Note: This page contains sample records for the topic atomic structure chemical from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: August 15, 2014.
1

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

PubMed

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

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

2

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

NASA Astrophysics Data System (ADS)

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, ?, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from the questionnaires were formed from the combination of items found to measure different aspects of a specific topic area using a reliability analysis. Average scores for the subgroups were compared to results obtained by students on the diagnostic instrument targeting the same topic area. There were no significant differences of the scores on both of the diagnostic instruments between the levels of undergraduate chemistry students. There were, however, significant differences on certain items of the diagnostic instruments between upper and lower class students. Additionally, misconceptions were identified within all levels of these undergraduate students that corresponded to previous results reported in the literature. A significant relationship was found to exist between the scores obtained on the two diagnostic instruments, as well as strong correlations between specific items and the total scores of the instruments. Response to the expectations questionnaires revealed no differences between the chemical industry and chemical academia, but did provide information concerning the chemical community's expectations of undergraduate chemistry students. Results indicate that undergraduate students majoring in chemistry have conceptions that are inconsistent with currently accepted scientific views. The findings also support the hypothesis that an understanding of the general structure of the atom and the roles played by electrons in molecular bonding and structure is important to an understanding of chemical properties and behavior.

Campbell, Erin Roberts

3

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

NASA Technical Reports Server (NTRS)

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.

Kahn, L. R.

1981-01-01

4

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

5

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

PubMed

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

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

6

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

ERIC Educational Resources Information Center

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

Tsaparlis, Georgios

1997-01-01

7

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

SciTech Connect

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.

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

8

Atomic structure and chemical order in Ge-As selenide and sulfoselenide glasses: An x-ray absorption fine structure spectroscopic study  

NASA Astrophysics Data System (ADS)

The nearest-neighbor coordination environments of Ge and As atoms in GexAsySe1-x-y glasses with x:y=1:2 and 1:1 and in Ge0.154As0.308 (S,Se)0.538 sulfoselenide glasses with wide-ranging Se contents have been studied with Ge and As K-edge extended x-ray absorption time spectra spectroscopy. The average coordination numbers of Ge and As atoms are found to be 4 and 3, respectively, in all glasses. The compositional makeup of the first coordination shells of Ge and As atoms indicate that chemical order is largely preserved in stoichiometric and Se-excess GexAsySe1-x-y glasses. On the other hand, chemical order is found to be strongly violated in the case of Se-deficient GexAsySe1-x-y glasses where the chalcogen deficiency is entirely taken up by the formation of As-As homopolar bonds at low and intermediate levels of Se deficiency. The Ge atoms take part in homopolar bonding only in strongly Se-deficient glasses indicating clustering of As atoms. In the case of sulfoselenide glasses the distribution of S and Se atoms in the first coordination shells of Ge and As atoms is found to be random, signifying a chemically ordered chalcogen ``sublattice.'' It is shown that the intermediate-range structural and topological aspects of such compositional variation of chemical order may play a central role in controlling properties such as the molar volume of chalcogenide glasses.

Sen, S.; Aitken, B. G.

2002-10-01

9

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

NASA Technical Reports Server (NTRS)

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.

Kahn, L. R.

1982-01-01

10

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

NASA Astrophysics Data System (ADS)

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.

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

2012-06-01

11

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

NASA Technical Reports Server (NTRS)

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.

Kahn, L. R.

1981-01-01

12

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

Microsoft Academic Search

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

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

1997-01-01

13

Atomic Structure Webquest  

NSDL National Science Digital Library

This web page outlines a student activity on atoms and the periodic table. The assignment includes instructions about how to write a children's book for 3rd and 4th graders on the topic of the elements from the cover to the end of the book. It is a performance-based activity designed to promote critical thinking about atomic and molecular structures as students characterize and model the structures in a storybook format. Grading rubrics are also included.

Stefaniak, Linda

2007-10-02

14

Atomic Scale Properties of Chemically Doped Graphene  

NASA Astrophysics Data System (ADS)

In monolayer graphene, substitutional doping during growth can be used to alter its electronic properties. We used scanning tunneling microscopy, Raman spectroscopy, x-ray spectroscopy, and first principles calculations to characterize individual nitrogen dopants in monolayer graphene grown on a copper substrate. Individual nitrogen atoms were incorporated as graphitic dopants, and a fraction of the extra electron on each nitrogen atom was delocalized into the graphene lattice. The electronic structure of nitrogen-doped graphene was strongly modified only within a few lattice spacings of the site of the nitrogen dopant. These findings show that chemical doping is a promising route to achieving high-quality graphene films with a large carrier concentration. Ref: L. Zhao et al, Science 333,999 (2011).

Pasupathy, Abhay

2012-02-01

15

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

PubMed

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

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

2014-06-26

16

Atomic and electronic structure of carbon strings.  

PubMed

This paper presents an extensive study of various string and tubular structures formed by carbon atomic chains. Our study is based on first-principles pseudopotential plane wave and finite-temperature ab initio molecular dynamics calculations. Infinite- and finite-length carbon chains exhibit unusual mechanical and electronic properties such as large cohesive energy, axial strength, high conductance, and overall structural stability even at high temperatures. They are suitable for structural and chemical functionalizations. Owing to their flexibility and reactivity they can form linear chain, ring, helix, two-dimensional rectangular and honeycomb grids, three-dimensional cubic networks, and tubular structures. Metal-semiconductor heterostructures and various quantum structures, such as multiple quantum wells and double-barrier resonant tunnelling structures, can be formed from the junctions of metallic carbon and semiconducting BN linear chains. Analysis of atomic and electronic structures of these periodic, finite, and doped structures reveals fundamentally and technologically interesting features, such as structural instabilities and chiral currents. The double covalent bonding of carbon atoms depicted through self-consistent charge density analysis underlies the chemical, mechanical, and electronic properties. PMID:21690699

Tongay, S; Dag, S; Durgun, E; Senger, R T; Ciraci, S

2005-06-29

17

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

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)

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

18

Universal bosonic tetramers of dimer-atom-atom structure  

NASA Astrophysics Data System (ADS)

Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.

Deltuva, A.

2012-04-01

19

BOOK REVIEW: Computational Atomic Structure  

NASA Astrophysics Data System (ADS)

The primary purpose of `Computational Atomic Structure' is to give a potential user of the Multi-Configuration Hartree-Fock (MCHF) Atomic Structure Package an outline of the physics and computational methods in the package, guidance on how to use the package, and information on how to interpret and use the computational results. The book is successful in all three aspects. In addition, the book provides a good overview and review of the physics of atomic structure that would be useful to the plasma physicist interested in refreshing his knowledge of atomic structure and quantum mechanics. While most of the subjects are covered in greater detail in other sources, the book is reasonably self-contained, and, in most cases, the reader can understand the basic material without recourse to other sources. The MCHF package is the standard package for computing atomic structure and wavefunctions for single or multielectron ions and atoms. It is available from a number of ftp sites. When the code was originally written in FORTRAN 77, it could only be run on large mainframes. With the advances in computer technology, the suite of codes can now be compiled and run on present day workstations and personal computers and is thus available for use by any physicist, even those with extremely modest computing resources. Sample calculations in interactive mode are included in the book to illustrate the input needed for the code, what types of results and information the code can produce, and whether the user has installed the code correctly. The user can also specify the calculational level, from simple Hartree-Fock to multiconfiguration Hartree-Fock. The MCHF method begins by finding approximate wavefunctions for the bound states of an atomic system. This involves minimizing the energy of the bound state using a variational technique. Once the wavefunctions have been determined, other atomic properties, such as the transition rates, can be determined. The book begins with an introduction to atomic structure. It covers single and many electron systems, how to set up a basis set of wavefunctions for a many electron system, LS coupling, single and multi-electron Hamiltonians, the elementary Hartree-Fock approximation and how variational methods are used to determine the ground state energy and wavefunctions. The computational methods used in the codes are outlined and there are exercises at the end of each chapter. For a number of candidate atomic configurations, explicit examples are given that illustrate the physics, the approximations and the computational methods involved, and which provide the reader with the opportunity to check that he is using the suite of codes correctly. Relativistic effects are covered as perturbations with Breit-Pauli Hamiltonians. Isotope and hyperfine level splitting are also covered. A summary chapter covers allowed and forbidden bound-bound transitions. It describes how to set up the matrix elements for transition operators, and the determination of selection rules and computational aspects of the methods for allowed and forbidden lines. The last chapter provides a brief introduction to continuum transitions, including how to compute the necessary wavefunctions to calculate photoionization or photodetachment and autoionization processes. Several appendices provide a summary of angular momentum theory, an introduction to the Dirac and Breit-Pauli theory for relativistic processes, and a description of the input parameters needed to run the programs. In summary, the book is an almost essential guide to anyone planning to use the Multi-Configuration Hartree-Fock suite of codes. With this guide, even someone not thoroughly familiar with the details of the subject or the codes should be able to use them to obtain energy levels, wavefunctions and transition rates for any atomic system of interest. This book serves as a model example for the general computational physics community of how to document an important suite of codes for a wide number of researchers and really make the suite usable to the general physics c

Post, Douglass E.

1998-02-01

20

Hyperfine Structure of Atomic Nitrogen  

Microsoft Academic Search

The hyperfine structure of the ground state of N14 and N15 has been determined by optical pumping with spin exchange. A circulation system, which forced the nitrogen through an electrodeless rf discharge into the resonance bulb, provided a continuous source of atomic nitrogen. Optically-pumped cesium was used to polarize and analyze the nitrogen. The zero-field intervals extrapolated to zero pressure

W. W. Jr. Holloway; E. Luescher; R. Novick

1962-01-01

21

Atomic structure of titania nanosheet with vacancies  

PubMed Central

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.

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

2013-01-01

22

Chemical control of electrical contact to sp2 carbon atoms  

NASA Astrophysics Data System (ADS)

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.

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

2014-04-01

23

Atomic structures and compositions of internal interfaces  

SciTech Connect

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.

Seidman, D.N. (Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering); Merkle, K.L. (Argonne National Lab., IL (United States))

1992-03-01

24

Atomic oxygen-MoSâ chemical interactions  

Microsoft Academic Search

The present study shows that, at 1.5 eV O-atom translation energy, SOâ is generated and outgases from an anhydrous MoSâsurface with an initial reactivity nearly 50% that of kapton. The reaction of atomic oxygen with MoSâ has little or no translational energy barier; i.e., thermally generated atomic oxygen reacts as readily as that having 1.5 eV of translational energy. It

J. B. Cross; J. A. Martin; L. E. Pope; S. L. Koontz

1989-01-01

25

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

NASA Astrophysics Data System (ADS)

We report a chemically specific x-ray photoelectron diffraction (XPD) investigation using synchrotron radiation of the thermally induced growth of epitaxial graphene on the 6H-SiC(0001). The XPD results show that the buffer layer on the SiC(0001) surface is formed by two domain regions rotated by 60? with respect to each other. The experimental data supported by a comprehensive multiple scattering calculation approach indicates the existence of a long-range ripple due the (63×63)R30? reconstruction, in addition to a local range buckling in the (0001) direction of the two sublattices that form the honeycomb structure of the buffer layer. This displacement supports the existence of an sp2-to-sp3 rehybridization in this layer. For the subsequent graphene layer this displacement is absent, which can explain several differences between the electronic structures of graphene and the buffer layer.

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

2013-02-01

26

Atomic structures and compositions of interfaces  

SciTech Connect

This research program focuses on an experimental study of the structure and chemistry of metal/metal oxide internal interfaces; the latter are mainly created, although not exclusively, by internal oxidation of binary or ternary metal alloys that are solid-solution phases prior to the internal oxidation treatment. The principal research tools are transmission electron microscopy (TEM), high resolution microscopy (HREM), analytical electron microscopy (AEM) and atom-probe field-ion microscopy (APFIM). The APFIM technique is used to determine the chemical composition of the interfacial region on an atomic scale. Initial studies are foucused on Pd/NiO, Cu/MgO, Cu/Al{sub 2}O{sub 3}, Cu/SiO{sub 2} interfaces, as well as metal oxides in Pt-based alloys. Topics of importance include coherency effects, misfit dislocations, structure of the terminating layer between the metal and the metal oxide, microstoichiometry, dipole space charge effects, and distributions of impurities and point defects at the interfacial region.

Seidman, D.N. (Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering); Merkle, K.L. (Argonne National Lab., IL (United States))

1990-09-01

27

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.  

PubMed

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment. PMID:20429589

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

28

Evolution of atomic structure during nanoparticle formation  

PubMed Central

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.

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

2014-01-01

29

A Thermo-Chemical Reactor for analytical atomic spectrometry  

NASA Astrophysics Data System (ADS)

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.

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

2009-01-01

30

Interferometer-type structures for guided atoms.  

PubMed

We experimentally demonstrate interferometer-type guiding structures for neutral atoms based on dipole potentials created by microfabricated optical systems. As a central element we use an array of atom waveguides being formed by focusing a red-detuned laser beam with an array of cylindrical microlenses. Combining two of these arrays, we realize X-shaped beam splitters and more complex systems like the geometries for Mach-Zehnder and Michelson-type interferometers for atoms. PMID:12485053

Dumke, R; Müther, T; Volk, M; Ertmer, W; Birkl, G

2002-11-25

31

Digital Resource Package for Teaching Atomic Structure  

NSDL National Science Digital Library

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

Moin, Laura

32

Introduction to Atomic Structure: Demonstrations and Labs.  

ERIC Educational Resources Information Center

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)

Ciparick, Joseph D.

1988-01-01

33

Unraveling the Atomic Structure of Ultrafine Iron Clusters  

NASA Astrophysics Data System (ADS)

Unraveling the atomic structures of ultrafine iron clusters is critical to understanding their size-dependent catalytic effects and electronic properties. Here, we describe the stable close-packed structure of ultrafine Fe clusters for the first time, thanks to the superior properties of graphene, including the monolayer thickness, chemical inertness, mechanical strength, electrical and thermal conductivity. These clusters prefer to take regular planar shapes with morphology changes by local atomic shuffling, as suggested by the early hypothesis of solid-solid transformation. Our observations differ from observations from earlier experimental study and theoretical model, such as icosahedron, decahedron or cuboctahedron. No interaction was observed between Fe atoms or clusters and pristine graphene. However, preferential carving, as observed by other research groups, can be realized only when Fe clusters are embedded in graphene. The techniques introduced here will be of use in investigations of other clusters or even single atoms or molecules.

Wang, Hongtao; Li, Kun; Yao, Yingbang; Wang, Qingxiao; Cheng, Yingchun; Schwingenschlögl, Udo; Zhang, Xi Xiang; Yang, Wei

2012-12-01

34

Unraveling the Atomic Structure of Ultrafine Iron Clusters  

PubMed Central

Unraveling the atomic structures of ultrafine iron clusters is critical to understanding their size-dependent catalytic effects and electronic properties. Here, we describe the stable close-packed structure of ultrafine Fe clusters for the first time, thanks to the superior properties of graphene, including the monolayer thickness, chemical inertness, mechanical strength, electrical and thermal conductivity. These clusters prefer to take regular planar shapes with morphology changes by local atomic shuffling, as suggested by the early hypothesis of solid-solid transformation. Our observations differ from observations from earlier experimental study and theoretical model, such as icosahedron, decahedron or cuboctahedron. No interaction was observed between Fe atoms or clusters and pristine graphene. However, preferential carving, as observed by other research groups, can be realized only when Fe clusters are embedded in graphene. The techniques introduced here will be of use in investigations of other clusters or even single atoms or molecules.

Wang, Hongtao; Li, Kun; Yao, Yingbang; Wang, Qingxiao; Cheng, Yingchun; Schwingenschlogl, Udo; Zhang, Xi Xiang; Yang, Wei

2012-01-01

35

Polar and chemical domain structures of lead scandium tantalate (PST).  

National Technical Information Service (NTIS)

The local structure of chemical and polar domains and domain walls is determined directly by atomic resolution high-resolution electron microscopy. Thus the Pb, Ta and Sc atomic positions may be located in the images of very thin crystals. Furthermore the...

J. L. Peng L. A. Bursill

1993-01-01

36

Iodine Atoms Structured in (SN)x  

NASA Astrophysics Data System (ADS)

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

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

1985-05-01

37

Direct atomic structure determination by the inspection of structural phase  

PubMed Central

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

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

2013-01-01

38

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

SciTech Connect

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.

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

2008-03-29

39

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

PubMed Central

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

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

2013-01-01

40

Energy band of manipulated atomic structures on an insulator substrate  

Microsoft Academic Search

Stimulated by recent progress in atom manipulation technology, the electronic properties of periodic structures artificially created with atoms on a substrate surface are studied, where constituent atoms are isolated from substrate atoms and interact with one another through neighboring?atom interactions. By reducing the lattice constant from infinity, the neighboring?atom interaction is gradually turned on, and discrete atomic states broaden to

Toshishige Yamada; Yoshihisa Yamamoto; W. A. Harrison

1996-01-01

41

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

ERIC Educational Resources Information Center

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)

Whitman, Mark

1984-01-01

42

Spatial chemical distance based on atomic property fields  

Microsoft Academic Search

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

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

2010-01-01

43

Semiempirical studies of atomic structure  

NASA Astrophysics Data System (ADS)

The energy level structure, transition probabilities, and general spectroscopic properties of highly-ionized many-electron systems are studied through the combined use of sensitive semiempirical data systematizations, selected precision experimental measurements, and specialized theoretical computations. Measurements are made primarily through the use of fast ion beam excitation methods, which are combined with available data from laser- and tokamak-produced plasmas, astrophysical sources, and conventional light sources. The experimental studies are strengthened through large scale ab initio calculations. Large blocks of data are predictively systematized and parameterized along isoelectric, homologous, isoionic, Rydberg, and yrast series, to provide a comprehensive and reliable data base.

Curtis, L. J.

44

Semiempirical studies of atomic structure  

SciTech Connect

The energy level structure, transition probabilities, and general spectroscopic properties of highly-ionized many-electron systems are studied through the combined use of sensitive semiempirical data systematizations, selected precision experimental measurements, and specialized theoretical computations. Measurements are made primarily through the use of fast ion beam excitation methods, which are combined with available data from laser- and tokamak-produced plasmas, astrophysical sources, and conventional light sources. The experimental studies are strengthened through large scale ab initio calculations. Large blocks of data are predictively systematized and parameterized along isoelectric, homologous, isoionic, Rydberg, and yrast series, to provide a comprehensive and reliable data base.

Curtis, L.J.

1992-01-01

45

Making Matter: The Atomic Structure of Materials  

NSDL National Science Digital Library

The Institut Laue Langevin provides the Making Matter: The Atomic Structure of Materials Website. This site offers information as well as 3D structures of inorganic materials (such as salt) in the Inorganic Crystal Structure Database. Sections included at the site are Close Packing, Compounds, Bonding, and Gems & Minerals, among others. This site provides spectacular 3D images (.gif and VRML format) of inorganic materials and is well worth the visit.

46

Recent progress in atomic and chemical group effective potentials.  

PubMed

Recent progress on atomic and chemical group effective potentials is presented. The reviewed effective potentials follow a shape-consistent extraction technique from ab initio data, within a scalar relativistic approximation. Two types of averaged relativistic effective core potentials are considered: the correlated ones where a part of the correlation energy is included in the effective potential, and the polarized ones for which only the core polarization effects are taken into account. In addition spin-orbit polarized pseudopotentials have been extracted, and the effects of the core polarization are tested on the atomic spectroscopy of iodine. Finally a very recent chemical group effective methodology is presented, reducing the number of both electrons and nuclei explicitly treated. Chemical transferability is investigated, and test calculations on a cyclopentadienyl effective group potential are presented. PMID:11206381

Maron, L; Teichteil, C; Poteau, R; Alary, F

2001-01-01

47

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

SciTech Connect

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.

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

1989-02-01

48

A relationship between chemical structure and the critical temperature  

NASA Technical Reports Server (NTRS)

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.

Fedors, R. F.

1982-01-01

49

Atomic force microscopy of histological sections using a chemical etching method  

Microsoft Academic Search

Physiology and pathology have a big deal on tissue morphology, and the intrinsic spatial resolution of an atomic force microscope (AFM) is able to observe ultrastructural details. In order to investigate cellular and subcellular structures in histological sections with the AFM, we used a new simple method for sample preparation, i.e. chemical etching of semithin sections from epoxy resin-embedded specimens:

B. Tiribilli; D. Bani; F. Quercioli; A. Ghirelli; M. Vassalli

2005-01-01

50

Chemical infiltration during atomic layer deposition: metalation of porphyrins as model substrates.  

PubMed

New uses for ALD: By applying standard metal oxide atomic layer deposition (ALD) to two types of porphyrins, site-specific chemical infiltration of substrate molecules is achieved: Diethylzinc can diffuse into the interior of porphyrin supramolecular structures and induce metalation of the porphyrin molecules from the vapor phase. A = Ph, p-HO(3)SC(6)H(4). PMID:19492376

Zhang, Lianbing; Patil, Avinash J; Li, Le; Schierhorn, Angelika; Mann, Stephen; Gösele, Ulrich; Knez, Mato

2009-01-01

51

Atomic Structure Calculations from the Los Alamos Atomic Physics Codes  

DOE Data Explorer

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.

Cowan, R. D.

52

Atomic structure of Tb(11 2 0)  

SciTech Connect

A low-energy electron-diffraction intensity analysis of a Tb(11{bar 2}0) surface finds that the atomic structure of this surface is different from bulk structure in two ways: The spacing between the first and the second layer, which have two inequivalent atoms in the unit mesh, is contracted by 3.3% (0.06 A), and the two inequivalent atoms in the first layer translate parallel to the surface by equal and opposite amounts of 0.21 A. Thus the change in registration of the composite surface layer preserves both the size and the symmetry of the unit mesh of parallel bulk layers. This kind of surface rearrangement is different from that reported by others for the (11{bar 2}0) surfaces of other rare-earth metals, such as Y, Gd, and Ho.

Li, Y.S.; Quinn, J.; Jona, F. (College of Engineering and Applied Science, State University of New York, Stony Brook, New York 11794 (United States)); Marcus, P.M. (IBM Research Center, Yorktown Heights, New York 10598 (United States))

1992-08-15

53

Structural materials: understanding atomic scale microstructures  

SciTech Connect

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.

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

2009-01-01

54

Contrast Reversal in Atomic-Resolution Chemical Mapping  

SciTech Connect

We report an unexpected result obtained using chemical mapping on the new, aberration corrected Nion UltraSTEM at Daresbury. Using different energy windows above the L{sub 2,3} edge in <011> silicon to map the position of the atomic columns we find a contrast reversal which produces an apparent and misleading translation of the silicon columns. Using simulations of the imaging process, we explain the intricate physical mechanisms leading to this effect.

Wang, P.; Bleloch, A. L. [UK SuperSTEM Laboratory, Daresbury Laboratory, Cheshire WA4 4AD (United Kingdom); D'Alfonso, A. J.; Allen, L. J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Findlay, S. D. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo, 113-8656 (Japan)

2008-12-05

55

Atom Optics and Quantum Information Processing with Atoms in Optical Micro-Structures  

NASA Astrophysics Data System (ADS)

We experimentally demonstrate interferometer-type guiding structures for neutral atoms and novel structures for the realization of registers of atomic qubits based on dipole potentials created by micro-fabricated optical systems.

Volk, M.; Müther, T.; Scharnberg, F.; Lengwenus, A.; Dumke, R.; Ertmer, W.; Birkl, G.

2004-12-01

56

Atomic Structure and the Periodic Table  

NSDL National Science Digital Library

Any online chemistry textbook that contains a photograph of Max Planck and Albert Einstein on its first page definitely sets the right tone, and Stephen Lower's textbook certainly falls into that category. Over the past several years Lower has been working on this textbook, and for students looking for a bit of refresher on the world of the structure of atoms and the periodic table, this is the right place in which to spend a bit of time. Through the use of short and concise chapters, the textbook provides six different lesson titles which cover the world of quantum physics, the Bohr atom, and the periodic properties of the elements. Within each chapter, users will also find illustrations and a "What you need to know" section that effectively summarizes the key principles and concepts in each section.

Lower, Stephen

57

On role of the 3d atomic orbital in the chemical bonding of sulfur fluorides  

NASA Astrophysics Data System (ADS)

The electronic structure of SF2, SF4, SF6 and S2F2 was studied, using the DV-X[alpha] molecular orbital method. The chemical bonding of these sulfur fluorides was characterized using the Mulliken population analysis. We determined the 1s~3d as an appropriate basis set for sulfur atom. Near-linear correlations were found between the valence of sulfur and the 3d orbital population and between the valence of the sulfur atom and the effective charge. We confirm that the 3d orbital of sulfur should be taken as a valence orbital.

Tanaka, Kumiko; Sekine, Rika; Onoe, Jun; Nakamatsu, Hirohide

58

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

PubMed Central

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

2014-01-01

59

Atomic structure of ion tracks in Ceria  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

60

Synthesis, atomic structures and properties of carbon and boron nitride fullerene materials  

Microsoft Academic Search

Carbon (C) and boron nitride (BN) fullerene materials (clusters, onions, intercalation, nanopolyhedra, nanotubes and nanocapsules) were synthesized by polymer pyrolysis, chemical reaction, arc-melting and electron-beam irradiation. Atomic structure and formation mechanism were investigated by high-resolution electron microscopy, energy dispersive spectroscopy and electron energy-loss spectroscopy. Fullerene clusters and atomic clouds (atom hopping) were formed on the surface of the C and

Takeo Oku; Takanori Hirano; Masaki Kuno; Takafumi Kusunose; Koichi Niihara; Katsuaki Suganuma

2000-01-01

61

Automated extraction of chemical structure information from digital raster images  

PubMed Central

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

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

2009-01-01

62

Chemical and dielectrical characteristics of ultrathin oxides grown by atomic force microscopy and scanning electron beam  

SciTech Connect

We report a comparative study on the chemical and dielectrical properties of ultrathin oxides grown by atomic force microscopy (AFM) and scanning electron beam (SEB) techniques. Oxide grown by AFM (AFM oxide) shows preferential etching as compared to oxide grown by SEB (SEB oxide). The structural and chemical features of these oxides were probed using time-of-flight secondary ion mass spectrometry (TOF-SIMS) time profiling. It was found that AFM oxide is richer in Si-H and Si-OH content, while SEB oxide is oxygen rich and relatively dense in structure. The dielectric strength of AFM and SEB oxides were further evaluated by conducting AFM (c-AFM). The current-voltage characteristics and dielectric breakdown probability of these oxides were compared. The correlation between Si-H and Si-OH site formation and its impact on the chemical and dielectrical stability of AFM and SEB oxides was discussed.

Xie, X.N.; Chung, H.J.; Sow, C.H.; Wee, A.T.S. [NUS Nanoscience and Nanotechnology Initiative, National University of Singapore, 2 Science Drive 3, Singapore 117542 (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore and NUS Nanoscience and Nanotechnology Initiative, National University of Singapore, 2 Science Drive 3, Singapore 117542 (Singapore)

2005-05-09

63

Chemical Correlations in Atomic Size-Mismatch Disordered Alloys Predicted from KKR-DCA  

NASA Astrophysics Data System (ADS)

The dynamical cluster approximation (DCA) has been implemented in a Korringa-Kohn-Rostoker (KKR) electronic-structure method to predict electronic and structural properties of disordered alloys, in particular, chemical short-range order (SRO). We adapted an optimal-basis methodootnotetextA. Alam and D.D. Johnson, Phys. Rev. B 80, 125123 (2009) to the KKR-DCA to account for variations in atomic size due to different configurations present in size-mismatch alloys. In comparison to experiment, we find excellent agreement for predicted lattice constants and SRO, with origins identified in the electronic structure and affecting mechanical properties at finite temperatures. We also show how coarse-grained symmetry of the DCA can be exploited to reduce memory and computation time, allowing us to perform for the first time self-consistent KKR-DCA calculations with 2^16 or more configurations (and atoms) on a single compute node.

