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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. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

    Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

  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

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

    PubMed Central

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

    2015-01-01

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

  5. Determining chemically and spatially resolved atomic profile of low contrast interface structure with high resolution.

    PubMed

    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

  6. 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

  7. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  10. Local atomic and electronic structure of boron chemical doping in monolayer graphene.

    PubMed

    Zhao, Liuyan; Levendorf, Mark; Goncher, Scott; Schiros, Theanne; Pálová, Lucia; Zabet-Khosousi, Amir; Rim, Kwang Taeg; Gutiérrez, Christopher; Nordlund, Dennis; Jaye, Cherno; Hybertsen, Mark; Reichman, David; Flynn, George W; Park, Jiwoong; Pasupathy, Abhay N

    2013-10-01

    We use scanning tunneling microscopy and X-ray spectroscopy to characterize the atomic and electronic structure of boron-doped and nitrogen-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 carriers into the graphene sheet per dopant. Density functional theory calculations indicate that boron dopants interact strongly with the underlying copper substrate while nitrogen dopants do not. The local bonding differences between graphitic boron and nitrogen dopants lead to large scale differences in dopant distribution. The distribution of dopants is observed to be completely random in the case of boron, while nitrogen displays strong sublattice clustering. Structurally, nitrogen-doped graphene is relatively defect-free while boron-doped graphene films show a large number of Stone-Wales defects. These defects create local electronic resonances and cause electronic scattering, but do not electronically dope the graphene film. PMID:24032458

  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. Atomic-level structural and chemical analysis of Cr-doped Bi2Se3 thin films

    PubMed Central

    Ghasemi, A.; Kepaptsoglou, D.; Collins-McIntyre, L. J.; Ramasse, Q.; Hesjedal, T.; Lazarov, V. K.

    2016-01-01

    We present a study of the structure and chemical composition of the Cr-doped 3D topological insulator Bi2Se3. Single-crystalline thin films were grown by molecular beam epitaxy on Al2O3 (0001), and their structural and chemical properties determined on an atomic level by aberration-corrected scanning transmission electron microscopy and electron energy loss spectroscopy. A regular quintuple layer stacking of the Bi2Se3 film is found, with the exception of the first several atomic layers in the initial growth. The spectroscopy data gives direct evidence that Cr is preferentially substituting for Bi in the Bi2Se3 host. We also show that Cr has a tendency to segregate at internal grain boundaries of the Bi2Se3 film. PMID:27221782

  13. Atomic-level structural and chemical analysis of Cr-doped Bi2Se3 thin films.

    PubMed

    Ghasemi, A; Kepaptsoglou, D; Collins-McIntyre, L J; Ramasse, Q; Hesjedal, T; Lazarov, V K

    2016-01-01

    We present a study of the structure and chemical composition of the Cr-doped 3D topological insulator Bi2Se3. Single-crystalline thin films were grown by molecular beam epitaxy on Al2O3 (0001), and their structural and chemical properties determined on an atomic level by aberration-corrected scanning transmission electron microscopy and electron energy loss spectroscopy. A regular quintuple layer stacking of the Bi2Se3 film is found, with the exception of the first several atomic layers in the initial growth. The spectroscopy data gives direct evidence that Cr is preferentially substituting for Bi in the Bi2Se3 host. We also show that Cr has a tendency to segregate at internal grain boundaries of the Bi2Se3 film. PMID:27221782

  14. Atomic-level structural and chemical analysis of Cr-doped Bi2Se3 thin films

    NASA Astrophysics Data System (ADS)

    Ghasemi, A.; Kepaptsoglou, D.; Collins-McIntyre, L. J.; Ramasse, Q.; Hesjedal, T.; Lazarov, V. K.

    2016-05-01

    We present a study of the structure and chemical composition of the Cr-doped 3D topological insulator Bi2Se3. Single-crystalline thin films were grown by molecular beam epitaxy on Al2O3 (0001), and their structural and chemical properties determined on an atomic level by aberration-corrected scanning transmission electron microscopy and electron energy loss spectroscopy. A regular quintuple layer stacking of the Bi2Se3 film is found, with the exception of the first several atomic layers in the initial growth. The spectroscopy data gives direct evidence that Cr is preferentially substituting for Bi in the Bi2Se3 host. We also show that Cr has a tendency to segregate at internal grain boundaries of the Bi2Se3 film.

  15. 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

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

    SciTech Connect

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

    2014-09-25

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

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

    DOE PAGESBeta

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

    2014-09-25

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

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

    SciTech Connect

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

    2012-09-12

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

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

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1982-01-01

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  3. 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.

  4. Atomic Scale Chemical and Structural Characterization of Ceramic Oxide Heterostructure Interfaces

    SciTech Connect

    Singh, R. K.

    2003-04-16

    The research plan was divided into three tasks: (a) growth of oxide heterostructures for interface engineering using standard thin film deposition techniques, (b) atomic level characterization of oxide heterostructure using such techniques as STEM-2 combined with AFM/STM and conventional high-resolution microscopy (HRTEM), and (c) property measurements of aspects important to oxide heterostructures using standard characterization methods, including dielectric properties and dynamic cathodoluminescence measurements. Each of these topics were further classified on the basis of type of oxide heterostructure. Type I oxide heterostructures consisted of active dielectric layers, including the materials Ba{sub x}Sr{sub 1-x}TiO{sub 3} (BST), Y{sub 2}O{sub 3} and ZrO{sub 2}. Type II heterostructures consisted of ferroelectric active layers such as lanthanum manganate and Type III heterostructures consist of phosphor oxide active layers such as Eu-doped Y{sub 2}O{sub 3}.

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

    DOE PAGESBeta

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

    2014-11-18

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

  6. Chemical identification of individual surface atoms by atomic force microscopy.

    PubMed

    Sugimoto, Yoshiaki; Pou, Pablo; Abe, Masayuki; Jelinek, Pavel; Pérez, Rubén; Morita, Seizo; Custance, Oscar

    2007-03-01

    Scanning probe microscopy is a versatile and powerful method that uses sharp tips to image, measure and manipulate matter at surfaces with atomic resolution. At cryogenic temperatures, scanning probe microscopy can even provide electron tunnelling spectra that serve as fingerprints of the vibrational properties of adsorbed molecules and of the electronic properties of magnetic impurity atoms, thereby allowing chemical identification. But in many instances, and particularly for insulating systems, determining the exact chemical composition of surfaces or nanostructures remains a considerable challenge. In principle, dynamic force microscopy should make it possible to overcome this problem: it can image insulator, semiconductor and metal surfaces with true atomic resolution, by detecting and precisely measuring the short-range forces that arise with the onset of chemical bonding between the tip and surface atoms and that depend sensitively on the chemical identity of the atoms involved. Here we report precise measurements of such short-range chemical forces, and show that their dependence on the force microscope tip used can be overcome through a normalization procedure. This allows us to use the chemical force measurements as the basis for atomic recognition, even at room temperature. We illustrate the performance of this approach by imaging the surface of a particularly challenging alloy system and successfully identifying the three constituent atomic species silicon, tin and lead, even though these exhibit very similar chemical properties and identical surface position preferences that render any discrimination attempt based on topographic measurements impossible. PMID:17330040

  7. Chemical bonding and atomic structure of Rb + exchanged KTiOPO4 waveguides probed by micro-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Tuschel, David D.; Paz-Pujalt, Gustavo R.; Risk, William P.

    1995-02-01

    Channel waveguides of Rb+ exchanged single-crystal KTiOPO4 were studied by micro-Raman spectroscopy. Rb+ exchange causes a disruption of the long-range translational (crystal) symmetry of the lattice and a tilting of the TiO6 octahedra. The ability to nondestructively map the chemical and physical structure related to the optical properties of channel waveguides is demonstrated.

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    A significant BN-to-graphene charge donation is evident in the electronic structure of a graphene/h-BN(0001) heterojunction grown by chemical vapor deposition and atomic layer deposition directly on Ru(0001), consistent with density functional theory. This filling of the lowest unoccupied state near the Brillouin zone center has been characterized by combined photoemission/k vector resolved inverse photoemission spectroscopies, and Raman and scanning tunneling microscopy/spectroscopy. The unoccupied σ*(Γ1 +) band dispersion yields an effective mass of 0.05 me for graphene in the graphene/h-BN(0001) heterostructure, in spite of strong perturbations to the graphene conduction band edge placement.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  11. 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…

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

    SciTech Connect

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

    2014-11-18

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

  13. 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

  14. 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)

  15. 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

  16. Gauge theory and chemical structure.

    PubMed

    Mattingly, James

    2003-05-01

    The possibility of chemical structure in the context of quantized matter is examined by way of Richard Bader's Atoms in Molecules. I critically examine his notion of "electronic charge density"-showing that he cannot really mean "density of charge"-and I argue that the appropriate concept is expectation value of charge. This still allows him to define chemical structure, but it makes problematic his appeals to the explanatory power of structure. This is because, as Rosenfeld and Bohr showed, the expectation value of charge cannot be taken as the electronic field experienced by other charges. I suggest that we can recover the efficacy of structure by thinking of chemistry as a gauge theory. Current consensus in the study of gauge theories indicates that gauge potentials represent a new type of property; while no member of the family of functions comprising the gauge potential is real, the potential itself is causally potent. I illustrate this in the case of electrodynamics, where the vector potential can causally influence charges in the absence of electric or magnetic fields. I show how chemical structure can be considered to be a gauge field. Following Bader, I take it to be a family of geometric configurations, no one of which is possessed by a given molecule. I claim that current research in gauge theory licenses the attribution of causal potency to this notion of structure, despite its lack of reality. I thus begin the process of freeing the explanatory resources of gauge theory from physics alone. PMID:12796102

  17. 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

  18. 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

  19. Atomic structure of titania nanosheet with vacancies

    PubMed Central

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

    2013-01-01

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

  20. Chemical structure of interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, F. J.

    1985-01-01

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

  1. Chemical control of electrical contact to sp2 carbon atoms

    PubMed Central

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

    2014-01-01

    Carbon-based nanostructures are attracting tremendous interest as components in ultrafast electronics and optoelectronics. The electrical interfaces to these structures play a crucial role for the electron transport, but the lack of control at the atomic scale can hamper device functionality and integration into operating circuitry. Here we study a prototype carbon-based molecular junction consisting of a single C60 molecule and probe how the electric current through the junction depends on the chemical nature of the foremost electrode atom in contact with the molecule. We find that the efficiency of charge injection to a C60 molecule varies substantially for the considered metallic species, and demonstrate that the relative strength of the metal-C bond can be extracted from our transport measurements. Our study further suggests that a single-C60 junction is a basic model to explore the properties of electrical contacts to meso- and macroscopic sp2 carbon structures. PMID:24736561

  2. Atomic structures and compositions of internal interfaces

    SciTech Connect

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

    1992-03-01

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

  3. Quantum Theory of Atomic and Molecular Structures and Interactions

    NASA Astrophysics Data System (ADS)

    Makrides, Constantinos

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

  4. 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)

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

    NASA Astrophysics Data System (ADS)

    Izquierdo-Aymerich, Mercè; Adúriz-Bravo, Agustín

    2009-04-01

    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 of evidence construction, new contributions from physicists and physical chemists that were incorporated to chemical research acquired ‘chemical’ meaning, since they were related to research questions that genuinely came from chemistry. Conversely, the core ideas of 19th-century chemical atomism, among which we must highlight valence and Mendeleev’s periodic system, provided ‘clues’ for imagining an atom in terms of the elements adjusted to their chemical behaviour, which changed periodically as a function of atomic mass. With this, chemistry ceased to be a descriptive science and began to be a ‘law-based’, theoretical science. Little by little, chemistry teaching became the teaching of the internal structure of atoms, which were arranged in the Periodic Table according to criteria and ‘construction rules’ related to quantum mechanics. We pose the question: ‘how can we now teach general chemistry in a way that does not disregard current knowledge about the structure of the atom yet, at the same time, gives priority to chemical criteria, thus making such structure useful to interpret chemical change?’.

  6. The Chemical Structure and Acid Deterioration of Paper.

    ERIC Educational Resources Information Center

    Hollinger, William K., Jr.

    1984-01-01

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

  7. 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.

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

    SciTech Connect

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

    1996-09-01

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

  9. A Thermo-Chemical Reactor for analytical atomic spectrometry

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  10. Evolution of atomic structure during nanoparticle formation

    PubMed Central

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

    2014-01-01

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

  11. Evolution of atomic structure during nanoparticle formation.

    PubMed

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

    2014-05-01

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

  12. Electrochemical Potential Derived from Atomic Cluster Structures.

    PubMed

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

    2016-02-01

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

  13. 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)

  14. 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)

  15. 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….

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  18. 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.

  19. 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.

  20. 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)

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

    SciTech Connect

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

    2007-01-01

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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

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

    DOE Data Explorer

    Cowan, R. D.

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

  7. 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. A relationship between chemical structure and the critical temperature

    NASA Technical Reports Server (NTRS)

    Fedors, R. F.

    1982-01-01

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

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

    PubMed

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

    2007-01-01

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

  11. 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}.

  12. Atomic scale interface structure in metallic superlattices

    NASA Astrophysics Data System (ADS)

    Uzdin, V. M.; Keune, W.

    2007-04-01

    We present an atomistic model of interface alloying that presupposes exchange of adatoms with substrate atoms and floating of adatoms on the upper layers during deposition. Due to the existence of a preferred direction (the growth direction), the chemical profile near the interface proves to be asymmetrical. The floating algorithm combined with self-consistent calculations of atomic magnetic moments is used as a model for interpreting Mössbauer data obtained from 57Fe-enriched interfacial tracer layers in Fe/Cr(001) superlattices. The superlattices were grown at different temperatures in order to modify their interface roughness. A linear correlation between calculated moment peaks and observed distinct magnetic hyperfine fields was found. Our experimental samples exhibit larger intermixing than the simplified theoretical model we used. The experimental giant magnetoresistance ratio was observed to increase with the decreasing fraction of certain 57Fe atoms located in the interfacial region. Therefore, bulk scattering from impurity atoms appears to provide the main contribution to the giant magnetoresistance in Fe/Cr. Moreover, our theoretical results clarify the dependence of the short-wavelength period of interlayer coupling on the interface roughness in Fe/Cr.

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

    PubMed

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

    2015-08-12

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

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

    NASA Astrophysics Data System (ADS)

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

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

  16. Atomic Structure of Ultrathin Gold Nanowires.

    PubMed

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

    2016-05-11

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

  17. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

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

    PubMed

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

    2014-08-12

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

  20. 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

  1. 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.

  2. 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

  3. MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES

    SciTech Connect

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

    2000-09-01

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

  4. The electronic structure and chemical bonding of vitamin B12

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

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

    PubMed

    Murshudov, G N

    2016-01-01

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

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

    SciTech Connect

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

    2014-12-02

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

  8. Atomic vapor spectroscopy in integrated photonic structures

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    We investigate an integrated optical chip immersed in atomic vapor providing several waveguide geometries for spectroscopy applications. This includes integrated ring resonators, Mach Zehnder interferometers, slot waveguides and counterpropagating coupling schemes. 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 strong atom light coupling. Cooperativities on the order of 1 are within reach.

