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1

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

E-print Network

LETTERS Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy identification of all the atoms in a material with unknown three-dimensional structure would con- stitute a very that scatter strongly from individual atoms and whose wavelengths are about 50 times smaller than an atom

Pennycook, Steve

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

Atomic Structure: Investigating Atoms  

NSDL National Science Digital Library

Science Objects are two hour on-line interactive inquiry-based content modules that help teachers better understand the science content they teach. This Science Object is the first of three Science Objects in the Atomic Structure SciPack. It discusses the

National Science Teachers Association (NSTA)

2010-05-24

4

Probing Atomic and Electronic Structure of Catalysts by Combination of In Situ and Ex Situ Chemical Imaging  

E-print Network

Probing Atomic and Electronic Structure of Catalysts by Combination of In Situ and Ex Situ Chemical: "Atomic level investigation of the phase stability of transition metal surfaces under reactive environmentnm [001] [110] [001] 2 nm HAADF STEM atomic level of -Al2O3 from several low index zone axis. Derived

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

Chemical generation of iodine atoms  

Microsoft Academic Search

The chemical generation of atomic iodine using a chemical combustor to generate the atomic fluorine intermediate, from the reaction of F2 + H2, followed by the production of atomic iodine, from the reaction of F + HI, was investigated. The maximum conversion efficiency of HI into atomic iodine was observed to be approximately 75%, which is in good agreement with

Kevin B. Hewett; Gordon D. Hager; Peter G. Crowell

2005-01-01

7

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

8

Chemical generation of iodine atoms  

Microsoft Academic Search

The chemical generation of atomic iodine using a chemical combustor to generate the atomic fluorine intermediate, from the reaction of F2+H2, followed by the production of atomic iodine, from the reaction of F+HI, was investigated. The maximum conversion efficiency of HI into atomic iodine was observed to be approximately 75%, which is in good agreement with the theoretical model. The

Kevin B. Hewett; Gordon D. Hager; Peter G. Crowell

2005-01-01

9

Atomic Structure: Properties of Atoms  

NSDL National Science Digital Library

Science Objects are two hour on-line interactive inquiry-based content modules that help teachers better understand the science content they teach. This Science Object is the second of three Science Objects in the Atomic Structure SciPack. It explores the

National Science Teachers Association (NSTA)

2010-05-24

10

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

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

Reactions to Atomic Structure  

NSDL National Science Digital Library

Middle level students are in a concrete stage of psychosocial development and often have difficulty comprehending something as abstract as atomic structure. Students may simply memorize and "brain dump" information about atoms instead of truly internalizing and understanding the concepts. To help students grasp this abstract concept, the lesson described here engages them in an inquiry-based activity in which they build their own model of the atom.

Galus, Pamela

2003-01-01

13

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

PubMed

Monolayer molybdenum disulfide (MoS2) has attracted tremendous attention due to its promising applications in high-performance field-effect transistors, phototransistors, spintronic devices and nonlinear optics. The enhanced photoluminescence effect in monolayer MoS2 was discovered and, as a strong tool, was employed for strain and defect analysis in MoS2. Recently, large-size monolayer MoS2 has been produced by chemical vapour deposition, but has not yet been fully explored. Here we systematically characterize chemical vapour deposition-grown MoS2 by photoluminescence spectroscopy and mapping and demonstrate non-uniform strain in single-crystalline monolayer MoS2 and strain-induced bandgap engineering. We also evaluate the effective strain transferred from polymer substrates to MoS2 by three-dimensional finite element analysis. Furthermore, our work demonstrates that photoluminescence mapping can be used as a non-contact approach for quick identification of grain boundaries in MoS2. PMID:25404060

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

2014-01-01

14

Insights From Atomic-Resolution X-Ray Structures Of Chemically-Synthesized Hiv-1 Protease In Complex With Inhibitors  

PubMed Central

Summary The HIV-1 protease is an aspartyl protease essential for HIV-1 viral infectivity. HIV-1 protease has one catalytic site formed by the homodimeric enzyme. We have chemically synthesized fully active HIV-1 protease using modern ligation methods. When complexed with the classic substrate-derived inhibitors JG-365 and MVT-101, the synthetic HIV-1 protease formed crystals that diffracted to 1.04 and 1.2Å resolution, respectively. These atomic resolution structures revealed additional structural details of the HIV-1 protease interactions with its active site ligands. Heptapeptide inhibitor JG-365, which has a hydroxyethylamine moiety in place of the scissile bond, binds in two equivalent antiparallel orientations within the catalytic groove, whereas the reduced isostere hexapeptide MVT-101 binds in a single orientation. When JG-365 was converted into the natural peptide substrate for molecular dynamic simulations, we found putative catalytically competent reactant states for both lytic water and direct nucleophilic attack mechanisms. Moreover, free energy perturbation calculations indicated that the insertion of catalytic water into the catalytic site is an energetically favorable process. PMID:17869270