Biava, D. A.; Johnson, D. D.

2011-03-01

64

Te atom splitting and modulated structure in calaverite  

Microsoft Academic Search

By a crystal structure refinement of calaverite, (Au, Ag) Te2, it was found that Te atom is split symmetrically to the both-side of mirror plane where Te atoms are supposed to exist. We assumed a regular wavy displacement of Te atom in the calaverite structure and tried to explain the superstructure observed in this mineral.

Shigeho Sueno; Mitsuyoshi Kimata; Masaaki Ohmasa

1979-01-01

65

Mechanism of atomic-scale passivation and flattening of semiconductor surfaces by wet-chemical preparations  

NASA Astrophysics Data System (ADS)

Atomic arrangements of Si(001), Si(110) and 4H-SiC(0001) surfaces after wet-chemical preparations are investigated with scanning tunneling microscopy. Their passivated structures as well as the surface formation mechanisms in aqueous solutions are discussed. On both Si(001) and Si(110) surfaces, simple 1 × 1 phases terminated by H atoms are clearly resolved after dilute HF dipping. Subsequent etching with water produces the surfaces with 'near-atomic' smoothness. The mechanisms of atomic-scale preferential etching in water are described in detail together with first-principles calculations. Furthermore, 4H-SiC(0001), which is a hard material and where it is difficult to control the surface structure by solutions, is flattened on the atomic scale with Pt as a catalyst in HF solution. After a mechanism is proposed based on electroless oxidation, the flattened surface mainly composed of a 1 × 1 phase is analyzed. The obtained results will be helpful from various scientific and technological viewpoints.

Arima, Kenta; Endo, Katsuyoshi; Yamauchi, Kazuto; Hirose, Kikuji; Ono, Tomoya; Sano, Yasuhisa

2011-10-01

66

Mechanism of atomic-scale passivation and flattening of semiconductor surfaces by wet-chemical preparations.  

PubMed

Atomic arrangements of Si(001), Si(110) and 4H-SiC(0001) surfaces after wet-chemical preparations are investigated with scanning tunneling microscopy. Their passivated structures as well as the surface formation mechanisms in aqueous solutions are discussed. On both Si(001) and Si(110) surfaces, simple 1 × 1 phases terminated by H atoms are clearly resolved after dilute HF dipping. Subsequent etching with water produces the surfaces with 'near-atomic' smoothness. The mechanisms of atomic-scale preferential etching in water are described in detail together with first-principles calculations. Furthermore, 4H-SiC(0001), which is a hard material and where it is difficult to control the surface structure by solutions, is flattened on the atomic scale with Pt as a catalyst in HF solution. After a mechanism is proposed based on electroless oxidation, the flattened surface mainly composed of a 1 × 1 phase is analyzed. The obtained results will be helpful from various scientific and technological viewpoints. PMID:21921316

Arima, Kenta; Endo, Katsuyoshi; Yamauchi, Kazuto; Hirose, Kikuji; Ono, Tomoya; Sano, Yasuhisa

2011-10-01

67

The electronic structure and chemical bonding of vitamin B12  

NASA Astrophysics Data System (ADS)

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.

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

2003-05-01

68

MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES  

SciTech Connect

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.

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

2000-09-01

69

Atomic fidelity of subunit-based chemically-synthesized antimalarial vaccine components.  

PubMed

The tri-dimensional (3D) structure determined by NMR of functionally relevant High Activity Binding Peptides (HABPs) of chemically-synthesized malarial proteins, involved in invasion to target cells, is practically identical, at the atomic level, to their corresponding recombinantly produced proteins, determined by X-ray crystallography. Both recombinant proteins as well as these chemically-synthesized HABPs bind to host-cell receptors through channels or troughs formation, stabilized by hydrogen bonding; most of them are located on distant segments to the highly polymorphic, highly antigenic, strain specific amino acid sequences the parasite uses to evade immune pressure. When these immunologically silent conserved HABPs are specifically modified, they become highly immunogenic and capable of inducing protective immune responses, supporting the specifically modified minimal subunit-based, multiepitopic, chemically-synthesized vaccines concept. PMID:19961869

Patarroyo, Manuel E; Cifuentes, Gladys; Martínez, Nora L; Patarroyo, Manuel A

2010-01-01

70

Polar and chemical domain structures of lead scandium tantalate (PST)  

NASA Astrophysics Data System (ADS)

The local structure of chemical and polar domains and domain walls is determined directly by atomic resolution high-resolution electron microscopy. Thus, the Pb, Ta, and Sc atomic positions may be located in the images of very thin crystals. Furthermore, the Pb cation displacements away from the ideal perovskite A-site have been measured directly for the first time. Local variations in polarization direction may be mapped directly off the images, provided certain electron optical conditions are met. Results are relevant to recent theories of polar-glass behavior in relaxor-type complex oxide functional ceramics.

Peng, J. L.; Bursill, L. A.

71

Polar and Chemical Domain Structures of Lead Scandium Tantalate (pst)  

NASA Astrophysics Data System (ADS)

The local structure of chemical and polar domains and domain walls is determined directly by atomic resolution high-resolution electron microscopy (HRTEM). Thus the Pb, Ta, and Sc atomic positions may be located in the images of very thin crystals. Furthermore, the Pb cation displacements away from the ideal perovskite A-site have been measured directly for the first time. Local variations in polarization direction may be mapped directly off the images, provided certain electron optical conditions are met. The results are relevant to recent theories of polar-glass behaviour in relaxor-type complex oxide functional ceramics.

Peng, Julin; Bursill, L. A.

72

Atomic resolution chemical bond analysis of oxygen in La2CuO4  

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

73

Electronic structure and chemical bonding of zirconium disulfide  

Microsoft Academic Search

This paper involves the carrying out of the first-principle molecular-orbital calculations for ZrS2 with a model cluster composed of 129 atoms. The nature and intensity of intra- and interlayer chemical bondings are also\\u000a investigated by use of the bond overlap population. The valence band structure produced by this calculation agrees well with\\u000a experimental results reported from X-ray photoelectron spectroscopy. Each

Yang-Soo Kim; Hyun-Chul Ko; Hwa-Soo Park

2000-01-01

74

ChemTeacher Resource: Atomic Structure  

NSDL National Science Digital Library

This applet allows students to build atoms by combining different amounts of protons, neutrons, and electrons. The atomic number, charge, and radioactivity are displayed after each additional particle is added. Questions throughout the applet allow students to check their understanding of the concepts with instantaneous feedback.

Consortium, The C.

2011-01-01

75

Chemical reactivity of iron atoms near room temperature  

Microsoft Academic Search

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

S. A. Mitchell; P. A. Hackett

1990-01-01

76

Local functional derivative of the total energy and the shell structure in atoms and molecules  

Microsoft Academic Search

The full and local Thomas–Fermi–Dirac energy functional derivatives are evaluated at Hartree–Fock densities for several atoms and molecules. These functions are interpreted as local chemical potentials and related mainly to kinetic energy functional derivatives. They are able to reveal the shell structure of atoms, and the resulting radial extrema are compared with the ones obtained from the radial density, the

R Pino Plasencia; A. J. Markvoort; R. A. van Santen; P. A. J. Hilbers

2003-01-01

77

A Variational Monte Carlo Approach to Atomic Structure  

ERIC Educational Resources Information Center

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.

Davis, Stephen L.

2007-01-01

78

Sharing chemical relationships does not reveal structures.  

PubMed

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

Matlock, Matthew; Swamidass, S Joshua

2014-01-27

79

Chemical Design of Structural Ceramics.  

National Technical Information Service (NTIS)

A major aim of this program was to establish computational techniques based on statistical methodologies for the compositional design of structural ceramics. For the purposes of this study we are focusing on silicon nitride based ceramics. The enhancement...

K. Rajan

2001-01-01

80

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

SciTech Connect

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

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

2009-05-12

81

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

NASA Astrophysics Data System (ADS)

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 Er2O3 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 ErFeO3 and ErFe2O4 phases develop following subsequent thermal annealing processes at 850 °C in air and N2. 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.

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

2014-05-01

82

Quantum chemical studies of protein structure  

PubMed Central

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

Oldfield, Eric

2004-01-01

83

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

84

Local structure, chemical bond parameters and hyperfine magnetic interactions of 57Fe and doped 119Sn atoms in the orthoferrites TlFeO3 and TlFe0.99Sn0.01O3  

NASA Astrophysics Data System (ADS)

Mössbauer spectroscopy has been applied to study the magnetic hyperfine interactions of 57Fe and 119Sn probe atoms within TlFeO3 and TlFe0.99Sn0.01O3 ferrites. According to the magnetic measurements, the magnetic ordering temperature TN (= 560 K) for TlFeO3 is much lower than that for any other orthoferrites RFeO3 (R = rare earth). It is suggested that such difference in TN may be explained by different characteristics of the Tl-O and R-O chemical bonds involved and the induced competition with the Fe-O bonds. The effects of covalency and overlap distortion on the spin and charge densities at 57Fe nuclei are discussed in relation with the hyperfine interactions observed. By using cluster molecular orbital (MO) calculations, it was shown that the low value of the hyperfine magnetic field HFe(= 538 kOe) at 57Fe nuclei in TlFeO3 is strongly associated with a decrease of the covalent mixing parameter (b?)2 = 0.048 and (b?)2 = 0.009 values, which characterize the Fe-O bond covalence. It was elucidated that the value of super-transferred hyperfine field (HSTHF) at 119Sn nuclei in TlFe0.99Sn0.01O3 is sensitive mainly to the angle of the Sn-O-Fe bonds.

Presniakov, I. A.; Sobolev, A. V.; Baranov, A. V.; Demazeau, G.; Rusakov, V. S.

2006-10-01

85

Crystal Structure, Chemical Binding, and Lattice Properties  

NASA Astrophysics Data System (ADS)

This chapter starts with an overview of the ZnO crystal structure and its conjunction to the chemical binding. ZnO commonly occurs in the wurtzite structure. This fact is closely related to its tetrahedral bond symmetry and its prominent bond polarity. The main part of the first section deals with the ZnO wurtzite crystal lattice, its symmetry properties, and its geometrical parameters. Besides wurtzite ZnO, the other polytypes, zinc-blende and rocksalt ZnO are also briefly discussed. Subsequently, lattice constant variations and crystal lattice deformations are treated. This discussion starts with static lattice constant variations, induced by temperature or by pressure, as well as strain-induced static lattice deformation, which reduces the crystal symmetry. The impact of this symmetry reduction on the electrical polarization is the piezo effect, which is very much pronounced in ZnO and is exploited in many applications. See also Chap. 13. Dynamic lattice deformations manifest themselves as phonons and, in case of doping, as phonon-plasmon mixed states. The section devoted to phonons starts with a consideration of the vibration eigenmodes and their dispersion curves. Special attention is paid to the investigation of phonons by optical spectroscopy. The methods applied for this purpose are infrared spectroscopy and, more often, Raman spectroscopy. The latter method is very common for the structural quality assessment of ZnO bulk crystals and layers; it is also frequently used for the study of the incorporation of dopant and alloying atoms in the ZnO crystal lattice. Thus, it plays an important role with regard to possible optoelectronics and spintronics applications of ZnO. The final section of this chapter focuses on phonon-plasmon mixed states. These eigenstates occur in doped ZnO due to the strong coupling between collective free-carrier oscillations and lattice vibrations, which occurs due to the high bond polarity. Owing to the direct correlation of the plasmon-phonon modes to the electronic doping, they are an inherent property of ZnO samples, when applied in (opto-) electronics and spintronics. See also Chap. 12.

Geurts, J.

86

Atomic structure of novel epitaxial oxide\\/semiconductor interfaces  

Microsoft Academic Search

Further scaling of complementary metal-oxide-silicon field-effect transistors may require alternative gate dielectrics. Ultimately, interfaces between Si and these new gate dielectrics need to be atomically abrupt, which may require epitaxial interfaces. In this presentation, we identify the interfacial atomic structure of novel epitaxial Si\\/oxide interfaces and address some of the challenges in obtaining high-quality heterostructures. We report atomic resolution observations

Susanne Stemmer

2005-01-01

87

Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures  

USGS Publications Warehouse

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.

Dowty, E.; Clark, J. R.

1972-01-01

88

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

PubMed

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. PMID:24794852

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

2014-05-14

89

Tuning the electronic structures of armchair graphene nanoribbons through chemical edge modification: A theoretical study  

Microsoft Academic Search

We report combined first-principle and tight-binding (TB) calculations to simulate the effects of chemical edge modifications on structural and electronic properties. The C-C bond lengths and bond angles near the GNR edge have considerable changes when edge carbon atoms are bounded to different atoms. By introducing a phenomenological hopping parameter $t_{1}$ for nearest-neighboring hopping to represent various chemical edge modifications,

Z. F. Wang; Qunxiang Li. Huaixiu Zheng; Hao Ren; Haibin Su; Q. W. Shi; Jie Chen

2007-01-01

90

Annual Report 2000. Chemical Structure and Dynamics  

SciTech Connect

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.

Colson, Steven D.; McDowell, Robin S.

2001-04-15

91

Atomic oxygen-MoS/sub 2/ chemical interactions  

SciTech Connect

The present study shows that, at 1.5 eV O-atom translation energy, SO/sub 2/ is generated and outgases from an anhydrous MoS/sub 2/surface with an initial reactivity nearly 50% that of kapton. The reaction of atomic oxygen with MoS/sub 2/ has little or no translational energy barier; i.e., thermally generated atomic oxygen reacts as readily as that having 1.5 eV of translational energy. It is also shown that water, present in the flowing afterglow apparatus used to study thermal O-atom reactivity, formed sulfates on the MoS/sub 2/ surface and that the sulfate is not likely in the form of sulfuric acid. These results imply that water dumps or outgasing in low earth orbit have the potential of forming sulfuric acid covered surfaces on MoS/sub 2/ lubricants. For MoS/sub 2/ films sputter-deposited at 50-70/degree/C, friction measurements show a high initial friction coefficient for O-atom exposed MoS/sub 2/ surfaces (up to 0.25) which drops to the normal low values after several cycles of operation in air and ultrahigh vacuum. For MoS/sub 2/ films deposited at 200/degree/C, the friction coefficient was not affected by the O-atom exposure. 11 refs., 3 figs.

Cross, J.B.; Martin, J.A.; Pope, L.E.; Koontz, S.L.

1989-01-01

92

Three-Dimensional Atomic Structure of Metastable Nanoclusters in Doped Semiconductors  

NASA Astrophysics Data System (ADS)

Aberration-corrected scanning transmission electron microscopy is used to determine the atomic structure of nanoclusters of cerium dopant atoms embedded in silicon. By channeling electrons along two crystallographic orientations, we identify a characteristic zinc-blende chemical ordering within CeSi clusters coherent with the silicon host matrix. Strain energy limits the size of these ordered arrangements to just above 1 nm. With the local order identified, we then determine the atomic configuration of an individual subnanometer cluster by quantifying the scattering intensity under weak channeling condition in terms of the number of atoms. Analysis based on single-atom visualization also evidences the presence of split-vacancy impurity complexes, which supports the hypothesis of a vacancy-assisted formation of these metastable CeSi nanophases.

Couillard, Martin; Radtke, Guillaume; Knights, Andrew P.; Botton, Gianluigi A.

2011-10-01

93

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

ERIC Educational Resources Information Center

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)

Eilks, Ingo; Leerhoff, Gabriele

2001-01-01

94

Hyperspectral imaging of structure and composition in atomically thin heterostructures.  

PubMed

Precise vertical stacking and lateral stitching of two-dimensional (2D) materials, such as graphene and hexagonal boron nitride (h-BN), can be used to create ultrathin heterostructures with complex functionalities, but this diversity of behaviors also makes these new materials difficult to characterize. We report a DUV-vis-NIR hyperspectral microscope that provides imaging and spectroscopy at energies of up to 6.2 eV, allowing comprehensive, all-optical mapping of chemical composition in graphene/h-BN lateral heterojunctions and interlayer rotations in twisted bilayer graphene (tBLG). With the addition of transmission electron microscopy, we obtain quantitative structure-property relationships, confirming the formation of interfaces in graphene/h-BN lateral heterojunctions that are abrupt on a micrometer scale, and a one-to-one relationship between twist angle and interlayer optical resonances in tBLG. Furthermore, we perform similar hyperspectral imaging of samples that are supported on a nontransparent silicon/SiO2 substrate, enabling facile fabrication of atomically thin heterostructure devices with known composition and structure. PMID:23841492

Havener, Robin W; Kim, Cheol-Joo; Brown, Lola; Kevek, Joshua W; Sleppy, Joel D; McEuen, Paul L; Park, Jiwoong

2013-08-14

95

Protein structure determination from NMR chemical shifts.  

PubMed

NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques. PMID:17535901

Cavalli, Andrea; Salvatella, Xavier; Dobson, Christopher M; Vendruscolo, Michele

2007-06-01

96

Protein structure determination from NMR chemical shifts  

PubMed Central

NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 ? or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.

Cavalli, Andrea; Salvatella, Xavier; Dobson, Christopher M.; Vendruscolo, Michele

2007-01-01

97

Relating Dynamic Properties to Atomic Structure in Metallic Glasses  

SciTech Connect

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.

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

2012-07-18

98

Atomic Structure of Graphene on SiO 2  

Microsoft Academic Search

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

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

2007-01-01

99

Archimedean polyhedron structure yields a lower energy atomic cluster  

Microsoft Academic Search

Icosahedral structures are generally accepted as the lowest energy geometries for clusters of 13 ? n ? 147 atoms of the same type. Here we propose a novel structure for the 38-atoms cluster, possessing remarkable characteristics: 1.(i) its Lennard-Jones potential energy is below the minimum reported in the literature;2.(ii) as it can be embedded in a face-centered cubic lattice, it

D. Romero

1996-01-01

100

The PubChem chemical structure sketcher  

PubMed Central

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

2009-01-01

101

Localizing Chemical Groups while Imaging Single Native Proteins by High-Resolution Atomic Force Microscopy.  

PubMed

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

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

2014-05-14

102

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

NASA Astrophysics Data System (ADS)

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

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

2012-11-01

103

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

PubMed

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

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

2012-11-01

104

Making Matter: The atomic structure of materials  

NSDL National Science Digital Library

This site offers information as well as 3D images (gif and vrml) of the structures of inorganic materials (such as salt) in the Inorganic Crystal Structure Database. Sections included at the site are Close Packing, Compounds, Bonding, and Gems & Minerals, among others.

Hewat, Alan

2003-10-10

105

Direct imaging of the atomic structure inside a nanowire by scanning tunnelling microscopy  

NASA Astrophysics Data System (ADS)

Semiconductor nanowires are expected to be important components in future nano-electronics and photonics. Already a wide range of applications has been realized, such as high-performance field-effect transistors, bio/chemical sensors, diode logics and single-nanowire lasers. As nanowires have small cross-sections and large surface-to-bulk ratios, their properties can be significantly influenced by individual atomic-scale structural features, and they can have properties or even atomic arrangements with no bulk counterparts. Hence, experimental methods capable of directly addressing the atomic-scale structure of nanowires are highly desirable. One such method is scanning tunnelling microscopy (STM), which, by direct imaging of the atomic and electronic structure of surfaces has revolutionized the perception of nanoscale objects and low-dimensional systems. Here we demonstrate how combining STM with an embedding scheme allows us to image the interior of semiconductor nanowires with atomic resolution. Defect structures such as planar twin segments and single-atom impurities are imaged inside a GaAs nanowire. Further, we image an intriguing GaAs nanowire that is separated into two distinct nanocrystallites along the growth direction of the wire.

Mikkelsen, Anders; Sköld, Niklas; Ouattara, Lassana; Borgström, Magnus; Andersen, Jesper N.; Samuelson, Lars; Seifert, Werner; Lundgren, Edvin

2004-08-01

106

The atomic and electron structure of ZrO 2  

Microsoft Academic Search

The atomic structure of amorphous and crystalline zirconium dioxide (ZrO2) films is studied using X-ray diffraction and extended X-ray absorption fine structure techniques. The electron structure\\u000a of ZrO2 is experimentally determined using X-ray and UV photoelectron spectroscopy, and the electron energy band structure is theoretically\\u000a calculated using electron density functional method. According to these data, the valence band of ZrO2

A. V. Shaposhnikov; D. V. Gritsenko; I. P. Petrenko; O. P. Pchelyakov; V. A. Gritsenko; S. B. Érenburg; N. V. Bausk; A. M. Badalyan; Yu. V. Shubin; T. P. Smirnova; H. Wong; C. W. Kim

2006-01-01

107

Graph kernels for chemical compounds using topological and three-dimensional local atom pair environments  

Microsoft Academic Search

Approaches that can predict the biological activity or properties of a chemical compound are an important application of machine learning. In this paper, we introduce a new kernel function for measuring the similarity between chemical compounds and for learning their related properties and activities. The method is based on local atom pair environments which can be rapidly computed by using

Georg Hinselmann; Nikolas Fechner; Andreas Jahn; Matthias Eckert; Andreas Zell

2010-01-01

108

Editorial . Quantum fluctuations and coherence in optical and atomic structures  

Microsoft Academic Search

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.

Jürgen Eschner; Alessandra Gatti; Agnès Maître; Giovanna Morigi

2003-01-01

109

Direct experimental determination of the atomic structure at internal interfaces  

SciTech Connect

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.

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

1995-07-01

110

Physico-chemical environment of Al impurity atoms in amorphous silica  

NASA Astrophysics Data System (ADS)

The physico-chemical environment around the aluminum impurity atoms in commercial Herasil silica is studied by electron-induced X-ray emission spectroscopy. Despite the low concentration of aluminum and the charging effect occurring upon electron irradiation, we have been able to characterize the environment of the Al atoms. We show that the Al atoms are in an octahedral environment, i.e. surrounded by 6 oxygen atoms. The presence of Al clusters, whose metallic character would make them candidates to be ultraviolet absorption centers, is ruled out.

Jonnard, Ph.; Morreeuw, J.-P.; Bercegol, H.

2003-02-01

111

Atomic structure analysis of stabilized toxic wastes  

Microsoft Academic Search

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

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

1986-01-01

112

Structural effects of atomic substitutions in silicates  

NASA Astrophysics Data System (ADS)

Structural transformations, thermal expansion, and thermochemistry of stuffed quartz phases in the Lisb1-xAlsb1-xSisb1+xOsb4 system were investigated by high- and low-temperature powder synchrotron X-ray and neutron diffraction, and high-temperature drop-solution calorimetry. Rietveld analysis of diffraction data reveals an Al/Si order-disorder transition at x = ˜0.3 and a beta-alpha displacive transformation at ˜0.65. Although the stuffed beta-quartz compounds (0 ? x <\\ ˜0.65) expand within (001) and contract along c with increasing temperature, this thermal anisotropy is more pronounced for 0 ? x <\\ ˜0.3 than for ˜0.3 ? x <\\ ˜0.65. The disparity can be attributed to tetrahedral tilting that only occurs in the ordered structures. The alpha-quartz-stuffed phases (˜0.65 ? x ? 1) exhibit positive thermal expansion along both a and c, which arises from a rotation of rigid Si(Al)-tetrahedra about <100>. As Li+Al content increases, the critical temperature of the alpha-beta quartz transition decreases linearly, and the first-order character of this transition becomes weaker. Variations in the enthalpy of drop-solution with composition show a trend change at x = ˜0.3 that corresponds to the Al/Si order-disorder transition. However, since the enthalpy of the alpha-beta transformation is rather small, no significant discontinuity is observed at x = ˜0.65. The alpha-beta quartz transition, the P 1-I 1 anorthite transition, and the order-disorder transition of Li ions in beta-eucryptite were examined by in situ transmission electron microscopy. Structural defects appear to interact strongly with displacive transitions as manifested by the memory effects associated with the transition-induced domains. Dauphine twins in alpha-quartz are pinned by both extended and point defects, and an Arrhenius analysis of the memory degrading behavior involving point defects yields an activation energy for point defect diffusion of 68.5 ± 4.1 kJ/mol. By contrast, c-antiphase domain boundaries of anorthite exhibit a nearly perfect memory, because they are fixed by localized Al/Si disorder. Electron diffraction analysis of beta-eucryptite reveals modulated structures that result from superperiodic stacking of two structural units with different Li configurations parallel to (100). Upon heating, these structures transform to the modification with a disordered Li distribution due to positional disordering of Li along the structural channels.

Xu, Hongwu

1998-12-01

113

Multi-million atom electronic structure calculations for quantum dots  

Microsoft Academic Search

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

Muhammad Usman

2010-01-01

114

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

NASA Astrophysics Data System (ADS)

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.

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

2010-04-01

115

Atomic structure of quasicrystalline Al sub 65 Ru sub 15 Cu sub 20  

SciTech Connect

The atomic structure and chemical ordering of Al{sub 65}Ru{sub 25}Cu{sub 20} quasicrystals was studied by anomalous-x-ray-diffraction measurements of powder samples carried out at the Ru and Cu {ital K} edges. The differential atomic pair distribution function of Ru, and partial structure factor of Ru and Cu, were obtained. The results suggest that a strong covalent bonding between Al and Ru is contributing to the stability of this phase. A structural model obtained by a direct projection of a six-dimensional hypercubic lattice with the vertex decoration using a non-Penrose window is shown to account for the results quite well. Compositional ordering is specified by subdividing the window for each composition. The structure of this phasonless quasicrystal is fundamentally different from the structures of other quasicrystals with phasons.

Hu, R.; Egami, T. (Department of Materials Science and Engineering and Laboratory for Research on the Structure of Matter, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6272 (United States)); Tsai, A.; Inoue, A.; Masumoto, T. (Institute for Materials Research, Tohoku University, Sendai 980 (Japan))

1992-09-01

116

Chemical profiling of silicon nitride structures  

NASA Technical Reports Server (NTRS)

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

Vasquez, R. P.

1989-01-01

117

Crystal structure solution from experimentally determined atomic pair distribution functions  

SciTech Connect

An extension of the Liga algorithm for structure solution from atomic pair distribution functions (PDFs), to handle periodic crystal structures with multiple elements in the unit cell, is described. The procedure is performed in three separate steps. First, pair distances are extracted from the experimental PDF. In the second step the Liga algorithm is used to find unit-cell sites consistent with these pair distances. Finally, the atom species are assigned over the cell sites by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron X-ray PDF data from 16 test samples. The structure solution was successful for 14 samples, including cases with enlarged supercells. The algorithm success rate and the reasons for the failed cases are discussed, together with enhancements that should improve its convergence and usability.

Juhas, P.; Granlund, L.; Gujarathi, S.R.; Duxbury, P.M.; Billinge, S.J.L. (MSU); (Columbia)

2010-05-25

118

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

PubMed

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

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

2013-09-01

119

Self-organized atomic nanowires of noble metals on Ge(001): atomic structure and electronic properties  

NASA Astrophysics Data System (ADS)

Atomic structures of quasi-one-dimensional (1D) character can be grown on semiconductor substrates by metal adsorption. Significant progress concerning study of their 1D character has been achieved recently by condensing noble metal atoms on the Ge(001) surface. In particular, Pt and Au yield high quality reconstructions with low defect densities. We report on the self-organized growth and the long-range order achieved, and present data from scanning tunneling microscopy (STM) on the structural components. For Pt/Ge(001), we find hot substrate growth is the preferred method for self-organization. Despite various dimerized bonds, these atomic wires exhibit metallic conduction at room temperature, as documented by low-bias STM. For the recently discovered Au/Ge(001) nanowires, we have developed a deposition technique that allows complete substrate coverage. The Au nanowires are extremely well separated spatially, exhibit a continuous 1D charge density, and are of solid metallic conductance. In this review, we present structural details for both types of nanowires, and discuss similarities and differences. A perspective is given for their potential to host a 1D electron system. The ability to condense different noble metal nanowires demonstrates how atomic control of the structure affects the electronic properties.