  9. 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…

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

    PubMed

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

    2016-04-21

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

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

    PubMed

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

    2016-01-01

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

  1. 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).

  2. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  4. Probing Atomic Dynamics and Structures Using Optical Patterns

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2015-05-01

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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina

    2016-07-01

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

  7. 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.

  8. 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

  9. 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.

  10. 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…

  11. 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.

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

    DOE PAGESBeta

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

    2015-04-03

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  14. 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…

  15. Renyi complexities and information planes: Atomic structure in conjugated spaces

    NASA Astrophysics Data System (ADS)

    Antolín, J.; López-Rosa, S.; Angulo, J. C.

    2009-05-01

    Generalized Renyi complexity measures are defined and numerically analyzed for atomic one-particle densities in both conjugated spaces. These complexities provide, as particular cases, the previously known statistical and Fisher-Shannon complexities. The generalized complexities provide information on the atomic shell structure and shell-filling patterns, allowing to appropriately weight different regions of the electronic cloud.

  16. 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.

  17. 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.

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

    SciTech Connect

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

  19. 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)

  20. 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.

  1. 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.

  2. Chemical structure and dynamics. Annual report 1995

    SciTech Connect

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

    1996-05-01

    The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

  3. Annual Report 2000. Chemical Structure and Dynamics

    SciTech Connect

    Colson, Steve D; McDowell, Rod 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 and 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.

  4. 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.

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

    PubMed

    Hendrickson, Wayne A

    2016-06-01

    Membrane proteins are substantially more challenging than natively soluble proteins as subjects for structural analysis. Thus, membrane proteins are greatly underrepresented in structural databases. Recently, focused consortium efforts and advances in methodology for protein production, crystallographic analysis and cryo-EM analysis have accelerated the pace of atomic-level structure determination of membrane proteins. PMID:27273628

  6. 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.

  7. Localizing chemical groups while imaging single native proteins by high-resolution atomic force microscopy.

    PubMed

    Pfreundschuh, Moritz; Alsteens, David; Hilbert, Manuel; Steinmetz, Michel O; Müller, Daniel J

    2014-05-14

    Simultaneous high-resolution imaging and localization of chemical interaction sites on single native proteins is a pertinent biophysical, biochemical, and nanotechnological challenge. Such structural mapping and characterization of binding sites is of importance in understanding how proteins interact with their environment and in manipulating such interactions in a plethora of biotechnological applications. Thus far, this challenge remains to be tackled. Here, we introduce force-distance curve-based atomic force microscopy (FD-based AFM) for the high-resolution imaging of SAS-6, a protein that self-assembles into cartwheel-like structures. Using functionalized AFM tips bearing Ni(2+)-N-nitrilotriacetate groups, we locate specific interaction sites on SAS-6 at nanometer resolution and quantify the binding strength of the Ni(2+)-NTA groups to histidine residues. The FD-based AFM approach can readily be applied to image any other native protein and to locate and structurally map histidine residues. Moreover, the surface chemistry used to functionalize the AFM tip can be modified to map other chemical interaction sites. PMID:24766578

  8. 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.

  9. Evaluating and Interpreting the Chemical Relevance of the Linear Response Kernel for Atoms.

    PubMed

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

    2013-02-12

    Although a lot of work has been done on the chemical relevance of the atom-condensed linear response kernel χAB regarding inductive, mesomeric, and hyperconjugative effects as well as (anti)aromaticity of molecules, the same cannot be said about its not condensed form χ(r,r'). Using a single Slater determinant KS type ansatz involving second order perturbation theory, we set out to investigate the linear response kernel for a number of judiciously chosen closed (sub)shell atoms throughout the periodic table and its relevance, e.g., in relation to the shell structure and polarizability. The numerical results are to the best of our knowledge the first systematic study on this noncondensed linear response function, the results for He and Be being in line with earlier work by Savin. Different graphical representations of the kernel are presented and discussed. Moreover, a frontier orbital approach has been tested illustrating the sensitivity of the nonintegrated kernel to the nodal structure of the orbitals. As a test of our method, a numerical integration of the linear response kernel was performed, yielding an accuracy of 10(-4). We also compare calculated values of the polarizability tensor and their evolution throughout the periodic table to high-level values found in the literature. PMID:26588743

  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. Direct experimental determination of the atomic structure at internal interfaces

    SciTech Connect

    Browning, N.D. |; Pennycook, S.J.

    1995-07-01

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

  13. 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

  14. Glass formation and local topological instability of atomic structure

    SciTech Connect

    Egami, T.

    1997-12-31

    A direct connection between the local topology of the atomic structure of liquids and glasses and thermodynamic quantities through the atomic level stresses is suggested for metallic alloys. In particular the role of local topological instability in the phase transformation involving liquid and glass will be discussed. It is pointed out that a single local geometrical criterion can explain various phase transformations, such as melting, glass transition, and glass formation by solid state reaction and liquid quenching.

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

    ERIC Educational Resources Information Center

    Rittenhouse, Robert C.

    2015-01-01

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

  16. 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.

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

    SciTech Connect

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

    2004-11-30

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

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

    NASA Technical Reports Server (NTRS)

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

    1979-01-01

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

  19. 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.

  20. 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.

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

    PubMed

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

    2013-09-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. 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.

  4. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    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).

  5. 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).

  6. 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.

  7. 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

  8. 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.

  9. 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).

  10. 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

  11. 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.

  12. 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

  13. 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.

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

    DOE PAGESBeta

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

    2014-12-02

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

  15. Local atomic structure around Ni, Nb, and Zr atoms in Ni-Nb-Zr-H glassy alloys

    NASA Astrophysics Data System (ADS)

    Oji, H.; Handa, K.; Ide, J.; Honma, T.; Umesaki, N.; Yamaura, S.; Fukuhara, M.; Inoue, A.; Emura, S.

    2009-11-01

    In order to elucidate the hydrogen effect on the atomic configuration in the Ni-Nb-Zr glassy alloys, we measured Ni, Nb, and Zr K-edge XAFS spectra of the Ni-Nb-Zr glassy alloy films with two different chemical compositions, i.e., Ni42Nb28Zr30 and Ni36Nb24Zr40, and their hydrogen-charged ones, i.e., (Ni42Nb28Zr30)0.91H0.09 and (Ni36Nb24Zr40)0.89H0.11. The Fourier transforms of the XAFS oscillations of these samples clearly shows that there is a significant difference in the structural response between the Zr30at.% and the Zr40at.% alloys when hydrogen atoms are charged. The curve-fitting analysis indicates that the hydrogenation does not alter the local alignment around the three metal atoms for the Zr30at.% alloy, but for the Zr40at.% alloy; it elongates the inter-atomic distances of Zr-Zr, Zr-Nb and Nb-Ni. On the basis of the curve fitting analysis, we propose the distorted icosahedral Zr5Ni5Nb3 cluster models. The XANES spectra at each (Ni, Zr and Nb) edge of (Ni36Nb24Zr40)0.89H0.11 also present the distinct shape from the other samples. The pre-edge peak (shoulder) vanishes or weakens, suggesting the conversion of the electronic state of the metal ions owing to the hydrogenation. The post-edge energy region shows clear multi-scattering effects from hydrogen atoms by charging these.

  16. Metal Atom Endohedrally Doped C20 CAGE Structure:

    NASA Astrophysics Data System (ADS)

    Erkoç, Şakir

    The C20 cage structure (X@C20; X =Fe, Co, Ni) endohedrally doped with a metal atom has been investigated theoretically by performing molecular-mechanics optimizations, and semi-empirical PM3 level and density functional theory B3LYP/6-31G* level calculations within UHF formalism. Calculations have been performed with different spin configurations for the neutral systems.

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

    SciTech Connect

    1981-03-01

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

  18. Guiding of atoms in helical optical potential structures

    NASA Astrophysics Data System (ADS)

    Rsheed, Anwar Al; Lyras, Andreas; Lembessis, Vassilis E.; Aldossary, Omar M.

    2016-06-01

    The classical dynamics of a cold atom trapped inside a static helical optical potential is investigated based on the Lagrangian formalism, which takes into account both the optical light field and the gravitational field. The resulting equations of motion are solved numerically and analytically. The topology of the helical optical potential, which drives the trapped cold atom, is responsible for two different types of oscillations, namely: the local oscillations, whereby the atomic motion is confined in a region smaller than the light field wavelength (z\\lt λ ) and the global oscillations, when the atomic motion is extended to larger regions comparable to the beam Rayleigh range (z\\lt {z}{{R}}). Local oscillations guide the atom along the helical structure of the optical potential. The global oscillations, which constitute the main topic of our paper, define the atomic motion along the z-axis as an oscillation between two turning points. For typical values of the beam waist {w}{{o}} the turning points are symmetrical around the origin. For large values of the beam waist {w}{{o}}, the global oscillations become asymmetric because the optical dipole potential weakens and the gravitational potential contributes to the determination of the turning points. For sufficiently large values of the beam waist {w}{{o}}, there are no global oscillations and only one upper turning point defines the atom’s global motion.

  19. A quantum interface between single atoms and nanophotonic structures

    NASA Astrophysics Data System (ADS)

    Thompson, Jeffrey Douglas

    Strong interactions between light and atoms at the single-quantum level are an important ingredient for quantum technologies, as well as for studies of fundamental effects in quantum optics. This thesis describes the development of a novel experimental platform that allows for trapping a single rubidium atom in the evanescent mode of a nano-fabricated optical cavity with sub-wavelength dimensions. By virtue of their small size, these cavities provide extremely large atom-photon coupling strengths and good prospects for scalability and integration into complex quantum optical circuits. Positioning the atom near the nano-structure is accomplished using a scanning optical tweezer dipole trap. As a first application, we have demonstrated a coherent optical switch, where a single gate photon controls the propagation of many subsequent signal photons, with the interaction mediated by the atom and cavity. We have also shown that the optical response of the combined atom-cavity system is nonlinear at the level of one or two photons.

  20. Chemical and structural features influencing the biological activity of curcumin.

    PubMed

    Priyadarsini, K Indira

    2013-01-01

    Curcumin, a polyphenolic natural product, exhibits therapeutic activity against a number of diseases, attributed mainly to its chemical structure and unique physical, chemical, and biological properties. It is a diferuloyl methane molecule [1,7-bis (4-hydroxy-3- methoxyphenyl)-1,6-heptadiene-3,5-dione)] containing two ferulic acid residues joined by a methylene bridge. It has three important functionalities: an aromatic o-methoxy phenolic group, α, β-unsaturated β-diketo moiety and a seven carbon linker. Extensive research in the last two decades has provided evidence for the role of these different functional groups in its crucial biological activities. A few highlights of chemical structural features associated with the biological activity of curcumin are: The o-methoxyphenol group and methylenic hydrogen are responsible for the antioxidant activity of curcumin, and curcumin donates an electron/ hydrogen atom to reactive oxygen species. Curcumin interacts with a number of biomolecules through non-covalent and covalent binding. The hydrogen bonding and hydrophobicity of curcumin, arising from the aromatic and tautomeric structures along with the flexibility of the linker group are responsible for the non-covalent interactions. The α, β-unsaturated β-diketone moiety covalently interacts with protein thiols, through Michael reaction. The β-diketo group forms chelates with transition metals, there by reducing the metal induced toxicity and some of the metal complexes exhibit improved antioxidant activity as enzyme mimics. New analogues with improved activity are being developed with modifications on specific functional groups of curcumin. The physico-chemical and structural features associated with some of the biological activities of curcumin and important analogues are summarized in this article. PMID:23116315

  1. 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.

  2. Structure and production of deeply bound pionic atoms

    SciTech Connect

    Toki, H. )

    1991-04-10

    We study the structure and production of deeply bound pionic atoms in heavy nuclei, which are found quasi-stable due to the repulsive pion-nucleus optical potential and the attractive Coulomb potential. The bound pion forms a pionic halo just outside of nucleus. We discuss then the use of pion transfer reactions such as (n,p) and (d, {sup 2}He) to form these states. In addition, we study other processes such as (n,d) and (d, {sup 3}He) and the use of the inverse kinematics for formation of deeply bound pionic atoms.

  3. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-08-23

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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. Atomic and electronic structures of a transition layer at the CrN/Cr interface

    NASA Astrophysics Data System (ADS)

    Zhang, Zaoli; Daniel, Rostislav; Mitterer, Christain

    2011-08-01

    By spherical aberration (CS)-corrected high-resolution transmission electron microscopy (HRTEM) and electron energy-loss spectroscopy (EELS), the atomic and electronic structures at the CrN/Cr interface are studied. A transition layer is formed at the CrN/Cr interface, which is identified as hexagonal Cr2N. The atomic structures at the interfaces are revealed. The elemental concentration distribution across the interface was quantified by EELS. The fine structures of Cr-L2,3 in Cr, CrN, and Cr2N exhibit a subtle difference. The Cr-L2,3 edge in CrN shows a noticeable chemical shift as compared to Cr and Cr2N, accompanied by a slight variation at the corresponding N-K edge.

  13. 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.

  14. Stable atomic structure of NiTi austenite

    NASA Astrophysics Data System (ADS)

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2014-08-01

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

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. Vibrational structure in atomic emission spectra: Hg atoms in molecular matrices

    NASA Astrophysics Data System (ADS)

    Crépin, C.; Tramer, A.

    1997-08-01

    Mercury atoms excited to the 3P1 state in rare gas and molecular (CH4, CD4, CF4, and SF6) matrices relax by a direct 3P1→1S0 fluorescence with a ca. 60 ns lifetime or by the 3P1⇝3P0 radiationless transition followed by the 3P0→1S0 long-lived (τ in the 10 to 500 ms range) emission. The main difference between atomic and molecular hosts is the appearance, in the latter case, of a well resolved vibrational structure in the spectrum of the 3P0→1S0 transition involving the frequencies of nontotally symmetric modes of the host molecules. This structure, related to a shortening of the lifetime of the 3P0→1S0 emission is explained by the intensity borrowing from the allowed 3P1→1S0 transition, i.e., by the 3P1↔3P0 mixing induced by nontotally symmetric vibrations of neighbor molecules (analog of the Herzberg-Teller effect). Relative intensities of bands corresponding to different vibrational modes may be deduced from estimation of electric fields induced in the Hg atom by displacements of electric charges of the vibrating molecule

  2. 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.

  3. 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.

  4. Ground-State Structures of Atomic Metallic Hydrogen

    NASA Astrophysics Data System (ADS)

    McMahon, Jeffrey M.; Ceperley, David M.