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

2007-01-01

15

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

16

Extended study of the atomic step-terrace structure on hexagonal SiC (0 0 0 1) by chemical-mechanical planarization  

NASA Astrophysics Data System (ADS)

The atomic step-terrace structure on hexagonal silicon carbide (0 0 0 1) surface is significant in that it guides the improvement of chemical-mechanical planarization (CMP) and epitaxial technique. The final state of atomic step-terrace structure can be used as a feedback for improving the CMP process, the formula of slurry and the epitaxial technique. In this paper an extended study of the atomic step-terrace structure on 4H- and 6H-SiC (0 0 0 1) planarized by CMP is presented. Surface topography of the (0 0 0 1) facet plane of 4H- and 6H-SiC wafers during CMP process was studied by atomic force microscopy (AFM). The results demonstrate that high-definition atomic step-terrace structure of the (0 0 0 1) facet plane of both 4H- and 6H-SiC can be obtained by appropriate CMP process, and during CMP process, the formation of step-terrace structure had a certain rule. We studied the relationship between the CMP process and the characteristics of the atomic step-terrace structure, and analyzed the possible impact of the CMP process on the status of terraces. We studied the distribution of terraces in different areas of the wafer, and the origin of this distribution was discussed briefly. We also describe the formation of dislocations in hexagonal SiC. The results of this paper may provide some ideas and suggestions for CMP, crystal growth and epitaxy research.

Shi, Xiaolei; Pan, Guoshun; Zhou, Yan; Zou, Chunli; Gong, Hua

2013-11-01

17

Chemical identification of individual surface atoms by atomic force microscopy.  

PubMed

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

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

2007-03-01

18

Atom Probe Tomography Frontiers in Chemical Imaging  

E-print Network

Atom Probe Tomography Frontiers in Chemical Imaging Seminar Series Presented by... M.K. Miller overview of the history of the atom probe tomography (APT) technique and instruments will be presented, from the early field ion microscopy experiments in which images of individual atoms were obtained

19

N-Linear Algebraic Maps for Chemical Structure Codification: A Suitable Generalization for Atom-pair Approaches?  

PubMed

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

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

2014-01-01

20

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

ERIC Educational Resources Information Center

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

Wang, Chia-Yu; Barrow, Lloyd H.

2013-01-01

21

Chemical factors influencing selenium atomization  

E-print Network

gas flow during the atomization cycle) and with manual or microprocessor control modes. The source was a Westinghouse Hollow Cathode Lamp (Model JA 45 477, Fisher Sc1entific) operated at 10 ma. The 196. 0 nm 11ne of selen1um was used with entrance... Time Function Ouration 000 005 010 015 025 165 Flag 1. Lower the dispenser Flag 5. Fill sample loop on stream sampler (pneumatic) Flag 4, Start AA Flag 2. Remove the dispenser Flag 7. Switch stream sample to by-pass and dispense sample...

Buren, Mary Sue

2012-06-07

22

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

2014-07-21

23

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

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

24

Origin of Oxygen Reduction Reaction Activity on "Pt3Co" Nanoparticles: Atomically Resolved Chemical Compositions and Structures  

E-print Network

Compositions and Structures Shuo Chen, Wenchao Sheng, Naoaki Yabuuchi, Paulo J. Ferreira,§ Lawrence F. Allard, Materials Science and Engineering Program, UniVersity of Texas at Austin, Austin, Texas 78712, and High-treated "Pt3Co" nanoparticles showed specific oxygen reduction reaction (ORR) activity (0.7 mA/cmPt 2 at 0.9 V

Ferreira, Paulo J.

25

RADIOACTIVE CHEMICAL ELEMENTS IN THE ATOMIC TABLE.  