Schäfer, J.; Meyer, S.; Blumenstein, C.; Roensch, K.; Claessen, R.; Mietke, S.; Klinke, M.; Podlich, T.; Matzdorf, R.; Stekolnikov, A. A.; Sauer, S.; Bechstedt, F.

2009-12-01

120

Hydrogen atom initiated chemistry. [chemical evolution in planetary atmospheres  

NASA Technical Reports Server (NTRS)

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.

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

1979-01-01

121

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

PubMed

Boron and nitrogen doped graphenes are highly promising materials for electrochemical applications, such as energy storage, generation and sensing. The doped graphenes can be prepared by a broad variety of chemical approaches. The substitution of a carbon atom should induce n-type behavior in the case of nitrogen and p-type behavior in the case of boron-doped graphene; however, the real situation is more complex. The electrochemical experiments show that boron-doped graphene prepared by hydroboration reaction exhibits similar properties as the nitrogen doped graphene; according to theory, the electrochemical behavior of B and N doped graphenes should be opposite. Here we analyze the electronic structure of N/B-doped graphene (at ?5% coverage) by theoretical calculations. We consider graphene doped by both substitution and addition reactions. The density of states (DOS) plots show that graphene doped by substitution of the carbon atom by N/B behaves as expected, i.e., as an n/p-doped material. N-doped graphene also has a lower value of the workfunction (3.10 eV) with respect to that of the pristine graphene (4.31 eV), whereas the workfunction of B-doped graphene is increased to the value of 5.57 eV. On the other hand, the workfunctions of graphene doped by addition of -NH2 (4.77 eV) and -BH2 (4.54 eV) groups are both slightly increased and therefore the chemical nature of the dopant is less distinguishable. This shows that mode of doping depends significantly on the synthesis method used, as it leads to different types of behaviour, and, in turn, different electronic and electrochemical properties of doped graphene, as observed in electrocatalytic experiments. This study has a tremendous impact on the design of doped graphene systems from the point of view of synthetic chemistry. PMID:24912566

Lazar, Petr; Zbo?il, Radek; Pumera, Martin; Otyepka, Michal

2014-07-21

122

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

123

Determination of the fine structure constant from atom interferometry  

NASA Astrophysics Data System (ADS)

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

Guellati, Saida

2012-06-01

124

Theoretical atomic physics code development I: CATS: Cowan Atomic Structure Code  

SciTech Connect

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.

Abdallah, J. Jr.; Clark, R.E.H.; Cowan, R.D.

1988-12-01

125

Editorial . Quantum fluctuations and coherence in optical and atomic structures  

NASA Astrophysics Data System (ADS)

From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures. This special issue is dedicated to recent developments in this area. It presents a selection of examples where quantum dynamics, fluctuations, and coherence generate structures in time or in space or where such structures are observed experimentally. The examples range from coherence phenomena in condensed matter, over atoms in optical structures, entanglement in light and matter, to quantum patterns in nonlinear optics and quantum imaging. The combination of such seemingly diverse subjects formed the basis of a successful European TMR network, "Quantum Structures" (visit http://cnqo.phys.strath.ac.uk/~gianluca/QSTRUCT/). This special issue partly re.ects the results and collaborations of the network, going however well beyond its scope by including contributions from a global community and from many related topics which were not addressed directly in the network. The aim of this issue is to present side by side these di.erent topics, all of which are loosely summarized under quantum structures, to highlight their common aspects, their di.erences, and the progress which resulted from the mutual exchange of results, methods, and knowledge. To guide the reader, we have organized the articles into subsections which follow a rough division into structures in material systems and structures in optical .elds. Nevertheless, in the following introduction we point out connections between the contributions which go beyond these usual criteria, thus highlighting the truly interdisciplinary nature of quantum structures. Much of the progress in atom optics has been generated by the application of concepts from wave optics to matter waves. An example is the contribution by Franke-Arnold et al. The authors investigate the coherence properties of two trapped cold atoms using concepts developed in wave optics. Nevertheless, novel features appear in this system due to the quantum statistics - as atoms may be bosons or fermions - and due to interactions. Matter waves find a spectacular manifestation in Bose-Einstein condensates (BECs) of cold dilute atomic gases. Several concepts of wave optics, like the laser, have been discussed in relation to BECs, and the .eld of atom optics with BECs is rapidly developing. The similarity between the theoretical description of a weakly interacting BEC with that of a non-linear optical system has motivated a series of experiments that led to the observation of, e.g., solitons, vortices and vortex crystallization in matter waves. In this context, the paper by Josopait et al. describes the dynamics of a Bose-Einstein condensate containing a vortex. The vortex stability is discussed as a function of the interparticle interaction, which can be tuned using Feshbach resonances, and the dynamics of the BEC reflected by an atomic mirror is investigated. Non-linear optics merges with atomic physics also in a relatively new research area which aims at quantum non-linear optics with cold atomic gases. Labeyrie et al. use a dense, laser-cooled atomic gas as a non-linear medium for light propagation, and discuss the conditions for observing optical patterns in the transmitted beam. Pattern formation in non-linear optical media is one of the numerous forms of self-organization that these systems display, including also turbulence and optical solitons. With respects to other physical systems, where these phenomena are commonly observed, optical systems are however special: at optical frequencies thermal .uctuations are negligible and do not hide the presence of quantum .uctuations, even at room temperature. Remarkably, the interplay between non-linearity and quantum noise leads to novel

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

2003-03-01

126

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

127

Polymorphism of dislocation core structures at the atomic scale  

NASA Astrophysics Data System (ADS)

Dislocation defects together with their associated strain fields and segregated impurities are of considerable significance in many areas of materials science. However, their atomic-scale structures have remained extremely challenging to resolve, limiting our understanding of these ubiquitous defects. Here, by developing a complex modelling approach in combination with bicrystal experiments and systematic atomic-resolution imaging, we are now able to pinpoint individual dislocation cores at the atomic scale, leading to the discovery that even simple magnesium oxide can exhibit polymorphism of core structures for a given dislocation species. These polymorphic cores are associated with local variations in strain fields, segregation of defects, and electronic states, adding a new dimension to understanding the properties of dislocations in real materials. The findings advance our fundamental understanding of basic behaviours of dislocations and demonstrate that quantitative prediction and characterization of dislocations in real materials is possible.

Wang, Zhongchang; Saito, Mitsuhiro; McKenna, Keith P.; Ikuhara, Yuichi

2014-01-01

128

Atomic and electronic structure of Ni-Nb metallic glasses  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

129

DFT study of the structures and energetics of 98-atom AuPd clusters  

NASA Astrophysics Data System (ADS)

The energetics, structures and segregation of 98-atom AuPd nanoclusters are investigated using a genetic algorithm global optimization technique with the Gupta empirical potential (comparing three different potential parameterisations) followed by local minimizations using Density Functional Theory (DFT) calculations. A shell optimization program algorithm is employed in order to study the energetics of the highly symmetric Leary Tetrahedron (LT) structure and optimization of the chemical ordering of a number of structural motifs is carried out using the Basin Hopping Monte Carlo approach. Although one of the empirical potentials is found to favour the LT structure, it is shown that Marks Decahedral and mixed FCC-HCP motifs are lowest in energy at the DFT level.The energetics, structures and segregation of 98-atom AuPd nanoclusters are investigated using a genetic algorithm global optimization technique with the Gupta empirical potential (comparing three different potential parameterisations) followed by local minimizations using Density Functional Theory (DFT) calculations. A shell optimization program algorithm is employed in order to study the energetics of the highly symmetric Leary Tetrahedron (LT) structure and optimization of the chemical ordering of a number of structural motifs is carried out using the Basin Hopping Monte Carlo approach. Although one of the empirical potentials is found to favour the LT structure, it is shown that Marks Decahedral and mixed FCC-HCP motifs are lowest in energy at the DFT level. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr32517a

Bruma, Alina; Ismail, Ramli; Oliver Paz-Borbón, L.; Arslan, Haydar; Barcaro, Giovanni; Fortunelli, Alessandro; Li, Z. Y.; Johnston, Roy L.

2012-12-01

130

MCHF atomic-structure package: support libraries and utilities  

NASA Astrophysics Data System (ADS)

The libraries and utilities that form part of the MCHF atomic-structure package are described. Among the utilities is a LEVELS program that produces an energy level table and a LINES program that process the transition data from a series of LSJ calculations as a line list.

Fischer, Charlotte Froese

1991-06-01

131

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

NASA Astrophysics Data System (ADS)

Structural defects in SiO2 glasses implanted with Li+, N+, O+, F+, Si+, and P+ ions were examined by vacuum-ultraviolet-absorption and electron-paramagnetic-resonance spectroscopies as well as thermal-gas-release analysis. The chemical interaction of implanted ions with substrate structure was considered on the basis of the obtained results. It is found that the type of predominant defects is controlled by the electronegative nature of implants. Silicon-silicon homobonds, which are oxygen-vacancy-type defects, are produced by electropositive implants (i.e., Li, P, and Si) at concentrations comparable to those of the implants. On the other hand, in the case of electronegative implants (F and O) O2 molecules and peroxy radicals (POR), both of which may be regarded as oxygen-interstitial-type defects, are the major defects and the total concentrations of these two defects are comparable to implant concentrations. These results indicate that chemical interaction of implanted ions with SiO2 is primarily controlled by the electronegative nature of implants. Electropositive implants (M) react chemically with oxygen atoms in the substrate structure to form M-O bonds, leaving Si-Si bonds. Electronegative implants (A) react chemically with silicon atoms to form Si-A bonds and oxygen atoms recoiled with implants combine with each other to form O2 molecules or react with the silica-network structure to form POR's. Concentrations of these predominant defects relative to implants can be used quantitatively to describe the strength of chemical interactions. When the chemical interaction is strong, both concentrations are comparable. On the other hand, when the chemical interaction is weak, concentrations of these defects are much smaller than those of implants because the major fraction of implants occur in a neutral state without forming chemical bonds with constituents of the substrate. Nitrogen is an example of this category and the major fraction of implanted nitrogen atoms are present as N2 molecules.

Hosono, Hideo; Matsunami, Noriaki

1993-11-01

132

Atomic Structure and Properties of Extended Defects in Silicon  

SciTech Connect

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.

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

1998-10-15

133

Local atomic structure of Ca-Mg-Zn metallic glasses  

NASA Astrophysics Data System (ADS)

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

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

2010-09-01

134

Chemical identity of atoms using core electron annihilations  

SciTech Connect

Positron annihilation spectroscopy is a sensitive probe for studying the electronic structure of defects in solids. The high momentum part of the Doppler-broadened annihilation spectra can be used to distinguish different elements. This is achieved by using a new two-detector coincidence system and by imposing appropriate kinematic cuts to exclude background events. The new setup improves the peak to background ratio in the annihilation spectrum to {approximately}10{sup 5}. As a result, the line shape variations arising from different core electrons can be studied. The new approach adds elemental specificity to the Doppler broadening technique, and is useful in studying elemental variations around a defect site. Results from several case studies are reviewed.

Asoka-Kumar, P.

1997-06-27

135

Properties of Individual Dopant Atoms in Single-Layer MoS2 : Atomic Structure, Migration, and Enhanced Reactivity.  

PubMed

Single-layered MoS2 doped with Re (n-type) and Au (p-type) are investigated by in situ scanning transmission electron microscopy. Re atoms substituting Mo sites enhance the local chemical affinity, evidenced by agglomeration of other dopant/impurity atoms. Au atoms exist as adatoms and show larger mobility under the electron beam. These behaviors are consistent with density functional theory calculations. PMID:24677145

Lin, Yung-Chang; Dumcenco, Dumitru O; Komsa, Hannu-Pekka; Niimi, Yoshiko; Krasheninnikov, Arkady V; Huang, Ying-Sheng; Suenaga, Kazu

2014-05-01

136

Insight into Amyloid Structure Using Chemical Probes  

PubMed Central

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

Reinke, Ashley A.; Gestwicki, Jason E.

2011-01-01

137

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

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.

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

1982-09-02

138

Modifications of the electronic structure of GaSb surface by chalcogen atoms: S, Se, and Te  

Microsoft Academic Search

Modifications to the electronic properties and chemical structures of the GaSb surface using the chalcogen atoms S, Se, and Te were investigated theoretically and experimentally. A self-consistent density-functional theory study indicates that an adsorption of a full monolayer coverage of chalcogen atoms on a Ga-terminated surface reduces the density of gap region states significantly. A greater photoluminescence enhancement was observed

Z. Y. Liu; A. A. Gokhale; M. Mavrikakis; D. A. Saulys; T. F. Kuech

2004-01-01

139

Structural and chemical heterogeneity of natural crystals and microgeochemical line of research in ontogeny of minerals  

NASA Astrophysics Data System (ADS)

A review of the current state of genetic mineralogy in the field of the chemical heterogeneity of mineral individuals is presented. Due to advances in the local analysis of matter, the ontogenetic approach is now being focused on the chemical anatomy of minerals. A new line of research, microgeochemistry, deals with the migration of chemical elements in natural crystals caused by defects in the crystal lattice. It becomes evident that structural and chemical heterogeneity is an intrinsic property of mineral individuals. Phenomenological laws of this heterogeneity and the interaction of atoms with lattice defects are stated.

Alekseev, V. I.; Marin, Yu. B.

2012-12-01

140

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

Microsoft Academic Search

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

F W Meyer; L I Vergara; H F Krause

2006-01-01

141

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins.  

PubMed

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of ?-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems. PMID:22988857

Tamiola, Kamil; Mulder, Frans A A

2012-10-01

142

Direct measurement of fine structure in the ground state of atomic carbon by laser magnetic resonance  

NASA Astrophysics Data System (ADS)

Laser magnetic resonance measurements of fine-structure intervals in the ground state of atomic carbon, which have made possible the detection of far infrared line emissions from C-12 in several interstellar sources, are reported. The 3P0 to 3P1 and 3P1 to 3P2 transitions in C-12 and C-13 atoms in a methane-fluorine atom flame were observed at 10 different optically pumped far infrared laser lines, and the C-12 fine structure intervals were determined from the combined data of all 10 lines and g-factors from the atomic beam experiments of Wolber et al. (1970). Interval spacings of 809.3446 (29) and 492.1623 (7) GHz are obtained for the 3P0-3P1 and 3P1-3P2 transitions, respectively. It is pointed out that the further detection of these transitions should lead to information regarding atomic abundances, isotope ratios, chemical fractionation effects, processes involving interstellar dust grains and the physical conditions of the interstellar medium

Saykally, R. J.; Evenson, K. M.

1980-06-01

143

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

SciTech Connect

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

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

2010-11-05

144

Atomic structures of Si(111) surface during silicon epitaxial growth  

NASA Astrophysics Data System (ADS)

Atomic structures during homoepitaxial growth on a Si(111)7 × 7 surface are investigated by reflection high-energy electron diffraction (RHEED) and scanning tunneling microscopy (STM). Analyzing RHEED intensity rocking curves by dynamical calculations, we conclude that backbonds of adatoms on the dimer-adatom-stacking-fault (DAS) structure are broken by two adsorbed silicon atoms at an initial stage of the deposition. Subsequently the structure is reconstructed into a pyramidal cluster-type one. At temperatures higher than 400°C, rocking curves during growth are very similar to that of the Si(111)7 × 7 DAS structure. It is concluded that the surface structures during growth at the high temperatures are the DAS structures including 3 × 3, 5 × 5 and 9 × 9. At 280°C, however, the rocking curve is very different from the curves by the DAS structures. Analyzing the curve by RHEED dynamical calculations, we have found that the pyramidal cluster-type structure is formed on the surface during growth. From these results and instability of the pyramidal cluster-type structure, we conclude that the formation of the metastable structure promotes successive epitaxial growth accompanied with stacking-fault dissolution at the dimer-stacking-fault framework. At substrate temperatures from 400 to 600°C a mixed phase of 5 × 5 and 7 × 7 structures is observed with RHEED intensity oscillation during growth. In STM images of isolated silicon hillocks formed on the Si(111)7 × 7 surface, we observed stable (long lifetime) shapes of 5 × 5 hillocks, and found magic numbers of the 5 × 5 units in the hillocks. For 7 × 7 hillocks, however, it is hard to find stable ones in STM images. We discuss the relation between the formation of the 5 × 5 DAS structure at the growth surface and the stability of the isolated 5 × 5 hillocks.

Ichimiya, Ayahiko; Nakahara, Hitoshi; Tanaka, Yoriko

1996-05-01

145

Optical gain and grating structure in the collective atomic recoil laser  

NASA Astrophysics Data System (ADS)

Considering atoms entering an interaction region with limited length, then continuously running away, we show the features of the optical gain and atomic grating structure in the collective atomic recoil laser (CARL).

Wang, Jun-Li; Qiao, Yao-Jun; Fan, Wen-Jun; Zhai, Peng-Wang; Gao, Jin-Yue

1999-04-01

146

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

PubMed Central

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.

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

2008-01-01

147

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

PubMed Central

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

March, Norman H.; Parr, Robert G.

1980-01-01

148

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

SciTech Connect

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted directly without the need for preconceived atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementary chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25{degree} symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}.

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

1994-05-01

149

Optomechanical self-structuring in a cold atomic gas  

NASA Astrophysics Data System (ADS)

The rapidly developing field of optomechanics aims at the combined control of optical and mechanical modes. In cold atoms, the spontaneous emergence of spatial structures due to optomechanical back-action has been observed in one dimension in optical cavities or highly anisotropic samples. Extensions to higher dimensions that aim to exploit multimode configurations have been suggested theoretically. Here, we describe a simple experiment with many spatial degrees of freedom, in which two continuous symmetries--rotation and translation in the plane orthogonal to a pump beam axis--are spontaneously broken. We observe the simultaneous long-range spatial structuring (with hexagonal symmetry) of the density of a cold atomic cloud and of the pump optical field, with adjustable length scale. Being based on coherent phenomena (diffraction and the dipole force), this scheme can potentially be extended to quantum degenerate gases.

Labeyrie, G.; Tesio, E.; Gomes, P. M.; Oppo, G.-L.; Firth, W. J.; Robb, G. R. M.; Arnold, A. S.; Kaiser, R.; Ackemann, T.

2014-04-01

150

Imaging of zeolite surface structures by atomic force microscopy  

NASA Astrophysics Data System (ADS)

Atomic force microscopy has been employed to study the (010) surface structure of the natural zeolite heulandite. Images on a macroscopic scale exhibit large terraces separated from each other by half of the unit cell length b. Molecular resolution is obtained when measured in 0.1M NaOH. The surface ac unit cell is about 26% larger in area than the bulk unit cell.

Scandella, L.; Kruse, N.; Prins, R.

151

Imaging of zeolite surface structures by atomic force microscopy  

NASA Astrophysics Data System (ADS)

Atomic force microscopy has been employed to study the (010) surface structure of the natural zeolite heulandite. Images on a macroscopic scale exhibit large terraces separated from each other by half of the unit cell length b. Molecular resolution is obtained when measured in 0.1M NaOH. The surface ac unit cell is about 26% larger in area than the bulk unit cell.

Scandella, L.; Kruse, N.; Prins, R.

1993-02-01

152

The local atomic structure of superconducting Fe-Se-Te  

Microsoft Academic Search

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

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

2009-01-01

153

Magnetism and surface structure of atomically controlled ultrathin metal films.  

SciTech Connect

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.

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

2007-01-01

154

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

NASA Astrophysics Data System (ADS)

This dissertation examines the modification and characterization of hydrogen-terminated silicon surfaces in organic liquids. Conductive atomic force microscope (cAFM) lithography is used to fabricate structures with sub-100 nm line width on H:Si(111) in n-alkanes, 1-alkenes, and 1-alkanes. Nanopatterning is accomplished by applying a positive (n-alkanes and 1-alkenes) or a negative (1-alkanes) voltage pulse to the silicon substrate with the cAFM tip connected to ground. The chemical and kinetic behavior of the patterned features is characterized using AFM, lateral force microscopy, time-of-flight secondary ion mass spectroscopy (TOF SIMS), and chemical etching. Features patterned in hexadecane, 1-octadecene, and undecylenic acid methyl ester exhibited chemical and kinetic behavior consistent with AFM field induced oxidation. The oxide features are formed due to capillary condensation of a water meniscus at the AFM tip-sample junction. A space-charge limited growth model is proposed to explain the observed growth kinetics. Surface modifications produced in the presence of neat 1-dodecyne and 1-octadecyne exhibited a reduced lateral force compared to the background H:Si(111) substrate and were resistant to a hydrofluoric acid etch, characteristics which indicate that the patterned features are not due to field induced oxidation and which are consistent with the presence of the methyl-terminated 1-alkyne bound directly to the silicon surface through silicon-carbon bonds. In addition to the cAFM patterned surfaces, full monolayers of undecylenic acid methyl ester (SAM-1) and undec-10-enoic acid 2-bromoethyl ester (SAM-2) were grown on H:Si(111) substrates using ultraviolet light. The structure and chemistry of the monolayers were characterized using AFM, TOF SIMS, X-ray photoelectron spectroscopy (XPS), X-ray reflectivity (XRR), X-ray standing waves (XSW), and X-ray fluorescence (XRF). These combined analyses provide evidence that SAM-1 and SAM-2 form dense monolayers with areal densities corresponding to 50% and 57% of the Si(111) surface bonds. XPS and XSW analyses of SAM-2 reveal that Br abstraction by reactive silicon dangling bonds competes with olefin addition to the surface so that 0.48 monolayer (ML) of a total Br coverage of 0.58 ML is bound to the Si(111) lattice position.

Kinser, Christopher Reagan

155

The accurate electron crystallographic refinement of organic structures containing heavy atoms.  

PubMed

Prospects for the accurate structure determination of heavy-atom-containing organic crystals were evaluated with electron diffraction data from perchloro and perbromo derivatives of copper phthalocyanine. While the extensive overlap of experimental Patterson maps (from 1200kV intensities) with respective crystal autocorrelation functions explains the success of previous direct structure analyses, it is clear that multiple-scattering perturbations still evident at high voltage will frustrate the determination of accurate bond distances and angles. If, however, the result obtained after direct structure analysis and Fourier refinement is used to position an idealized molecular model (i.e. with chemically reasonable bonding parameters), the correct structure can then be justified by a rotational search coupled with a multislice dynamical calculation. Even though dynamical scattering is not the only major perturbation to such data sets, the resolution-limited correction is still sufficient to identify the correct molecular orientation in the unit cell. Alternatively, an acceptable unconstrained structure refinement can be carried out via a procedure proposed by Huang, Liu, Gu, Xiong, Fan & Li [Acta Cryst. (1996), A52, 152-157]. A phenomenological adjustment of observed intensities, based initially on the heavy-atom positions found in a high-resolution electron micrograph, will permit all light atoms to be observed near their ideal positions in the ensuing Fourier refinement. PMID:9175261

Dorset, D L

1997-05-01

156

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

NASA Astrophysics Data System (ADS)

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

Kraj?í, M.; Hafner, J.; Mihalkovi?, M.

2000-07-01

157

Structure of a Quantized Vortex in Fermi Atom Gas  

SciTech Connect

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.

Machida, Masahiko [CCSE, Japan Atomic Energy Research Institute, 6-9-3 Higashi-Ueno, Taito-ku, Tokyo 110-0015 (Japan) and CREST (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan); Koyama, Tomio [IMR, Tohoku University 2-1-1 Katahira Aoba-ku, Sendai 980-8577 (Japan) and CREST (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)

2006-09-07

158

Atomic- Resolution Crystal Structure of the Antiviral Lectin Scytovirin  

SciTech Connect

The crystal structures of the natural and recombinant antiviral lectin scytovirin (SVN) were solved by single-wavelength anomalous scattering and refined with data extending to 1.3 Angstroms and 1.0 Angstroms resolution, respectively. A molecule of SVN consists of a single chain 95 amino acids long, with an almost perfect sequence repeat that creates two very similar domains (RMS deviation 0.25 Angstroms for 40 pairs of Ca atoms). The crystal structure differs significantly from a previously published NMR structure of the same protein, with the RMS deviations calculated separately for the N- and C-terminal domains of 5.3 Angstroms and 3.7 Angstroms, respectively, and a very different relationship between the two domains. In addition, the disulfide bonding pattern of the crystal structures differs from that described in the previously published mass spectrometry and NMR studies.

Moulaei,T.; Botos, I.; Ziolkowska, N.; Bokesch, H.; Krumpe, L.; McKee, T.; O'Keefe, B.; Dauter, Z.; Wlodawer, A.

2007-01-01

159

Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion  

SciTech Connect

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.

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

2012-02-10

160

Electronic structure and reactivity of guanylthiourea: a quantum chemical study.  

PubMed

Electronic structure analysis of guanylthiourea (GTU) and its isomers has been carried out using quantum chemical methods. Two major tautomeric classes (thione and thiol) have been identified on the potential energy (PE) surface. In both the cases conjugation of pi-electrons and intramolecular H-bonds have been found to play a stabilizing role. Various isomers of GTU on its PE surface have been analyzed in two different groups (thione and thiol). The interconversion from the most stable thione conformer (GTU-1) to the most stable thiol conformer (GTU-t1) was found to take place via bimolecular process which involves protonation at sulfur atom of GTU-1 followed by subsequent C-N bond rotation and deprotonation. The detailed analysis of the protonation has been carried out in gas phase and aqueous phase (using CPMC model). Sulfur atom (S1) was found to be the preferred protonation site (over N4) in GTU-1 in gas phase whereas N4 was found to be the preferred site of protonation in aqueous medium. The mechanism of S-alkylation reaction in GTU has also been studied. The formation of alkylated analogs of thiol isomers (alkylated guanylthiourea) is believed to take place via bimolecular process which involves alkyl cation attack at S atom followed by C-N bond rotation and deprotonation. The reactive intermediate RS(NH(2))C-N-C(NH(2))(2)(+) belongs to the newly identified [symbol: see text]N(<--L)(2) class of species and provides the necessary dynamism for easy conversion of thione to thiol. PMID:19890877

Mehdi, Ahmed; Adane, Legesse; Patel, Dhilon S; Bharatam, Prasad V

2010-04-30

161

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

PubMed

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

Ivanciuc, Ovidiu

2013-06-01

162

Understanding chemical reactivity: the case for atom, proton and methyl transfers.  

PubMed

The concept of "chemical reactivity" assumes that atoms and molecules contain the necessary information to describe their evolution over time as they transform from reactants to products. This concept was useful in the past to rationalize reactivity trends and predict the behavior of new systems. Free-energy relationships have played a central role in this field. However, electronic effects often counter the energetic effects and give rise to "anomalies" or separate correlations. We discuss a quantification of the concept of "chemical reactivity", emphasizing the role of molecular and electronic factors in chemistry. PMID:18491307

Arnaut, Luis G; Formosinho, Sebastião J

2008-01-01

163

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

PubMed

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

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

2014-04-30

164

DFT study of the structures and energetics of 98-atom AuPd clusters.  