    2011-04-01

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

  5. Atomic and electronic structure of exfoliated black phosphorus

    SciTech Connect

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

    2015-11-15

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

  6. Cavities and Atomic Packing in Protein Structures and Interfaces

    PubMed Central

    Sonavane, Shrihari; Chakrabarti, Pinak

    2008-01-01

    A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues) lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 Å3 of cavity volume is found to accommodate single water, with another 40–45 Å3 needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface), residues in β-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein–protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein–protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure. PMID:19005575

  7. Chemical weathering within high mountain depositional structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    PubMed

    Fooshee, David; Andronico, Alessio; Baldi, Pierre

    2013-11-25

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

  9. 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

  10. 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.

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

    PubMed

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

    2016-05-01

    This work demonstrates a new halogenation reaction through sequential radical and halogen transfer reactions, named as "radical and atom transfer halogenation" (RATH). Both benzoxazine compounds and poly(2,6-dimethyl-1,4-phenylene oxide) have been demonstrated as active species for RATH. Consequently, the halogenated compound becomes an active initiator of atom transfer radical polymerization. Combination of RATH and sequential ATRP provides an convenient and effective approach to prepare reactive and crosslinkable polymers. The RATH reaction opens a new window both to chemical synthesis and molecular design and preparation of polymeric materials. PMID:27027639

  12. Spectroscopic elucidation of chemical structure of plasma-polymerized pyridine

    SciTech Connect

    Hozumi, K.; Kitamura, K.; Hashimoto, H.; Hamaoka, T.; Fujisawa, H.; Ishizawa, T.

    1983-05-01

    Chemical structure of the plasma-polymerized pyridine film produced on a glass reactor wall by means of the plasma technique in which the pyridine vapor was electronically excited by high-frequency power under a reduced pressure was elucidated. The polymer was highly hydrophilic and was soluble to some of the polar organic solvents so that nitrogen-containing polar functional groups were predicted to participate in the chemical structure of the polymer molecules. /sup 1/H-NMR, /sup 13/CNMR, and IR spectroscopies, high-resolution mass spectral data, and number-average molecular weight determination with some aid of microelemental analysis revealed the presence of various functional groups such as imine, nitrile, amine, pyridine ring, its N-oxide, and even amide. The oxygen atoms involved in the last two groups were supposedly introduced by contact with ambient air after the plasma process. The hydrophilic nature of the polymer which was essential for preparing reverse osmosis membrane was therefore due to the overall hydration effect of these polar functional groups.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  14. 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.

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

    PubMed

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Usman, Muhammad

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

  17. 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

  18. Chemical Structure of Trichomonas vaginalis Surface Lipoglycan

    PubMed Central

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

    2011-01-01

    The extracellular parasite Trichomonas vaginalis contains a surface glycoconjugate that appears to mediate parasite-host cell interaction via binding to human galectin-1. This glycoconjugate also elicits cytokine production from human vaginal epithelial cells, implicating its role in modulation of host immune responses. We have analyzed the structure of this glycoconjugate, previously described to contain the sugars rhamnose (Rha), N-acetylglucosamine (GlcNAc), galactose (Gal), xylose (Xyl), N-acetylgalactosamine (GalNAc), and glucose (Glc), using gas chromatograph mass spectrometry (GC-MS), matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF), electrospray MS/MS, and nuclear magnetic resonance (NMR), combined with chemical and enzymatic digestions. Our data reveal a complex structure, named T. vaginalis lipoglycan (TvLG), that differs markedly from Leishmania lipophosphoglycan and Entamoeba lipopeptidophosphoglycan and is devoid of phosphosaccharide repeats. TvLG is composed of an α1–3 linked polyrhamnose core, where Rha residues are substituted at the 2-position with either β-Xyl or chains of, on average, five N-acetyllactosamine (-3Galβ1–4GlcNAcβ1-) (LacNAc) units and occasionally lacto-N-biose (-3Galβ1-3GlcNAcβ1-) (LNB). These chains are themselves periodically substituted at the Gal residues with Xyl-Rha. These structural analyses led us to test the role of the poly-LacNAc/LNB chains in parasite binding to host cells. We found that reduction of poly-LacNAc/LNB chains decreased the ability of TvLG to compete parasite binding to host cells. In summary, our data provide a new model for the structure of TvLG, composed of a polyrhamnose backbone with branches of Xyl and poly-LacNAc/LNB. Furthermore, the poly-LacNAc side chains are shown to be involved in parasite-host cell interaction. PMID:21900246

  19. 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.

  20. Spatial multimode structure of atom-generated squeezed light

    NASA Astrophysics Data System (ADS)

    Zhang, Mi; Lanning, R. Nicholas; Xiao, Zhihao; Dowling, Jonathan P.; Novikova, Irina; Mikhailov, Eugeniy E.

    2016-01-01

    We investigated the spatial distribution of quantum fluctuations in a squeezed vacuum field, generated via polarization self-rotation (PSR) interaction of an ensemble of Rb atoms and a strong near-resonant linearly polarized laser field. We found that the noise suppression is greatly effected by the transverse profile of a spatial mask, placed in both the squeezed field and the local oscillator, as well as its position along the focused beam near the focal point. These observations indicate the spatial multimode structure of the squeezed vacuum field. We have developed a theoretical model that describes the generation of higher-order Laguerre-Gauss modes as a result of PSR light-atom interaction. The prediction of this model is in a good qualitative agreement with the experimental measurements.

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

    SciTech Connect

    Goeken, M.; Vehoff, H.

    1996-10-15

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

  2. Deciphering Adsorption Structure on Insulators at the Atomic Scale

    SciTech Connect

    Thurmer, Konrad; Feibelman, Peter J.

    2014-09-01

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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

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

    PubMed

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

    2011-05-27

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

  9. 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.

  10. Chemical syntheses of inulin and levan structures.

    PubMed

    Oscarson, Stefan; Sehgelmeble, Fernando W

    2002-11-29

    A fructofuranosyl thiglycoside donor, ethyl 6-O-acetyl-3-O-benzyl-1,4-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-2-thio-beta-D-fructofuranoside (11), designed to yield stereospecifically beta-linkages and also to allow subsequent elongation in the 6- and/or 1-positions, was prepared and used in syntheses of levan and inulin structures. DMTST-promoted glycosylation between 11 (1.3 mol equiv) and methyl beta-D-fructofuranoside 6-OH and 1-OH acceptors (3 and 6) gave stereospecifically the protected methyl levanobioside 12 and inulinobioside 17 in excellent yields (80 and 86%), respectively. Protecting group manipulations on these afforded new disaccharide 6'-OH and 1'-OH acceptors (13 and 19), which were coupled again with donor 11 (1.0 mol equiv) to yield methyl levanotrioside 14 and inulinotrioside 20 in high yields, 65 and 67%, respectively. These were transformed into new acceptors and also fully deprotected to afford the methyl glycosides of levanotriose and inulinotriose, all structures that have earlier not been accessible by chemical synthesis. PMID:12444625

  11. 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

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

    SciTech Connect

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

    2011-01-01

    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

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

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

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

    PubMed

    Yong, Chin W

    2016-08-22

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

  16. 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.

  17. 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.

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    SciTech Connect

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

    2013-06-15

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

  1. Local atomic structure around Ni, Nb, and Zr atoms in Ni-Nb-Zr-H glassy alloys studied by x-ray absorption fine structure method

    NASA Astrophysics Data System (ADS)

    Oji, H.; Handa, K.; Ide, J.; Honma, T.; Yamaura, S.; Inoue, A.; Umesaki, N.; Emura, S.; Fukuhara, M.

    2009-06-01

    To elucidate hydrogen effects on the atomic configuration of Ni-Nb-Zr-H glassy alloys exhibiting proton-tunneling-induced Coulomb oscillation, we investigated the local atomic configuration around the Ni, Nb, and Zr atoms by x-ray absorption fine structure (XAFS) method. The analysis of the XAFS spectra indicates that there is the significant difference in structural response between the Zr 30 and the Zr 40 at. % alloys when hydrogen atoms are charged; charging the hydrogen atoms basically does not alter the local structures around the three atoms for the Zr 30 at. % alloy but induces the elongation of the Zr-Zr, Zr-Nb, and Nb-Ni distances for the Zr 40 at. % alloy. The distorted icosahedral Zr5Ni5Nb3 clusters assembled in randomly packed manners for the possible models in the Ni-Nb-Zr glassy alloy are proposed. The sites where hydrogen atoms occupy are also inferred.

  2. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    PubMed

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

    2016-08-01

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

  3. Chemical and structural modifications of RNAi therapeutics.

    PubMed

    Ku, Sook Hee; Jo, Sung Duk; Lee, Yeon Kyung; Kim, Kwangmeyung; Kim, Sun Hwa

    2016-09-01

    Small interfering RNA (siRNA), a 21-23nt double-stranded RNA responsible for post-transcriptional gene silencing, has attracted great interests as promising genomic drugs, due to its strong ability to silence target genes in a sequence-specific manner. Despite high silencing efficiency and on-target specificity, the clinical translation of siRNA has been hindered by its inherent features: poor intracellular delivery, limited blood stability, unpredictable immune responses and unwanted off-targeting effects. To overcome these hindrances, researchers have made various advances to modify siRNA itself and to improve its delivery. In this review paper, first we briefly discuss the innate properties and delivery barriers of siRNA. Then, we describe recent progress in (1) chemically and structurally modified siRNAs to solve their intrinsic problems and (2) siRNA delivery formulations including siRNA conjugates, polymerized siRNA, and nucleic acid-based nanoparticles to improve in vivo delivery. PMID:26549145

  4. Conservation-dissipation structure of chemical reaction systems.

    PubMed

    Yong, Wen-An

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  6. 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

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

    PubMed Central

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

    2015-01-01

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

  8. 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

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

    PubMed

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

    2009-11-01

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

  10. 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

  11. Images of Atoms.

    ERIC Educational Resources Information Center

    Wright, Tony

    2003-01-01

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

  12. 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

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

    PubMed

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

    2014-07-15

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

  14. Structural relaxation in atomic clusters: Master equation dynamics

    NASA Astrophysics Data System (ADS)

    Miller, Mark A.; Doye, Jonathan P. K.; Wales, David J.

    1999-10-01

    The role of the potential energy landscape in determining the relaxation dynamics of model clusters is studied using a master equation. Two types of energy landscape are examined: a single funnel, as exemplified by 13-atom Morse clusters, and the double funnel landscape of the 38-atom Lennard-Jones cluster. Interwell rate constants are calculated using Rice-Ramsperger-Kassel-Marcus theory within the harmonic approximation, but anharmonic model partition functions are also considered. Decreasing the range of the potential in the Morse clusters is shown to hinder relaxation toward the global minimum, and this effect is related to the concomitant changes in the energy landscape. The relaxation modes that emerge from the master equation are interpreted and analyzed to extract interfunnel rate constants for the Lennard-Jones cluster. Since this system is too large for a complete characterization of the energy landscape, the conditions under which the master equation can be applied to a limited database are explored. Connections are made to relaxation processes in proteins and structural glasses.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

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

    2016-08-01

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

  17. 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

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

    SciTech Connect

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

    2015-06-24

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

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

    SciTech Connect

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

    2011-08-15

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

  20. 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

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

    PubMed

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

    2015-10-15

    We re-examine the prototypical roaming reaction--hydrogen atom roaming in formaldehyde decomposition--from a phase space perspective. Specifically, we address the question "why do trajectories roam, rather than dissociate through the radical channel?" We describe and compute the phase space structures that define and control all possible reactive events for this reaction, as well as provide a dynamically exact description of the roaming region in phase space. Using these phase space constructs, we show that in the roaming region, there is an unstable periodic orbit whose stable and unstable manifolds define a conduit that both encompasses all roaming trajectories exiting the formaldehyde well and shepherds them toward the H2···CO well. PMID:26499774

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed Central

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

    2012-01-01

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

  4. Atomic structure of the actin: DNase I complex

    NASA Astrophysics Data System (ADS)

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

    1990-09-01

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

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

    SciTech Connect

    Harris, J.C.

    2001-04-16

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

  6. The Oil, Chemical, and Atomic Workers International Union: refining strategies for labor.

    PubMed

    Wooding, J; Levenstein, C; Rosenberg, B

    1997-01-01

    In a period of declining union membership and severe economic and environmental crisis it is important that labor unions rethink their traditional roles and organizational goals. Responding to some of these problems and reflecting a history of innovative and progressive unionism, the Oil, Chemical and Atomic Workers Union (OCAW) has sought to address occupational and environmental health problems within the context of a political struggle. This study suggests that by joining with the environmental movement and community activists, by pursuing a strategy of coalition building, and by developing an initiative to build and advocate for a new political party, OCAW provides a model for reinvigorating trade unionism in the United States. PMID:9031016

  7. 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

  8. 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.

  9. On the atomic structure of cocaine in solution.

    PubMed

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

    2016-01-14

    Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ∼5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function. PMID:26660073

  10. 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

  11. 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.

  12. 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.

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

    SciTech Connect

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

    2015-10-15

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

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

    SciTech Connect

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

    2005-06-01

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

  15. 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

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

    SciTech Connect

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

    1992-03-01

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

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

    SciTech Connect

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

    2011-12-09

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

  18. 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.

  19. Dopant distributions in n-MOSFET structure observed by atom probe tomography.

    PubMed

    Inoue, K; Yano, F; Nishida, A; Takamizawa, H; Tsunomura, T; Nagai, Y; Hasegawa, M

    2009-11-01

    The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted. PMID:19775815

  20. 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.

  1. 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.

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

    PubMed

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

    2015-07-15

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

  3. 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.

  4. An atomic structure of human γ-secretase

    PubMed Central

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

    2015-01-01

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

  5. 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. Application of electrospray and fast atom bombardment mass spectrometry to the identification of post-translational and other chemical modifications of proteins and peptides.

    PubMed

    Kouach, M; Belaïche, D; Jaquinod, M; Couppez, M; Kmiecik, D; Ricart, G; Van Dorsselaer, A; Sautière, P; Briand, G

    1994-05-01

    Mass spectrometry is a very powerful tool in the identification of chemical modifications of proteins and peptides. Often these modifications cannot be determined by conventional techniques. This report describes the combined use of electrospray ionization mass spectrometry and fast atom bombardment mass spectrometry to complete the primary structure of proteins and peptides. Examples illustrate how mass spectrometry is used to locate sites of phosphorylation, methylation and acetylation, and identify blocking groups and unexpected side reactions such as deamidation or alkylation. PMID:8204685

  7. 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

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

    PubMed

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

    2009-05-01

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

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

    SciTech Connect

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

    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.

  10. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

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

  11. New version: GRASP2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  12. 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.…

  13. 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.