SciTech Connect

In the 1949 Report of the Atomic Weights Commission, a series of new elements were added to the Atomic Weights Table. Since these elements had been produced in the laboratory and were not discovered in nature, the atomic weight value of these artificial products would depend upon the production method. Since atomic weight is a property of an element as it occurs in nature, it would be incorrect to assign an atomic weight value to that element. As a result of that discussion, the Commission decided to provide only the mass number of the most stable (longest-lived) known isotope as the number to be associated with these entries in the Atomic Weights Table. As a function of time, the mass number associated with various elements has changed as longer-lived isotopes of a particular elements has been found in nature, or as improved half-life values of an element's isotopes might cause a shift in the longest-lived isotope from one mass number to another. In the 1957 Report of the Atomic Weights Commission, it was decided to discontinue the listing of the mass number in the Atomic Weights Table on the grounds that the kind of information supplied by the mass number is inconsistent with the primary purpose of the Table, i.e., to provide accurate values of ''these constants'' for use in chemical calculations. In addition to the Table of Atomic Weights, the Commission included an auxiliary Table of Radioactive Elements for the first time, where the entry would be the isotope of that element which was most stable, i.e., it had the longest known half-life. In their 1973 report, the Commission noted that the users of the Atomic Weights Table were dissatisfied with the omission of values in the Table for some elements and it was decided to reintroduce the mass number for elements. In their 1983 report, the Commission decided that radioactive elements were considered to lack a characteristic terrestrial isotopic composition, from which an atomic weight value could be calculated to five or more figure accuracy, without prior knowledge of the sample. These elements were again listed in the table with no further information, is., no mass number or atomic weight value. For the elements, which have no stable or long-lived isotopes, the data on radioactive half-lives and relative atomic masses for the nuclides of interest have been evaluated. The values of the half-lives their uncertainties are listed. The uncertainties are given in the last digit quoted of the half-life vale and shown in parentheses. The criteria for consideration of entries in this Table continue to be the same as it has been for over fifty years. It is the same criteria, which are used for all data that are evaluated for inclusion in the Atomic Weight's Table. If a report of data is published in a peer-reviewed journal, that data is evaluated and considered for inclusion in the appropriate table of the biennial report of the Atomic Weights Commission. As better data might become available in the future, the information that is contained in either of the tables may be modified. The information contained in the Table of Radioactive Elements should enable the user to calculate the atomic weight for any sample of radioactive material, which might have a variety of isotopic compositions. The atomic mass values have been taken from the 2003 Atomic Mass Table. Most of these half-lives have already been documented in various sources.

HOLDEN, N.E.

2005-08-13

26

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.

27

Atomic Structure in Black Hole  

E-print Network

We propose that any black hole has atomic structure in its inside and has no horizon as a model of black holes. Our proposal is founded on a mean field approximation of gravity. The structure of our model consists of a (charged) singularity at the center and quantum fluctuations of fields around the singularity, namely, it is quite similar to that of atoms. Any properties of black holes, e.g. entropy, can be explained by the model. The model naturally quantizes black holes. In particular, we find the minimum black hole, whose structure is similar to that of the hydrogen atom and whose Schwarzschild radius is approximately 1.1287 times the Planck length. Our approach is conceptually similar to the Bohr's model of the atomic structure, and the concept of the minimum Schwarzschild radius is similar to that of the Bohr radius. The model predicts that black holes carry baryon number, and the baryon number is rapidly violated. This baryon number violation can be used as verification of the model.

Yukinori Nagatani

2006-11-27

28

Chemical evolution STRUCTURE OF GALAXIES  

E-print Network

Outline Absorption Chemical evolution STRUCTURE OF GALAXIES 8. Absorption; chemical evolution Piet Piet van der Kruit, Kapteyn Astronomical Institute Absorption; chemical evolution #12;Outline Absorption Chemical evolution Outline Absorption Holmberg's analysis Analysis of Disney et al. Edge

Kruit, Piet van der

29

Experimental results on chemical generation of atomic iodine via Cl atoms for chemical oxygen-iodine laser  

Microsoft Academic Search

An alternative chemical way of atomic iodine generation for the chemical oxygen-iodine laser (COIL) was studied. This development was aimed at the laser power increase and simplification of the laser operation control. The method is based on the fast reaction of hydrogen iodide with chemically produced chlorine atoms. Kinetics of the process was studied in two types of the small-scale

Otomar Spalek; Vít Jirásek; Miroslav Censky; Jarmila Kodymová; Ivo Jakubec; Gordon D. Hager

2003-01-01

30

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

31

Chemical oxygen-iodine laser with atomic iodine generated via Cl or F atoms  

Microsoft Academic Search

Two alternative chemical methods of atomic iodine generation for a chemical oxygen-iodine laser (COIL) were studied. These methods are based on fast reactions of gaseous hydrogen iodide with chemically produced chlorine and fluorine atoms. Both processes were studied first in small-scale reactors. A yield of atomic iodine in the Cl system and nitrogen (non-reactive) atmosphere exceeded 80%, while in the

Otomar Spalek; Vit Jirasek; Miroslav Censky; Jarmila Kodymova; Ivo Jakubec; Gordon D. Hager

2005-01-01

32

Theoretical studies on structures, 13 C NMR chemical shifts, aromaticity,  

E-print Network

of capping hydrogen atoms at the open ends of a SWCNT changes the chemical activity of the SWCNTTheoretical studies on structures, 13 C NMR chemical shifts, aromaticity, and chemical reactivity The geometries, chemical shifts, aromaticity, and reactivity of finite-length open-ended armchair single- walled

Wang, Yan Alexander

33

The Chemical Structure and Acid Deterioration of Paper.  