PubMed

The energetics, structures and segregation of 98-atom AuPd nanoclusters are investigated using a genetic algorithm global optimization technique with the Gupta empirical potential (comparing three different potential parameterisations) followed by local minimizations using Density Functional Theory (DFT) calculations. A shell optimization program algorithm is employed in order to study the energetics of the highly symmetric Leary Tetrahedron (LT) structure and optimization of the chemical ordering of a number of structural motifs is carried out using the Basin Hopping Monte Carlo approach. Although one of the empirical potentials is found to favour the LT structure, it is shown that Marks Decahedral and mixed FCC-HCP motifs are lowest in energy at the DFT level. PMID:23223667

Bruma, Alina; Ismail, Ramli; Paz-Borbón, L Oliver; Arslan, Haydar; Barcaro, Giovanni; Fortunelli, Alessandro; Li, Z Y; Johnston, Roy L

2013-01-21

165

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

ScienceCinema

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

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

2013-04-19

166

Relativistic total energy and chemical potential of heavy atoms and positive ions  

Microsoft Academic Search

The relativistic Thomas-Fermi theory, with a finite nucleus, is used to study the variation of the chemical potential mu with atomic number Z and number of electrons N(N

S. H. Hill; P. J. Grout; N. H. March

1984-01-01

167

Atomic-Hydrogen Mapping in Hot-Filament Chemical-Vapor Deposition  

NASA Astrophysics Data System (ADS)

Two-dimensional maps of the atomic-hydrogen concentration distribution were acquired with two-photon laser-induced fluorescence. The environment was a hot-filament chemical-vapor-deposition reactor used for polycrystalline diamond-film deposition. The maps were measured in situ under diamond-deposition conditions with variation of the growth parameters. The parameters investigated were filament temperature, input methane concentration, and total pressure.

Larjo, Jussi; Koivikko, Heidi; Li, Daming; Hernberg, Rolf

2001-02-01

168

Autocorrelation method adapted to generate new atomic environments: application for the prediction of 13-C chemical shifts of alkanes.  

PubMed

The concept of the multifunctional autocorrelation method governing global description of molecules was changed in order to take into account the structural environment of each atom. New atomic environments are generated as possible descriptors in QSARs and can be useful for database characterization. The principles of this approach are widely explained through a case study dealing with the design of a model allowing the simulation of the carbon-13 nuclear magnetic spectra for alkanes. Carbon atoms in alkanes are described by using as structural descriptors a vector corresponding to only four components vectors of the multifunctional autocorrelation method. The statistical method used for deriving the model was a classical three-layer feedforward neural network trained by the back-propagation algorithm and multilinear regression (MLR). The predictive ability of the ANN model was tested by -10%-out(L10%O) cross-validation method, demonstrating the superior quality of the neural model. The established model allows us the prediction of the 13-C chemical shifts with success because since all types of carbons are taken into account without distinction of connectivity. The neural network possessed a 4:7:1 architecture with a sigmoid shape as a activation function. The model produced a cross-validation standard coefficient r between delta(exp) and delta(calc) about 0.99, while the cross-validation standard s and the mean error are equal to 0.87 and 0.60 ppm, respectively. PMID:12086518

Nohair, M; Zakarya, D; Berrada, A

2002-01-01

169

Atomic and electronic structures of divacancy in graphene nanoribbons  

NASA Astrophysics Data System (ADS)

First principles calculations have been performed to investigate the electronic structures and transport properties of defective graphene nanoribbons (GNRs) in the presence of pentagon-octagon-pentagon (5-8-5) defects. Electronic band structure results reveal that 5-8-5 defects in the defective zigzag graphene nanoribbon (ZGNR) is unfavorable for electronic transport. However, such defects in the defective armchair graphene nanoribbon (AGNR) give rise to smaller band gap than that in the pristine AGNR, and eventually results in semiconductor to metal-like transition. The distinct roles of 5-8-5 defects in two kinds of edged-GNR are attributed to the different coupling between ?* and ? subbands influenced by the defects. Our findings indicate the possibility of a new route to improve the electronic transport properties of graphene nanoribbons via tailoring the atomic structures by ion irradiation.

Zhao, Jun; Zeng, Hui; Wei, Jianwei

2012-01-01

170

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

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.

Gurovich, B. A.; Prikhod'ko, K. E., E-mail: kirill@irmrnt.kiae.ru; Kuleshova, E. A.; Maslakov, K. I.; Komarov, D. A. [National Research Center Kurchatov Institute (Russian Federation)

2013-06-15

171

Understanding the structure of the first atomic contact in gold  

PubMed Central

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

2013-01-01

172

Viral structural transitions: an all-atom multiscale theory.  

PubMed

An all-atom theory of viral structural transitions (STs) is developed based on a multiscale analysis of the N-atom Liouville equation. The approach yields an understanding of viral STs from first principles and a calibrated interatomic force field. To carry out the multiscale analysis, we introduce slow variables characterizing the whole-virus dynamics. Use of the "nanocanonical ensemble" technique and the fundamental hypothesis of statistical mechanics (i.e., the equivalence of long-time and ensemble averages) is shown to imply a Fokker-Planck equation yielding the coarse-grained evolution of the slow variables. As viral STs occur on long time scales, transition state theory is used to estimate the energy barrier of transition between free energy wells implied by observed hysteresis in viral STs. Its application to Nudaurelia capensis omega virus provides an upper bound on the free energy barrier when a single dilatational order parameter is used. The long time scale of viral STs is shown to follow from the aggregate effect of inertia, energy barrier, and entropic effects. Our formulation can be generalized for multiple order parameter models to account for lower free energy barrier pathways for transition. The theory with its all-atom description can be applied to nonviral nanoparticles as well. PMID:17166043

Miao, Yinglong; Ortoleva, Peter J

2006-12-01

173

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

PubMed

High quality and purity single crystal ZnO samples doped with single isotopes of (63)Cu and (65)Cu, with equal concentrations of both these isotopes, and with natural Cu using a wet chemical atomic substitution reaction and anneal were studied using low temperature optical spectroscopy. Our data on the zero phonon line of the structured green band in ZnO confirm unambiguously the involvement of a single Cu atom in this defect emission. These data allow us to confirm the main features of the assignment proposed by Dingle in 1969 and to comment further on the defect structure. PMID:22575904

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

2012-05-30

174

Nanoscale chemical and structural characterization of transient metallic nanowires using aberration-corrected STEM-EELS.  

PubMed

Direct chemical and structural characterization of transient iron-nickel alloy nanowires was performed at subnanometer spatial resolution using probe spherical aberration-corrected scanning transmission electron microscopy and electron energy-loss spectroscopy. Nanowires with diameter less than 2 nm retaining their nominal bulk alloy composition were observed. In some cases, the nanowires were oxidized. Before rupture, a nanojunction as thin as three atoms in width could be imaged. The time-dependent structural analyses revealed the nanowire rupture mechanisms. It is found that the atoms on the {111} planes were the easiest to be removed by electron irradiation and fluctuations between low-energy and high-energy facets were observed. The hitherto unknown rich variety of structural and chemical behavior in alloyed magnetic nanojunctions should be considered for understanding their physical properties. PMID:22554271

Eswara Moorthy, Santhana K; Rousseau, Olivier; Viret, Michel; Kociak, Mathieu

2012-06-13

175

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

PubMed

Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes. PMID:24586129

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

2014-02-01

176

Effects of Xenon Insertion into Hydrogen Bromide. Comparison of the Electronic Structure of the HBr···CO2 and HXeBr···CO2 Complexes Using Quantum Chemical Topology Methods: Electron Localization Function, Atoms in Molecules and Symmetry Adapted Perturbation Theory.  

PubMed

Quantum chemistry methods have been applied to study the influence of the Xe atom inserted into the hydrogen-bromine bond (HBr ? HXeBr), particularly on the nature of atomic interactions in the HBr···CO2 and HXeBr···CO2 complexes. Detailed analysis of the nature of chemical bonds has been carried out using topological analysis of the electron localization function, while topological analysis of electron density was used to gain insight into the nature of weak nonbonding interactions. Symmetry-adapted perturbation theory within the orbital approach was applied for greater understanding of the physical contributions to the total interaction energy. PMID:24865594

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

2014-06-01

177

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

178

Chemical and Structural Variations at Augite (100) Twin Boundaries  

NASA Astrophysics Data System (ADS)

Twins and stacking faults on (100) are far less abundant in calcic pyroxenes like augite than they are in low-Ca compositions, such as pigeonite and orthopyroxene. The paucity of such twinning in augite has been attributed to high energies associated with octahedral skew reversals in pyroxenes where the M2 site is occupied by cations larger than Mg or Fe (e.g., Ca, Na). Deformation-twin boundaries in augite occurring in a pyroxene granulite from Hamnoy, Lofoten, Norway, were examined using high-resolution transmission electron microscopy. HRTEM images are consistent with Ca depletion at (100) twin boundaries, which can be interpreted structurally as a single unit cell of the low-Ca protoenstatite structure, or one-half unit cell of orthopyroxene. The high-resolution images show that the augite (100) twin planes are coherent or semi-coherent and are, in some cases, associated with (100) stacking faults. Although some of the twin planes have only a single, 0.9-nm layer of Ca-depleted pyroxene, most of them have been replaced by several unit cells of low-Ca clinopyroxene (pigeonite or clinoenstatite) that apparently nucleated on the low-Ca twin plane. We predict that future energy-filtered compositional imaging (EFTEM) investigations will confirm that the simple twin boundaries are, in fact, depleted in Ca. These nanometer-scale, Ca-depleted twin planes, and the pigeonite lamellae that nucleate on them, may result from a protracted thermal high during deformation, or from a later, retrograde metamorphic event experienced by these rocks. The atomic structure at the deformation-twin boundaries is topologically identical to that of the (100) herringbone twin planes that are found almost universally in augite from basalts and gabbros. Future investigations of (100) twin planes in augite from basalts and gabbros therefore should indicate whether or not long annealing times are required for Ca depletion at (100) twin planes in high-Ca pyroxenes. These results also suggest that traditional structural models of twin boundaries in complex inorganic solids are oversimplified. In cases such as this, chemical diffusion results in a different chemical composition, and, no doubt, in concomitant structural variations in the vicinity of the twin plane, compared to that of the host structure.

Zhang, S.; Veblen, D. R.

2006-05-01

179

Structural and chemical derivatization of graphene for electronics and sensing  

NASA Astrophysics Data System (ADS)

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

Mohanty, Nihar Ranjan

180

Atomic-scale structure of Mo6S6 nanowires.  

PubMed

We have studied the atomic-scale structure of the Mo6S6 nanowires using scanning tunneling microscopy and spectroscopy (STM and STS) and density functional theory (DFT). A novel synthesis route based on metallic Mo precursors is presented for the selective formation of elementary pure Mo6S6 nanowires. The Mo6S6 nanowires selectively organize as trimer bundles, and each of the Mo6S6 nanowires consists of an electrically conducting Mo backbone dressed with a sulfur exterior cap. The Mo6S6 nanowires may thus be of interest as novel building blocks in nanoelectronics because the Mo6S6 nanowires exist in a robust, singular structural conformation with uniquely defined electrical (metallic) properties. PMID:18950238

Kibsgaard, Jakob; Tuxen, Anders; Levisen, Martin; Laegsgaard, Erik; Gemming, Sibylle; Seifert, Gotthard; Lauritsen, Jeppe V; Besenbacher, Flemming

2008-11-01

181

Images of Atoms.  

ERIC Educational Resources Information Center

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)

Wright, Tony

2003-01-01

182

Atomic structure of DUSP26, a novel p53 phosphatase  

PubMed Central

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

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

2013-01-01

183

Enhanced Sensitivity of Micro Mechanical Chemical Sensors Through Structural Variation  

SciTech Connect

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.

Harris, J.C.

2001-04-16

184

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

185

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

PubMed

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

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

2013-07-24

186

Trends in information theory-based chemical structure codification.  

PubMed

This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed. PMID:24705993

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

2014-08-01

187

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

NASA Astrophysics Data System (ADS)

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

Xu, Ye

188

The structure of chemically modified detonation-synthesized nanodiamond particles  

Microsoft Academic Search

The results of studies of the structure of chemically modified detonation-synthesized nanodiamond (ND) particles by a set\\u000a of physical and chemical methods are reported. It is shown that the crystal structure, size, and the paramagnetic properties\\u000a of the particles persist during chemical modification processes. No nondiamond sp\\u000a 2 carbon is observed in the composition of the particles. The first experimental

I. I. Kulakova; V. V. Korol’kov; R. Yu. Yakovlev; G. V. Lisichkin

2010-01-01

189

Atomic Defects on the Surface of Quasi Two-Dimensional Layered Titanium Dichalcogenides: Stm Experiment and Quantum Chemical Simulation  

Microsoft Academic Search

The atomic surface structure of layered dichalcogenide 1T-TiSe2 is studied by scanning tunneling microscopy (STM) at room temperature. In STM images, the ordered structures in the form\\u000a of 6 ×6 ×6 triangles of Se atoms extending for 0.3 ±0.20 Å above the crystal surface are observed. The effect of a series\\u000a of different atomic structural defects on the surface topology

A. S. Razinkin; A. N. Enyashin; T. V. Kuznetsova; A. N. Titov; M. V. Kuznetsov; A. L. Ivanovskii

2010-01-01

190

Chromosome structure investigated with the atomic-force microscope  

NASA Astrophysics Data System (ADS)

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

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

1992-05-01

191

An atomic force microscopy investigation of cyanophage structure.  

PubMed

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

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

2012-12-01

192

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

NASA Astrophysics Data System (ADS)

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

Özer, Mustafa M.; Weitering, Hanno H.

2013-07-01

193

Flow injection-chemical vapor generation atomic fluorescence spectrometry hyphenated system for organic mercury determination: A step forward  

Microsoft Academic Search

Monomethylmercury and ethylmercury were determined on line using flow injection-chemical vapor generation atomic fluorescence spectrometry without neither requiring a pre-treatment with chemical oxidants, nor UV\\/MW additional post column interface, nor organic solvents, nor complexing agents, such as cysteine. Inorganic mercury, monomethylmercury and ethylmercury were detected by atomic fluorescence spectrometry in an Ar\\/H2 miniaturized flame after sodium borohydride reduction to Hg0,

Valeria Angeli; Simona Biagi; Silvia Ghimenti; Massimo Onor; Alessandro D'Ulivo; Emilia Bramanti

194

Defects in p-GaN and their atomic structure  

SciTech Connect

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

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

2004-10-08

195

Temperature-dependent local atomic structure in the colossal magnetoresistive manganese oxide lanthanum strontium manganese oxide  

NASA Astrophysics Data System (ADS)

Extended X-ray Absorption Fine Structure (XAFS) measurements at the Mn, Sr, and La K-edges of the colossal magnetoresistive (CMR) manganese oxide La1.2Sr1.8 Mn2O7 show that the local atomic structure is coupled to the metal-insulator and paramagnetic-ferromagnetic transitions. These polarized and temperature dependent XAFS measurements are the first performed on a layered CMR manganite in an effort to further elucidate the strong interplay between charge, spin, and lattice degrees of freedom in these hole doped oxides. The polarization dependence of the XAFS indicates that the local distortions accompanying this electronic and magnetic phase transition are associated with Jahn-Teller type distortions to the apical (lying perpendicular to the perovskite MnO planes) oxygen distribution around the MN cations. The metal-insulator transition is accompanied by a sudden increase in the number of Jahn-Teller distorted Mn sites as well as anomalous increases in the thermal Debye-Waller factor indicating increased fluctuations of the local atomic arrangements. A possibility for the La and Sr cations to influence the electronic and magnetic transitions is suggested by their tendency to stabilize differing local arrangements of the nearest neighbor oxygen atoms. The contrasting temperature dependence of the La-oxygen and Sr-oxygen distributions shows that the temperature dependent local atomic distortions observed in the apical oxygen distribution around the Mn ions are primarily associated with Sr atoms. The observed differences in the local atomic structures surrounding Sr and La are supported by similar results in the non-CMR oxide LaSrMnO4. This element specific interaction suggests the possibility that the local dopant concentration could enhance or induce electronic, magnetic, and structural phase separation. Thus, the XAFS experiments documented here have supported the general view that local lattice distortions can play a role in the MI transition and the CMR effect in the bilayer manganite La1.2 Sr1.8Mn2O 7 while also indicating that the effects of the local chemical environment of the Mn ions may play a role in determining the nature of the phase transitions.

Villella, Phillip Michael

2002-09-01

196

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

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.

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

2011-12-09

197

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

SciTech Connect

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

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

2005-11-01

198

Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons  

PubMed Central

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.

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

2012-01-01

199

Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons  

NASA Astrophysics Data System (ADS)

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.

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

2012-12-01

200

Atomic and electronic structure of divacancies in carbon nanotubes  

NASA Astrophysics Data System (ADS)

We present atomic and electronic structure of divacancies in carbon nanotubes, which is calculated using the density functional theory. Divacancies in carbon nanotubes self-heal by spontaneous reconstructions, which consist of concerted bond formations. Divacancy formation energies EDV , which strongly depend on the divacancy orientation with respect to the tube axis, are in the range of 2.8 4.3 eV for favorable orientations in the nanotubes of 4 9Å diameter, making divacancies more probable than monovacancies in carbon nanotubes. Defect related states lead to a higher density of states around the Fermi level. Semiconducting nanotubes develop midgap levels that may adversely affect the functionality of carbon nanotube based devices. Our spin polarized density functional calculations show that the exchange splitting of defect-related bands in nonsemiconducting defective nanotubes leads to net spin polarizations of ??-???0.5?B per divacancy for some divacancy orientations.

Berber, Savas; Oshiyama, Atsushi

2008-04-01

201

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

NASA Astrophysics Data System (ADS)

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

Kuznetsov, V.; Papastavrou, G.

2012-11-01

202

17O NMR spectroscopy of substituted methyleneindanones: relationship between chemical shift and oxygen atom electron density  

NASA Astrophysics Data System (ADS)

17O NMR spectroscopic data for eigth ?-substituted methyleneindanones obtained at natural abundance in acetonitrile at 75°C are reported. 17O NMR data for ten para-substituted E-benzalindanones, enriched with 17O, were recorded in acetonitrile at 75°C. The 17O NMR data for the E-benzalindanones gave good correlations with sigma plus values, with literature carbonyl IR stretching frequencies, and with literature 17O NMR carbonyl data of chalcones and 5-aryl-2,3-furandiones. The carbonyl oxygen atom electron density (AM1) gave good correlation with the carbonyl 17O NMR chemical shift of both ?-substituted methyleneindanones and the E-benzalindanones.

Kumar, Arvind; Boykin, David W.

1993-07-01

203

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

SciTech Connect

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.

Seidman, D.N. [Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering; Merkle, K.L. [Argonne National Lab., IL (United States)

1992-03-01

204

Electronic structures and chemical bonds of cobaltite and Ni-doped  

Microsoft Academic Search

The relation among electronic structure, chemical bond and thermoelectric property of Ca3 Co2 O6 and Ni-doped was studied by density function theory and discrete variation method (DFT-DVM). The results indicate that the\\u000a highest valence band (HVB) and the lowest conduction, band(LCB) are mainly attributed to Co3d, Ni3d and O2p atomic orbitals.\\u000a The property of a semiconductor is shown from the

Min Xinmin; Xing Xueling; Zhu Lei

2005-01-01

205

Structural Investigations of Chemically and Electrochemically Deposited Metals on Silicon and Germanium Surfaces  

Microsoft Academic Search

X-ray Standing Wave (XSW) studies of the atomic structure of the metal-semiconductor interface have been carried out for the systems Ni\\/Si(111), Ni\\/Ge(111) and Ga\\/Si(111). Monolayer and sub monolayer coverages of the metals were deposited on chemically cleaned surfaces of Si and Ge by chemisorption (wet chemistry), electrochemical, photoelectrochemical and U.H.V. deposition techniques. Besides yielding positional information, the XSW technique is

Thomas George Thundat

1987-01-01

206

Structural analysis of TiO 2 films grown using microwave-activated chemical bath deposition  

Microsoft Academic Search

TiO2 layer films were grown using the microwave (MW)-activated chemical bath deposition technique on two different indium tin oxide substrates. The TiO2 films are studied to determine their structural response when changing the MW heating power. Thickness (areal density), oxygen concentration profile, composition and surface homogeneity were determined using Rutherford backscattering spectrometry, nuclear reaction analysis and atomic force microscopy. The

F. Fernández-Lima; D. L Baptista; I Zumeta; E Pedrero; R Prioli; E Vigil; F. C Zawislak

2002-01-01

207

First Optical Hyperfine Structure Measurement in an Atomic Anion  

NASA Astrophysics Data System (ADS)

We have investigated the hyperfine structure of the transition between the 5d76s2 F9/2e4 ground state and the 5d66s26p DJo6 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 Os-187 and Os-189 the yet unknown total angular momentum of the bound excited state was found to be J=9/2. The hyperfine structure constants of the F9/2e4 ground state and the D9/2o6 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 Os-192 in an external magnetic field was calculated, revealing possible laser cooling transitions.

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

2010-02-01

208

Chemical structure representations and applications in computational toxicity.  

PubMed

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

Karthikeyan, Muthukumarasamy; Vyas, Renu

2012-01-01

209

Low temperature hydrogen plasma assisted chemical vapor generation for Atomic Fluorescence Spectrometry.  

PubMed

Chemical vapor generation techniques have long been considered as important ways of sample introduction for analytical atomic spectrometry. In this paper, a low temperature plasma assisted chemical vapor generation method which avoids the massive use of consumptive chemical agents was proposed by using atmospheric pressure dielectric barrier discharge. The plasma was generated by hydrogen doped argon gas flow through a quartz tube, serving as a dielectric barrier, which had a copper wire inner electrode and a copper foil outer electrode. An alternative high voltage was applied to electrodes to ignite and sustain the plasma. Sample solutions were converted to aerosol by a nebulizer and then mixed with the plasma to generate hydrides. To confirm the utility of this method, four hydride forming elements, As, Te, Sb and Se, were determined by coupling the low temperature plasma assisted chemical vapor generation system with an atomic fluorescence spectrometer. Responses of As, Te, Sb and Se were linear in the range of 0.5-20?gmL(-1). The RSDs of As, Te, Sb and Se in the present method were less than 4.1% and the absolute detection limits for As, Te, Sb and Se were 0.6ng, 1.0ng, 1.4ng and 1.2ng, respectively. Furthermore, four arsenic species were determined after HPLC separation. The method is green and simple compared with hydride generation with tetrahydroborate and the most attractive characteristic is micro-sampling. In principle, the method offers potential advantages of miniaturization, less consumption and ease of automation. PMID:24881527

Yang, Meng; Xue, Jiao; Li, Ming; Han, Guojun; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong

2014-08-01

210

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

211

The grasp2K relativistic atomic structure package  

NASA Astrophysics Data System (ADS)

This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel Xeon, 3.06 GHz Operating system: Suse LINUX RAM: 500 MB or more Classification: 2.1 Nature of problem: Prediction of atomic spectra—atomic energy levels, oscillator strengths, and radiative decay rates—using a 'fully relativistic' approach. Solution method: Atomic orbitals are assumed to be four-component spinor eigenstates of the angular momentum operator, j=l+s, and the parity operator ?=??. Configuration state functions (CSFs) are linear combinations of Slater determinants of atomic orbitals, and are simultaneous eigenfunctions of the atomic electronic angular momentum operator, J, and the atomic parity operator, P. Approximate atomic state functions (ASFs) are linear combinations of CSFs. A variational functional may be constructed by combining expressions for the energies of one or more ASFs. Average energy level (EAL) functionals are weighted sums of energies of all possible ASFs that may be constructed from a set of CSFs; the number of ASFs is then the same as the number of CSFs. Extended optimal level (EOL) functionals are weighted sums of energies of some subset of ASFs. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Hartree-Fock (MCDHF) equations that define an extremum of the variational functional by the self-consistent-field (SCF) method. Lists of CSFs are generated from a set of reference CSFs and rules for deriving other CSFs from these. Expansion coefficients are obtained using sparse-matrix methods for solving the relativistic configuration interaction (CI) problem. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. Biorthogonal transformation methods are employed so that all matrix elements between CSFs can be evaluated using Racah algebra. Restrictions: The maximum number of radial orbitals is limited to 120 by the packing algorithm used for 32-bit integers. The maximum size of a multiconfiguration (MC) calculation, as measured by the length of the configuration state function (CSF) list, is limited by numerical st

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

2007-10-01

212

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

SciTech Connect

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.

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

1993-12-01

213

Chemical Bondings around Intercalated Li Atoms in LiTiX2 (X=S, Se, and Te)  

NASA Astrophysics Data System (ADS)

A systematic study of the electronic structure and chemical bonding of the Li-intercalated titanium dichalcogenides, LiTiX2 (X=S, Se, and Te), is performed by a first-principles molecular-orbital method using a model cluster composed of 75 atoms. The discrete-variational (DV)-X? method was employed and Mulliken's population analyses were thoroughly conducted. The net charge of Li is found to be approximately 0.1 independently of X-species. Net charges of Ti and X are not significantly affected by the Li intercalation. Strong covalent bonding is formed between Li and X with a bond-overlap population (BOP) of 0.173 0.176. The BOP of Ti X bonding decreases by about 10% due to the presence of Li. These results should be important for determining battery properties when the dichalcogenide are used for positive electrodes.

Kim, Yang-Soo; Koyama, Yukinori; Tanaka, Isao; Adachi, Hirohiko

1998-12-01

214

Atomic-scale graded structure formed by sedimentation of substitutional atoms in a Bi-Sb alloy  

NASA Astrophysics Data System (ADS)

An atomic-scale graded structure was formed by the sedimentation of component atoms in an all-proportional miscible alloy under a strong gravitational field of 1 million g in maximum acceleration at high temperature. Continuous composition gradients of Sb (about 20-0 wt. %) and Bi (about 80-100 wt. %) and the resultant continuous change in the lattice constants were observed in the ultracentrifuged Bi-Sb (70:30 in mol %) alloy bulk body. Crystal growth in the direction of acceleration field was also observed. It must be noted that the substitutional solute atoms with component level rate acted in the sedimentation of this system, while interstitial solutes (Au) at an impurity level rate acted in some elemental metals with low melting temperature in the previous studies. It is expected that the sedimentation of substitutional atoms can be used to control the compositions and structure of alloys or compounds.

Mashimo, Tsutomu; Ikeda, Taiki; Minato, Ichiro

2001-07-01

215

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

SciTech Connect

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.

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

216

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

SciTech Connect

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.

Valentini, J.J. (Columbia Univ., New York, NY (United States))

1991-01-01

217

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

SciTech Connect

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.

Valentini, J.J. [Columbia Univ., New York, NY (United States)

1991-12-31

218

Structural studies on MOCVD grown GaN and AlGaN using atomic force microscopy  

Microsoft Academic Search

Surface morphology studies of GaN and AlGaN grown by metalorganic chemical vapor deposition (MOCVD) have been carried out using atomic force microscopy. The open core dislocation and steps connecting two threading dislocations of opposite direction are commonly observed in undoped and doped GaN. Structural studies on AlGaN epitaxial layers grown on undoped GaN revealed the formation of open-core dislocation with

R. S Qhalid Fareed; S Juodkazis; S. H Chung; T Sugahara; S Sakai

2000-01-01

219

Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: A chemical chaperone at atomic resolution  

PubMed Central

Proteins are very sensitive to their solvent environments. Urea is a common chemical denaturant of proteins, yet some animals contain high concentrations of urea. These animals have evolved an interesting mechanism to counteract the effects of urea by using trimethylamine N-oxide (TMAO). The molecular basis for the ability of TMAO to act as a chemical chaperone remains unknown. Here, we describe molecular dynamics simulations of a small globular protein, chymotrypsin inhibitor 2, in 8 M urea and 4 M TMAO/8 M urea solutions, in addition to other control simulations, to investigate this effect at the atomic level. In 8 M urea, the protein unfolds, and urea acts in both a direct and indirect manner to achieve this effect. In contrast, introduction of 4 M TMAO counteracts the effect of urea and the protein remains well structured. TMAO makes few direct interactions with the protein. Instead, it prevents unfolding of the protein by structuring the solvent. In particular, TMAO orders the solvent and discourages it from competing with intraprotein H bonds and breaking up the hydrophobic core of the protein.

Bennion, Brian J.; Daggett, Valerie

2004-01-01

220

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

PubMed Central

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.

Hay, Mark E.