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

    PubMed

    Buehler, Markus J

    2013-02-01

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

  15. Interface structure and atomic bonding characteristics in silicon nitride ceramics.

    PubMed

    Ziegler, A; Idrobo, J C; Cinibulk, M K; Kisielowski, C; Browning, N D; Ritchie, R O

    2004-12-01

    Direct atomic resolution images have been obtained that illustrate how a range of rare-earth atoms bond to the interface between the intergranular phase and the matrix grains in an advanced silicon nitride ceramic. It has been found that each rare-earth atom bonds to the interface at a different location, depending on atom size, electronic configuration, and the presence of oxygen at the interface. This is the key factor to understanding the origin of the mechanical properties in these ceramics and will enable precise tailoring in the future to critically improve the materials' performance in wide-ranging applications. PMID:15576617

  16. 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

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

    PubMed

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

    2015-12-01

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

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Hay, Mark E.

    2009-01-01

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

  20. Atomic structures and electronic properties of phosphorene grain boundaries

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

    Sobolev, Andrey; Mirzoev, Alexander

    2015-08-17

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

  3. 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

  4. The Intersection of Structural and Chemical Biology - An Essential Synergy.

    PubMed

    Zuercher, William J; Elkins, Jonathan M; Knapp, Stefan

    2016-01-21

    The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas. PMID:26933743

  5. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

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

    2009-01-01

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

  6. PREDICTING MODES OF TOXIC ACTION FROM CHEMICAL STRUCTURE: AN OVERVIEW

    EPA Science Inventory

    In the field of environmental toxicology, and especially aquatic toxicology, quantitative structure activity relationships (QSARS) have developed as scientifically-credible tools for predicting the toxicity of chemicals when little or no empirical data are available. asic and fun...

  7. 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.

  8. Wet Etching of Heat Treated Atomic Layer Chemical Vapor Deposited Zirconium Oxide in HF Based Solutions

    NASA Astrophysics Data System (ADS)

    Balasubramanian, Sriram; Raghavan, Srini

    2008-06-01

    Alternative materials are being considered to replace silicon dioxide as gate dielectric material. Of these, the oxides of hafnium and zirconium show the most promise. However, integrating these new high-k materials into the existing complementary metal-oxide-semiconductor (CMOS) process remains a challenge. One particular area of concern is the wet etching of heat treated high-k dielectrics. In this paper, work done on the wet etching of heat treated atomic layer chemical vapor deposited (ALCVD) zirconium oxide in HF based solutions is presented. It was found that heat treated material, while refractory to wet etching at room temperature, is more amenable to etching at higher temperatures when methane sulfonic acid is added to dilute HF solutions. Selectivity over SiO2 is still a concern.

  9. 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.

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

    SciTech Connect

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

    1997-04-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

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

  13. Structural motifs, mixing, and segregation effects in 38-atom binary clusters

    NASA Astrophysics Data System (ADS)

    Paz-Borbón, Lauro Oliver; Johnston, Roy L.; Barcaro, Giovanni; Fortunelli, Alessandro

    2008-04-01

    Thirty eight-atom binary clusters composed of elements from groups 10 and 11 of the Periodic Table mixing a second-row with a third-row transition metal (TM) (i.e., clusters composed of the four pairs: Pd-Pt, Ag-Au, Pd-Au, and Ag-Pt) are studied through a combined empirical-potential (EP)/density functional (DF) method. A "system comparison" approach is adopted in order to analyze a wide diversity of structural motifs, and the energy competition among different structural motifs is studied at the DF level for these systems, mainly focusing on the composition 24-14 (the first number refers to the second-row TM atom) but also considering selected motifs with compositions 19-19 (of interest for investigating surface segregation effects) and 32-6 (also 14-24 and 6-32 for the Pd-Au pair). The results confirm the EP predictions about the stability of crystalline structures at this size for the Au-Pd pair but with decahedral or mixed fivefold-symmetric/closed-packed structures in close competition with fcc motifs for the Ag-Au or Ag-Pt and Pd-Pt pairs, respectively. Overall, the EP description is found to be reasonably accurate for the Pd-Pt and Au-Pd pairs, whereas it is less reliable for the Ag-Au and Ag-Pt pairs due to electronic structure (charge transfer or directionality) effects. The driving force to core-shell chemical ordering is put on a quantitative basis, and surface segregation of the most cohesive element into the core is confirmed, with the exception of the Ag-Au pair for which charge transfer effects favor the segregation of Au to the surface of the clusters.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Structural examination of lithium niobate ferroelectric crystals by combining scanning electron microscopy and atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Efremova, P. V.; Ped'ko, B. B.; Kuznecova, Yu. V.

    2016-02-01

    The structure of lithium niobate single crystals is studied by a complex technique that combines scanning electron microscopy and atomic force microscopy. By implementing the piezoresponse force method on an atomic force microscope, the domain structure of lithium niobate crystals, which was not revealed without electron beam irradiation, is visualized

  19. Laser-induced resonant structure in electron-atom scattering

    NASA Astrophysics Data System (ADS)

    Flegel, A. V.; Frolov, M. V.; Manakov, N. L.; Starace, Anthony F.

    2009-11-01

    Orders of magnitude increases are predicted in the cross sections for electron-atom scattering accompanied by absorption or emission of n laser photons for incident electron energies at which the electron, by emitting μ laser photons, can be captured by the atom to form a negative ion. Resonance enhancements are most significant in the plateau region (n gg μ) of the scattered electron spectrum, whose shape is predicted to replicate that of the ion's (n + μ)-photon detachment spectrum.

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

    NASA Astrophysics Data System (ADS)

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

    1999-06-01

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

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

    PubMed

    Helmich, Benjamin; Sierka, Marek

    2012-01-15

    An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms. PMID:21997798

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

    SciTech Connect

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

    2015-08-07

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

  5. 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

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

    PubMed Central

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

    2014-01-01

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

  7. Chemical structure and pharmacokinetics of novel quinolone agents represented by avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and nemonoxacin.

    PubMed

    Kocsis, Bela; Domokos, J; Szabo, D

    2016-01-01

    Quinolones are potent antimicrobial agents with a basic chemical structure of bicyclic ring. Fluorine atom at position C-6 and various substitutions on the basic quinolone structure yielded fluoroquinolones, namely norfloxacin, ciprofloxacin, levofloxacin, moxifloxacin and numerous other agents. The target molecules of quinolones and fluoroquinolones are bacterial gyrase and topoisomerase IV enzymes. Broad-spectrum and excellent tissue penetration make fluoroquinolones potent agents but their toxic side effects and increasing number of resistant pathogens set limits on their use. This review focuses on recent advances concerning quinolones and fluoroquinolones, we will be summarising chemical structure, mode of action, pharmacokinetic properties and toxicity. We will be describing fluoroquinolones introduced in clinical trials, namely avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and non-fluorinated nemonoxacin. These agents have been proved to have enhanced antibacterial effect even against ciprofloxacin resistant pathogens, and found to be well tolerated in both oral and parenteral administrations. These features are going to make them potential antimicrobial agents in the future. PMID:27215369

  8. Band-Structure Engineering of Gold Atomic Wires on Silicon by Controlled Doping

    NASA Astrophysics Data System (ADS)

    Choi, Won Hoon; Kang, Pil Gyu; Ryang, Kyung Deuk; Yeom, Han Woong

    2008-03-01

    We report on the systematic tuning of the electronic band structure of atomic wires by controlling the density of impurity atoms. The atomic wires are self-assembled on Si(111) by substitutional gold adsorbates and extra silicon atoms are deposited as the impurity dopants. The one-dimensional electronic band of gold atomic wires, measured by angle-resolved photoemission, changes from a fully metallic to semiconducting one with its band gap increasing above 0.3 eV along with an energy shift as a linear function of the Si dopant density. The gap opening mechanism is suggested to be related to the ordering of the impurities.

  9. 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.

  10. The atomic structure of ternary amorphous TixSi1-xO2 hybrid oxides.

    PubMed

    Landmann, M; Köhler, T; Rauls, E; Frauenheim, T; Schmidt, W G

    2014-06-25

    Atomic length-scale order characteristics of binary and ternary amorphous oxides are presented within the framework of ab initio theory. A combined numerically efficient density functional based tight-binding molecular dynamics and density functional theory approach is applied to model the amorphous (a) phases of SiO2 and TiO2 as well as the amorphous phase of atomically mixed TixSi1-xO2 hybrid-oxide alloys over the entire composition range. Short and mid-range order in the disordered material phases are characterized by bond length and bond-angle statistics, pair distribution function analysis, coordination number and coordination polyhedra statistics, as well as ring statistics. The present study provides fundamental insights into the order characteristics of the amorphous hybrid-oxide frameworks formed by versatile types of TiOn and SiOm coordination polyhedra. In a-SiO2 the fourfold crystal coordination of Si ions is almost completely preserved and the atomic structure is widely dominated by ring-like mid-range order characteristics. In contrast, the structural disorder of a-TiO2 arises from short-range disorder in the local coordination environment of the Ti ion. The coordination number analysis indicates a large amount of over and under-coordinated Ti ions (coordination defects) in a-TiO2. Aside from the ubiquitous distortions of the crystal-like coordinated polyhedra, even the basic coordination-polyhedra geometry type changes for a significant fraction of TiO6 units (geometry defects). The combined effects of topological and chemical disorder in a-TixSi1-xO2 alloys lead to a continuos increase in both the Si as well as the Ti coordination number with the chemical composition x. The important roles of intermediate fivefold coordination states of Ti and Si cations are highlighted for ternary a-TixSi1-xO2 as well as for binary a-TiO2. The continuous decrease in ring size with increasing Ti content reflects the progressive loss of mid-range order structure

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

    PubMed

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

    2015-01-01

    The measurement conditions for determining boron using graphite furnace-atomic absorption spectrometry (GF-AAS) were investigated. Differences in the boron absorbance profiles were found using three different commercially available GF-AAS instruments when the graphite atomizers in them were not tuned. The boron absorbances found with and without adjusting the graphite atomizers suggested that achieving an adequate absorbance for the determination of boron requires a sharp temperature profile that overshoots the target temperature during the atomization process. Chemical modifiers that could improve the boron absorbance without the need for using coating agents were tested. Calcium carbonate improved the boron absorbance but did not suppress variability in the peak height. Improvement of boron absorbance was comparatively less using iron nitrate or copper nitrate than using calcium carbonate, but variability in the peak height was clearly suppressed using iron nitrate or copper nitrate. The limit of detection was 0.0026 mg L(-1) when iron nitrate was used. It appears that iron nitrate is a useful new chemical modifier for the quick and simple determination of boron using GF-AAS. PMID:25958863

  12. Chemical composition in relation with biomass ash structure

    NASA Astrophysics Data System (ADS)

    Holubcik, Michal; Jandacka, Jozef

    2014-08-01

    Biomass combustion can be more complicated like combustion of fossil fuels because it is necessary to solve problems with lower ash melting temperature. It can cause a lot of problems during combustion process. Chemical composition of biomass ash has great impact on sinters and slags creation in ash because it affects structure of heated ash. In this paper was solved relation between chemical composition and structure of heated ash from three types of biomass (spruce wood, miscanthus giganteus and wheat straw). Amount of SiO2, CaO, MgO, Al2O3 and K2O was determined. Structure of heated ash was optically determined after heating to 1000 °C or 1200 °C. Results demonstrated that chemical composition has strong effect on structure and color of heated ash.

  13. Forgotten topological index of chemical structure in drugs.

    PubMed

    Gao, Wei; Siddiqui, Muhammad Kamran; Imran, Muhammad; Jamil, Muhammad Kamran; Farahani, Mohammad Reza

    2016-05-01

    A massive of early drug tests implies that there exist strong inner relationships between the bio-medical and pharmacology characteristics of drugs and their molecular structures. The forgotten topological index was defined to be used in the analysis of drug molecular structures, which is quite helpful for pharmaceutical and medical scientists to grasp the biological and chemical characteristics of new drugs. Such tricks are popularly employed in developing countries where enough money is lacked to afford the relevant chemical reagents and equipment. In our article, by means of drug molecular structure analysis and edge dividing technology, we present the forgotten topological index of several widely used chemical structures which often appear in drug molecular graphs. PMID:27275112

  14. 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

  15. 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.

  16. 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.

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

    PubMed

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

    2016-03-01

    Magnetic tunnel junctions (MTJs) constitute a promising building block for future nonvolatile memories and logic circuits. Despite their pivotal role, spatially resolving and chemically identifying each individual stacking layer remains challenging due to spatially localized features that complicate characterizations limiting understanding of the physics of MTJs. Here, we combine advanced electron microscopy, spectroscopy, and first-principles calculations to obtain a direct structural and chemical imaging of the atomically confined layers in a CoFeB-MgO MTJ, and clarify atom diffusion and interface structures in the MTJ following annealing. The combined techniques demonstrate that B diffuses out of CoFeB electrodes into Ta interstitial sites rather than MgO after annealing, and CoFe bonds atomically to MgO grains with an epitaxial orientation relationship by forming Fe(Co)-O bonds, yet without incorporation of CoFe in MgO. These findings afford a comprehensive perspective on structure and chemistry of MTJs, helping to develop high-performance spintronic devices by atomistic design. PMID:26905782

  18. 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).

  19. Atomic-scale calculations of interfacial structures and their properties in electronic materials

    NASA Astrophysics Data System (ADS)

    Liang, Tao

    With the tremendous increase in computational power over the last two decades as well as the continuous shrinkage of Si-based Metal Oxide Semiconductor Field Effect Transistors (MOSFET), quantum mechanically based ab initio methods become indispensable tools in nano-scale device engineering. In this work, atomistic simulations including ab initio, nudged elastic band (NEB) and kinetic Monte Carlo methods have been used to (1) calculate the dopant segregation energy at silicon/gate oxide interfaces; (2) characterize the Si:Ge/SiO2 interfacial structure; (3) study the effects of impurity atoms on the diffusion process at Al and Al(Cu) grain boundaries. Using VASP, an ab initio simulation package, we calculated B segregation energy at different atomic sites in perfect and defected Si/SiO 2 interfaces and arsenic segregation energy in Si/LaAlO3 structures. With the presence of O vacancies and H in B doped systems, the predicted segregation energy is 0.85 eV for neutral systems and 1.12 eV for negatively charged systems, which is consistent with experimental measurements (0.51 to 1.47 eV). Recent ab initio structure calculations have examined the stability of various Si(001)/LaAlO3 interfaces and find that a LaO terminated interface with La deficiency or perfect stoichiometry depending on oxygen partial pressure has the lowest energy. Focussing on the La deficient Si/LaAlO3 interfacial structure, we find that the arsenic prefers energetically not to segregate into LaAlO3 nor does it pile up in front of the interface. In combation of atomic-resolution Z-contrast imaging and electron energy loss spectroscopy (EELS), we theorectically calculated the band structure and EELS of a Ge/SiO2 interface. We actually found a chemically abrupt Ge/SiO2 interface, which has never been reported before and which is quite desirable for applications. Furthermore, we formulated a kinetic Monte Carlo model to simulate the oxidation process of Ge ion-implanted Si. Our modeling suggests the

  20. From electron microscopy maps to atomic structures using normal mode-based fitting.

    PubMed

    Hinsen, Konrad; Beaumont, Edward; Fournier, Bertrand; Lacapère, Jean-Jacques

    2010-01-01

    Electron microscopy (EM) has made possible to solve the structure of many proteins. However, the resolution of some of the EM maps is too low for interpretation at the atomic level, which is particularly important to describe function. We describe methods that combine low-resolution EM data with atomic structures for different conformations of the same protein in order to produce atomic models compatible with the EM map.We illustrate these methods with EM data from decavanadate-induced tubular crystals of a pseudo-phosphorylated intermediate of Ca-ATPase and the various atomic structures of other intermediates available in the Protein Data Bank (PDB). Determination of atomic structure permits not only to analyse protein-protein interactions in the crystals, but also to localize residues in the proximity of the crystallizing agent both within Ca-ATPase and between Ca-ATPase molecules. PMID:20665270

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Roland, Elizabeth Anne Edwards

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

  3. Chemical and structural characterization of carbon nanotube surfaces.

    PubMed

    Wepasnick, Kevin A; Smith, Billy A; Bitter, Julie L; Howard Fairbrother, D

    2010-02-01

    To utilize carbon nanotubes (CNTs) in various commercial and scientific applications, the graphene sheets that comprise CNT surfaces are often modified to tailor properties, such as dispersion. In this article, we provide a critical review of the techniques used to explore the chemical and structural characteristics of CNTs modified by covalent surface modification strategies that involve the direct incorporation of specific elements and inorganic or organic functional groups into the graphene sidewalls. Using examples from the literature, we discuss not only the popular techniques such as TEM, XPS, IR, and Raman spectroscopy but also more specialized techniques such as chemical derivatization, Boehm titrations, EELS, NEXAFS, TPD, and TGA. The chemical or structural information provided by each technique discussed, as well as their strengths and limitations. Particular emphasis is placed on XPS and the application of chemical derivatization in conjunction with XPS to quantify functional groups on CNT surfaces in situations where spectral deconvolution of XPS lineshapes is ambiguous. PMID:20052581

  4. CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

    PubMed

    Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

    2014-07-01

    In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

  5. 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

  6. 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.