ERIC Educational Resources Information Center

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

Hollinger, William K., Jr.

1984-01-01

34

Development of a chemical oxygen - iodine laser with production of atomic iodine in a chemical reaction  

SciTech Connect

The alternative method of atomic iodine generation for a chemical oxygen - iodine laser (COIL) in chemical reactions with gaseous reactants is investigated experimentally. The influence of the configuration of iodine atom injection into the laser cavity on the efficiency of the atomic iodine generation and small-signal gain is studied. (lasers)

Censky, M; Spalek, O; Jirasek, V; Kodymova, J [Institute of Physics, Czech Academy of Sciences, Prague (Czech Republic); Jakubec, I [Institute of Inorganic Chemistry, Czech Academy of Sciences, Rez (Czech Republic)

2009-11-30

35

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

PubMed

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

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

2014-03-26

36

Chemical Bonding: The Classical Description sharing or transferring electrons between atoms  

E-print Network

Chemical Bonding: The Classical Description sharing or transferring electrons between atoms LEWIS electron dot diagram -> formula (SF6) VSEPR (valence-shell electron-pair repulsion) theory Molecular Structure (w/o quantum mechanics) Chapter. 3 Two or more atoms approach -> their electrons interact and form

Ihee, Hyotcherl

37

Chemical generation of atomic iodine for the chemical oxygen–iodine laser. II. Experimental results  

Microsoft Academic Search

A new method for the chemical generation of atomic iodine intended for use in a chemical oxygen–iodine laser (COIL) was investigated experimentally. The method is based on the fast reaction of hydrogen iodide with chemically produced chlorine atoms. Effects of the initial ratio of reactants and their mixing in a flow of nitrogen were investigated experimentally and interpreted by means

Otomar Špalek; V??t Jirásek; Miroslav ?enský; Jarmila Kodymová; Ivo Jakubec; Gordon D. Hager

2002-01-01

38

Relationship between chemical shift value and accessible surface area for all amino acid atoms  

Microsoft Academic Search

BACKGROUND: Chemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and

Wim F Vranken; Wolfgang Rieping

2009-01-01

39

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

40

About the atomic structures of icosahedral quasicrystals  

NASA Astrophysics Data System (ADS)

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

Quiquandon, Marianne; Gratias, Denis

2014-01-01

41

Chemical generation of atomic iodine for chemical oxygen–iodine laser. I. Modelling of reaction systems  

Microsoft Academic Search

The mathematical modelling of reaction systems for chemical generation of atomic iodine is presented. This process is aimed to be applied in the chemical oxygen–iodine laser (COIL), where it can save a substantial part of energy of singlet oxygen and so increase the laser output power. In the suggested method, gaseous reactants for I atoms generation are admixed into the

V??t Jirásek; Otomar Špalek; Jarmila Kodymová; Miroslav ?enský

2001-01-01

42

Chemical structure and dynamics: Annual report 1993  

SciTech Connect

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

Colson, S.D.

1994-07-01

43

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. PMID:23251781

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

2012-01-01

44

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

45

Continuous wave chemically pumped atomic iodine laser  

SciTech Connect

Cw laser action achieved on the 2p178-2p3/2 transition of the iodine atom by energy transfer from the 1 delta metastable state of O2 is discussed. The effluent from a conventional oxygen generator was mixed with molecular iodine at the entrance of a longitudinal flow laser cavity where the I2 was dissociated by a small amount of O2 (1 sigma ) that was present in the flow due to energy pooling processes. The measured output power was greater than 4MW

Benard, D.J.; Bousek, R.R.; Mcdermott, W.E.; Pchelkin, N.R.