2012-01-01

221

PATENTS, LICENSING, AND MARKET STRUCTURE IN THE CHEMICAL INDUSTRY  

Microsoft Academic Search

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

Ashish Arora

1996-01-01

222

Structure of acidic haloaluminate melts: Neutron diffraction and quantum chemical calculations  

SciTech Connect

The structure of molten mixtures of (KX){sub {ital y}}(AlX{sub 3}){sub 1{minus}{ital y}} was investigated by neutron diffraction for X=Cl and Br and {ital y}=0.25 and 0.33. These melts, known as acidic haloaluminates, contain different ionic species such as AlX{sup {minus}}{sub 4},Al{sub 2}X{sup {minus}}{sub 7}, Al{sub 3}X{sup {minus}}{sub 10}. The diffraction patterns were similar, although not identical, for the same halide pairs and showed features indicative of short-range and intermediate-range order. Quantum chemical calculations were carried out on AlX{sup {minus}}{sub 4}, Al{sub 2}X{sup {minus}}{sub 7}, and Al{sub 3}X{sup {minus}}{sub 10} to provide information needed to interpret the structural results within the framework of the random packing of structural units model. It is shown that the bent Al--X--Al bridge for Al{sub 2}X{sup {minus}}{sub 7}, obtained from the quantum chemical calculations, is necessary to represent well the structure, and that the values of the bond angles at the central halide atoms are around 110{degree}. Aluminum atoms are found to be tetrahedrally coordinated by the halide atoms, and information on the orientational correlations of neighboring Al{sub 2}X{sup {minus}}{sub 7} is derived.

Blander, M.; Bierwagen, E.; Calkins, K.G.; Curtiss, L.A.; Price, D.L.; Saboungi, M. (Argonne National Laboratory, Argonne, Illinois 60439 (United States))

1992-08-15

223

Composition and Structure of Chemically Deposited PbS.  

National Technical Information Service (NTIS)

In a study of the fundamental properties of chemically deposited lead sulfide, new instrumental techniques-scanning electron microscopy (SEM) and mass spectroscopy--were applied to the analysis of structure and composition. Lead sulfide samples were prepa...

M. H. Ritchie C. M. Drew

1969-01-01

224

A Method for the Automatic Classification of Chemical Structures  

ERIC Educational Resources Information Center

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

Adamson, George W.; Bush, Judith A.

1973-01-01

225

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...

226

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

227

Physical and chemical characterization of multilayered structures  

SciTech Connect

It is important to know the physical and chemical properties of a multilayer if its performance is to be compared to theoretical predictions, or if guidance is needed for the production of superior multilayers. Accurate, nondestructive analytical methods, such as neutron activation analysis, are restricted to certain elements. Certain destructive methods, such as total carbon analysis by combustion, can be sensitive enough for use with very small samples. The method of choice depends upon sensitivity and specificity, both of which are discussed in this paper. 6 refs., 3 figs., 2 tabs.

Thorne, J.M.; Knight, L.V.; Peterson, B.G.

1985-01-01

228

Fast-ion-beam laser probing of ion-source energy distributions and atomic structure  

NASA Astrophysics Data System (ADS)

Collinear fast-ion-beam laser spectroscopy is a very high resolution probe for measuring ion-beam energy distributions and atomic structure parameters of interest in nuclear physics, atomic physics, and astrophysics. We have used offline 10-keV beams of atomic ions and a CW laser system to study the behavior of a Penning ion source and to measure hyperfine structure, isotope shifts, atomic lifetimes, spontaneous-emission branching fractions, oscillator strengths, and absolute wavelengths of a variety of atomic species from the lanthanide and transition-metal groups.

Holt, Richard A.; Rosner, S. David

2013-04-01

229

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

NASA Astrophysics Data System (ADS)

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

Katskov, Dmitri; Darangwa, Nicholas; Grotti, Marco

2006-05-01

230

Electronic structure and atomic arrangement in VPt system  

NASA Astrophysics Data System (ADS)

We present a study on the electronic structure of Pt and ordered compounds in the V-Pt system, based on photoemission (XPS and UPS) measurements and on the examination of previous susceptibility and specific heat results. Photoemission spectra on pure Pt are discussed. The experimental results of compounds allow an evaluation of the partial densities of states (PDOS's) in particular for Platinum. The shape of this PDOS varies appreciably with Pt concentration and can be analyzed in terms of local environments and local symmetry in the various compounds. For "isolated" Pt atoms in a Vanadium environment (V 3Pt) the Pt electronic states are mainly located toward the bottom of the valence band. With an increasing of Pt neighbours a broad contribution appears in the middle of the band and is attributable to Pt-Pt hybridization ; more and more electronic states are available in the upper part of the band An evaluation of the PDOS's at the Fermi level n(E F)'s is presented. It is suggested that n(E F) for Vanadium is constant for V, V 3Pt and VPt and decreases for VPt 2 whereas the Pt n(E F) increases slowly from V 3Pt to VPt 2 and increases rapidly from VPt 3 to Pt.

Amamou, A.; Kuentzler, R.

1982-08-01

231

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses  

PubMed Central

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

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

2010-01-01

232

Atomic structures and compositions of interfaces. Progress report, September 1, 1989--August 31, 1990  

SciTech Connect

This research program focuses on an experimental study of the structure and chemistry of metal/metal oxide internal interfaces; the latter are mainly created, although not exclusively, by internal oxidation of binary or ternary metal alloys that are solid-solution phases prior to the internal oxidation treatment. The principal research tools are transmission electron microscopy (TEM), high resolution microscopy (HREM), analytical electron microscopy (AEM) and atom-probe field-ion microscopy (APFIM). The APFIM technique is used to determine the chemical composition of the interfacial region on an atomic scale. Initial studies are foucused on Pd/NiO, Cu/MgO, Cu/Al{sub 2}O{sub 3}, Cu/SiO{sub 2} interfaces, as well as metal oxides in Pt-based alloys. Topics of importance include coherency effects, misfit dislocations, structure of the terminating layer between the metal and the metal oxide, microstoichiometry, dipole space charge effects, and distributions of impurities and point defects at the interfacial region.

Seidman, D.N. [Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering; Merkle, K.L. [Argonne National Lab., IL (United States)

1990-09-01

233

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

PubMed

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

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

2013-06-01

234

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

PubMed

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

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

2008-12-01

235

Melt processible polyimides and their chemical structures  

Microsoft Academic Search

A series of aromatic ether diamines having different numbers of benzene rings, different amino-substituted positions and different moieties in their structures was synthesized. By using these synthesized ether diamines and commercially available tetracarboxylic dianhydrides, various kinds of polyimides having almost the same molecular weights were synthesized. The glass transition temperature (Tg) values and thermoplasticity were studied by focusing on the

M. Ohta

1996-01-01

236

Chemical Structure, Conjugation, and Cross-Reactivity of Bacillus pumilus Sh18 Cell Wall Polysaccharide  

Microsoft Academic Search

Bacillus pumilus strain Sh18 cell wall polysaccharide (CWP), cross-reactive with the capsular polysaccharide of Haemophilus influenzae type b, was purified and its chemical structure was elucidated using fast atom bombardment mass spectrometry, nuclear magnetic resonance techniques, and sugar-specific degradation procedures. Two major structures, 1,5-poly(ribitol phosphate) and 1,3-poly(glycerol phosphate), with the latter partially substituted by 2-acetamido-2-deoxy--galactopyranose (13%) and 2-acetamido-2-deoxy--glucopyr- anose (6%)

Joanna Kubler-Kielb; Bruce Coxon; Rachel Schneerson

2004-01-01

237

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

PubMed

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

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

2014-05-30

238

Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances  

Microsoft Academic Search

Finding optimal three-dimensional molecular configurations based on a limited amount of experimental and\\/or theoretical data requires efficient nonlinear optimization algorithms. Optimization methods must be able to find atomic configurations that are close to the abso- lute, or global, minimum error and also satisfy known physical constraints such as minimum separation distances between atoms (based on van der Waals interactions). The

Glenn A. Williams; Jonathan M. Dugan; Russ B. Altman

2001-01-01

239

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

NASA Astrophysics Data System (ADS)

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

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

2008-07-01

240

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

NASA Astrophysics Data System (ADS)

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.

Balasubramanian, Sriram; Raghavan, Srini

2008-06-01

241

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

NASA Astrophysics Data System (ADS)

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.

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

2009-10-01

242

Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery.  

PubMed

All molecules of up to 11 atoms of C, N, O, and F possible under consideration of simple valency, chemical stability, and synthetic feasibility rules were generated and collected in a database (GDB). GDB contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple bonds. By comparison, only 63 857 compounds of up to 11 atoms were found in public databases (a combination of PubChem, ChemACX, ChemSCX, NCI open database, and the Merck Index). A total of 538 of the 1208 ring systems in GDB are currently unknown in the CAS Registry and Beilstein databases in any carbon/heteroatom/multiple-bond combination or as a substructure. Over 70% of GDB molecules are chiral. Because of their small size, all compounds obey Lipinski's bioavailability rule. A total of 13.2 million compounds also follow Congreve's "Rule of 3" for lead-likeness. A Kohonen map trained with autocorrelation descriptors organizes GDB according to compound classes and shows that leadlike compounds are most abundant in chiral regions of fused carbocycles and fused heterocycles. The projection of known compounds into this map indicates large uncharted areas of chemical space. The potential of GDB for drug discovery is illustrated by virtual screening for kinase inhibitors, G-protein coupled receptor ligands, and ion-channel modulators. The database is available from the author's Web page. PMID:17260980

Fink, Tobias; Reymond, Jean-Louis

2007-01-01

243

Chemical Activity of Oxygen Atoms in Magnetron Sputter-Deposited ZnO Films during Film Growth  

NASA Astrophysics Data System (ADS)

The role of oxygen atoms in the growth of magnetron sputter-deposited ZnO films was studied by alternating the deposition of a several-nanometer-thick ZnO layer and an O2/Ar mixed plasma exposure, i.e., a layer-by-layer (LbL) technique. Film crystallization was promoted by suppressing the formation of oxygen vacancies and interstitial defects by adjusting the exposure conditions of the O2/Ar plasma. These findings suggest that the chemical potential of oxygen atoms influences film crystallization and the electronic state. The diffusion and effusion of oxygen atoms at the growing surface have effects similar to those of thermal annealing, namely, the promotion of film crystallization and the creation and annihilation of oxygen- and zinc-related defects. The role of oxygen atoms reaching the growing film surface is discussed in terms of chemical annealing, and a possible oxygen diffusion mechanism is proposed.

Morita, Aya; Watanabe, Ikuo; Ohta, Naoki; Shirai, Hajime

2011-08-01

244

Chemical and electronic properties of silver atoms supported on sulfur and molybdenum sulfide surfaces  

NASA Astrophysics Data System (ADS)

The chemical and electronic properties of a series of Ag/S mult/Mo(110) and {Ag}/{MoSX} systems have been investigated using X-ray photoemission, thermal desorption mass spectroscopy, hydrogen (H 2, D 2, or D) chemisorption and molecular orbital calculations. At 100 K, sulfur multilayers supported on Mo(110) react with silver to form sulfide compounds. Upon annealing to high temperature, the silver sulfides promote the sulfidation of the Mo support leading to the formation MoS X. Silver atoms deposited on molybdenum sulfide surfaces remain in a metallic state at temperatures below 300 K. The results of INDO/S and ab initio self-consistent-field calculations indicate that the Ag?MoS 2 bond is best described as covalent with a small degree of ionic character. On MoS 2 surfaces, Ag is a poor electron donor compared with Co and Ni. At temperatures above 400 K Ag diffuses into the bulk of molybdenum sulfide, forming AgMoS X compounds. These bimetallic sulfides decompose at high temperatures (> 800 K) with Ag desorbing and MoS X remaining solid. The {AgSY}/{MoSX} and AgMoS X systems were unreactive towards molecular hydrogen under ultrahigh vacuum conditions. However, gas-phase atomic hydrogen reacted with the surfaces to form gaseous hydrogen sulfide and led to sorption of hydrogen by the {AgSY}/{MoSX} and AgMoS X systems. Compared with other similar systems (MoS X, {NiSY}/{MoSX}, {CoSY}/{MoSX}, {ZnSY}/{MoSX}), the {AgSY}/{MoSX} systems show the lowest rate of hydrogenation of Mo-bonded S atoms. The Ag adatoms are very efficient for blocking D?S interactions.

Li, S. Y.; Rodriguez, J. A.; Hrbek, J.; Huang, H. H.; Xu, G.-Q.

1998-01-01

245

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

USGS Publications Warehouse

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.

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

1982-01-01

246

Electronic structure and chemical bonding in nonstoichiometric zirconium nitrides  

Microsoft Academic Search

X-ray emission spectra were taken and band calculations using the Green function LMTO method and cluster calculations using the discrete variational Xa method were carried out for the electronic structure and chemical bonding parameters for nonstoichiometric zirconium nitrides containing metallic and metalloid vacancies. The existence of structural defects leads to a redistribution of the occupancies of the major sub-bands of

D. L. Novikov; Yu. M. Yarmoshenko; A. L. Ivanovskii; V. A. Gubanov

1989-01-01

247

Recent Strategies for Retrieving Chemical Structure Information on the Web.  

ERIC Educational Resources Information Center

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

Lo, Mei Ling

1997-01-01

248

Structure and Atomization Properties of Dense Turbulent Sprays. (Reannouncement with New Availability Information).  

National Technical Information Service (NTIS)

Aspects of the structure and atomization properties of the near injector (dense spray) region of turbulent sprays are reviewed, considering the following: spray breakup regimes, dense-spray structure, and liquid breakup processes. The discussion is limite...

G. M. Faeth

1990-01-01

249

Field emission spectra of single-atom tips with thermodynamically stable structures  

Microsoft Academic Search

Energy spectra of field emitted electrons from well-characterized tungsten nanoemitters covered with different metals have been measured in detail while changing the electric field and the topmost atomic structure. At very high electric fields, additional humps appear in the spectra of a single-atom tip. Their energy positions depend on both the coated material and structure termination but not on the

E. Rokuta; H.-S. Kuo; T. Itagaki; K. Nomura; T. Ishikawa; B.-L. Cho; I.-S. Hwang; T. T. Tsong; C. Oshima

2008-01-01

250

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

SciTech Connect

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

Parpia, F.A.; Grant, I.P. (Department of Theoretical Chemsitry, 5 South Parks Road, Oxford OX1 3UB (United Kingdom))

1991-08-05

251

An Automatic Symmetry-Leveraging Approach for Solving Incomplete Many-Atom Crystal Structures  

Microsoft Academic Search

We present a new first principles-based method, called a symmetry-leveraging genetic algorithm (SLGA), for fully and automatically solving large crystal structures when experimental diffraction studies do not identify all internal atomic positions. Such incomplete structural refinements may occur when crystals contain light atoms or when the characterization is performed under extreme conditions such as high pressure. We apply our method

Bryce Meredig; Chris Wolverton

2011-01-01

252

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

SciTech Connect

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.

Dembczynski, J. [Chair of Quantum Engineering and Metrology, Faculty of Technical Physics, Poznan University of Technology, Nieszawska 13B, 60-965 Poznan (Poland)]. E-mail: Jerzy.Dembczynski@put.poznan.pl; Elantkowska, M. [Chair of Quantum Engineering and Metrology, Faculty of Technical Physics, Poznan University of Technology, Nieszawska 13B, 60-965 Poznan (Poland); Ruczkowski, J. [Chair of Quantum Engineering and Metrology, Faculty of Technical Physics, Poznan University of Technology, Nieszawska 13B, 60-965 Poznan (Poland); Stefanska, D. [Chair of Quantum Engineering and Metrology, Faculty of Technical Physics, Poznan University of Technology, Nieszawska 13B, 60-965 Poznan (Poland)

2007-01-15

253

Polarization-gradient laser cooling as a way to create strongly localized structures for atom lithography  

SciTech Connect

Generally, conditions for deep sub-Doppler laser cooling do not match conditions for strong atomic localization, that takes place in a deeper optical potential and leads to higher temperature. Moreover, for a given detuning in a deep optical potential the secular approximation, which is frequently used for a quantum description of laser cooling, fails. Here we investigate the atomic localization in optical potential, using a full quantum approach for atomic density matrix beyond the secular approximation. It is shown that laser cooling in a deep optical potential, created by a light field with polarization gradients, can be used as an alternative method for the formation of high contrast spatially localized structures of atoms for the purposes of atom lithography and atomic nanofabrication. Finally, we analyze possible limits for the width and contrast of localized atomic structures that can be reached in this type of light mask.

Prudnikov, O. N.; Taichenachev, A. V.; Tumaikin, A. M.; Yudin, V. I. [Novosibirsk State University, Pirogova 2, Novosibirsk 630090 (Russian Federation); Institute of Laser Physics SB RAS, Lavrentyeva 13/3, Novosibirsk 630090 (Russian Federation)

2007-02-15

254

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

PubMed

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 characteristics and the competing roles of network forming and network modifying SiOm and TiOn units in the mixed hybrid oxides. PMID:24848713

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

2014-06-25

255

The atomic structure of ternary amorphous TixSi1?xO2 hybrid oxides  

NASA Astrophysics Data System (ADS)

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 characteristics and the competing roles of network forming and network modifying SiOm and TiOn units in the mixed hybrid oxides.

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

2014-06-01

256

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

PubMed

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

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

2013-11-01

257

chem-path-tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures.  

PubMed

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

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

2014-07-01

258

Atomic shell structure from the Single-Exponential Decay Detector.  

PubMed

The density of atomic systems is analysed via the Single-Exponential Decay Detector (SEDD). SEDD is a scalar field designed to explore mathematical, rather than physical, properties of electron density. Nevertheless, it has been shown that SEDD can serve as a descriptor of bonding patterns in molecules as well as an indicator of atomic shells [P. de Silva, J. Korchowiec, and T. A. Wesolowski, ChemPhysChem 13, 3462 (2012)]. In this work, a more detailed analysis of atomic shells is done for atoms in the Li-Xe series. Shell populations based on SEDD agree with the Aufbau principle even better than those obtained from the Electron Localization Function, which is a popular indicator of electron localization. A link between SEDD and the local wave vector is given, which provides a physical interpretation of SEDD. PMID:24784264

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

2014-04-28

259

Atomic shell structure from the Single-Exponential Decay Detector  

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

260

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

SciTech Connect

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. The high-resolution Z-contrast imaging technique in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition can be interpreted intuitively. This direct image allows the electron probe to be positioned over individual atomic columns for parallel detection electron energy loss spectroscopy (EELS) at a spatial resolution approaching 0.22nm. In this paper we have combined the structural information available in the Z-contrast images with the bonding information obtained from the fine structure within the EELS edges to determine the grain boundary structure in a SrTiO{sub 3} bicrystal.

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

1993-12-01

261

Secondary structural effects on protein NMR chemical shifts  

Microsoft Academic Search

For an amino acid in protein, its chemical shift, d(?, ?)s, is expressed as a function of its backbone torsion angles (? and ?) and secondary state (s): d(?, ?)s=d?, ?)_coil+?d(?, ?)_s, where d(?, ?)coil represents its chemical shift at coil state (s=coil); ? d(?, ?)s (s=sheet or helix) is herein defined as secondary structural effect correction factor, which are

Yunjun Wang

2004-01-01

262

Annealing effect on the chemical structure of diamondlike carbon  

Microsoft Academic Search

The effect of annealing in an ultrahigh vacuum on the chemical structure of diamondlike carbon (DLC) was investigated using photoelectron spectroscopy, thermal desorption spectroscopy, electrical resistivity, and micro-Raman spectroscopy measurements. The line shapes of the C 1s photoelectron spectra depended on annealing temperature. The relative intensities of four chemical components in the spectra were quantitatively evaluated: sp3 carbon with carbon-carbon

Susumu Takabayashi; Keishi Okamoto; Hiroyuki Sakaue; Takayuki Takahagi; Tatsuyuki Nakatani

2008-01-01

263

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

PubMed Central

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

Andujar-De Sanctis, Ivonne L.

2012-01-01

264

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

PubMed Central

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

2013-01-01

265

Atom-decorated nanotubes  

Microsoft Academic Search

Quantum chemical and molecular dynamics studies of nanotubes decorated with atoms of various elements are surveyed. The effect of adsorption of hydrogen, oxygen, alkali metal, alkaline earth metal, d-metal, halogen, and inert gas atoms on external walls of carbon nanotubes on the structure and electronic or other physicochemical properties of nanotubes is considered. The results of simulation of the properties

Victoria V. Ivanovskaya; Alexander L. Ivanovskii

2011-01-01

266

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

SciTech Connect

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.

Luo,W.; Ma, E.

2008-01-01

267

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

NASA Astrophysics Data System (ADS)

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).

Fitting Kourkoutis, L.

2010-03-01

268

Atomic-Scale Structure of Co–Mo–S Nanoclusters in Hydrotreating Catalysts  

Microsoft Academic Search

By means of scanning tunneling microscopy (STM), it has been possible to obtain the first atomic-scale images of the Co–Mo–S structure present in hydrodesulfurization (HDS) catalysts. Information on the catalytically important edge structures has been obtained by synthesizing single-layer Co–Mo–S nanoclusters using the Au(111) herringbone structure as a template. It is observed that the presence of the Co promoter atoms

J. V Lauritsen; S Helveg; E Lægsgaard; I Stensgaard; B. S Clausen; H Topsøe; F Besenbacher

2001-01-01

269

What is the best reference state for designing statistical atomic potentials in protein structure prediction?  

PubMed Central

Many statistical potentials were developed in last two decades for protein folding and protein structure recognition. The major difference of these potentials is on the selection of reference states to offset sampling bias. However, since these potentials used different databases and parameter cutoffs, it is difficult to judge what the best reference states are by examining the original programs. In this work, we aim to address this issue and evaluate the reference states by a unified database and programming environment. We constructed distance-specific atomic potentials using six widely-used reference states based on 1,022 high-resolution protein structures, which are applied to rank modeling in six sets of structure decoys. The reference state on random-walk chain outperforms others in three decoy sets while those using ideal-gas, quasi-chemical approximation and averaging sample stand out in one set separately. Nevertheless, the performance of the potentials relies on the origin of decoy generations and no reference state can clearly outperform others in all decoy sets. Further analysis reveals that the statistical potentials have a contradiction between the universality and pertinence, and optimal reference states should be extracted based on specific application environments and decoy spaces.

Deng, Haiyou; Jia, Ya; Wei, Yanyu; Zhang, Yang

2012-01-01

270

Role of chemical potential in relaxation of faceted crystal structure  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

271

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

ERIC Educational Resources Information Center

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)

Harrison, Allan G.; Treagust, David F.

2000-01-01

272

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

NASA Astrophysics Data System (ADS)

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

Volynsky, Anatoly B.

1998-01-01

273

Structural, optical and photoelectrochemical characterization of CdS nanowire synthesized by chemical bath deposition and wet chemical etching  

NASA Astrophysics Data System (ADS)

Nanocrystalline thin films of CdS have been grown onto flexible plastic and titanium substrates by a simple and environmentally benign chemical bath deposition (CBD) method at room temperature. The films consist of clusters of CdS nanoparticles. The clusters of CdS nanoparticles in the films were successfully converted into nanowire (NW) networks using chemical etching process. The possible mechanism of the etching phenomenon is discussed. These films were examined for their structural, surface morphological and optical properties by means of X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM) and UV-vis spectrophotometry techniques, respectively. Photoelectrochemical (PEC) investigations were carried out using cell configuration as n-CdS/(1 M NaOH + 1 M Na 2S + 1 M S)/C. The film of nanowires was found to be hexagonal in structure with the preferential orientation along the (0 0 2) plane. The nanowires have widths in the range of 50-150 nm and have lengths of the order of a few micrometers. Optical studies reveal that the CdS nanowires have value of band gap 2.48 eV, whereas it is 2.58 eV for nanoparticles of CdS. Finally, we report on the ideality of junction improvement of PEC cells when CdS nanoparticles photoelectrode converted into nanowires photoelectrode.

Dongre, J. K.; Nogriya, Vikas; Ramrakhiani, M.

2009-04-01

274

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

DOEpatents

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.

Lim, Chong Wee (Urbana, IL); Ohmori, Kenji (Urbana, IL); Petrov, Ivan Georgiev (Champaign, IL); Greene, Joseph E. (Champaign, IL)

2004-07-13

275

Electronic Structures and Chemical Bonding of TiX2 (X=S, Se, and Te)  

NASA Astrophysics Data System (ADS)

A systematic study of the electronic structures and chemical bonding of the titanium dichalcogenide TiX2 (X=S, Se, and Te) layered structures is performed by a first-principles molecular orbital calculation using the discrete-variational (DV)-X? cluster method. The intra- and interlayer chemical bonding properties are also investigated using the bond overlap population. Valence band structures obtained by the calculation are in good agreement with experimental results obtained by X-ray photoemission spectroscopy. Each peak in the density of states (DOS) is identified from the viewpoint of chemical bonding. There is a considerably strong covalent bonding between Ti and chalcogen atoms in TiX2. The covalency of chemical bonding is shown to increase and the ionicity to decrease in the series of TiS2 TiSe2 TiTe2. Both in intra- and interlayer chalcogen-chalcogen bonding and intralayer Ti Ti bonding are much weaker than Ti-chalcogen intralayer bonding. However, interlayer interaction is found to be not purely of the van der Waals type.

Kim, Yang-Soo; Mizuno, Masataka; Tanaka, Isao; Adachi, Hirohiko

1998-09-01

276

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

NASA Astrophysics Data System (ADS)

Surface atomic structure analysis by low-energy ion scattering spectroscopy (ISS) is reviewed, with particular emphasis on quantitative surface atomic structure analysis by ISS. The important differences between ISS and Rutherford backscattering spectroscopy (RBS), some basic characteristics of ISS, a special type of ISS called impact-collision ion scattering spectroscopy (ICISS), and the general features of the shadow cone in the energy range of ISS are discussed as a basis for the description of particular examples of ISS studies which follow. The examples are mainly concerned with the analysis of the atomic arrangement, defect structure, thermal vibration, and electron spatial distribution of the (001) and (111) surfaces of TiC.

Aono, Masakazu; Souda, Ryutaro

1985-10-01

277

Atomic-level structures and physical properties of magnetic CoSiB metallic glasses  

NASA Astrophysics Data System (ADS)

Two CoSiB metallic glasses of low Co contents, which consist of different clusters, have recently been developed by addition of solute atoms. In this work, the atomic structure and the magnetic properties of the two CoBSi metallic glasses were elucidated by state-of-the-art extended X-ray absorption fine structure spectroscopy (EXAFS) combining with ab initio molecular-dynamics (AIMD) computational techniques. Besides, the origin of these magnetic behaviors was discussed in view of the EXAFS results and atomic structures of the metallic glasses.

Shan, Guangcun; Liang Zhang, Ji; Li, Jiong; Zhang, Shuo; Jiang, Zheng; Huang, Yuying; Shek, Chan-Hung

2014-02-01

278

[The relationship between the chemical structure and the antiarrhythmic action of ethacizine and its analogs].  