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

    PubMed

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

    2015-04-28

    We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations. PMID:25933773

  8. 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.

  9. 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)

  10. 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

  11. 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.

  12. 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

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

    NASA Astrophysics Data System (ADS)

    Okada, Kenji

    1996-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Billinge, Simon J. L.

    2008-07-01

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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Langhoff, Peter; Mills, Jeffrey; Boatz, Jerry

    2016-05-01

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

  2. Determination of cadmium in water samples by fast pyrolysis-chemical vapor generation atomic fluorescence spectrometry

    NASA Astrophysics Data System (ADS)

    Zhang, Jingya; Fang, Jinliang; Duan, Xuchuan

    2016-08-01

    A pyrolysis-vapor generation procedure to determine cadmium by atomic fluorescence spectrometry has been established. Under fast pyrolysis, cadmium ion can be reduced to volatile cadmium species by sodium formate. The presence of thiourea enhanced the efficiency of cadmium vapor generation and eliminated the interference of copper. The possible mechanism of vapor generation of cadmium was discussed. The optimization of the parameters for pyrolysis-chemical vapor generation, including pyrolysis temperature, amount of sodium formate, concentration of hydrochloric acid, and carrier argon flow rate were carried out. Under the optimized conditions, the absolute and concentration detection limits were 0.38 ng and 2.2 ng ml- 1, respectively, assuming that 0.17 ml of sample was injected. The generation efficiency of was 28-37%. The method was successfully applied to determine trace amounts of cadmium in two certified reference materials of Environmental Water (GSB07-1185-2000 and GSBZ 50009-88). The results were in good agreement with the certified reference values.

  3. Analysis of atomic scale chemical environments of boron in coal by 11B solid state NMR.

    PubMed

    Takahashi, Takafumi; Kashiwakura, Shunsuke; Kanehashi, Koji; Hayashi, Shunichi; Nagasaka, Tetsuya

    2011-02-01

    Atomic scale chemical environments of boron in coal has been studied by solid state NMR spectroscopy including magic angle spinning (MAS), satellite transition magic angle spinning (STMAS), and cross-polarization magic angle spinning (CPMAS). The (11)B NMR spectra can be briefly classified according to the degree of coalification. On the (11)B NMR spectra of lignite, bituminous, and sub-bituminous coals (carbon content of 70-90mass%), three sites assigned to four-coordinate boron ([4])B with small quadrupolar coupling constants (≤0.9 MHz) are observed. Two of the ([4])B sites in downfield are considered organoboron complexes with aromatic ligands, while the other in the most upper field is considered inorganic tetragonal boron (BO(4)). By contrast, on the (11)B NMR spectra of blind coal (carbon content >90mass%), the ([4])B which substitutes tetrahedral silicon of Illite is observed as a representative species. It has been considered that the organoboron is decomposed and released from the parent phase with the advance of coal maturation, and then the released boron reacts with the inorganic phase to substitute an element of inorganic minerals. Otherwise boron contained originally in inorganic minerals might remain preserved even under the high temperature condition that is generated during coalification. PMID:21175186

  4. Increase in the power of lasing on atomic and ion transitions in chemical elements

    SciTech Connect

    Klimkin, V M; Sokovikov, V G

    2007-02-28

    A method for increasing the power of pulsed lasing on atomic and ion transitions in chemical elements obtained by the conversion of the UV radiation of excimer lasers in cells with metal vapours is studied. A part of UV radiation transmitted through a cell with metal vapour is used for pumping a dye solution in such a way that the cell converter with metal vapour represents a master oscillator, while the dye cell represents an amplifier. The study is performed by the example of amplification of weak spectral components of radiation from a XeCl* laser converted in mercury and barium vapours. In the amplifying stage the longitudinal pumping of the dye is used and a scheme for suppressing self-excitation is employed. It is found by selecting dyes that the alcohol solution of uranin is nearly optimal for amplification of the 546.1-nm laser line of mercury, while the best results in amplification of the 533-nm and 648.2-nm laser lines of barium were obtained by using alcohol solutions of rhodamine 6G and oxazine 17, respectively. The power of the 546.1-nm mercury line was increased by an order of magnitude, while the power of the 533-nm and 648.2-nm lines of barium - almost by a factor of twenty-five. (lasers)

  5. 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

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

    PubMed

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

    2014-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    Suewattana, Malliga

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

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

    SciTech Connect

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

    2012-03-09

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

  9. Structure, Chemical Synthesis, and Biosynthesis of Prodiginine Natural Products.

    PubMed

    Hu, Dennis X; Withall, David M; Challis, Gregory L; Thomson, Regan J

    2016-07-27

    The prodiginine family of bacterial alkaloids is a diverse set of heterocyclic natural products that have likely been known to man since antiquity. In more recent times, these alkaloids have been discovered to span a wide range of chemical structures that possess a number of interesting biological activities. This review provides a comprehensive overview of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, research toward chemical synthesis of the prodiginine alkaloids over the last several decades is extensively reviewed. Finally, the current, evidence-based understanding of the various biosynthetic pathways employed by bacteria to produce prodiginine alkaloids is summarized. PMID:27314508

  10. The atomic and electronic structure of nitrogen- and boron-doped phosphorene.

    PubMed

    Boukhvalov, Danil W

    2015-10-28

    First principles modeling of nitrogen- and boron-doped phosphorene demonstrates the tendency toward the formation of highly ordered structures. Nitrogen doping leads to the formation of -N-P-P-P-N- lines. Further transformation into -P-N-P-N- lines across the chains of phosphorene occurs with increasing band gap and increasing nitrogen concentration, which coincides with the decreasing chemical activity of N-doped phosphorene. In contrast to the case of nitrogen, boron atoms prefer to form -B-B- pairs with the further formation of -P-P-B-B-P-P- patterns along the phosphorene chains. The low concentration of boron dopants converts the phosphorene from a semiconductor into a semimetal with the simultaneous enhancement of its chemical activity. Co-doping of phosphorene by both boron and nitrogen starts from the formation of -B-N- pairs, which provides flat bands and further transformation of these pairs into hexagonal BN lines and ribbons across the phosphorene chains. PMID:26417893

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2007-11-01

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

  13. Spectacular enhancement of thermoelectric phenomena in chemically synthesized graphene nanoribbons with substitution atoms.

    PubMed

    Zberecki, K; Swirkowicz, R; Wierzbicki, M; Barnaś, J

    2016-07-21

    We analyze theoretically the transport and thermoelectric properties of graphene nanoribbons of a specific geometry, which have been synthesized recently from polymers [Cai, et al., Nature, 2011, 466, 470]. When such nanoribbons are modified at one of the two edges by Al or N substitutions, they acquire a ferromagnetic moment localized at the modified edge. We present numerical results on the electronic structure and thermoelectric properties (including also spin thermoelectricity) of the modified nanoribbons. The results show that such nanoribbons can display large thermoelectric efficiency in certain regions of chemical potential, where the corresponding electric and spin figures of merit achieve unusually large values. The enhancement of thermoelectric efficiency follows from a reduced phonon heat conductance of the nanoribbons and from their peculiar electronic band structure. Thus, such nanoribbons are promising for practical applications in nanoelectronic and spintronic devices. PMID:27331357

  14. 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

  15. 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.}

  16. NMR structure note: Structure of the Membrane Protein MerF, a Bacterial Mercury Transporter, Improved by the Inclusion of Chemical Shift Anisotropy Constraints

    PubMed Central

    Tian, Ye; Lu, George J.; Marassi, Francesca M.; Opella, Stanley J.

    2014-01-01

    SUMMARY MerF is a mercury transport membrane protein from the bacterial mercury detoxification system. By performing a solid-state INEPT experiment and measuring chemical shift anisotropy frequencies in aligned samples, we are able to improve on the accuracy and precision of the initial structure that we presented. MerF has four N-terminal and eleven C-terminal residues that are mobile and unstructured in phospholipid bilayers. The structure presented here has average pairwise RMSDs of 1.78 Å for heavy atoms and 0.92 Å for backbone atoms. PMID:25103921

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

    ERIC Educational Resources Information Center

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

    2002-01-01

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

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

    ERIC Educational Resources Information Center

    Park, Eun Jung; Light, Gregory

    2009-01-01

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

  19. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation

    PubMed Central

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

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures. PMID:18787110

  20. 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.

  1. 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

  2. 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

  3. Ultrathin atomic vapor film transmission spectroscopy: analysis of Dicke narrowing structure

    NASA Astrophysics Data System (ADS)

    Li, Yuanyuan; Zhang, Yanpeng; Gan, Chenli

    2005-11-01

    Transmission sub-Doppler spectroscopy with confined atomic vapor film between two dielectric walls is theoretically studied. Because of atoms flying from wall to wall, where they get de-excited, the atom-field interaction time is anisotropic so that the contribution of slow atoms is enhanced, a sub-Doppler transmission spectroscopy (Dicke narrowing effect) can be obtained when the thickness of the film is much small or comparable with the wavelength even at small angle oblique incidence. It is feasible to get a sub-Doppler structure in a new region (L < ?/4) in experiments.

  4. 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.

  5. 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.

  6. Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes.

    PubMed

    Ismer, Jochen; Rose, Alexander S; Tiemann, Johanna K S; Goede, Andrean; Rother, Kristian; Hildebrand, Peter W

    2013-01-01

    Voronoia4RNA (http://proteinformatics.charite.de/voronoia4rna/) is a structural database storing precalculated atomic volumes, atomic packing densities (PDs) and coordinates of internal cavities for currently 1869 RNAs and RNA-protein complexes. Atomic PDs are a measure for van der Waals interactions. Regions of low PD, containing water-sized internal cavities, refer to local structure flexibility or compressibility. RNA molecules build up the skeleton of large molecular machineries such as ribosomes or form smaller flexible structures such as riboswitches. The wealth of structural data on RNAs and their complexes allows setting up representative data sets and analysis of their structural features. We calculated atomic PDs from atomic volumes determined by the Voronoi cell method and internal cavities analytically by Delaunay triangulation. Reference internal PD values were derived from a non-redundant sub-data set of buried atoms. Comparison of internal PD values shows that RNA is more tightly packed than proteins. Finally, the relation between structure size, resolution and internal PD of the Voronoia4RNA entries is discussed. RNA, protein structures and their complexes can be visualized by the Jmol-based viewer Provi. Variations in PD are depicted by a color code. Internal cavities are represented by their molecular boundaries or schematically as balls. PMID:23161674

  7. 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

  8. 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…

  9. 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…

  10. 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.

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

    SciTech Connect

    Curtis, L. J.

    2004-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Barton, Jeffrey Thomas

    Processes for depositing thin films with various electronic, optical, mechanical, and chemical properties are indispensable in many industries today. Of the many deposition methods available, chemical vapor deposition (CVD) has proved over time to be one of the most flexible, efficient, and cost-effective. Atomic layer deposition (ALD) is a newer process that is gaining favor as a method for depositing films with excellent properties and unparalleled precision. This work describes the development of novel CVD and ALD processes to deposit a variety of materials. Hafnium oxide and zirconium oxide show promise as replacements for SiO 2 as gate dielectrics in future-generation transistors. These high-k materials would provide sufficient capacitance with layers thick enough to avoid leakage from tunneling. An ALD method is presented here for depositing conformal hafnium oxide from tetrakis-(diethylamido)hafnium and oxygen gas. A CVD method for depositing zirconium oxide from tetrakis-(dialkylamido)zirconium and either oxygen gas or water vapor is also described. The use of copper for interconnects in integrated circuits requires improved diffusion barrier materials, given its high diffusivity compared to the previously-used aluminum and tungsten. Tungsten nitride has a low resistivity among barrier materials, and can be deposited in amorphous films that are effective diffusion barriers in layers as thin as a few nanometers. Here we demonstrate CVD and plasma-enhanced CVD methods to deposit tungsten nitride films from bis-(dialkylamido)bis-( tert-butylimido)tungsten precursors and ammonia gas. Recent findings had shown uniform copper growth on tantalum silicate films, without the dewetting that usually occurs on oxide surfaces. Tantalum and tungsten silicates were deposited by a CVD reaction from the reaction of either tris-(diethylamido)ethylimido tantalum or bis-(ethylmethylamido)-bis-( tert-butylimido)tungsten with tris-(tert-butoxy)silanol. The ability of evaporated

  13. 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

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

    PubMed

    Aguado, Andrés; López, José M

    2010-09-01

    The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions. PMID:20831313

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  16. 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

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

    PubMed

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

    2015-01-01

    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

  18. Weighted voting-based consensus clustering for chemical structure databases.

    PubMed

    Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

    2014-06-01

    The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures. PMID:24830925

  19. 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

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Driver, Marcus Sky

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

  3. Effects of atomic oxygen treatment on structures, morphologies and electrical properties of ZnO:Al films

    NASA Astrophysics Data System (ADS)

    Wang, Wenwen; Li, Chunzhi; Zhang, Junying; Diao, Xungang

    2010-05-01

    ZnO:Al (ZAO) film has a potential application in providing spacecrafts the protection against atomic oxygen (AO) erosion. To advance the understanding of the AO resisting mechanisms and the relationships between the structures, morphologies and conductive properties of ZAO film, direct current magnetron sputtered ZAO films with different thicknesses were treated with AO in a ground-based simulation facility. The microstructure, surface chemical state, morphologies and electrical properties of pristine films and irradiated ones were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, atomic force microscopy and Hall measurement. It is found that AO exposure produces novel, oriented recrystallization of the surface particles. It also increases the content of oxygen ions in fully oxidized stoichiometric surroundings on the surface, resulting in the decrease of the conductivity. As the thickness of ZAO film increases, the crystallinity, conductivity and resistance to AO erosion are all improved.