1981-05-12

46

Electronic Structure: Electronic Structure of atoms (theory)  

Microsoft Academic Search

The analysis of the spectrum of the hydrogen atom has been the starting point of the development of Quantum Mechanics at the beginning of the last century. The calcula- tion of the energy eigenvalues and of the corresponding eigenfunctions of this one-electron system is simple enough both in non -relativistic and in relativistic quantum mechanics. When the number of the

Vincenzo Marigliano Ramaglia

47

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. PMID:23940343

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

2013-01-01

48

PHYSICAL REVIEW B 85, 205417 (2012) Chemically ordered MnPt ultrathin films on Pt(001) substrate: Growth, atomic structure, and  

E-print Network

PHYSICAL REVIEW B 85, 205417 (2012) Chemically ordered MnPt ultrathin films on Pt(001) substrate; published 10 May 2012) Ultrathin MnPt films have been grown on Pt(001) single crystals by alternate leads to a disordered and rough MnPt film. After annealing at 770 K, chemical order develops

Paris-Sud XI, Université de

49

Quantitative Chemical Imaging of Atomic-Scale Chemistry Changes at Interfaces Research Team: Nigel Browning, Hao Yang  

E-print Network

Quantitative Chemical Imaging of Atomic-Scale Chemistry Changes at Interfaces Research Team: Nigel method to quantify atomic-scale changes in structure, composition, and bonding that occur at interfaces Make use of advanced capabilities for chemical imaging under varied environmental conditions afforded

50

Quantum Structures of the Hydrogen Atom  

E-print Network

Modern quantum theory introduces quantum structures (decompositions into subsystems) as a new discourse that is not fully comparable with the classical-physics counterpart. To this end, so-called Entanglement Relativity appears as a corollary of the universally valid quantum mechanics that can provide for a deeper and more elaborate description of the composite quantum systems. In this paper we employ this new concept to describe the hydrogen atom. We offer a consistent picture of the hydrogen atom as an open quantum system that naturally answers the following important questions: (a) how do the so called "quantum jumps" in atomic excitation and de-excitation occur? and (b) why does the classically and seemingly artificial "center-of-mass + relative degrees of freedom" structure appear as the primarily operable form in most of the experimental reality of atoms?

J. Jeknic-Dugic; M. Dugic; A. Francom; M. Arsenijevic

2012-04-14

51

Chemical analysis of impurity boron atoms in diamond using soft X-ray emission spectroscopy.  

PubMed

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. PMID:18614820

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

2008-07-01

52

Local atomic structure in disordered and nanocrystalline catalytic materials.  

SciTech Connect

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

Dmowski, W. [University of Tennessee, Knoxville (UTK); Egami, T. [University of Tennessee, Knoxville (UTK); Swider-Lyons, K. [Naval Research Laboratory, Washington, D.C.; Dai, Sheng [ORNL; Overbury, Steven {Steve} H [ORNL

2007-01-01

53

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

54

Molecular structures derived from deterministic theory of atomic structure  

NASA Astrophysics Data System (ADS)

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

Lu, K. U.

1996-07-01

55

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

56

Chemical-potential standard for atomic Bose-Einstein condensates  

E-print Network

When subject to an external time periodic perturbation of frequency $f$, a Josephson-coupled two-state Bose-Einstein condensate responds with a constant chemical potential difference $\\Delta\\mu=khf$, where $h$ is Planck's constant and $k$ is an integer. We propose an experimental procedure to produce ac-driven atomic Josephson devices that may be used to define a standard of chemical potential. We investigate how to circumvent some of the specific problems derived from the present lack of advanced atom circuit technology. We include the effect of dissipation due to quasiparticles, which is essential to help the system relax towards the exact Shapiro resonance, and set limits to the range of values which the various physical quantities must have in order to achieve a stable and accurate chemical potential difference between the macroscopic condensates.

Sigmund Kohler; Fernando Sols

2003-05-02

57

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

58

Atom structures of relation algebras Ian Hodkinson \\Lambda  

E-print Network

Atom structures of relation algebras Ian Hodkinson \\Lambda October 24, 1995 Abstract We study atom structures of relation algebras. We prove that the class of atom structures that arise from representable atomic relation algebras is elementary, but is not definable by a sentence of the infinitary logic L ! 1

Hodkinson, Ian

59

Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality  

E-print Network

The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

Mikhail M. Labushev

2012-06-20

60

Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality  

E-print Network

The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

Labushev, Mikhail M

2012-01-01

61

PROTEIN STRUCTURE REPORT Atomic resolution structure of the  

E-print Network

PROTEIN STRUCTURE REPORT Atomic resolution structure of the cytoplasmic domain of Yersinia pestis III secretion system (T3SS) in Yersinia pestis, have been solved by single-wavelength anomolous; YscU Introduction Yersinia pestis is the causative agent of plague, one of the most deadly diseases

62

Contrast reversal in atomic-resolution chemical mapping.  