PubMed

The relationship between the chemical structure and the antiarrhythmic activity of phenothiazine derivatives--ethacizine and its analogues--was estimated quantitatively by the value of the antiarrhythmic effect on aconitine model in conscious rats. The lengthening of the side chain of nitrogen atom in position 10 of phenothiazine cycle by one methylene group as well as the substitution of demethylamine radical for diethylamine one increased the antiarrhythmic activity; the toxicity of the compound being also increased. Ethacizine was found to possess the highest antiarrhythmic activity and the greatest antiarrhythmic index. PMID:2081560

Turilova, A I; Berdiaev, S Iu; Grishchenko, A N; Senova, Z P

1990-01-01

279

Flow of thin liquid films on chemically structured substrates  

Microsoft Academic Search

Chemically patterned surfaces are of significant interest in the context of microfluidic applications. Miniaturization of such devices will eventually lead to structures on the nano-scale. Whereas on the micron scale purely macroscopic descriptions of liquid flow are valid, on the nanometer scale long-ranged inter-molecular interactions, thermal fluctuations such as capillary waves, and finally the molecular structure of the liquid become

Markus Rauscher; S. Dietrich

2003-01-01

280

Chemical Structure of Organic N and Organic P in Soil  

Microsoft Academic Search

Although much progress has been achieved in revealing more about the chemical structure of soil organic N and P and the mechanisms\\u000a involved in their formation, we are still far from completely knowing the structures and understanding the formation and dynamics\\u000a of these major soil organic matter components.\\u000a \\u000a There is now consensus that a major part of the SON is

Ingrid Kögel-Knabner

281

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

PubMed

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

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

2014-01-01

282

The stability and electronic structure of Fe atoms embedded in zigzag graphene nanoribbons  

NASA Astrophysics Data System (ADS)

The stability and electronic properties of the Fe atoms embedded in divacancy defects in graphene nanoribbons (GNR) with zigzag-shaped edges have been studied by first-principles calculations. When Fe is positioned in the middle of the ribbon, it has little effect on the edge C atoms, which reserves the flat edges of graphene nanoribbons. On the other hand, when Fe atom is near the edge, structural distortion takes place resulting in tilted-edge structure with low energies. This indicates that the Fe atoms prefer to occupy divacancy sites near the edges. This is also in consistent with the analyses of electronic structures. Meanwhile, our results reveal that embedding Fe atom in the graphene nanoribbons is an effective method to make the GNR possessing metallic properties.

Li, Hengshuai; Hu, Haiquan; Bao, Chunjiang; Zhang, Xiaoming; Wang, Aizhu; Zhou, Hongcai; Zhao, Mingwen

2014-05-01

283

The Chemical and Physical Structure of Giant Molecular Cloud Cores  

Microsoft Academic Search

We present the results of a study of the emission from 33 molecular transitions in the GMC cores Orion A, M17, and Cepheus A. We have mapped the emission over a 4' × 12' area in Orion, and a 4' × 5' area in M17 and Cepheus A. We have used these observations to probe the physical and chemical structure

Edwin Anthony Bergin

1995-01-01

284

STRUCTURAL FEATURES ASSOCIATED WITH DEGRADABLE AND PERSISTENT CHEMICALS  

EPA Science Inventory

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

285

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

SciTech Connect

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)

Klimkin, V M; Sokovikov, V G [Institute of Atmospheric Optics, Siberian Branch, Russian Academy of Sciences, Tomsk (Russian Federation)

2007-02-28

286

Investigation of chemical modifiers for phosphorus in a graphite furnace using high-resolution continuum source atomic absorption spectrometry  

NASA Astrophysics Data System (ADS)

Phosphorus is not one of the elements that are typically determined by atomic absorption spectrometry, but this technique nevertheless offers several advantages that make it attractive, such as the relatively great freedom from interferences. As the main resonance lines for phosphorus are in the vacuum-ultraviolet, inaccessible by conventional atomic absorption spectrometry equipment, ?vov and Khartsyzov proposed to use the non-resonance doublet at 213.5 / 213.6 nm. Later it turned out that with conventional equipment it is necessary to use a chemical modifier in order to get reasonable sensitivity, and lanthanum was the first one suggested for that purpose. In the following years more than 30 modifiers have been proposed for the determination of this element, and there is no consensus about the best one. In this work high-resolution continuum source atomic absorption spectrometry has been used to investigate the determination of phosphorus without a modifier and with the addition of selected modifiers of very different nature, including the originally recommended lanthanum modifier, several palladium-based modifiers and sodium fluoride. As high-resolution continuum source atomic absorption spectrometry is revealing the spectral environment of the analytical line at high resolution, it became obvious that without the addition of a modifier essentially no atomic phosphorus is formed, even at 2700 °C. The absorption measured with line source atomic absorption spectrometry in this case is due to the PO molecule, the spectrum of which is overlapping with the atomic line. Palladium, with or without the addition of calcium or ascorbic acid, was found to be the only modifier to produce almost exclusively atomic phosphorus. Lanthanum and particularly sodium fluoride produced a mixture of P and PO, depending on the atomization temperature. This fact can explain at least some of the discrepancies found in the literature and some of the phenomena observed in the determination of phosphorus using line source atomic absorption spectrometry.

Lepri, Fábio G.; Dessuy, Morgana B.; Vale, Maria Goreti R.; Borges, Daniel L. G.; Welz, Bernhard; Heitmann, Uwe

2006-08-01

287

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

PubMed

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

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

2014-02-17

288

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

PubMed Central

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.

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

2013-01-01

289

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

ERIC Educational Resources Information Center

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'…

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

2002-01-01

290

Mixing of gaseous reactants in chemical generation of atomic iodine for COIL: two-dimensional study  

NASA Astrophysics Data System (ADS)

Two-dimensional CFD model was applied for the study of mixing and reaction between gaseous chlorine dioxide and nitrogen monoxide diluted with nitrogen during atomic iodine generation. The influence of molecular diffusion on the production of atomic chlorine as a precursor of atomic iodine was predominantly studied. The results were compared with one-dimensional modeling of the system.

Jirásek, Vít; Spalek, Otomar; Kodymová, Jarmila; Censky, Miroslav

2003-12-01

291

Electron correlation and relativistic effects in atomic structure calculations of the thorium atom.  

PubMed

Relativistic two-component ab initio calculations have been performed for the Th atom. The spin free low lying states have been calculated at state-averaged complete active space self-consistent field (SA-CASSCF) and multi-state complete active space second-order perturbation (MS-CASPT2) level of theories using different sets of active orbitals. The spin-orbit states have been computed using Douglas-Kroll type of atomic mean-field integral approach. The effects of dynamic electron correlation have been studied at the MS-CASPT2 level. The energy levels of spin-orbit states below 30,000 cm(-1) obtained by the inclusion of dynamic electron correlation are in very good agreement with the experimental values. The radiative properties such as weighted transition probabilities (gA) and oscillator strengths (gf) among several spin-orbit states have been calculated at the SA-CASSCF and MS-CASPT2 levels and are expected to be very helpful for future experiments. PMID:21702551

Roy, S K; Prasad, Rajendra; Chandra, P

2011-06-21

292

Electronic structure, magnetic structure, and metal-atom site preferences in CrMnAs  

NASA Astrophysics Data System (ADS)

Density functional theory was used to examine stoichiometric CrMnAs, one of a class of 3d-metal arsenides that exhibit cooperative magnetic ordering. CrMnAs is a tetragonal structure with two inequivalent metal sites: M(I), which is tetrahedral coordinate, and M(II), which is square pyramidal coordinate. CrMnAs thus presents a "coloring problem," the question of how the two types of metal atoms are distributed between the two types of metal sites. Previous diffraction studies have determined that CrMnAs is antiferromagnetic with the M(I) site primarily occupied by Cr. TB-LMTO-ASA local density approximation (LDA) calculations showed indications of instability in the nonmagnetic structure, which could be resolved either by structural distortion or by spin polarization. LDA crystal orbital Hamilton population (COHP) curves were used to predict the nature of particular direct-exchange interactions upon spin polarization. Spin-polarized total energy calculations were performed using VASP with the generalized gradient approximation (GGA). The lowest-energy structure had Mn at the M(I) site and a different antiferromagnetic ordering than previously observed. The structure with the second-lowest calculated total energy also had Mn at M(I). Next lowest were four structures with Cr at M(I), including the experimentally observed structure. Those four had calculated total energies ranging from 154.2 to 167.8 meV/f.u. higher than the lowest-energy case. The number of possible structures with small energy differences suggests that the observed magnetic ordering and coloring may be due to entropy rather than reflecting a true electronic ground state.

Lutz, Laura Christine

293

Atomic volumes and local structure of metallic glasses  

Microsoft Academic Search

The composition dependence of the room-temperature average atomic volume is analysed for early and late transition metal (TE–TL type) and metal–metalloid (TL–MD type) amorphous alloys. For the Zr–Cu, Ti–Cu and Hf–Ni sytems, the data suggest an ideal solid solution behaviour. For the other TE–TL systems, two composition ranges can be distinguished (20–70 at.% TL and 84–93 at.% TL). For each

I. Bakonyi

2005-01-01

294

Linking surface stress to surface structure: measurement of atomic strain in a surface alloy using scanning tunneling microscopy.  

PubMed

Annealed submonolayer CoAg/Ru(0001) films form an alloy with a structure that contains droplets of Ag surrounded by Co [G. E. Thayer, V. Ozolins, A. K. Schmid, N. C. Bartelt, M. Asta, J. J. Hoyt, S. Chiang, and R. Q. Hwang, Phys. Rev. Lett. 86, 660 (2001)]. To understand how surface stress contributes to the formation of this structure, we use scanning tunneling microscopy to extract atomic displacements at the boundaries between regions of Co and Ag. Comparing our measurements to Frenkel-Kontorova model calculations, we show how stress due to lattice mismatch contributes to the formation of the alloy droplet structure. In particular, we quantitatively evaluate how competing strain and chemical energy contributions determine surface structure. PMID:12144406

Thayer, G E; Bartelt, N C; Ozolins, V; Schmid, A K; Chiang, S; Hwang, R Q

2002-07-15

295

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

PubMed

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

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

2013-01-01

296

Weighted voting-based consensus clustering for chemical structure databases.  

PubMed

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

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

2014-06-01

297

Inaccurate chemical structures of dyes and fluorochromes found in the literature can be problematic for teaching and research.  

PubMed

Abstract Representations of the chemical structures of dyes and fluorochromes often are used to illustrate staining mechanisms and histochemical reactions. Unfortunately, inaccurate chemical structures sometimes are used, which results in problems for teaching and research in histochemistry. We comment here on published examples of inadequate chemical drawing and modeling. In particular, omission of hydrogen atoms can lead to misleading hydrogen-bonding interactions, and inaccurate drawing and modeling procedures result in a variety of implausible molecular structures. The examples and arguments given here are easily intelligible for non-chemists and could be used as part of a training approach to help avoid publication of misleading or puzzling dye structures and molecular models for illustrating biological staining and histochemical studies. PMID:20500122

Stockert, J C; Abasolo, M I

2011-02-01

298

Evolution of Theoretical Concepts Concerning the Structure of Atomic Nuclei after the Discovery of a Neutron.  

National Technical Information Service (NTIS)

The theoretical concepts concerning the structure of atomic nuclei after the discovery of a neutron which underlie theoretical treatment of experimental facts, such as the drop model, the shell model and the optical model, the generalized model and the ph...

A. S. Davydov G. F. Filippov

1981-01-01

299

Correlation between local atomic structure and ultraviolet luminescence of AlGdN thin films  

NASA Astrophysics Data System (ADS)

The present study reports on the correlation between the local atomic structure and cathodoluminescent properties of Al1-xGdxN thin films grown by reactive rf magnetron sputtering at ultra-high vacuum conditions. Those thin films were characterised using X-ray absorption fine structure (XAFS) and cathodoluminescence (CL). From the CL measurements, we have observed a narrow intense ultraviolet emission at 318 nm which is originated from the intra-orbital f-f transition in Gd3+ ions. In order to understand the local atomic structure around the Al1-xGdxN (x=0.1 to 6.0 mol%) thin film, XAFS measurements have been carried out. Analysis of the local atomic structural results showed that both the large distance among Gd atoms and nitrogen vacancies in Al1-xGdxN lattice significantly contribute to the richness in the ultraviolet emission intensity.

Ichii, Kuniyuki; Kitayama, Shinya; Iwahashi, Shinya; Nakamura, Junya; Sagar Reddithota, Vidya; Kita, Takashi; Chigi, Yoshitaka; Nishimoto, Tetsurou; Tanaka, Hiroyuki; Kobayashi, Mikihiro; Ishihara, Tsuguo; Izumi, Hirokazu

2013-03-01

300

H atom positions and nuclear magnetic resonance chemical shifts of short H bonds in photoactive yellow protein.  

PubMed

Recent neutron diffraction studies on photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore-ionized p-coumaric acid (pCA) is a low-barrier H bond (LBHB) mainly because the H atom position was assigned at the midpoint of the O(Glu46)-O(pCA) bond. However, the (1)H nuclear magnetic resonance (NMR) chemical shift (?(H)) was 15.2 ppm, which is lower than the values of 17-19 ppm for typical LBHBs. We evaluated the dependence of ?(H) on an H atom position in the O(Glu46)-O(pCA) bond in the PYP ground state by using a quantum mechanical/molecular mechanical (QM/MM) approach. The calculated chemical shift unambiguously suggested that a ?(H) of 15.2 ppm for the O(Glu46)-O(pCA) bond in NMR studies should correspond to the QM/MM geometry (?(H) = 14.5 ppm), where the H atom belongs to the Glu moiety, rather than the neutron diffraction geometry (?(H) = 19.7 ppm), where the H atom is near the midpoint of the donor and acceptor atoms. PMID:22263543

Saito, Keisuke; Ishikita, Hiroshi

2012-02-14

301

Role of preferential weak hybridization between the surface-state of a metal and the oxygen atom in the chemical adsorption mechanism.  

PubMed

We report on the chemical adsorption mechanism of atomic oxygen on the Pt(111) surface using angle-resolved-photoemission spectroscopy (ARPES) and density functional calculations. The detailed band structure of Pt(111) from ARPES reveals that most of the bands near the Fermi level are surface-states. By comparing band maps of Pt and O/Pt, we identify that dxz (dyz) and dz(2) orbitals are strongly correlated in the surface-states around the symmetry point M and K, respectively. Additionally, we demonstrate that the s- or p-orbital of oxygen atoms hybridizes preferentially with the dxz (dyz) orbital near the M symmetry point. This weak hybridization occurs with minimal charge transfer. PMID:24097254

Kim, Yong Su; Jeon, Sang Ho; Bostwick, Aaron; Rotenberg, Eli; Ross, Philip N; Walter, Andrew L; Chang, Young Jun; Stamenkovic, Vojislav R; Markovic, Nenad M; Noh, Tae Won; Han, Seungwu; Mun, Bongjin Simon

2013-11-21

302

A bond-topological approach to theoretical mineralogy: crystal structure, chemical composition and chemical reactions  

NASA Astrophysics Data System (ADS)

Here, I describe a theoretical approach to the structure and chemical composition of minerals based on their bond topology. This approach allows consideration of many aspects of minerals and mineral behaviour that cannot be addressed by current theoretical methods. It consists of combining the bond topology of the structure with aspects of graph theory and bond-valence theory (both long range and short range), and using the moments approach to the electronic energy density-of-states to interpret topological aspects of crystal structures. The structure hierarchy hypothesis states that higher bond-valence polyhedra polymerize to form the (usually anionic) structural unit, the excess charge of which is balanced by the interstitial complex (usually consisting of large low-valence cations and (H2O) groups). This hypothesis may be justified within the framework of bond topology and bond-valence theory, and may be used to hierarchically classify oxysalt minerals. It is the weak interaction between the structural unit and the interstitial complex that controls the stability of the structural arrangement. The principle of correspondence of Lewis acidity-basicity states that stable structures will form when the Lewis-acid strength of the interstitial complex closely matches the Lewis-base strength of the structural unit, and allows us to examine the factors that control the chemical composition and aspects of the structural arrangements of minerals. It also provides a connection between a structure, the speciation of its constituents in aqueous solution and its mechanism of crystallization. The moments approach to the electronic energy density-of-states provides a link between the bond topology of a structure and its thermodynamic properties, as indicated by correlations between average anion coordination number and reduced enthalpy of formation from the oxides for [6]Mg{/m [4]}Si n O( m+2 n) and MgSO4(H2O) n .

Hawthorne, Frank C.

2012-11-01

303

Structural, electronic and magnetic properties of C atom doped AlN nanoribbons  

NASA Astrophysics Data System (ADS)

First-principles calculations are performed to study the structural, electronic and magnetic properties of pure and C atom doped AlN nanoribbons with both zigzag edge (ZAlNNR) and armchair edge (AAlNNR). With the substitution of one N (Al) atom by a single C atom, a local expansion (a local contraction) takes place, and the C atom is preferred to substituting an edge N or Al atom in 7-ZAlNNR or 7-AAlNNR. Furthermore, by substituting C atom at different positions, the systems may turn into magnetic semiconductors or show a metallic character, which may open a way to design magnetic nanodevices based on AlNNR.

Sun, Ting-ting; Wang, Yong-xin; Du, Xiu-juan; Ke, Bo

2014-05-01

304

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

SciTech Connect

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).

Curtis, L. J.

2004-05-01

305

Structure of adsorbed monolayers. The surface chemical bond  

SciTech Connect

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

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

1984-06-01

306

Ab initio study on atomic and electronic structures of epitaxial graphene  

Microsoft Academic Search

Recently, lots of efforts have been devoted to the growth of epitaxial graphene and its geometric and electronic structure measurements. Several models for the interface structure have been suggested but never been successful in explaining the observations from various experiments. Using density functional theory (DFT) calculations, we find an interface atomic structure of graphene on hexagonal silicon carbide which agrees

Seungchul Kim; Jisoon Ihm; Hyoung Joon Choi; Young-Woo Son

2008-01-01

307

Chemical structural effects on ?-ray spectra of positron annihilation in fluorobenzenes  

NASA Astrophysics Data System (ADS)

Spectra of ?-ray Doppler shifts for positron annihilation in benzene and its fluoro-derivatives are simulated using low energy plane wave positron (LEPWP) approximation. The results are compared with available measurements. It is found that the Doppler shifts in these larger aromatic compounds are dominated by the contributions of the valence electrons and that the LEPWP model overestimates the measurements by approximately 30%, in agreement with previous findings in noble gases and small molecules. It is further revealed that the halogen atoms not only switch the sign of the charges on carbon atoms that they bond to, but that they also polarize other C-H bonds in the molecule leading to a redistribution of the molecular electrostatic potentials. As a result, it is likely that the halogen atoms contribute more significantly to the annihilation process. The present study also suggests that, while the Doppler shifts are sensitive to the number of valence electrons in the molecules, they are less sensitive to the chemical structures of isomers that have the same numbers and type of atoms and, hence, the same numbers of electrons. Further investigation of this effect is warranted.

Wang, F.; Ma, X. G.; Selvam, L.; Gribakin, G. F.; Surko, C. M.

2012-04-01

308

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

SciTech Connect

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.

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

2013-05-01

309

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

SciTech Connect

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

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

2009-06-05

310

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

NASA Astrophysics Data System (ADS)

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.

Aguado, Andrés; López, José M.

2010-09-01

311

Atomic structure of the Ga nanoclusters on Si(111)-(7x7)  

SciTech Connect

Atomic structures of Ga nanoclusters formed on the Si(111)-(7x7) surface have been studied. Combination of scanning tunneling microscopy and rocking-curve analysis of reflection high-energy electron diffraction enables us to study detailed structure of the Ga-adsorbed surface. Highly ordered arrays of nanoclusters, consisting of six Ga and three Si atoms, have been confirmed, in good agreement with the previous studies. We found that the formation of Ga nanoclusters is accompanied by the partial ({approx}40%) substitution of the Si adatoms, surrounding the nanoclusters, by the deposited Ga atoms.

Ohtake, Akihiro [National Institute for Materials Science (NIMS), Tsukuba 305-0044 (Japan)

2006-01-15

312

Atomic accuracy in predicting and designing non-canonical RNA structure  

PubMed Central

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

Das, Rhiju; Karanicolas, John; Baker, David

2010-01-01

313

Atomic Structure of Highly Strained BiFeO3 Thin Films  

SciTech Connect

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

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

2012-01-01

314

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

ERIC Educational Resources Information Center

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

Schoch-Grubler, Ursula

1990-01-01

315

Direct imaging of covalent bond structure in single-molecule chemical reactions.  

PubMed

Observing the intricate chemical transformation of an individual molecule as it undergoes a complex reaction is a long-standing challenge in molecular imaging. Advances in scanning probe microscopy now provide the tools to visualize not only the frontier orbitals of chemical reaction partners and products, but their internal covalent bond configurations as well. We used noncontact atomic force microscopy to investigate reaction-induced changes in the detailed internal bond structure of individual oligo-(phenylene-1,2-ethynylenes) on a (100) oriented silver surface as they underwent a series of cyclization processes. Our images reveal the complex surface reaction mechanisms underlying thermally induced cyclization cascades of enediynes. Calculations using ab initio density functional theory provide additional support for the proposed reaction pathways. PMID:23722428

de Oteyza, Dimas G; Gorman, Patrick; Chen, Yen-Chia; Wickenburg, Sebastian; Riss, Alexander; Mowbray, Duncan J; Etkin, Grisha; Pedramrazi, Zahra; Tsai, Hsin-Zon; Rubio, Angel; Crommie, Michael F; Fischer, Felix R

2013-06-21

316

Synthesis-dependent atomic surface structures of oxide nanoparticles.  

PubMed

Using SrTiO3 nanocuboids as a model system, we show with aberration-corrected high resolution electron microscopy at sub-Å resolution that surface relaxations or reconstructions are present on the nanocuboids, depending on the synthetic process. Oleic acid synthesis, acetic acid synthesis, and microwave-assisted acetic acid synthesis result in a SrO termination, TiO2-rich reconstruction, and mixed termination, respectively. The experimental atomic positions are in better agreement with density functional theory calculations using an exact-exchange corrected PBEsol functional than the Perdew-Burke-Ernzerhof (PBE) functional. PMID:24160614

Lin, Yuyuan; Wen, Jianguo; Hu, Linhua; Kennedy, Robert M; Stair, Peter C; Poeppelmeier, Kenneth R; Marks, Laurence D

2013-10-11

317

Analysis of Surface Fine Structures Using Atomic Force Microscopy  

NSDL National Science Digital Library

In this exercise, you will use an AFM to monitor the surface roughness of PMMA/PS blends versus PMMA/PS copolymers. You will use phase imaging to detect the differences in surface morphology for the blend versus the copolymer. After in-class presentation, completion of hands-on laboratory experiment and review of the information provided, you should be able to: ⢠Confidently discuss the theory and applications of atomic force microscopy for use to characterize polymers and other materials. ⢠Understand the importance of the surface state of polymeric materials.

Derosa, Rebecca L.

2008-09-26

318

Microstructural Characterization of Hierarchical Structured Surfaces by Atomic Force Microscopy  

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

319

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

SciTech Connect

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.

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

320

Applications of the Cambridge Structural Database in chemical education1  

PubMed Central

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.

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

2010-01-01

321

Structure of Intracellular Mature Vaccinia Virus Visualized by In Situ Atomic Force Microscopy  

Microsoft Academic Search

Vaccinia virus, the basis of the smallpox vaccine, is one of the largest viruses to replicate in humans. We have used in situ atomic force microscopy (AFM) to directly visualize fully hydrated, intact intracellular mature vaccinia virus (IMV) virions and chemical and enzymatic treatment products thereof. The latter included virion cores, core-enveloping coats, and core substructures. The isolated coats appeared

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

2003-01-01

322

Imaging the atomic surface structures of CeO2 nanoparticles.  

PubMed

Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear experimental determination of the oxygen atom positions. In this study, with oxygen atoms clearly observed using aberration-corrected high-resolution electron microscopy, we determined the atomic structures of the (100), (110), and (111) surfaces of CeO2 nanocubes. The predominantly exposed (100) surface has a mixture of Ce, O, and reduced CeO terminations, underscoring the complex structures of this polar surface that previously was often oversimplified. The (110) surface shows "sawtooth-like" (111) nanofacets and flat CeO2-x terminations with oxygen vacancies. The (111) surface has an O termination. These findings can be extended to the surfaces of differently shaped CeO2 nanoparticles and provide insight about face-selective catalysis. PMID:24295383

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

2014-01-01

323

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

NASA Technical Reports Server (NTRS)

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.

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

1986-01-01

324

Structural changes of diamond-like carbon films due to atomic hydrogen exposure during annealing  

NASA Astrophysics Data System (ADS)

We have deposited diamond-like carbon (DLC) films by radio-frequency magnetron sputtering, and have annealed the films under various conditions to investigate the effects of annealing on the structural properties by visible Raman spectroscopy, X-ray photoelectron spectroscopy and atomic force microscopy. The structural ordering of hydrogenated DLC films occurs during annealing below 400 °C in a vacuum and a hydrogen gas atmosphere, while unhydrogenated DLC films are not ordered during annealing even at 700 °C. On the other hand, the ordering and the decrease of the sp 3 content are observed for both the films after annealing under an atomic hydrogen exposure. The ordering progresses as the annealing temperature and time are increased. The reduction of the film thickness after annealing is suppressed with increasing annealing temperature. The results suggest that both the preferential etching by atomic hydrogen and the hydrogen evolution encourage the structural changes under an atomic hydrogen exposure.

Nakazawa, H.; Kawabata, T.; Kudo, M.; Mashita, M.

2007-02-01

325

Structure, Electronic Spectrum, and Chemical Bonding of Fullerene-like Nanoparticles Based on MB2(M = Mg, Al, Sc, Ti) Layered Diborides  

Microsoft Academic Search

The structure, electronic spectrum, and interatomic interaction parameters of ?nB2n (n = 10, 30, 90, 120, 160; M = Mg, Al, Sc, Ti) fullerene-like molecules based on MB2 layered diborides are assessed using quantum-chemical modeling and are analyzed in relation to the atomic configuration, size, and chemical composition of ?nB2n?. The electronic structure of concentric nanoparticles consisting of ?nB2n cage

V. V. Ivanovskaya; A. N. Enyashin; A. L. Ivanovskii

2004-01-01

326

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

PubMed

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

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

1999-01-19

327

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

328

Protein secondary structure prediction using NMR chemical shift data.  

PubMed

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes. PMID:20981892

Zhao, Yuzhong; Alipanahi, Babak; Li, Shuai Cheng; Li, Ming

2010-10-01

329

Composition and chemical structure of oceanic mantle plumes  

Microsoft Academic Search

The average compositions (including H2O, Cl, F, and S contents) and chemical structure of oceanic mantle plumes were estimated on the basis of the ratios of incompatible\\u000a volatile components, potassium, and some other elements in the basaltic magmas of ocean islands (melt inclusions and quenched\\u000a glasses). The following average concentrations were estimated for the plume mantle: 510 ppm K2O, 520

V. I. Kovalenko; V. B. Naumov; A. V. Girnis; V. A. Dorofeeva; V. V. Yarmolyuk

2006-01-01

330

The chemical and physical structure of giant molecular cloud cores  

Microsoft Academic Search

The author presents the results of a study of the emission from 33 molecular transitions in the GMC cores Orion A, M17, and Cepheus A. The observations were used to probe the physical and chemical structure within each core. To derive the temperature the J = 6-->5 (K = 0,1,2) transitions of CH3CCH and the J = 1-->0 transition of

E. A. Bergin

1995-01-01

331

Correlating chemical structure and physical properties of vegetable oil esters  

Microsoft Academic Search

The influence of FA ester chemical structures on the rheology and crystallization temperature of those compounds was evaluated\\u000a using methyl, n-butyl, n-octyl, and 2-ethyl-1-hexyl FA esters with different chain lengths and different degrees of unsaturation. The rheological\\u000a properties were analyzed in a high-precision rheometer at various temperatures, and the crystallization temperatures were\\u000a determined by DSC. Esters produced from the esterification

Jorge de A. Rodrigues; Fabianne de P. Cardoso; Elizabeth R. Lachter; Luciana R. M. Estevão; Edson Lima; Regina S. V. Nascimento

2006-01-01

332

Chemical and structural characterization of carbon nanotube surfaces  

Microsoft Academic Search

To utilize carbon nanotubes (CNTs) in various commercial and scientific applications, the graphene sheets that comprise CNT\\u000a surfaces are often modified to tailor properties, such as dispersion. In this article, we provide a critical review of the\\u000a techniques used to explore the chemical and structural characteristics of CNTs modified by covalent surface modification strategies\\u000a that involve the direct incorporation of

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

2010-01-01

333

Three dimensionally structured transducers for chemical and biochemical sensors  

Microsoft Academic Search

Chemical sensors and biosensors based on three-dimensionally structured silicon transducers have been developed. With the inclusion of the third wafer dimension some severe problems related to the combination of IC-fabrication technologies and the technologies for the integration of membranes and biological sensor components have been minimized. Two transducer concepts are presented which both are full mass-production compatible in all fabrication

N. Conrath; N. Czupor; R. Steinkuhl; C. Sundermeier; D. Trau; M. Wittkampf; H. Hinkers; M. Meusel; G. Chemnitius; M. Knoll; F. Spener; K. Cammann

1997-01-01

334

Real-space imaging of molecular structure and chemical bonding by single-molecule inelastic tunneling probe.  