  4. Comparison of structures of gas atomized and of emulsified highly undercooled Ni-Sn alloy droplets

    NASA Technical Reports Server (NTRS)

    Yamamoto, M.; Wu, Y.; Shiohara, Y.; Flemings, M. C.

    1986-01-01

    A comparison is made of microstructures of droplets of Ni-Sn alloys rapidly solidified by gas atomization and in a glass emulsifying medium. Cooling rate of the gas atomized particles ranged from 10 to the 3rd to 10 to the 6th K/s depending on droplet diameter (20-230 microns). In the hypoeutectic alloy studied, /Ni-(25 wt pct Sn)/, most particles showed a dendritic structure. These same particles, melted and resolidified in a glass medium using DTA (Differential Thermal Analysis), showed undercoolings up to 280 K: the structures were dendritic at low undercoolings and nondendritic at undercoolings above 220 K. It is concluded that the gas atomized particles exhibited little or no undercooling before nucleation; the solidification time of the undercooled emulsified droplets is substantially less than that of gas atomized droplets, and the undercooling required to achieve nondendritic structure depends on sample size.

  5. 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.

  6. 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.

  7. 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.

  8. Structure-activity relationship analysis of N-benzoylpyrazoles for elastase inhibitory activity: a simplified approach using atom pair descriptors.

    PubMed

    Khlebnikov, Andrei I; Schepetkin, Igor A; Quinn, Mark T

    2008-03-15

    Previously, we utilized high throughput screening of a chemical diversity library to identify potent inhibitors of human neutrophil elastase and found that many of these compounds had N-benzoylpyrazole core structures. We also found individual ring substituents had significant impact on elastase inhibitory activity and compound stability. In the present study, we utilized computational structure-activity relationship (SAR) analysis of a series of 53 N-benzoylpyrazole derivatives to further optimize these lead molecules. We present an improved approach to SAR methodology based on atom pair descriptors in combination with 2-dimensional (2D) molecular descriptors. This approach utilizes the rich representation of chemical structure and leads to SAR analysis that is both accurate and intuitively easy to understand. A sequence of ANOVA, linear discriminant, and binary classification tree analyses of the molecular descriptors led to the derivation of SAR rule-based algorithms. These rules revealed that the main factors influencing elastase inhibitory activity of N-benzoylpyrazole molecules were the presence of methyl groups in the pyrazole moiety and ortho-substituents in the benzoyl radical. Furthermore, our data showed that physicochemical characteristics (energy of frontier molecular orbitals, molar refraction, lipophilicity) were not necessary for achieving good SAR, as comparable quality of SAR classification was obtained with atom pairs and 2D descriptors only. This simplified SAR approach may be useful to qualitative SAR recognition problems in a variety of data sets. PMID:18234502

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Senga, Ryosuke; Komsa, Hannu-Pekka; Liu, Zheng; Hirose-Takai, Kaori; Krasheninnikov, Arkady V.; Suenaga, Kazu

    2014-11-01

    Materials with reduced dimensionality have attracted much interest in various fields of fundamental and applied science. True one-dimensional (1D) crystals with single-atom thickness have been realized only for few elemental metals (Au, Ag) or carbon, all of which showed very short lifetimes under ambient conditions. We demonstrate here a successful synthesis of stable 1D ionic crystals in which two chemical elements, one being a cation and the other an anion, align alternately inside carbon nanotubes. Unusual dynamical behaviours for different atoms in the 1D lattice are experimentally corroborated and suggest substantial interactions of the atoms with the nanotube sheath. Our theoretical studies indicate that the 1D ionic crystals have optical properties distinct from those of their bulk counterparts and that the properties can be engineered by introducing atomic defects into the chains.

  12. 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.

  13. 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 metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  14. Applications of the Cambridge Structural Database in chemical education.

    PubMed

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

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  15. 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.

  16. Finding the minimum-energy atomic configuration in large multi-atom structures: Genetic Algorithm versus the Virtual-Atom Approach

    NASA Astrophysics Data System (ADS)

    D'Avezac, Mayeul; Zunger, Alex

    2007-03-01

    In many problems in molecular and solid state structures one needs to determine the energy-minimizing decoration of sites by different atom-types (i. e.configuration). The sheer size of this configurational space can be horrendous even if the underlying lattice-type is known. The ab-initio total-energy surface for different (relaxed) configurations can often be parameterized by a spin-like Hamiltonian (Cluster-Expansion) with discrete spin -variables denoting the type of atom occupying each site. We compare two search strategies for the energy-minimizing configuration: (i) A discrete-variable genetic-algorithm approach( S. V. Dudiy and A. Zunger, PRL 97, 046401 (2006) ) and (ii) a continuous-variable approach (M. Wang et al, J. Am. Chem. Soc. 128, 3228 (2006) ) where the discrete-spin functional is mapped onto a continuous-spin functional (virtual atoms) and the search is guided by local gradients with respect to each spin. We compare their efficiency at locating the ground-state configurations of fcc Au-Pd Alloy in terms of number of calls to the functional. We show that a GA approach with diversity-enhancing constraints and reciprocal-space mating easily outperforms the VA approach.

  17. 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

  18. Electronic structure and magnetic properties of substitutional transition-metal atoms in GaN nanotubes

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Shi, Jun-Jie

    2014-01-01

    The electronic structure and magnetic properties of the transition-metal (TM) atoms (Sc—Zn, Pt and Au) doped zigzag GaN single-walled nanotubes (NTs) are investigated using first-principles spin-polarized density functional calculations. Our results show that the bindings of all TM atoms are stable with the binding energy in the range of 6-16 eV. The Sc- and V-doped GaN NTs exhibit a nonmagnetic behavior. The GaN NTs doped with Ti, Mn, Ni, Cu and Pt are antiferromagnetic. On the contrary, the Cr-, Fe-, Co-, Zn- and Au-doped GaN NTs show the ferromagnetic characteristics. The Mn- and Co-doped GaN NTs induce the largest local moment of 4μB among these TM atoms. The local magnetic moment is dominated by the contribution from the substitutional TM atom and the N atoms bonded with it.

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

    NASA Astrophysics Data System (ADS)

    Ünlü, Pervin

    2010-07-01

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

  20. Ultracold Chemical Reactions of a Single Rydberg Atom in a Dense Gas

    NASA Astrophysics Data System (ADS)

    Schlagmüller, Michael; Liebisch, Tara Cubel; Engel, Felix; Kleinbach, Kathrin S.; Böttcher, Fabian; Hermann, Udo; Westphal, Karl M.; Gaj, Anita; Löw, Robert; Hofferberth, Sebastian; Pfau, Tilman; Pérez-Ríos, Jesús; Greene, Chris H.

    2016-07-01

    Within a dense environment (ρ ≈1014 atoms /cm3 ) at ultracold temperatures (T <1 μ K ), a single atom excited to a Rydberg state acts as a reaction center for surrounding neutral atoms. At these temperatures, almost all neutral atoms within the Rydberg orbit are bound to the Rydberg core and interact with the Rydberg atom. We have studied the reaction rate and products for n S 87Rb Rydberg states, and we mainly observe a state change of the Rydberg electron to a high orbital angular momentum l , with the released energy being converted into kinetic energy of the Rydberg atom. Unexpectedly, the measurements show a threshold behavior at n ≈100 for the inelastic collision time leading to increased lifetimes of the Rydberg state independent of the densities investigated. Even at very high densities (ρ ≈4.8 ×1014 cm-3 ), the lifetime of a Rydberg atom exceeds 10 μ s at n >140 compared to 1 μ s at n =90 . In addition, a second observed reaction mechanism, namely, Rb2+ molecule formation, was studied. Both reaction products are equally probable for n =40 , but the fraction of Rb2+ created drops to below 10% for n ≥90 .

  1. 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

  2. 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

  3. Regularities and symmetries in atomic structure and spectra

    NASA Astrophysics Data System (ADS)

    Pain, Jean-Christophe

    2013-09-01

    The use of statistical methods for the description of complex quantum systems was primarily motivated by the failure of a line-by-line interpretation of atomic spectra. Such methods reveal regularities and trends in the distributions of levels and lines. In the past, much attention was paid to the distribution of energy levels (Wigner surmise, random-matrix model…). However, information about the distribution of the lines (energy and strength) is lacking. Thirty years ago, Learner found empirically an unexpected law: the logarithm of the number of lines whose intensities lie between 2kI0 and 2k+1I0, I0 being a reference intensity and k an integer, is a decreasing linear function of k. In the present work, the fractal nature of such an intriguing regularity is outlined and a calculation of its fractal dimension is proposed. Other peculiarities are also presented, such as the fact that the distribution of line strengths follows Benford's law of anomalous numbers, the existence of additional selection rules (PH coupling), the symmetry with respect to a quarter of the subshell in the spin-adapted space (LL coupling) and the odd-even staggering in the distribution of quantum numbers, pointed out by Bauche and Cossé.

  4. 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.

  5. 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.

  6. Atomic structure of interface states in silicon heterojunction solar cells.

    PubMed

    George, B M; Behrends, J; Schnegg, A; Schulze, T F; Fehr, M; Korte, L; Rech, B; Lips, K; Rohrmüller, M; Rauls, E; Schmidt, W G; Gerstmann, U

    2013-03-29

    Combining orientation dependent electrically detected magnetic resonance and g tensor calculations based on density functional theory we assign microscopic structures to paramagnetic states involved in spin-dependent recombination at the interface of hydrogenated amorphous silicon crystalline silicon (a-Si:H/c-Si) heterojunction solar cells. We find that (i) the interface exhibits microscopic roughness, (ii) the electronic structure of the interface defects is mainly determined by c-Si, (iii) we identify the microscopic origin of the conduction band tail state in the a-Si:H layer, and (iv) present a detailed recombination mechanism. PMID:23581355

  7. 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.

  8. Chemical compatibility of structural materials in alkali metals

    SciTech Connect

    Natesan, K.; Rink, D.L.; Haglund, R.

    1995-04-01

    The objectives of this task are to (a) evaluate the chemical compatibility of structural alloys such as V-5 wt.%Cr-5 wt.%Ti alloy and Type 316 stainless steel for application in liquid alkali metals such as lithium and sodium-78 wt.% potassium (NaK) at temperatures in the range that are of interest for International Thermonuclear Experimental Reactor (ITER); (b) evaluate the transfer of nonmetallic elements such as oxygen, nitrogen, carbon, and hydrogen between structural materials and liquid metals; and (c) evaluate the effects of such transfers on the mechanical and microstructural characteristics of the materials for long-term service in liquid-metal-environments.

  9. 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.

  10. 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.

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

    SciTech Connect

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

    2013-12-12

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

  12. 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

  13. Structure stabilities and transitions in polyhedral metal nanocrystals: An atomic-bond-relaxation approach

    NASA Astrophysics Data System (ADS)

    Zhang, Ai; Zhu, Ziming; He, Yan; Ouyang, Gang

    2012-04-01

    We present an atomic-bond-relaxation (ABR) method to illustrate a deeper insight on structure stabilities and transitions of metal nanocrystals with polyhedral structure based on the thermodynamic consideration. It has been found that the end effects in polyhedral nanocrystals induced by the atoms located at edges, side facets, and vertexes play the dominant roles for their structure performances. The theoretical predictions are well consistent with the experimental measurements and simulations, which suggest the ABR model can be an effective method to understand solid-solid phase transition of polyhedral metal nanocrystals.

  14. Atomic structure and electronic properties of Ni3Al(111) and (011) surfaces

    NASA Astrophysics Data System (ADS)

    Jurczyszyn, L.; Krupski, A.; Degen, S.; Pieczyrak, B.; Kralj, M.; Becker, C.; Wandelt, K.

    2007-07-01

    We present results of theoretical studies of the structural and electronic properties of (111) and (011) surfaces of paramagnetic Ni3Al alloy. Atomic and electronic structures of these surfaces have been obtained from the density-functional calculations performed with the use of plane wave basis set. Our ab initio calculations show that for all considered surfaces, the topmost Al atoms are located above Ni atoms, and the structural parameters of relaxed surface systems well correspond to experimental data provided by earlier low-energy electron-diffraction measurements. The details of the calculated electronic structure of Ni3Al(111) in the vicinity of the Fermi level were compared with the results of scanning tunneling spectroscopy (STS) measurements which we have performed for this system, and a good agreement has been found between the calculated local-density-of-states distributions and the shape of obtained STS spectra.

  15. 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

  16. Organohelium compounds: structures, stabilities and chemical bonding analyses.

    PubMed

    Fourré, Isabelle; Alvarez, Elsa; Chaquin, Patrick

    2014-02-24

    This paper deals with the possibility of forming short and relatively strong carbon-helium bonds in small typical organic molecules through substitution of one or several H atoms by He(+). A structural and energetics study (based on high-level calculations) of this unusual bonding, as well as a topological characterization of the resulting cations, is undertaken. Stable species generally requires substitution of about half of the hydrogen atoms for formation. Under these conditions, the number of such species appears to be potentially unlimited. "True" C-He bonds exhibit equilibrium distances ranging from 1.327 (C2H2He2(2+)) to 1.129 Å (He2CO(2+)). The energies of neutral He releasing range from approximately 5 kcal mol(-1) [He2CO(2+), (Z)-C2H2He2(2+)] to 25 kcal mol(-1) (C2HHe3(3+)), but remain most frequently around 10 kcal mol(-1). However, most of He(+)-substituted hydrocarbons are metastable with respect to C-C cleavage, except derivatives of ethene. Atoms in molecules (AIM) and electron localization function (ELF) topological descriptors classify the C-He bond as a weak charge-shift interaction [S. Shaik, D. Danovich, B. Silvi, D. L. Lauvergnat, P. C. Hiberty, Chem. Eur. J. 2005, 11, 6358-6371] in agreement with a recent publication by Rzepa [S. H. Rzepa, Nat. Chem. 2010, 2, 390-393]. He2CO(2+) is the only investigated compound that presents a C-He bonding ELF basin, which indicates a non-negligible covalent contribution to the bond. Other modifications in the electronic structure, such as the breaking of the triple bond in ethyne derivatives or the loss of aromaticity in C6H3He3(3+), are also nicely revealed by the ELF topology. PMID:24488791

  17. Energy losses of fast heavy multiply charged structural ions in collisions with complex atoms

    NASA Astrophysics Data System (ADS)

    Matveev, V. I.; Sidorov, D. B.