PubMed

We report an unexpected result obtained using chemical mapping on the new, aberration corrected Nion UltraSTEM at Daresbury. Using different energy windows above the L2,3 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. PMID:19113568

Wang, P; D'Alfonso, A J; Findlay, S D; Allen, L J; Bleloch, A L

2008-12-01

63

Contrast Reversal in Atomic-Resolution Chemical Mapping  

NASA Astrophysics Data System (ADS)

We report an unexpected result obtained using chemical mapping on the new, aberration corrected Nion UltraSTEM at Daresbury. Using different energy windows above the L2,3 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.; D'Alfonso, A. J.; Findlay, S. D.; Allen, L. J.; Bleloch, A. L.

2008-12-01

64

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

SciTech Connect

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

Not Available

1989-12-15

65

Intra-atomic Charge and the Structure of the Atom  

Microsoft Academic Search

I AM very grateful to Mr. Soddy (NATURE, December 4, p. 399) that in accepting in principle the hypothesis that the intra-atomic charge of an element is determined by its place in the periodic table, he directed attention to the possible uncertainty of the absolute values of intra-atomic charge and of the number of intra-atomic electrons. Surely the absolute values

A. van den Broek

1913-01-01

66

Atomic-Scale Chemical Imaging via Combination of Scanning Tunneling and Electron Energy Loss Spectroscopies  

E-print Network

Atomic-Scale Chemical Imaging via Combination of Scanning Tunneling and Electron Energy Loss systems at atomic level Develop atomically resolved chemical imaging platform via combination of low-sensitive imaging at atomic/molecular level Key Success Completed and successfully tested molecular beam device

67

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

68

Chemical oxygen-iodine laser with a new method of atomic iodine generation  

Microsoft Academic Search

A study of recently proposed chemical method of atomic iodine production in the Chemical Oxygen-Iodine Laser (COIL) was performed. The process using gaseous reactants is based on the fast reaction of hydrogen iodide with chemically produced atomic chlorine. In the absence of singlet oxygen, the high yield of atomic iodine was attained (80 to 100 %). In the flow of

Otomar Spalek; Miroslav Censky; Vít Jirásek; Jarmila Kodymová; Ivo Jakubec; Gordon D. Hager

2003-01-01

69

Atomic Structures of Riboflavin (Vitamin B2) and its Reduced Form with Bond Lengths Based on Additivity of Atomic Radii  

E-print Network

It has been shown recently that chemical bond lengths, in general, like those in the components of nucleic acids, caffeine related compounds, all essential amino acids, methane, benzene, graphene and fullerene are sums of the radii of adjacent atoms constituting the bond. Earlier, the crystal ionic distances in all alkali halides and lengths of many partially ionic bonds were also accounted for by the additivity of ionic as well as covalent radii. Here, the atomic structures of riboflavin and its reduced form are presented based on the additivity of the same set of atomic radii as for other biological molecules.

Raji Heyrovska

2008-06-21

70

Atomic Structures of Riboflavin (Vitamin B2) and its Reduced Form with Bond Lengths Based on Additivity of Atomic Radii  

E-print Network

It has been shown recently that chemical bond lengths, in general, like those in the components of nucleic acids, caffeine related compounds, all essential amino acids, methane, benzene, graphene and fullerene are sums of the radii of adjacent atoms constituting the bond. Earlier, the crystal ionic distances in all alkali halides and lengths of many partially ionic bonds were also accounted for by the additivity of ionic as well as covalent radii. Here, the atomic structures of riboflavin and its reduced form are presented based on the additivity of the same set of atomic radii as for other biological molecules.

Heyrovska, Raji

2008-01-01

71

Chemical structure of multilayer oxidized epitaxial graphene  

NASA Astrophysics Data System (ADS)

In this work, density functional theory (DFT) calculations are used to interpret new X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and atomic force microscope (AFM) measurements of the oxide of epitaxial graphene. This layered carbon material is obtained by Hummers oxidation of 6- to 17-layer graphene films grown epitaxially at high temperature on a silicon carbide substrate. The extensive DFT calculations carried out to solve the inverse problem posed by the aforementioned measurements show that a most plausible molecular structure for the oxide of epitaxial graphene consists of mildly oxidized graphene layers covalently bridged by short polyoxymethylene chains. Possible chemical reactions leading to this form of graphene derivative are discussed.

Zhou, Si; Bongiorno, Angelo

2013-03-01

72

Predicting Chemical Carcinogenesis using Structural Information Only?  