PubMed

The arrangement of atoms and bonds in a molecule influences its physical and chemical properties. The scanning tunneling microscope can provide electronic and vibrational signatures of single molecules. However, these signatures do not relate simply to the molecular structure and bonding. We constructed an inelastic tunneling probe based on the scanning tunneling microscope to sense the local potential energy landscape of an adsorbed molecule with a carbon monoxide (CO)-terminated tip. The skeletal structure and bonding of the molecule are revealed from imaging the spatial variations of a CO vibration as the CO-terminated tip probes the core of the interactions between adjacent atoms. An application of the inelastic tunneling probe reveals the sharing of hydrogen atoms among multiple centers in intramolecular and extramolecular bonding. PMID:24855265

Chiang, Chi-lun; Xu, Chen; Han, Zhumin; Ho, W

2014-05-23

335

Resonance enhanced multiphoton ionization probing of H atoms and CH 3 radicals in a hot filament chemical vapour deposition reactor  

Microsoft Academic Search

Resonance enhanced multiphoton ionization spectroscopy has been used to provide spatially resolved in situ measurements of H atom and CH3 radical relative number densities and the local gas temperature in a hot filament reactor used for diamond chemical vapour deposition (CVD). Parameters varied include the hydrocarbon (CH4 and C2H2), the hydrocarbon\\/H2 process gas mixing ratio, the total pressure and flow

James A. Smith; Moray A. Cook; Stephen R. Langford; Stephen A. Redman; Michael N. R. Ashfold

2000-01-01

336

Atomic structure and chemistry of human serum albumin  

NASA Astrophysics Data System (ADS)

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 Å. 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 IIIA, 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.

He, Xiao Min; Carter, Daniel C.

1992-07-01

337

Atomic Models of Strong Solids Interfaces Viewed as Composite Structures  

NASA Astrophysics Data System (ADS)

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.

Staffell, I.; Shang, J. L.; Kendall, K.

2014-02-01

338

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

NASA Astrophysics Data System (ADS)

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

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

2009-01-01

339

Surface chemistry, structure, and electronic properties from microns to the atomic scale of axially doped semiconductor nanowires.  

PubMed

Using both synchrotron-based photoemission electron microscopy/spectroscopy and scanning tunneling microscopy/spectroscopy, we obtain a complete picture of the surface composition, morphology, and electronic structure of InP nanowires. Characterization is done at all relevant length scales from micrometer to nanometer. We investigate nanowire surfaces with native oxide and molecular adsorbates resulting from exposure to ambient air. Atomic hydrogen exposure at elevated temperatures which leads to the removal of surface oxides while leaving the crystalline part of the wire intact was also studied. We show how surface chemical composition will seriously influence nanowire electronic properties. However, opposite to, for example, Ge nanowires, water or sulfur molecules adsorbed on the exterior oxidized surfaces are of less relevance. Instead, it is the final few atomic layers of the oxide which plays the most significant role by strongly negatively doping the surface. The InP nanowires in air are rather insensitive to their chemical surroundings in contrast to what is often assumed for nanowires. Our measurements allow us to draw a complete energy diagram depicting both band gap and differences in electron affinity across an axial nanowire p-n junction. Our findings thus give a robust set of quantitative values relating surface chemical composition to specific electronic properties highly relevant for simulating the performance of nanoscale devices. PMID:23062066

Hjort, Martin; Wallentin, Jesper; Timm, Rainer; Zakharov, Alexei A; Håkanson, Ulf; Andersen, Jesper N; Lundgren, Edvin; Samuelson, Lars; Borgström, Magnus T; Mikkelsen, Anders

2012-11-27

340

Chemical activity of oxygen atoms in the magnetron sputter-deposited ZnO films during film growth.  

PubMed

The role of oxygen atoms in the growth of magnetron sputter-deposited ZnO films was studied in a deposition and post-deposition study in which the deposition of a several-nanometer-thick ZnO layer altered with an exposure to an O2/Ar mixed plasma, i.e., a layer-by-layer (LbL) technique. The film crystallization was promoted by suppressing the oxygen vacancy and interstitial defects by adjusting the exposure conditions of the O2/Ar plasma. These findings suggest that the chemical potential of the oxygen atom influences the film crystallization and the electronic state. The diffusion and effusion of oxygen atoms at the growing surface have an effect similar to that of thermal annealing, promoted film crystallization and the creation and the annihilation of oxygen- and zinc-related defects. The role of oxygen atoms reaching the growing film surface is discussed in terms of chemical annealing and a possible oxygen diffusion mechanism is proposed. PMID:22097531

Watanabe, Fumiya; Morita, Aya; Shirai, Hajime

2011-09-01

341

Atomic and electronic structures of divacancy in graphene nanoribbons  

Microsoft Academic Search

First principles calculations have been performed to investigate the electronic structures and transport properties of defective graphene nanoribbons (GNRs) in the presence of pentagon–octagon–pentagon (5–8–5) defects. Electronic band structure results reveal that 5–8–5 defects in the defective zigzag graphene nanoribbon (ZGNR) is unfavorable for electronic transport. However, such defects in the defective armchair graphene nanoribbon (AGNR) give rise to smaller

Jun Zhao; Hui Zeng; Jianwei Wei

342

Atomic Hydrogen: A Reagent for the Extraction of Chemical Species from Silicon Surfaces.  

National Technical Information Service (NTIS)

The surface chemistry of adsorbed halogen atoms on Si(100) has been studied using several surface science methods. It has been found that Cl atoms bond to dangling bonds on symmetric Si2 dimer sites, and that the Si-Cl bond angle is tilted from the normal...

J. T. Yates C. C. Cheng Q. Gao M. L. Colaianni W. J. Choyke

1992-01-01

343

Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures  

PubMed Central

Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability and dynamics, as well as interacting with the bulk water. Water potential functions are often parameterized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (?1.0 Å) protein crystal structures with a high level of hydration water by calculating the experimental water-protein radial distribution function or surface distribution function (SDF) and water radial distribution function (RDF). Two maxima are observed in SDF: the first maximum at a radius of 2.75 Å reflects first shell and hydrogen bond interactions between protein and water, the second maximum at 3.65 Å reflects second shell and van der Waals interactions between water and non-polar atoms of protein forming clathrate-hydrate-like structures. Thus, the two shells do not overlap. The RDF showed the features of liquid water rather than solid ice. The first and second maxima of RDF at 2.75 and 4.5 Å, respectively, are the same as for bulk water, but the peaks are sharper indicating hydration water is more stable than bulk water. Both distribution functions are inversely correlated with the distribution of B factors (atomic thermal factors) for the waters, suggesting that the maxima reflect stable positions. Therefore, the average water structure near the protein surface has experimentally observable differences from bulk water. This analysis will help improve the accuracy for models of water on the protein surface by providing rigorous data for the effects of the apparent chemical potential of the water near a protein surface.

Chen, Xianfeng; Weber, Irene; Harrison, Robert W.

2009-01-01

344

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.  

PubMed

The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding. Proteins 2014; 82:1186-1199. © 2013 Wiley Periodicals, Inc. PMID:24356941

van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; Pereira de Araújo, Antônio F

2014-07-01

345

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

346

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

PubMed

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

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

2014-02-01

347

Structural and optical properties of PbS thin films grown by chemical bath deposition  

SciTech Connect

Lead sulphide thin films are grown on glass substrates at various deposition times tD, in the range of 40-60 min per step of 2 min, using the chemical bath deposition technique. X-ray diffraction and atomic force microscopy are used to characterize the film structure. The surface composition is analysed by Auger electron spectroscopy. It appears that the as-prepared thin films are polycrystalline with cubic structure. Nanometric scale crystallites are uniformly distributed on the surface. They exhibit almost a stoechiometric composition with a [Pb]/[S] ratio equal to 1.10. Optical properties are studied in the range of 300-3300 nm by spectrophotometric measurements. Analysis of the optical absorption data of lead sulphide thin layers reveals a narrow optical direct band gap equal to 0.46 eV for the layer corresponding to a deposition time equal to 60 min.

Seghaier, S.; Kamoun, N. [Laboratoire de Physique de la Matiere Condensee, Faculte des Sciences de Tunis (2092) El Manar, Tunisie (Tunisia); Guasch, C. [Institut d'Electronique du Sud, UMR 5814, CNRS, Universite Montpellier Place Eugene Bataillon--CC082--34095 Montpellier cedex (France); Zellama, K. [Laboratoire de Physique de la Matiere Condensee, Faculte des Sciences d'Amiens, 33 rue Saint-Leu, 80039 Amiens (France)

2007-09-19

348

Atomic Structure of Interface States in Silicon Heterojunction Solar Cells  

NASA Astrophysics Data System (ADS)

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.

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.

2013-03-01

349

Atomic structure of interface states in silicon heterojunction solar cells.  

PubMed

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

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

350

Flow injection-chemical vapor generation atomic fluorescence spectrometry hyphenated system for organic mercury determination: A step forward  

NASA Astrophysics Data System (ADS)

Monomethylmercury and ethylmercury were determined on line using flow injection-chemical vapor generation atomic fluorescence spectrometry without neither requiring a pre-treatment with chemical oxidants, nor UV/MW additional post column interface, nor organic solvents, nor complexing agents, such as cysteine. Inorganic mercury, monomethylmercury and ethylmercury were detected by atomic fluorescence spectrometry in an Ar/H 2 miniaturized flame after sodium borohydride reduction to Hg 0, monomethylmercury hydride and ethylmercury hydride, respectively. The effect of mercury complexing agent such as cysteine, ethylendiaminotetracetic acid and HCl with respect to water and Ar/H 2 microflame was investigated. The behavior of inorganic mercury, monomethylmercury and ethylmercury and their cysteine-complexes was also studied by continuous flow-chemical vapor generation atomic fluorescence spectrometry in order to characterize the reduction reaction with tetrahydroborate. When complexed with cysteine, inorganic mercury, monomethylmercury and ethylmercury cannot be separately quantified varying tetrahydroborate concentration due to a lack of selectivity, and their speciation requires a pre-separation stage (e.g. a chromatographic separation). If not complexed with cysteine, monomethylmercury and ethylmercury cannot be separated, as well, but their sum can be quantified separately with respect to inorganic mercury choosing a suitable concentration of tetrahydroborate (e.g. 10 - 5 mol L - 1 ), thus allowing the organic/inorganic mercury speciation. The detection limits of the flow injection-chemical vapor generation atomic fluorescence spectrometry method were about 45 nmol L - 1 (as mercury) for all the species considered, a relative standard deviation ranging between 1.8 and 2.9% and a linear dynamic range between 0.1 and 5 ?mol L - 1 were obtained. Recoveries of monomethylmercury and ethylmercury with respect to inorganic mercury were never less than 91%. Flow injection-chemical vapor generation atomic fluorescence spectrometry method was validated by analyzing the TORT-1 certificate reference material, which contains only monomethylmercury, and obtaining 83 ± 5% of monomethylmercury recovered, respectively. This method was also applied to the determination of monomethylmercury in saliva samples.

Angeli, Valeria; Biagi, Simona; Ghimenti, Silvia; Onor, Massimo; D'Ulivo, Alessandro; Bramanti, Emilia

2011-11-01

351

Atomic and residue hydrophilicity in the context of folded protein structures.  

PubMed

Water-protein interactions drive protein folding, stabilize the folded structure, and influence molecular recognition and catalysis. We analyzed the closest protein contacts of 10,837 water molecules in crystallographic structures to define a specific hydrophilicity scale reflecting specific rather than bulk solvent interactions. The tendencies of different atom and residue types to be the nearest protein neighbors of bound water molecules correlated with other hydrophobicity scales, verified the relevance of crystallographically determined water positions, and provided a direct experimental measure of water affinity in the context of the folded protein. This specific hydrophilicity was highly correlated with hydrogen-bonding capacity, and correlated better with experimental than computationally derived measures of partitioning between aqueous and organic phases. Atoms with related chemistry clustered with respect to the number of bound water molecules. Neutral and negatively charged oxygen atoms were the most hydrophilic, followed by positively-charged then neutral nitrogen atoms, followed by carbon and sulfur atoms. Agreement between observed side-chain specific hydrophilicity values and values derived from the atomic hydrophilicity scale showed that hydrophilicity values can be synthesized for different functional groups, such as unusual side or main chains, discontinuous epitopes, and drug molecules. Two methods of atomic hydrophilicity analysis provided a measure of complementarity in the interfaces of trypsin:pancreatic trypsin inhibitor and HIV protease:U-75875 inhibitor complexes. PMID:8749849

Kuhn, L A; Swanson, C A; Pique, M E; Tainer, J A; Getzoff, E D

1995-12-01

352

Atomic Structure and Phase Transformations in Pu Alloys  

SciTech Connect

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.

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

353

Observing electronic scattering in atomic-scale structures on metals  

Microsoft Academic Search

The scanning tunneling microscope (STM) is a powerful spectroscopic probe of microscopic structures at metal surfaces. Here a series of STM studies are discussed that focus on the interaction of two-dimensional (2-d) electrons with surface nanostructures, and on the electronic properties of magnetic adsorbates. Spectroscopic imaging is shown to be a useful method for observing quantum interference patterns of 2-d

M. F. Crommie

2000-01-01

354

Atomic structure and spectral perturbations in hot dense plasmas  

NASA Astrophysics Data System (ADS)

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

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

1991-05-01

355

Interacting laser and Bose-Einstein-condensate atomic beams: Mutual guiding structures  

SciTech Connect

A basic set of equations describing the interaction of a Bose-Einstein condensate (BEC) with a laser field is derived based on a semiclassical model and applied to the problem of mutual guiding of laser and BEC atomic beams. Within this framework we have studied stationary spatially localized solutions of the nonlinear system which describe possible laser and BEC atomic beam guiding and have shown their stability as well. It is also shown that a self-guiding effect can be realized through both single- and multiple-scaled structures of a BEC atomic and a laser beam.

Cattani, F. [Department of Physics, Clarendon Laboratory, OX1 3PU, Oxford (United Kingdom); Geyko, V.; Kim, A. [Institute of Applied Physics, Russian Academy of Sciences, 603950 Nizhny Novgorod (Russian Federation); Anderson, D.; Lisak, M. [Department of Radio and Space Science, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)

2010-04-15

356

Atomic defects of the walls and the electronic structure of molybdenum disulfide nanotubes  

SciTech Connect

The method of the charge-density functional in the tight-binding approximation is used to study the effect of different types of wall atomic defects in the MoS{sub 2} nanotubes on their structural and electronic properties. It is shown that the atomic defects in the walls of the MoS{sub 2} nanotubes can be responsible for the semiconductor-metal transitions.

Enyashin, A. N.; Ivanovskii, A. L. [Russian Academy of Sciences, Institute of Solid State Chemistry, Ural Division (Russian Federation)], E-mail: ivanovskii@ihim.uran.ru

2007-01-15

357

Rubidium 52P fine-structure transitions induced by collisions with potassium and caesium atoms  

Microsoft Academic Search

A diode-laser fluorescence experiment was performed in order to study fine-structure transitions between 52P states of rubidium atoms colliding with ground-state potassium or caesium atoms. The Rb (52P32\\/) state was optically excited and the intensity ratio of sensitized to direct fluorescence was measured. The obtained cross sections for the excitation energy transfer Rb(2P32\\/) to Rb(2P12\\/) induced by collisions with K

C. Vadla; S. Knezovic; M. Movre

1992-01-01

358

Atomic oxygen fine-structure splittings with tunable far-infrared spectroscopy  

NASA Technical Reports Server (NTRS)

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.

Zink, Lyndon R.; Evenson, Kenneth M.; Matsushima, Fusakazu; Nelis, Thomas; Robinson, Ruth L.

1991-01-01

359

Correlation, relativistic, and quantum electrodynamics effects on the atomic structure of eka-thorium  

SciTech Connect

Large-scale multiconfiguration Dirac-Fock calculations have been performed for the superheavy element eka-thorium, Z=122. The resulting atomic structure is compared with that obtained by various computational approaches involving different degrees of approximation in order to elucidate the role that correlation, relativistic, Breit, and quantum electrodynamics corrections play in determining the low-energy atomic spectrum. The accuracy of the calculations is assessed by comparing theoretical results obtained for thorium with available experimental data.

Gaigalas, Gediminas; Gaidamauskas, Erikas; Rudzikas, Zenonas; Magnani, Nicola; Caciuffo, Roberto [Vilnius University Research Institute of Theoretical Physics and Astronomy, A. Gostauto 12, LT-01108 Vilnius (Lithuania); European Commission, Joint Research Centre, Institute for Transuranium Elements, Postfach 2340, D-76125 Karlsruhe (Germany)

2010-02-15

360

Atomic Structure of Defects in GaN:Mg Grown with Ga Polarity  

Microsoft Academic Search

The atomic structure of characteristic defects (Mg-rich hexagonal pyramids and truncated pyramids) in GaN:Mg thin films grown with Ga polarity was determined at atomic resolution by reconstruction of the scattered electron wave in a transmission electron microscope. Small cavities within the defects have inside walls covered by GaN of reverse polarity. We propose that lateral overgrowth of the cavities restores

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

2004-01-01

361

The electronic structure of oxygen atom vacancy and hydroxyl impurity defects on titanium dioxide (110) surface  

NASA Astrophysics Data System (ADS)

Introducing a charge into a solid such as a metal oxide through chemical, electrical, or optical means can dramatically change its chemical or physical properties. To minimize its free energy, a lattice will distort in a material specific way to accommodate (screen) the Coulomb and exchange interactions presented by the excess charge. The carrier-lattice correlation in response to these interactions defines the spatial extent of the perturbing charge and can impart extraordinary physical and chemical properties such as superconductivity and catalytic activity. Here we investigate by experiment and theory the atomically resolved distribution of the excess charge created by a single oxygen atom vacancy and a hydroxyl (OH) impurity defects on rutile TiO2(110) surface. Contrary to the conventional model where the charge remains localized at the defect, scanning tunneling microscopy and density functional theory show it to be delocalized over multiple surrounding titanium atoms. The characteristic charge distribution controls the chemical, photocatalytic, and electronic properties of TiO2 surfaces.

Minato, Taketoshi; Sainoo, Yasuyuki; Kim, Yousoo; Kato, Hiroyuki S.; Aika, Ken-Ichi; Kawai, Maki; Zhao, Jin; Petek, Hrvoje; Huang, Tian; He, Wei; Wang, Bing; Wang, Zhuo; Zhao, Yan; Yang, Jinlong; Hou, J. G.

2009-03-01

362

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

363

On Launching the First Principles Atomic Theory Using Common Sense Pressure Temperature Dynamism Analysis in Material Universe Vis a Vis Theories of Bohr (Atomic Theory) and Pauling (Chemical Bonding Theory)  

Microsoft Academic Search

Several of my recent papers in various areas of scientific and engineering investigations have been found to validate famous atomic theory of Bohr and chemical bonding theory of Pauling. In view of this, I thought of composing a paper to go alongside original Bohr and prior Rutherford work of attempting to launch an atomic (theory) picture using a special technique

Das Ashis

2004-01-01

364

Chemical Sputtering and Surface Damage of Graphite by Low Energy Atomic and Molecular Hydrogen and Deuterium Projectiles  

SciTech Connect

We present experimental methane production yields for H+, H2+, and H3+ ions incident on ATJ graphite in the energy range 10-250 eV/H. Below about 60 eV/H, the molecular H species give higher methane yields/H when compared with isovelocity H+. The results are interpreted by considering the differences of the maximum binary collision energy transfer in the ejection of chemical sputtering products associated with undissociated molecules and incident atomic ions, using the same analysis as developed by Yao et al. (PRL 81, 550(1998)) in comparing sputtering of Au by isovelocity N+ and N2+ ions. For both D and H atomic and molecular projectiles, the yields/atom coalesce onto a single curve below projectile energies of approximately 60 eV/atom, when plotted as function of maximum energy transfer, under the assumption that the incident molecular species are undissociated when ejecting the hydrocarbon chemical sputtering product. Raman spectroscopy of a graphite sample exposed to high fluences of D+ and D3+ beams at high and low energies, confirmed the expectation that, according to this argument, there should also be more surface damage by incident molecular species than by isovelocity atomic ions. The two high-energy beam-exposed spots showed similar damage, while the low-energy molecular-beam- exposed spot showed slightly more damage than the corresponding D+ beam exposed spot.

Meyer, Fred W [ORNL; Zhang, Hengda [ORNL; Lance, Michael J [ORNL; Krause, Herbert F [ORNL

2008-01-01

365

Electron spectra and structure of atomic and molecular clusters  

SciTech Connect

Changes in electronic structure that occur during the stepwise transition from gas phase monomers to large clusters which resemble the condensed phase were studied. This basic information on weakly bound clusters is critical to the understanding of such phenomena as nucleation, aerosol formation, catalysis, and gas-to-particle conversion, yet there exist almost no experimental data on neutral particle energy levels or binding energies as a function of cluster size. (GHT)

Dehmer, P.M.

1980-01-01

366

Structure and property correlations in heavy atom radical conductors.  

PubMed

The synthesis and solid-state characterization of the resonance-stabilized heterocyclic thia/selenazyl radicals 1a-4a is described. While all the radicals crystallize in undimerized slipped pi-stacked arrays, the four crystal structures do not constitute an isomorphous set; crystals of 1a and 3a belong to the orthorhombic space group P2(1)2(1)2(1), while those of 2a and 4a belong to the monoclinic space group P2(1)/n. The origin of the structural dichotomy can be traced back to the packing of the radicals in the P2(1)/n structure, which maximizes intermolecular Se-Se' contacts. There are marked differences in the transport properties of the two groups. Variable temperature conductivity measurements reveal high, but activated, conductivity for the monoclinic pair (2a/4a), with sigma(298 K) > 10(-3) S cm(-1). The application of physical pressure increases the conductivity of both compounds, with sigma(298 K) at 5 GPa reaching 0.5 S cm(-1) for 2a and 2 S cm(-1) for 4a. Variable-temperature magnetic susceptibility measurements indicate strong antiferromagnetic (AFM) coupling for the monoclinic pair 2a and 4a, the behavior of which has been modeled in terms of a molecular-field modified 1D Heisenberg chain of AFM coupled S = 1/2 centers. Extended Huckel theory band structure calculations and density functional theory first principles methods have been used to develop a qualitative understanding of the conductive and magnetic properties of radicals of the type 1-4 as a function of the degree and direction of slippage of the radical pi-stacks. PMID:19413327

Leitch, Alicea A; Yu, Xueyang; Winter, Stephen M; Secco, Richard A; Dube, Paul A; Oakley, Richard T

2009-05-27

367

Atomic Structure of Bacteriophage Sf6 Tail Needle Knob*  

PubMed Central

Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the “tail needle” likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 ? resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 ? resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.

Bhardwaj, Anshul; Molineux, Ian J.; Casjens, Sherwood R.; Cingolani, Gino

2011-01-01

368

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

PubMed

Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of gamma-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the gamma-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ((1)H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the (1)H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of gamma-oryzanol inside the lipid nanoparticles, the (1)H-NMR revealed that the chemical shifts of the liquid lipid in gamma-oryzanol loaded systems were found at rather higher field than those in gamma-oryzanol free systems, suggesting incorporation of gamma-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of gamma-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of gamma-oryzanol and lipids (solid and liquid) inside the lipid nanoparticle systems are proposed. PMID:20182010

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

2010-03-26

369

Excitation of the [sup 3][ital P][sub [ital J]=0,1,2] fine-structure levels of atomic oxygen in collisions with oxygen atoms  

SciTech Connect

A fully quantal calculation of the excitation cross sections for the fine-structure levels of ground-state atomic oxygen, in collisions with oxygen atoms at low energies, is presented. The results are compared with the cross sections obtained in a previous calculation.

Zygelman, B. (Department of Physics, University of Nevada at Las Vegas, Las Vegas, Nevada 89154 (United States)); Dalgarno, A. (Harvard Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138 (United States)); Sharma, R.D. (Optical Environment Division, Phillips Laboratory, 29 Randolph Road, Hanscom Air Force Base, Massachusetts 01731-3010 (United States))

1994-11-01

370

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...

371

STRUCTURAL BIOLOGY: A Chloride Pump at Atomic Resolution  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. In Halobacterium salinarum, a family of four archaeal rhodopsins performs several different signaling and cross-membrane transport functions. In this Perspective, Spudich discusses recent advances in understanding the molecular mechanism by which these homologous proteins perform this range of functions. A high-resolution structure of halorhodopsin (Kolbe et al., page 1390) provides insights into the relation between proton and chloride transport, representing an important step toward understanding the unifying principles in the archaeal rhodopsin family.

John L. Spudich (University of Texas-Houston Medical School;Department of Microbiology and Molecular Genetics)

2000-05-26

372

Atomic structures at cobalt silicide-silicon interfaces  

Microsoft Academic Search

The structure and chemistry at CoSi-Si(111) and CoSi2-Si(111) interfaces has been investigated in cross-section using high-resolution electron microscopy. After low-temperature annealing, evidence is shown for epitaxial CoSi growth; the corresponding orientation relationships are explained on the basis of a lattice-matching model. During the early stages of the CoSi-to-CoSi2 transformation, an epitaxial CoSi\\/CoSi2\\/Si system is observed, suggesting that CoSi2 nucleates at

A. Catana; P. E. Schmid; P. Lu; D. J. Smith

1992-01-01

373

Local atomic and electronic structures of epitaxial strained LaCoO3 thin films  

NASA Astrophysics Data System (ADS)

We have examined the atomic and electronic structures of perovskite lanthanum cobaltite (LaCoO3) thin films using Co K-edge x-ray absorption fine structure (XAFS) spectroscopy. Extended XAFS (EXAFS) demonstrates that a large difference between in-plane and out-of-plane Co-O bond lengths results from tetragonal distortion in highly strained films. The structural distortions are strongly coupled to the hybridization between atomic orbitals of the Co and O atoms, as shown by x-ray absorption near edge spectroscopy (XANES). Our results indicate that increased hybridization is not the cause of ferromagnetism in strained LaCoO3 films. Instead, we suggest that the strain-induced distortions of the oxygen octahedra increase the population of eg electrons and concurrently depopulate t2g electrons beyond a stabilization threshold for ferromagnetic order.

Sterbinsky, G. E.; Ryan, P. J.; Kim, J.-W.; Karapetrova, E.; Ma, J. X.; Shi, J.; Woicik, J. C.