    2007-07-01

    A nonperturbatve theory of energy losses of fast heavy multiply charged structural ions in collisions with neutral complex atoms is elaborated with allowance for simultaneous excitations of ionic and atomic electron shells. Formulas for the effective deceleration that are similar to the well-known Bethe-Bloch formulas are derived. By way of example, the energy lost by partially stripped U q+ ions (10 ≤ q ≤ 70) colliding with argon atoms and also the energy lost by Au, Pb, and Bi ions colliding with various targets are calculated. The results of calculation are compared with experimental data.

  18. 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.

  19. 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.

  20. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Wu, X.; Sha, W.

    2008-12-01

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.

  1. New horizons in chemical propulsion. [processes using free radicals, atomic hydrogen, excited species, etc

    NASA Technical Reports Server (NTRS)

    Cohen, W.

    1973-01-01

    After a review of the work of the late-Fifties on free radicals for propulsion, it is concluded that atomic hydrogen would provide a potentially large increase in specific impulse. Work conducted to find an approach for isolating atomic hydrogen is considered. Other possibilities for obtaining propellants of greatly increased capability might be connected with the technology for the generation of activated states of gases, metallic hydrogen, fuels obtained from other planets, and laser transfer of energy.

  2. Structure-activity Relationship Analysis of N-Benzoylpyrazoles for Elastase Inhibitory Activity: A Simplified Approach Using Atom Pair Descriptors

    PubMed Central

    Khlebnikov, Andrei I.; Schepetkin, Igor A.; Quinn, Mark T.

    2008-01-01

    Previously, we utilized high throughput screening of a chemical diversity library to identify potent inhibitors of human neutrophil elastase and found that many of these compounds had N-benzoylpyrazole core structures. We also found individual ring substituents had significant impact on elastase inhibitory activity and compound stability. In the present study, we utilized computational structure–activity relationship (SAR) analysis of a series of 53 N-benzoylpyrazole derivatives to further optimize these lead molecules. We present an improved approach to SAR methodology based on atom pair descriptors in combination with 2-dimentional (2D) molecular descriptors. This approach utilizes the rich representation of chemical structure and leads to SAR analysis that is both accurate and intuitively easy to understand. A sequence of ANOVA, linear discriminant, and binary classification tree analyses of the molecular descriptors led to the derivation of SAR rule-based algorithms. These rules revealed that the main factors influencing elastase inhibitory activity of N-benzoylpyrazole molecules were the presence of methyl groups in the pyrazole moiety and ortho-substituents in the benzoyl radical. Furthermore, our data showed that physicochemical characteristics (energy of frontier molecular orbitals, molar refraction, lipophilicity) were not necessary for achieving good SAR, as comparable quality of SAR classification was obtained with atom pairs and 2D descriptors only. This simplified SAR approach may be useful to qualitative SAR recognition problems in a variety of data sets. PMID:18234502

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

    PubMed Central

    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 population 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. PMID:22312477

  4. Structure and dynamics of dinucleosomes assessed by atomic force microscopy.

    PubMed

    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 population 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. PMID:22312477

  5. 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

  6. Structure of magnetic resonance in 87Rb atoms

    NASA Astrophysics Data System (ADS)

    Kozlov, A. N.; Zibrov, S. A.; Zibrov, A. A.; Yudin, V. I.; Taichenachev, A. V.; Yakovlev, V. P.; Tsygankov, E. A.; Zibrov, A. S.; Vassiliev, V. V.; Velichansky, V. L.

    2016-05-01

    Magnetic resonance at the F g = 1 rightleftarrows F e = 1 transition of the D 1 line in 87Rb has been studied with pumping and detection by linearly polarized radiation and detection at the double frequency of the radiofrequency field. The intervals of allowed values of the static and alternating magnetic fields in which magnetic resonance has a single maximum have been found. The structure appearing beyond these intervals has been explained. It has been shown that the quadratic Zeeman shift is responsible for the three-peak structure of resonance; the radiofrequency shift results in the appearance of additional extrema in resonance, which can be used to determine the relaxation constant Γ2. The possibility of application in magnetometry has been discussed.

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

    NASA Astrophysics Data System (ADS)

    Park, Eun Jung

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

  8. Fractional Band Filling in an Atomic Chain Structure

    NASA Astrophysics Data System (ADS)

    Crain, J. N.; Kirakosian, A.; Altmann, K. N.; Bromberger, C.; Erwin, S. C.; McChesney, J. L.; Lin, J.-L.; Himpsel, F. J.

    2003-05-01

    A new chain structure of Au is found on stepped Si(111) which exhibits a 1/4-filled band and a pair of ≥1/2-filled bands with a combined filling of 4/3. Band dispersions and Fermi surfaces for Si(553)-Au are obtained by photoemission and compared to that of Si(557)-Au. The dimensionality of both systems is determined using a tight binding fit. The fractional band filling makes it possible to preserve metallicity in the presence of strong correlations.

  9. 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.

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

    SciTech Connect

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

    2015-04-03

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

  11. Hydrogen atoms under magnification: direct observation of the nodal structure of Stark states.

    PubMed

    Stodolna, A S; Rouzée, A; Lépine, F; Cohen, S; Robicheaux, F; Gijsbertsen, A; Jungmann, J H; Bordas, C; Vrakking, M J J

    2013-05-24

    To describe the microscopic properties of matter, quantum mechanics uses wave functions, whose structure and time dependence is governed by the Schrödinger equation. In atoms the charge distributions described by the wave function are rarely observed. The hydrogen atom is unique, since it only has one electron and, in a dc electric field, the Stark Hamiltonian is exactly separable in terms of parabolic coordinates (η, ξ, φ). As a result, the microscopic wave function along the ξ coordinate that exists in the vicinity of the atom, and the projection of the continuum wave function measured at a macroscopic distance, share the same nodal structure. In this Letter, we report photoionization microscopy experiments where this nodal structure is directly observed. The experiments provide a validation of theoretical predictions that have been made over the last three decades. PMID:23745864

  12. Direct determination of cadmium in Orujo spirit samples by electrothermal atomic absorption spectrometry: comparative study of different chemical modifiers.

    PubMed

    Vilar Fariñas, M; Barciela García, J; García Martín, S; Peña Crecente, R; Herrero Latorre, C

    2007-05-22

    In this work, several analytical methods are proposed for cadmium determination in Orujo spirit samples using electrothermal atomic absorption spectrometry (ETAAS). Permanent chemical modifiers thermally coated on the platforms inserted in pyrolytic graphite tubes (such as W, Ir, Ru, W-Ir and W-Ru) were comparatively studied in relation to common chemical modifier mixtures [Pd-Mg(NO3)2 and (NH4)H2PO4-Mg(NO3)2] for cadmium stabilization. Different ETAAS Cd determination methods based on the indicated modifiers have been developed. In each case, pyrolysis and atomization temperatures, atomization shapes, characteristic masses and detection limits as well as other analytical characteristics have been determined. All the assayed modifiers (permanent and conventional) were capable of achieving the appropriate stabilization of the analyte, with the exception of Ru and W-Ru. Moreover, for all developed methods, recoveries (99-102%) and precision (R.S.D. lower than 10%) were acceptable. Taking into account the analytical performance (best detection limit LOD = 0.01 microg L(-1)), the ETAAS method based on the use of W as a permanent modifier was selected for further direct Cd determinations in Orujo samples from Galicia (NW Spain). The chosen method was applied in the determination of the Cd content in 38 representative Galician samples. The cadmium concentrations ranged

  13. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    PubMed Central

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-01-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature. PMID:27220411

  14. Atomic-scale study of lateral graphene/h-BN hybrid structure

    NASA Astrophysics Data System (ADS)

    Lee, Jaekwang; Park, Jewook; Li, An-Ping; Yoon, Mina

    2014-03-01

    Recently, atomically sharp 1D interfaces have been successfully implemented in lateral graphene/hexagonal boron nitride (h-BN) hybrid structures. Graphene/h-BN interfaces are of particular interest, because their bandgap and magnetic properties can be engineered by controlling the arrangement of nonmagnetic B, C and N atoms. Despite the enormous interest in graphene/h-BN, there has been very limited experimental success in determining the local atomic structure of the graphene/h-BN interface. Here, using state-of-the-art scanning tunneling microscopy, we report the direct and precise observation of a graphene/h-BN interface bonding structure at the atomic scale. Based on the detailed atomic structure, first-principles density-functional calculations show that graphene zigzag edge states and the h-BN polarity are strongly coupled to each other near the interface and induce spatial modulation of physical properties along the lateral direction. In addition, we investigate how the d-orbitals of metal surfaces (Cu (111), Cu (001)) and the pi-orbital of graphene/h-BN hybridize and predict resulting modification of the electronic properties of graphene/h-BN. This research was conducted at the CNMS, which is sponsored at ORNL by the Office of Basic Energy Sciences, U.S. Department of Energy. We acknowledge partial support provided by a Laboratory Directed Research and Development award (#7004).

  15. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures.

    PubMed

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-01-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature. PMID:27220411

  16. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    NASA Astrophysics Data System (ADS)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  18. 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.

  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. 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

  1. Ab initio prediction of protein structure with both all-atom and simplified force fields

    NASA Astrophysics Data System (ADS)

    Scheraga, Harold

    2004-03-01

    Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.

  2. Atomic calculations and search for variation of the fine-structure constant in quasar absorption spectra

    NASA Astrophysics Data System (ADS)

    Dzuba, V. A.; Flambaum, V. V.

    A brief review of the search for variation of the fine structure constant in quasar absorption spectra is presented. Special consideration is given to the role of atomic calculations in the analysis of the observed data. A range of methods which allow to perform calculations for atoms or ions with different electron structure and which cover practically all periodic table of elements is discussed. Critical compilation of the results of the calculations as well as a review of the most recent results of the analysis are presented.

  3. Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

    PubMed Central

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

    2007-01-01

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

  4. Structural and chemical profiling of the human cytosolic sulfotransferases.

    PubMed

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

    2007-05-01

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

  5. 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.

  6. 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.

  7. Atomic calligraphy: the direct writing of nanoscale structures using a microelectromechanical system.

    PubMed

    Imboden, Matthias; Han, Han; Chang, Jackson; Pardo, Flavio; Bolle, Cristian A; Lowell, Evan; Bishop, David J

    2013-07-10

    We present a microelectromechanical system (MEMS) based method for the resist-free patterning of nanostructures. Using a focused ion beam to customize larger MEMS machines, we fabricate apertures with features less than 50 nm in diameter on plates that can be moved with nanometer precision over an area greater than 20 × 20 μm(2). Depositing thermally evaporated gold atoms though the apertures while moving the plate results in the deposition of nanoscale metal patterns. Adding a shutter positioned micrometers above the aperture enables high speed control of not only where but also when atoms are deposited. With this shutter, different-sized apertures can be opened and closed selectively for nanostructure fabrication with features ranging from nano- to micrometers in scale. The ability to evaporate materials with high precision, and thereby fabricate circuits and structures in situ, enables new kinds of experiments based on the interactions of a small number of atoms and eventually even single atoms. PMID:23782403

  8. 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.

  9. Atomic and electronic structure of the corundum (0001) surface: comparison with surface spectroscopies

    NASA Astrophysics Data System (ADS)

    Puchin, V. E.; Gale, J. D.; Shluger, A. L.; Kotomin, E. A.; Günster, J.; Brause, M.; Kempter, V.

    1997-01-01

    The electronic structure and geometry of the Al-terminated corundum (0001) surface were studied using a slab model within the ab-initio Hartree-Fock technique. The distance between the top Al plane and the next O basal plane is found to be considerably reduced on relaxation (by 0.57 Å, i.e. by 68% of the corresponding interlayer distance in the bulk). An interpretation of experimental photoelectron spectra (UPS He I) and metastable impact electron spectra (MIES) is given using the calculated total density of states of the slab and the projections to the atoms, atomic orbitals, and He 1s floating atomic orbital at different positions above the surface. Calculated projected densities of states exhibit a strong dependence on the relaxation of surface atoms. The good agreement of simulated and experimental UPS and MIES spectra supports the correctness of calculated surface relaxation.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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 0.05-0.06 mmolg(dry)(-1) and a maximal adsorption capacity of 0.93-1.25 mmolg(dry)(-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 ∼1.95 Å 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

  18. Chemical structure and immunobiological activity of Porphyromonas gingivalis lipid A.

    PubMed

    Ogawa, Tomohiko; Asai, Yasuyuki; Makimura, Yutaka; Tamai, Riyoko

    2007-01-01

    In 1933, Boivin et al. extracted an endotoxin from Salmonella typhimurium for the first time, after which a variety of chemical and biological studies on endotoxins have been performed. In 1952, the structural and functional properties of endotoxic lipopolysaccharide (LPS), extracted by a hot phenol and water method devised by Westphal et al., were reported, which led to a number of studies of Gram-negative bacteria in regards to the host defense mechanism. Since 1960, the unique chemical structure and biological activity of Bacteroides species LPS have received a great deal of attention, and there is a long history of such studies. In addition, among oral bacterial strains that have received attention as causative periodontopathic bacteria, many have been classified as Bacteroides species. In particular, a number of researchers have investigated whether LPS of Porphyromonas gingivalis (formerly Bacteroides gingivalis), a black-pigmented oral anaerobic rod, is a virulent factor of the bacterium. The active center of the LPS of these Bacteroides species, the lipid A molecule, is known to be an active participant in endotoxic activation, though its other biological activities are weak, due to its unique chemical structure and action as an antagonist of LPS. On the other hand, many reports have noted that the LPS of those species activate cells in C3H/HeJ mice, which generally do not respond to LPS. We were the first to reveal the chemical structure of P. gingivalis lipid A and, together with other researchers, reported that P. gingivalis LPS and its lipid A have activities toward C3H/HeJ mice. Since that time, because of the popularity of Toll-like receptor (TLR) studies, a great deal of evidence has been reported indicating that P. gingivalis LPS and its lipid A are ligands that act on TLR2. In order to solve such problems as heterogeneity and contamination of the biologically active components of P. gingivalis lipid A, we produced a chemical synthesis counterpart

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

    PubMed

    Fredrickson, Daniel C

    2011-07-01

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

  20. 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

  1. 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.

  2. 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.