E-print Network

into the mechanistic paths and features that gov- ern chemical toxicity, since the solutions produced are readilyPredicting Chemical Carcinogenesis using Structural Information Only? Claire J. Kennedy1 of predicting the carcinogenic activity of chemical com- pounds from their molecular structure and the outcomes

Fernandez, Thomas

73

Atomic and electronic structure of gadolinium oxide  

NASA Astrophysics Data System (ADS)

Rare earth gadolinium oxide film has been studied by X-ray absorption fine structure (XAFS) at Gd L3-edge and energy electron loss spectroscopy (EELS) spectroscopies. XAFS data showed that the nearest Gd coordination shells consist of six oxygen atoms at ~2.308(2) Å and six gadolinium atoms at ~3.57(2) Å corresponding to Gd2O3 with a space group of Ia-3. EELS analysis of the film revealed excitations at the energies of 14.2, 19.9 eV which are due to electron transition from the valence band to the conductive one; excitations at the energies of 22.2-23.5 eV originated from valence electrons plasmon oscillations (bulk plasmons); and the excitation at 5.5 eV resulted from the electron transition at defects. When the photon energy changed from 1.5 to 5.0 eV the refractive index increased from 1.92 to 2.15.

Viktorovich Perevalov, Timofey; Evgenievich Dolbak, Andrey; Aleksandrovich Shvets, Vasilii; Alekseevich Gritsenko, Vladimir; Ivanovna Asanova, Tatijana; Borisovich Erenburg, Simon

2014-01-01

74

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

75

Chemical Etiology of Nucleic Acid Structure  

NSDL National Science Digital Library

Systematic chemical studies indicate that the capability of Watson-Crick base-pairing is widespread among potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. A comparison of RNA and such alternatives with regard to chemical properties that are fundamental to the biological function of RNA provides chemical facts that may contain clues to RNA's origin.

Albert Eschenmoser (The Scripps Research Institute ;)

1999-06-25

76

Functionalization of MWCNTs with atomic nitrogen: electronic structure  

NASA Astrophysics Data System (ADS)

The changes induced by exposing multi-walled carbon nanotubes (CNTs) to atomic nitrogen were analysed by high-resolution transmission electron microscopy (HRTEM), x-ray and ultraviolet photoelectron spectroscopy. It was found that the atomic nitrogen generated by a microwave plasma effectively grafts chemical groups onto the CNT surface altering the density of valence electronic states. HRTEM showed that the exposure to atomic nitrogen does not significantly damage the CNT surface.

Ruelle, Benoit; Felten, Alexandre; Ghijsen, Jacques; Drube, Wolfgang; Johnson, Robert L.; Liang, Duoduo; Erni, Rolf; Van Tendeloo, Gustaaf; Dubois, Philippe; Hecq, Michel; Bittencourt, Carla

2008-02-01

77

Using Spike-Anneal to Reduce Interfacial Layer Thickness and Leakage Current in Metal-Oxide-Semiconductor Devices with TaN/Atomic Layer Deposition-Grown HfAlO/Chemical Oxide/Si Structure  

NASA Astrophysics Data System (ADS)

In this study, the characteristics of Ta/chemical SiO2/Si devices with their chemical oxides formed by various chemicals, including HNO3, SC1, and H2SO4+H2O2 solutions, were first investigated. We found the HNO3 split depicts the lowest leakage current and the best hysteresis behavior. Next, chemical oxide formed by HNO3 was applied to form the interfacial SiO2 layer for metal-oxide-semiconductor (MOS) devices with Ta/HfAlO/chemical SiO2/Si structrue. The effects of a high-temperature spike anneal were then studied. We found that the spike-anneal process can effectively reduce the thickness of the chemical oxide from 10 to 7 Å, thus is beneficial in preserving the low effective oxide thickness (EOT) of the structure. Furthermore, both the gate leakage current and stress-induced leakage current (SILC) were also effectively suppressed by the high-temperature spike-anneal.

Tsai, Bo-An; Lee, Yao-Jen; Peng, Hsin-Yi; Tzeng, Pei-Jer; Luo, Chih-wei; Chang-Liao, Kuei-Shu

2008-04-01

78

Atomic Structure of Benzene Which Accounts for Resonance Energy  

E-print Network

Benzene is a hexagonal molecule of six carbon atoms, each of which is bound to six hydrogen atoms. The equality of all six CC bond lengths, despite the alternating double and single bonds, and the surplus (resonance) energy, led to the suggestion of two resonanting structures. Here, the new atomic structure shows that the bond length equality is due to three carbon atoms with double bond radii bound to three other carbon atoms with resonance bond radii (as in graphene). Consequently, there are two kinds of CH bonds of slightly different lengths. The bond energies account for the resonance energy.