2012-01-01

374

Pseudo-atomic-orbital band theory applied to electron-energy-loss near-edge structures  

Microsoft Academic Search

The near-edge structure in inner-shell spectroscopy is a product of the slowly varying matrix element and the appropriate projected density of states. We have made use of the self-consistent pseudo-atomic-orbital band-structure-calculation method to produce accurate projected density of states. Our calculation is in good agreement with the K near-edge structure of diamond, silicon, cubic SiC, and Be2C, and the L

Xudong Weng; Peter Rez; O. F. Sankey

1989-01-01

375

Atomic, electronic, and magnetic structure of the Au(100)/Fe3O4(100) interface: Density functional theory study  

NASA Astrophysics Data System (ADS)

The relative stability, the electronic structure, and the magnetic properties of the four models for Au(100)/Fe3O4(100) interface have been studied using density functional theory. From calculations, we find that all the interface energies of the four models are dependent linearly on the O chemical potential. At the same time, we predict the most stable structure of Au(100)/Fe3O4(100) interface. The density of states, the total energies, and the atomic spin magnetic moments of the four interface models are also calculated, which show that the half-metallic properties of bulk Fe3O4 are destroyed in the four models due to the charge transfer between Au layers and the Fe3O4 surface. In addition, from the total energies of the relaxed interface models in three magnetic states corresponding to ferromagnetic, antiferromagnetic, and nonmagnetic, we get the ground states of the four relaxed interface models, respectively.

Li, Y. L.; Yao, K. L.; Lu, Q. H.; Liu, Z. L.; Xi, D.; Luo, X. P.; Ning, Q.

2007-04-01

376

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

NASA Astrophysics Data System (ADS)

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

Shi, Ziliang

377

The double-layered chemical structure in DB white dwarfs  

NASA Astrophysics Data System (ADS)

The purpose of this work is to study the structure and evolution of white dwarf stars with helium-rich atmospheres (DB) in a self-consistent way with the predictions of time-dependent element diffusion. Specifically, we have considered white dwarf models with stellar masses in the range 0.60-0.85 M? and helium envelopes with masses from 10-2 to 10-4 M*. Our treatment of diffusion, appropriate for multicomponent gases, includes gravitational settling and chemical and thermal diffusion. OPAL radiative opacities for arbitrary metallicity and carbon-and oxygen-rich compositions are employed. Emphasis is placed on the evolution of the diffusion-modeled double-layered chemical structure. This structure, which is characterized by a pure helium envelope atop an intermediate remnant shell rich in helium, carbon and oxygen, is expected for pulsating DB white dwarfs, assuming that they are descendants of hydrogen-deficient PG 1159 post-AGB stars. We find that, depending on the stellar mass, if DB white dwarf progenitors are formed with a helium content smaller than ?10-3 M*, a single-layered configuration is expected to emerge during the DB pulsation instability strip. We also explore the consequences of diffusively evolving chemical stratifications on the adiabatic pulsational properties of our DB white dwarf models. In this context, we find that the evolving shape of the chemical profile translates into a distinct behaviour of the theoretical period distribution as compared with the case in which the shape of the profile is assumed to be fixed during the evolution across the instability strip. In particular, we find that the presence of a double-layered structure causes the period spacing diagrams to exhibit mode-trapping substructures. Finally, we extend the scope of the calculations to the domain of the helium-rich carbon-contaminated DQ white dwarfs. In particular, we speculate that DQ white dwarfs with low detected carbon abundances would not be descendants of the PG 1159 stars.

Althaus, L. G.; Córsico, A. H.

2004-04-01

378

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

PubMed

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

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

379

Atomic structure and ultrastructure of the Murex troscheli shell.  

PubMed

The structure of the gastropod Murex troscheli shell was investigated by using high-resolution scanning and transmission electron microscopies and high-resolution synchrotron X-ray powder diffraction. Rietveld refinement of X-ray diffraction patterns revealed anisotropic distortions of the orthorhombic aragonite unit cell, reaching a maximum of about 0.2% (along the c-direction) with respect to geological aragonite. Lattice distortions are effectively relieved under mild annealing at temperatures between 150 °C and 250 °C. This relaxation correlated well with the loss of organic substance during annealing, measured by thermal gravimetric analysis. The shell ultrastructure consists of three orders of hierarchy, which is typical for crossed-lamellar layers. The third-order fiber-like lamellae, nearly 50 × 250 nm² in cross-section, are heavily twinned, producing specific contrast features in transmission electron microscopy micrographs. So, higher orders of hierarchy are, in fact, twins, which boundaries are free of organic matter. PMID:23041491

Younis, Saeed; Kauffmann, Yaron; Pokroy, Boaz; Zolotoyabko, Emil

2012-12-01

380

ssDNA binding reveals the atomic structure of graphene.  

PubMed

We used AFM to investigate the interaction of polyelectrolytes such as ssDNA and dsDNA molecules with graphene as a substrate. Graphene is an appropriate substrate due to its planarity, relatively large surfaces that are detectable via an optical microscope, and straightforward identification of the number of layers. We observe that in the absence of the screening ions deposited ssDNA will bind only to the graphene and not to the SiO(2) substrate, confirming that the binding energy is mainly due to the ?-? stacking interaction. Furthermore, deposited ssDNA will map the graphene underlying structure. We also quantify the ?-? stacking interaction by correlating the amount of deposited DNA with the graphene layer thickness. Our findings agree with reported electrostatic force microscopy (EFM) measurements. Finally, we inspected the suitability of using a graphene as a substrate for DNA origami-based nanostructures. PMID:20977263

Husale, By Sudhir; Sahoo, Sangeeta; Radenovic, Aleksandra; Traversi, Floriano; Annibale, Paolo; Kis, Andras

2010-12-01

381

QED contributions to the atomic structure at strong central fields  

NASA Astrophysics Data System (ADS)

Precise determination of the accurate structure of highly charged, very heavy ions is the basis for a detailed understanding of QED at strong fields. The experimental advances in this field will be reviewed with special emphasis given to H-, He- and Li-like very heavy ions. For the heaviest species, U, the ground-state Lamb shift for H-like ions is measured with an accuracy of about 1%, the two-electron QED terms for He-like system are just being touched, and for the Li-like species already two-loop QED terms have been probed with ultimate accuracy. The different approaches to measure the strong field QED contributions will be elucidated and the results compared to theory. Emphasis will be given to results from the heavy ion storage ring ESR.

Mokler, P. H.

2006-11-01

382

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

PubMed

We show that quantitative internuclear (15)N-(13)C 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 (13)C sites in the beta1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-(13)C or 2-(13)C-glycerol as the (13)C source. Quantitative dipolar trajectories are extracted from two-dimensional (15)N-(13)C planes, in which approximately 750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one (13)C and several (15)N each), yielding quantitative precision as good as 0.1 A for approximately 350 sites, better than 0.3 A for another 150, and approximately 1.0 A for 150 distances in the range of 5-8 A. 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 A), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.79+/-0.03 A). Moreover, side chain heavy atoms are well restrained (0.76+/-0.06 A 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

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

2009-09-01

383

A knowledge-based structure-discriminating function that requires only main-chain atom coordinates  

PubMed Central

Background The use of knowledge-based potential function is a powerful method for protein structure evaluation. A variety of formulations that evaluate single or multiple structural features of proteins have been developed and studied. The performance of functions is often evaluated by discrimination ability using decoy structures of target proteins. A function that can evaluate coarse-grained structures is advantageous from many aspects, such as relatively easy generation and manipulation of model structures; however, the reduction of structural representation is often accompanied by degradation of the structure discrimination performance. Results We developed a knowledge-based pseudo-energy calculating function for protein structure discrimination. The function (Discriminating Function using Main-chain Atom Coordinates, DFMAC) consists of six pseudo-energy calculation components that deal with different structural features. Only the main-chain atom coordinates of N, C?, and C atoms for the respective amino acid residues are required as input data for structure evaluation. The 231 target structures in 12 different types of decoy sets were separated into 154 and 77 targets, and function training and the subsequent performance test were performed using the respective target sets. Fifty-nine (76.6%) native and 68 (88.3%) near-native (< 2.0 Å C? RMSD) targets in the test set were successfully identified. The average C? RMSD of the test set resulted in 1.174 with the tuned parameters. The major part of the discrimination performance was supported by the orientation-dependent component. Conclusion Despite the reduced representation of input structures, DFMAC showed considerable structure discrimination ability. The function can be applied to the identification of near-native structures in structure prediction experiments.

Makino, Yoshihide; Itoh, Nobuya

2008-01-01

384

Effect of substituents on the 13C chemical shifts of the azomethine carbon atom of N-(substituted phenylmethylene)-3- and -4-aminobenzoic acids  

NASA Astrophysics Data System (ADS)

13C chemical shifts of the azomethine carbon atom for N-(substituted phenylmethylene)-3- and -4-aminobenzoic acids having a wide range of substituent effects, were determined in deuterated DMSO solution. Good Hammett correlations of the 13C NMR chemical shifts of azomethine carbons with electrophilic substituent constants ?p+ for electron-donor substituents for both series of acids indicate an important resonance interaction of the substituents on the benzylidene ring with the azomethine carbon atom. On the other hand, good correlations of the 13C NMR chemical shifts of azomethine carbon atom of both series of acids with inductive substituent constants for electron-acceptor substituents in benzylidene ring indicates that the chemical shifts are influenced only by inductive effect of the substituents. The demand for electrons by the azomethine carbon atom in both investigated series have been compared, discussing the mode of transmission of substituent effects, both inductive and resonance, in relation to the geometry of investigated imines.

Jovanovi?, B. Ž.; Marinkovi?, A. D.; Assaleh, F. H.; Csanádi, J.

2005-06-01

385

Chemical space sampling by different scoring functions and crystal structures.  

PubMed

Virtual screening has become a popular tool to identify novel leads in the early phases of drug discovery. A variety of docking and scoring methods used in virtual screening have been the subject of active research in an effort to gauge limitations and articulate best practices. However, how to best utilize different scoring functions and various crystal structures, when available, is not yet well understood. In this work we use multiple crystal structures of PI3 K-gamma in both prospective and retrospective virtual screening experiments. Both Glide SP scoring and Prime MM-GBSA rescoring are utilized in the prospective and retrospective virtual screens, and consensus scoring is investigated in the retrospective virtual screening experiments. The results show that each of the different crystal structures that was used, samples a different chemical space, i.e. different chemotypes are prioritized by each structure. In addition, the different (re)scoring functions prioritize different chemotypes as well. Somewhat surprisingly, the Prime MM-GBSA scoring function generally gives lower enrichments than Glide SP. Finally we investigate the impact of different ligand preparation protocols on virtual screening enrichment factors. In summary, different crystal structures and different scoring functions are complementary to each other and allow for a wider variety of chemotypes to be considered for experimental follow-up. PMID:20401681

Brooijmans, Natasja; Humblet, Christine

2010-05-01

386

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

NASA Astrophysics Data System (ADS)

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

Li, Weiyin; Chen, Fuyi

2014-04-01

387

Spatially localized structures and oscillons in atomic Bose-Einstein condensates confined in optical lattices  

NASA Astrophysics Data System (ADS)

We consider the problem of formation of small-amplitude spatially localized oscillatory structures for atomic Bose-Einstein condensates confined in two- and three-dimensional optical lattices, respectively. Our approach is based on applying the regions with different signs of atomic effective masses where an atomic system exhibits effective hyperbolic dispersion within the first Brillouin zone. By using the kp method we have demonstrated mapping of the initial Gross-Pitaevskii equation on nonlinear Klein-Gordon and/or Ginzburg-Landau-Higgs equations, which is inherent in matter fields within ?4-field theories. Formation of breatherlike oscillating localized states—atomic oscillons—as well as kink-shaped states have been predicted in this case. Apart from classical field theories atomic field oscillons occurring in finite lattice structures possess a critical number of particles for their formation. The obtained results pave the way to simulating some analogues of fundamental cosmological processes occurring during our Universe's evolution and to modeling nonlinear hyperbolic metamaterials with condensed matter (atomic) systems.

Charukhchyan, M. V.; Sedov, E. S.; Arakelian, S. M.; Alodjants, A. P.

2014-06-01

388

An improved chemical scheme for the reactions of atomic oxygen and simple unsaturated hydrocarbons - implications for star-forming regions  

NASA Astrophysics Data System (ADS)

Recent laboratory experiments have demonstrated that even though contribution from other reaction channels cannot be neglected, unsaturated hydrocarbons easily break their multiple C-C bonds to form CO after their interactions with atomic oxygen. Here, we present an upgraded chemical modelling including a revision of the reactions between oxygen atoms and small unsaturated hydrocarbons for different astrochemical environments. The first conclusion is that towards hot cores/corinos atomic oxygen easily degrades unsaturated hydrocarbons directly to CO or to its precursor species (such as HCCO or HCO) and destroys the double or triple bond of alkenes and alkynes. Therefore, environments rich in atomic oxygen at a relatively high temperature are not expected to be rich in large unsaturated hydrocarbons or polycyclic aromatic hydrocarbons. In contrast, in O-poor and C-rich objects, hydrocarbon growth can occur to a large extent. In addition, new radical species, namely ketyl and vinoxy radicals, generated from other reaction channels can influence the abundances of hydrocarbons towards hot cores. We, therefore, suggest that they should be included in the available databases. Hydrocarbon column densities are calculated in the 1013-1015 cm-2 range, in good agreement with their observed values, despite the small number of data currently published in the literature.

Occhiogrosso, Angela; Viti, Serena; Balucani, Nadia

2013-07-01

389

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

SciTech Connect

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.

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

1996-12-31

390

Casimir-Polder force on a two-level atom in a structure containing metamaterials  

NASA Astrophysics Data System (ADS)

We study the Casimir-Polder (CP) force on an excited cold two-level atom in structures containing metamaterials. We adopt two kinds of metamaterials: left-handed materials (LHMs) and zero-index materials (ZIMs). The CP force on an excited atom can be divided into two parts: the dispersive force that responds to all frequencies of the electromagnetic mode and the resonant force, which is determined by the frequency at the atomic transition. Left-handed materials and ZIMs can significantly modify the resonant part of the CP force due to their unique character. It is found here that the presence of LHMs can enhance the force on the atom far away from the surface due to its phase compensation, while the presence of ZIMs can lead to a force that is independent of dipole orientation. The Casimir effect within the combination of LHMs and ZIMs leads us to realize a potential well that is insensitive to the orientation of atomic dipole. Due to the spontaneous decay, the resonant part of the CP force disappears eventually; however, the decay at the position with maximum force is inhibited. Therefore, during the time evolution, there are special positions (focuses) at which the force is significant for a longer time. Our results show the trap effect that can work on an atom with arbitrary dipole orientation. This provides a method to either trap or reflect an atom in a position far away from surface.

Xu, Jingping; Alamri, M.; Yang, Yaping; Zhu, Shi-Yao; Zubairy, M. Suhail

2014-05-01

391

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

PubMed

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

Ruiz-González, M Luisa; Cortés-Gil, Raquel; Torres-Pardo, Almudena; González-Merchante, Daniel; Alonso, José M; González-Calbet, José M

2014-01-27

392

Phase structure for lattice fermions with flavored chemical potential terms  

NASA Astrophysics Data System (ADS)

We discuss the chiral phase diagram in the parameter space of lattice QCD with minimal-doubling fermions, which can be seen as lattice fermions with flavored chemical potential terms. We study strong-coupling lattice QCD with the Karsten-Wilczek formulation, which has one relevant parameter ? 3 as well as gauge coupling and a mass parameter. We find a nontrivial chiral phase structure with a second-order phase transition between chiral symmetric and broken phases. To capture the whole structure of the phase diagram, we study the related lattice Gross-Neveu model. The result indicates that the chiral phase transition also exists in the weak-coupling region. From these results we speculate on the ? 3- g 2 chiral phase diagram in lattice QCD with minimal-doubling fermions, and discuss their application to numerical simulations.

Misumi, Tatsuhiro

2012-08-01

393

Formaldehyde adducts of glutathione. Structure elucidation by two-dimensional n.m.r. spectroscopy and fast-atom-bombardment tandem mass spectrometry.  

PubMed Central

Aqueous mixtures of formaldehyde and glutathione react to form a variety of cyclized adducts in addition to S-hydroxymethylglutathione. The adducts are in labile equilibrium with each other and are not readily separated. The structures of two of the other major adducts were determined by concerted application of 13C-1H two-dimensional chemical-shift correlation, fast-atom-bombardment mass spectrometry and tandem mass spectrometry to the adduct mixtures in aqueous solution.

Naylor, S; Mason, R P; Sanders, J K; Williams, D H; Moneti, G

1988-01-01

394

Atomic structure of the Si(001)-(2×1) surface  

NASA Astrophysics Data System (ADS)

We have performed an extensive set of first-principles self-consistent-field (SCF) pseudopotential total-energy and force calculations for Si(001)-(2×2) and -(2×1) surfaces to arrive at an optimized model for the 2×1 surface. We started with the symmetric dimer model proposed by Abraham and Batra (AB) based on the Stillinger-Weber potential as well as the Yin-Cohen (YC) asymmetric dimer model to carry out the optimization procedure. We confirm the short dimer bond length obtained by YC, unlike in the AB model. However, a symmetric dimer model with a substantial (0.45 Å) inward relaxation of the top layer is found to be lower in energy than the AB model and is highly competitive with a slightly modified YC model. This supports the use of the symmetric model by Pandey in the construction of the extended defect model and also in the recent spin-unrestricted model calculations. From the 2×2 cell calculations we conclude that in the small-buckling limit, some energy gain is possible, provided that the dimers are tilted in opposite directions. We also establish that there is no barrier associated with the surface dimer formation but twisting of the dimers is energetically unfavorable. A detailed account of the Hellmann-Feynman forces is given for various structures.

Batra, Inder P.

1990-03-01

395

Breit–Pauli atomic structure calculations for Fe XI  

SciTech Connect

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.

Aggarwal, Sunny, E-mail: sunny.du87@gmail.com; Singh, Jagjit; Mohan, Man

2013-11-15

396

Breit-Pauli atomic structure calculations for Fe XI  

NASA Astrophysics Data System (ADS)

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 3s3p43d and 3s3p33d2 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.

Aggarwal, Sunny; Singh, Jagjit; Mohan, Man

2013-11-01

397

Organic, inorganic and total mercury determination in fish by chemical vapor generation with collection on a gold gauze and electrothermal atomic absorption spectrometry  

Microsoft Academic Search

A method for organic, inorganic and total mercury determination in fish tissue has been developed using chemical vapor generation and collection of mercury vapor on a gold gauze inside a graphite tube and further atomization by electrothermal atomic absorption spectrometry. After drying and cryogenic grinding, potassium bromide and hydrochloric acid solution (1 mol L?1 KBr in 6 mol L?1 HCl) was added

Fábio Andrei Duarte; Cezar Augusto Bizzi; Fabiane Goldschmidt Antes; Valderi Luiz Dressler; Érico Marlon de Moraes Flores

2009-01-01

398

The chemical structure of the Hawaiian mantle plume.  

PubMed

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

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

2005-08-11

399

Structure and chemical properties of molybdenum oxide thin films  

SciTech Connect

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

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

2007-07-15

400

Annealing effect on the chemical structure of diamondlike carbon  

NASA Astrophysics Data System (ADS)

The effect of annealing in an ultrahigh vacuum on the chemical structure of diamondlike carbon (DLC) was investigated using photoelectron spectroscopy, thermal desorption spectroscopy, electrical resistivity, and micro-Raman spectroscopy measurements. The line shapes of the C 1s photoelectron spectra depended on annealing temperature. The relative intensities of four chemical components in the spectra were quantitatively evaluated: sp3 carbon with carbon-carbon bonds (C-C sp3 carbon), sp2 carbon with carbon-carbon bonds (C-C sp2 carbon), sp2 carbon with hydrogen-carbon bonds (H-C sp2 carbon), and sp3 carbon with hydrogen-carbon bonds (H-C sp3 carbon). The variation of the ratio of the components demonstrated that hydrogen in DLC is emitted to the outside in between 450 and 600 °C, and the remaining DLC is graphized above 600 °C. The increase in the asymmetry of the C 1s spectra and the decrease in the electrical resistivity of the DLC film with annealing temperature agree with the picture that the H-C bonds in DLC produces large free spaces in the structure, which inhibit conductive routes and lead to high electrical resistivity.

Takabayashi, Susumu; Okamoto, Keishi; Sakaue, Hiroyuki; Takahagi, Takayuki; Shimada, Kenya; Nakatani, Tatsuyuki

2008-08-01

401

Atomic-scale studies of electron transport through MOS structures  

NASA Astrophysics Data System (ADS)

The STM-based ballistic electron emission microscopy/spectroscopy (BEEM/BEES) in conjunction with theoretical modeling and Monte Carlo simulations are used to clarify intrinsic transport issues in metal-oxide-semiconductor (MOS) structures. Compared to conventional MOS transport studies, BEEM/BEES offers unique advantages that include, besides its unsurpassed spatial resolution, independent control over the energy of the electrons, which thereby can be injected directly into the SiO2 conduction band, as well as complete control over the electric field across the oxide. The MOS samples consist of thin Pd 'gate' dots deposited on 7-15 nm device-grade oxides thermally grown on Si(100). BEES measures the threshold energy for electron transmission over the potential barrier determined by the gate metal and oxide. This potential is strongly affected by the combination of screening effects due to the metal gate and an applied oxide field. Field dependent decreases of the injection thresholds follow classical image force theory, through which we have determined a dielectric response of ?ox = 2.74 for electrons in SiO2. Possible contributions to the threshold shifts from field induced tunneling through the oxide barrier were assessed with a WKB calculation and deemed unimportant. Justification for the measured ?ox = 2.74, as opposed to the 'established' value close to the optical dielectric constant of 2.15, is obtained from a novel theoretical model. The model, based on a classical particle subject to a time-dependent potential in a polarizable medium, predicts a dynamic dielectric response in the oxide to a moving charge near the metal interface of ?ox = 2.69. The image force induced distortion of the potential near the metal gate has a pronounced effect on the dynamics of the electrons reaching the oxide. Monte Carlo simulations show that this distortion strongly affects the phonon scattering rates in the immediate interface region. Energy and oxide-field dependent electron transmission probabilities were obtained from the simulations and were found to agree remarkably well with experimentally determined probabilities.

Wen, H. J.; Ludeke, R.; Newns, D. M.; Lo, S. H.; Cartier, E.

1998-01-01

402

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

NASA Technical Reports Server (NTRS)

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.

Ross, H. Richard

1993-01-01

403

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

PubMed

Most of the work done on the linear response kernel ?(r,r') has focussed on its atom-atom condensed form ?AB. 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 ?(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 ?(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

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

2014-06-25

404

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

ERIC Educational Resources Information Center

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

Tsai, Chin-Chung

1998-01-01

405

Atomic structure of a 6[degree][001]/(110) tilt grain boundary in aluminum by HREM  

SciTech Connect

A knowledge of the atomic structure of grain boundaries is central to a better understanding of the properties of polycrystalline materials. Attempts to predict grain boundary structure have so far led to the development of various geometrical models for grain boundaries. The concepts of coincident site lattice (CSL) (1), displacement shift complete (DSC) lattice (2,3,4) and the 0-lattice model (2), based on geometrical constructions of adjoining crystals forming boundaries, have been found useful in characterizing the structure of ideal grain boundaries. These models give suggestions regarding the atomic relaxation that occurs at the core of the boundary in the form of dislocations. The 0-lattice model is particularly useful in describing the primary dislocation content of low angle grain boundaries. In this paper the authors present a high resolution electron microscopy investigation of the core structure of a 6[degree][001] symmetrical tilt grain boundary in aluminum. For the first time the atomic structure of such a grain boundary in an FCC metal is resolved. The boundary structure obtained from the HREM images is compared to the corresponding structure predicted by the 0-lattice model and found to be in excellent agreement.

Shamsuzzoha, M.; Deymier, P.A. (Univ. of Arizona, Tucson (United States)); Smith, D.J. (Arizona State Univ., Tempe (United States))

1990-01-01

406

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

PubMed

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

Berns, Veronica M; Fredrickson, Daniel C

2013-11-18

407

Accessibility of selenomethionine proteins by total chemical synthesis: structural studies of human herpesvirus-8 MIP-II.  

PubMed

The determination of high resolution three-dimensional structures by X-ray crystallography or nuclear magnetic resonance (NMR) is a time-consuming process. Here we describe an approach to circumvent the cloning and expression of a recombinant protein as well as screening for heavy atom derivatives. The selenomethionine-modified chemokine macrophage inflammatory protein-II (MIP-II) from human herpesvirus-8 has been produced by total chemical synthesis, crystallized, and characterized by NMR. The protein has a secondary structure typical of other chemokines and forms a monomer in solution. These results indicate that total chemical synthesis can be used to accelerate the determination of three-dimensional structures of new proteins identified in genome programs. PMID:9877169

Shao, W; Fernandez, E; Wilken, J; Thompson, D A; Siani, M A; West, J; Lolis, E; Schweitzer, B I

1998-12-11

408

Structural and vibrational spectral investigations of melaminium maleate monohydrate by FTIR, FT-Raman and quantum chemical calculations.  

PubMed

The structural investigations of the molecular complex of melamine with maleic acid, namely melaminium maleate monohydrate have been carried out by quantum chemical methods in addition to FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical studies were performed with DFT (B3LYP) method using 6-31G(**), cc-pVDZ and 6-311++G(**) basis sets to determine the energy, structural and thermodynamic parameters of melaminium maleate monohydrate. The hydrogen atom from maleic acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak OH···O and NH···O hydrogen bonds shows notable vibrational effects. PMID:23416913

Arjunan, V; Kalaivani, M; Marchewka, M K; Mohan, S

2013-04-15

409

Structural and vibrational spectral investigations of melaminium maleate monohydrate by FTIR, FT-Raman and quantum chemical calculations  

NASA Astrophysics Data System (ADS)

The structural investigations of the molecular complex of melamine with maleic acid, namely melaminium maleate monohydrate have been carried out by quantum chemical methods in addition to FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical studies were performed with DFT (B3LYP) method using 6-31G**, cc-pVDZ and 6-311++G** basis sets to determine the energy, structural and thermodynamic parameters of melaminium maleate monohydrate. The hydrogen atom from maleic acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H⋯O and Nsbnd H⋯O hydrogen bonds shows notable vibrational effects.

Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

2013-04-01

410

International Atomic Energy Agency (IAEA) Coordinated Research Projects on Structural Integrity of Reactor Pressure Vessels  

Microsoft Academic Search

The International Atomic Energy Agency (IAEA) has conducted a series of Coordinated Research Projects (CRPs) that have focused on irradiated reactor pressure vessel (RPV) steel fracture toughness properties and approaches for assuring structural integrity of RPVs throughout operating life. A series of nine CRPs have been sponsored by the IAEA, starting in the early 1970s, focused on neutron radiation effects

William L. Server; Randy K. Nanstad; Jeremy T. Busby; Brady Hanson; S. W. Dean

2009-01-01

411

Imaging the atomic surface structures of CeO2 nanoparticles  

SciTech Connect

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

Lin, Yuyuan [Northwestern University, Evanston] [Northwestern University, Evanston; Wu, Zili [ORNL] [ORNL; Wen, Jianguo [Argonne National Laboratory (ANL)] [Argonne National Laboratory (ANL); Poeppelmeier, Kenneth R [Northwestern University, Evanston] [Northwestern University, Evanston; Marks, Laurence D [Northwestern University, Evanston] [Northwestern University, Evanston

2014-01-01

412

Atomic-scale structures and interactions between the guanine quartet and potassium.  

PubMed

The atomic-scale identification of the G4K1 structural motif is achieved using an interplay of STM imaging and DFT calculations. Its high stability is found to be caused by the delicate balance between hydrogen bonding and metal-ligand interaction, which is of utmost relevance to model interactions of the G-quadruplex with cations in vivo. PMID:23841112

Xu, Wei; Tan, Qinggang; Yu, Miao; Sun, Qiang; Kong, Huihui; Lægsgaard, Erik; Stensgaard, Ivan; Kjems, Jørgen; Wang, Jian-guo; Wang, Chen; Besenbacher, Flemming

2013-08-21