  3. ALD Zn(O,S) Thin Films’ Interfacial Chemical and Structural Configuration Probed by XAS

    PubMed Central

    2016-01-01

    The ability to precisely control interfaces of atomic layer deposited (ALD) zinc oxysulfide (Zn(O,S)) buffer layers to other layers allows precise tuning of solar cell performance. The O K- and S K-edge X-ray absorption near edge structure (XANES) of ∼2–4 nm thin Zn(O,S) films reveals the chemical and structural influences of their interface with ZnO, a common electrode material and diffusion barrier in solar cells. We observe that sulfate formation at oxide/sulfide interfaces is independent of film composition, a result of sulfur diffusion toward interfaces. Leveraging sulfur’s diffusivity, we propose an alternative ALD process in which the zinc precursor pulse is bypassed during H2S exposure. Such a process yields similar results to the nanolaminate deposition method and highlights mechanistic differences between ALD sulfides and oxides. By identifying chemical species and structural evolution at sulfide/oxide interfaces, this work provides insights into increasing thin film solar cell efficiencies. PMID:27223620

  4. 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

  5. ALD Zn(O,S) Thin Films' Interfacial Chemical and Structural Configuration Probed by XAS.

    PubMed

    Dadlani, Anup L; Acharya, Shinjita; Trejo, Orlando; Prinz, Fritz B; Torgersen, Jan

    2016-06-15

    The ability to precisely control interfaces of atomic layer deposited (ALD) zinc oxysulfide (Zn(O,S)) buffer layers to other layers allows precise tuning of solar cell performance. The O K- and S K-edge X-ray absorption near edge structure (XANES) of ∼2-4 nm thin Zn(O,S) films reveals the chemical and structural influences of their interface with ZnO, a common electrode material and diffusion barrier in solar cells. We observe that sulfate formation at oxide/sulfide interfaces is independent of film composition, a result of sulfur diffusion toward interfaces. Leveraging sulfur's diffusivity, we propose an alternative ALD process in which the zinc precursor pulse is bypassed during H2S exposure. Such a process yields similar results to the nanolaminate deposition method and highlights mechanistic differences between ALD sulfides and oxides. By identifying chemical species and structural evolution at sulfide/oxide interfaces, this work provides insights into increasing thin film solar cell efficiencies. PMID:27223620

  6. 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.

  7. 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.

  8. 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

  9. Atomic and electronic structures of lattice mismatched Cu2O/TiO2 interfaces

    NASA Astrophysics Data System (ADS)

    Wang, Shuzhi; Kavaipatti, Balasubramaniam; Kim, Sung-Joo; Pan, Xiaoqing; Ramesh, Ramamoorthy; Ager, Joel W.; Wang, Lin-Wang

    2014-05-01

    Heterojunction interfaces between metal oxides are often highly lattice mismatched. The atomic and electronic structures of such interfaces, however, are not well understood. We have synthesized Cu2O/TiO2 heterojunction thin films with 13% lattice mismatch and studied the interface via experimental methods and large-scale density function theory calculations of supercells containing ˜1300 atoms. We find that an interface of epitaxial quality is formed via a coincidence site lattice of 8 Cu2O unit cells matching 9 TiO2 unit cells. Calculations reveal the existence of a dislocation core of the O sublattices at the interface and a random arrangement of one layer of interfacial Cu atoms. The interfacial electronic structure is found to be mostly determined by the interfacial Cu distribution, rather than by the O dislocation core. The conduction band minimum and valence band maximum states are spatially separated, and there is no strongly localized state near the core.

  10. 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.

  11. Identification of ordered atomic structures of Ba on the Si(100) surface

    NASA Astrophysics Data System (ADS)

    Fan, W. C.; Ignatiev, A.

    1991-08-01

    Three long-range ordered atomic structures of (2 × 3), (1 × 2) and (2 × 4) phases have been observed by low-energy electron-diffraction (LEED) in the Ba/Si(100) surface at submonolayer Ba coverages (θ < 1 ML). The relationship between the observed phases for Ba on the Si(100) surface have been described as a function of Ba coverage and anneal temperature. Possible models of the surface atomic structures for the ordered phases are proposed by assuming Ba atomic chains in the Ba overlayer. A diffuse c(4 × 4)-like pattern has also been observed in the Ba/Si(100) system at high Ba exposure (> 2 ML), which might result from Ba diffusion and possible formation of a barium suicide.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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...

  17. 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...

  18. 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.

  19. 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

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

    SciTech Connect

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

    2005-11-15

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

  1. 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

  2. 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

  3. 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

  4. Determination of vanadium in mussels by electrothermal atomic absorption spectrometry without chemical modifiers.

    PubMed

    Saavedra, Y; Fernández, P; González, A

    2004-05-01

    A method was developed for the quantitative determination of total vanadium concentration in mussels via electrothermal atomic absorption spectrometry (ETAAS). After the microwave digestion of the samples, a program using temperatures of 1600 degrees C and 2600 degrees C for ashing and atomization respectively, without any matrix modifiers, allowed us to obtain results that were satisfactory since they agreed closely with certified reference material values. The detection limit was 0.03 mg kg(-1) (dry weight), indicating that the method is suitable for the analysis of mussel samples. This determination was compared with matrix modifiers that have been reported previously. The method was applied to various cultivated and wild mussels from the Galician coast, yielding levels below 1 mg kg(-1) (wet weight). PMID:14745471

  5. Effect of the chemical state of tin-117m atoms on their probability of decay

    SciTech Connect

    Bondarevskii, S.I.; Eremin, V.V.; Murin, A.N.

    1987-05-01

    The effect of the valence state of the tin atoms on the probability of radioactive decay has been studied by the ..delta..lambda/lambda and ..delta..I/I methods for the case of the isomeric M4-transition in the nucleus of tin-117m. The two methods gave concordant results: lambda(SnC/sub 2/O/sub 4/ x 2H/sub 2/O)-lambda(SnO/sub 2/) = + (7.5 +/- 1.5) x 10/sup -4/ x anti lambda; I (Sn(II) solution) - I (Sn(IV) solution) = + (7.0 +/- 1.0) x 10/sup -4/ x anti I. The values of the measured effects correspond, according to our estimates, to an overall decrease in electron density on the tin nucleus of 90 atomic units on transition from tin (II) to tin (IV).

  6. 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)

  7. 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…

  8. 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…

  9. Compensation of logarithmic corrections in calculating the fine structure of levels in hydrogen-like atoms

    SciTech Connect

    Boikova, N. A. Tyukhtyaev, Yu. N.; Faustov, R. N.

    2011-01-15

    Special features of the quasipotential approach to calculating logarithmic (in the fine-structure constant) contributions to the fine splitting of energy levels in hydrogen-like atoms are analyzed. The boundaries of the region of applicability of the Fell technique are indicated, and the order of corrections beyond this region is estimated.

  10. The role of bridged structures in the mechanism of the reaction between chlorine atom and ethylene

    NASA Astrophysics Data System (ADS)

    Braña, P.; Menéndez, B.; Fernández, T.; Sordo, J. A.

    2000-08-01

    The potential energy surface for the reaction between a chlorine atom and ethylene was extensively explored by using ab initio methodologies. Two different routes for the 1,2 migration of the chlorine atom were identified. One of them involves a C 2v ( 2B 2) transition structure (TS sb) that directly connects two equivalent structures (P and P') of the 2-chloroethyl radical with the chlorine atom attached either to C1 (P) or to C2 (P') carbon atoms in ethylene (shuttling motion). In the second pathway, the 2-chloroethyl radical (P) coverts into a C 2v ( 2A 1) intermediate (I add) through a C s ( 2A') transition structure (TS add ). Then I add leads to the 2-chloroethyl radical (P') through a transition structure equivalent to TS add (TS add' ). The `indirect shuttling motion' described along this latter route is notably lower in energy and allows one to rationalize some mechanistic aspects experimentally observed in reactions involving haloethyl radicals.

  11. 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…

  12. Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    We present calculations of nuclear structure effects to the Lamb shift in light muonic atoms. We adopt a modern ab-initio approach by combining state-of-the-art nuclear potentials with the hyperspherical harmonics method. Our calculations are instrumental to the determination of nuclear charge radii in the Lamb shift measurements, which will shed light on the proton radius puzzle.

  13. Electron in a homogeneous crystal of point atoms with internal structure. II

    SciTech Connect

    Kurasov, P.B.; Pavlov, B.S.

    1988-07-01

    A spectral analysis is made of a Schroedinger operator with zero-range potential of the type of one- or two-dimensional lattice in the presence of internal structure. The relationship between the resonances of an isolated atom and the spectral properties of the crystal is established.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  15. Chemical reaction of atomic oxygen with evaporated films of copper, part 4

    NASA Technical Reports Server (NTRS)

    Fromhold, A. T.; Williams, J. R.

    1990-01-01

    Evaporated copper films were exposed to an atomic oxygen flux of 1.4 x 10(exp 17) atoms/sq cm per sec at temperatures in the range 285 to 375 F (140 to 191 C) for time intervals between 2 and 50 minutes. Rutherford backscattering spectroscopy (RBS) was used to determine the thickness of the oxide layers formed and the ratio of the number of copper to oxygen atoms in the layers. Oxide film thicknesses ranged from 50 to 3000 A (0.005 to 0.3 microns, or equivalently, 5 x 10(exp -9) to 3 x 10(exp -7); it was determined that the primary oxide phase was Cu2O. The growth law was found to be parabolic (L(t) varies as t(exp 1/2)), in which the oxide thickness L(t) increases as the square root of the exposure time t. The analysis of the data is consistent with either of the two parabolic growth laws. (The thin-film parabolic growth law is based on the assumption that the process is diffusion controlled, with the space charge within the growing oxide layer being negligible. The thick-film parabolic growth law is also based on a diffusion controlled process, but space-charge neutrality prevails locally within very thick oxides.) In the absence of a voltage measurement across the growing oxide, a distinction between the two mechanisms cannot be made, nor can growth by the diffusion of neutral atomic oxygen be entirely ruled out. The activation energy for the reaction is on the order of 1.1 eV (1.76 x 10(exp -19) joule, or equivalently, 25.3 kcal/mole).

  16. Atomic Structure Study of the Quantum Spin-ice Pyrochlore Yb2Ti2O7

    NASA Astrophysics Data System (ADS)

    Mostaed, Ali; Balakrishnan, Geetha; Lees, Martin; Beanland, Richard; Microscopy Team; Superconductivity; Magnetism Team

    The quantum spin-ice candidate Yb2Ti2O7 (YTO) lies on the boundary between a number of competing magnetic ground states. Features in the low-temperature specific heat capacity are found to vary in sharpness and temperature depending on materials processing. It has been suggested that these changes in the magnetic ground state could be influenced by several factors, including the degree of cation stuffing, changes in oxygen occupancy and/or vacancies. In the present work, the structures of three different YTO samples, grown by the optical floating zone technique and that exhibit quite different heat capacity behaviour, have been studied by annular dark field scanning transmission microscopy (ADF-STEM). We show that the detailed intensity distribution around the visible atomic columns is sensitive to the presence of nearby atoms of low atomic number (in this case oxygen), even though they are not directly visible in the images. To the best of our knowledge, this is the first time that oxygen columns with a distance of ~30 pm have been distinguished in ADF-STEM images. Furthermore, by comparing atomic columns with different configurations of nearby oxygen atoms, we are able to distinguish between the different YTO samples Finally, the ADF data for the crystal that exhibits no specific heat anomaly shows signs of the substitution of Yb atoms on Ti sites, supporting the view that the magnetic ground state of YTO is extremely sensitive to disorder.

  17. Spontaneous emission of a photon: Wave-packet structures and atom-photon entanglement

    SciTech Connect

    Fedorov, M.V.; Efremov, M.A.; Kazakov, A.E.; Chan, K.W.; Eberly, J.H.; Law, C.K.

    2005-09-15

    Spontaneous emission of a photon by an atom is described theoretically in three dimensions with the initial wave function of a finite-mass atom taken in the form of a finite-size wave packet. Recoil and wave-packet spreading are taken into account. The total atom-photon wave function is found in the momentum and coordinate representations as the solution of an initial-value problem. The atom-photon entanglement arising in such a process is shown to be closely related to the structure of atom and photon wave packets which can be measured in the coincidence and single-particle schemes of measurements. Two predicted effects, arising under the conditions of high entanglement, are anomalous narrowing of the coincidence wave packets and, under different conditions, anomalous broadening of the single-particle wave packets. Fundamental symmetry relations between the photon and atom single-particle and coincidence wave-packet widths are established. The relationship with the famous scenario of Einstein-Podolsky-Rosen is discussed.

  18. Atomically precise self-assembly of one-dimensional structures on silicon

    NASA Astrophysics Data System (ADS)

    Barke, I.; Rügheimer, T. K.; Zheng, Fan; Himpsel, F. J.

    2007-10-01

    This work has three main themes: (1) fabricate atomically precise nanostructures at surfaces, particularly nanowires consisting of atom chains; (2) explore the behavior of one-dimensional electrons in atomic chains; (3) find the fundamental limits of data storage using an atomic scale memory. Semiconductor surfaces lend themselves towards self-assembly, because the broken covalent bonds create elaborate reconstruction patterns to minimize the surface energy. An example is the large 7 × 7 unit cell on Si(1 1 1), which can be used as building block. On semiconductors, the surface electrons completely de-couple from the substrate, as long as their energy lies in the band gap. Angle-resolved photoemission reveals surprising features, such as a fractional band filling and a spin-splitting at a non-magnetic surface. An interesting by-product is a memory structure with self-assembled tracks that are five atom rows wide and store a bit by the presence or absence of a single silicon atom. This toy memory is used to test the fundamental limits of data storage and to see how storage on silicon compares to storage in DNA.

  19. Segregation and temperature effect on the atomic structure of Bi30Ga70 liquid alloy

    NASA Astrophysics Data System (ADS)

    Sbihi, D. Es; Grosdidier, B.; Kaban, I.; Gruner, S.; Hoyer, W.; Gasser, J.-G.

    2009-06-01

    We investigate the structure of liquid monotectic alloy Bi30Ga70 above and below the critical point. The three-dimensional structure at 265 °C is modelled by means of the reverse Monte Carlo simulation technique using neutron and x-ray diffraction experimental data. It is shown that atomic segregation on the short-range scale exists in the liquid Bi30Ga70 slightly above the critical temperature (TC = 262 °C). We present also the structure factors of Bi30Ga70 liquid alloy under the critical point at 240 and 230 °C obtained with neutron diffraction to highlight the temperature effect in the atomic structure.

  20. Segregation and temperature effect on the atomic structure of Bi(30)Ga(70) liquid alloy.

    PubMed

    Sbihi, D Es; Grosdidier, B; Kaban, I; Gruner, S; Hoyer, W; Gasser, J-G

    2009-06-17

    We investigate the structure of liquid monotectic alloy Bi(30)Ga(70) above and below the critical point. The three-dimensional structure at 265 °C is modelled by means of the reverse Monte Carlo simulation technique using neutron and x-ray diffraction experimental data. It is shown that atomic segregation on the short-range scale exists in the liquid Bi(30)Ga(70) slightly above the critical temperature (T(C) = 262 °C). We present also the structure factors of Bi(30)Ga(70) liquid alloy under the critical point at 240 and 230 °C obtained with neutron diffraction to highlight the temperature effect in the atomic structure. PMID:21693940