Raji Heyrovska

2008-06-27

79

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

80

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

81

Evidence from Crystal Structures in Regard to Atomic Structures  

Microsoft Academic Search

The distribution of valence electrons in the diamond and similar crystals.-Because of the cubical symmetry, the equivalent scattering power of all the atoms, and the absence of pyro- and piezo-electric effect, the atoms in the diamond cannot be held together as a result of the transfer of electrons from atom to atom. Symmetry requirements also eliminate any cubical arrangement of

Maurice L. Huggins

1926-01-01

82

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

83

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

84

Valence-Bond Theory and Chemical Structure.  

ERIC Educational Resources Information Center

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

Klein, Douglas J.; Trinajstic, Nenad

1990-01-01

85

Direct chemical vapor deposition growth of WS2 atomic layers on hexagonal boron nitride.  

PubMed

Atomically thin transition metal dichalcogenides (TMDCs) have attracted considerable interest owing to the spin-valley coupled electronic structure and possibility in next-generation devices. Substrates are one of the most important factors to limit physical properties of atomic-layer materials, and among various substrates so far investigated, hexagonal boron nitride (hBN) is the best substrate to explore the intrinsic properties of atomic layers. Here we report direct chemical vapor deposition (CVD) growth of WS2 onto high-quality hBN using a 3-furnace CVD setup. Triangular-shaped WS2 grown on hBN have shown limited crystallographic orientation that is related to that of the underlying hBN. Photoluminescence spectra of the WS2 show an intense emission peak at 2.01 eV with a quite small fwhm of 26 meV. The sharp emission peak indicates the high quality of the present WS2 atomic layers with high crystallinity and clean interface. PMID:25093606

Okada, Mitsuhiro; Sawazaki, Takumi; Watanabe, Kenji; Taniguch, Takashi; Hibino, Hiroki; Shinohara, Hisanori; Kitaura, Ryo

2014-08-26

86

Structures of Molecules at the Atomic Level: Caffeine and Related Compounds  

E-print Network

Recent rsearches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. On investigating the bond length data for the molecular components of nucleic acids, all were found (for the first time) to be effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.

Heyrovska, Raji

2008-01-01

87

Structures of Molecules at the Atomic Level: Caffeine and Related Compounds  

E-print Network

Recent rsearches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. On investigating the bond length data for the molecular components of nucleic acids, all were found (for the first time) to be effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.

Raji Heyrovska; Saraswathi Narayan

2008-01-28

88

Recent results in the development of a chemical way of atomic iodine generation for a COIL  

Microsoft Academic Search

The results of theoretical and experimental investigation of gas phase chemical generation of atomic iodine, I(2P3\\/2), for stimulated emission in chemical oxygen-iodine laser (COIL) are presented. The method of I atoms generation employs a principal reaction X+HI implies I(2P3\\/2)+HX, where X equals F or Cl. A computational modeling was based on the 1D flow development exploring the chemical processes within

Jarmila Kodymova; Otomar Spalek; Vit Jirasek; Miroslav Censky; Gordon D. Hager

2002-01-01

89

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

90

Rutherford and Bohr describe atomic structure 1913  

NSDL National Science Digital Library

This page is from PBS A Science Odyssey: People and Discoveries. It describes Bohr's contribution to theories of the atom and its relationship to others' such as Rutherford's. Links to relevant pages are provided. An image of Bohr's conception drawn in his notebook is included.

1998-01-01

91

Critical adsorption at chemically structured substrates  

E-print Network

We consider binary liquid mixtures near their critical consolute points and exposed to geometrically flat but chemically structured substrates. The chemical contrast between the various substrate structures amounts to opposite local preferences for the two species of the binary liquid mixtures. Order parameters profiles are calculated for a chemical step, for a single chemical stripe, and for a periodic stripe pattern. The order parameter distributions exhibit frustration across the chemical steps which heals upon approaching the bulk. The corresponding spatial variation of the order parameter and its dependence on temperature are governed by universal scaling functions which we calculate within mean field theory. These scaling functions also determine the universal behavior of the excess adsorption relative to suitably chosen reference systems.

Monika Sprenger; Frank Schlesener; S. Dietrich

2005-01-25

92

Presentation of Atomic Structure in Turkish General Chemistry Textbooks  

ERIC Educational Resources Information Center

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

Niaz, Mansoor; Costu, Bayram

2009-01-01

93

Quantum Monte Carlo for the Electronic Structure of Atomic Systems  

Microsoft Academic Search

In this work we tackle the problem of the electronic structure of atoms by using Quantum Monte Carlo methods. The Variational Monte Carlo method has been extensively employed with trial wave functions which include different correlation mechanisms. A reliable description of different properties such as ionization potentials and electron affinities, or excitation energies is obtained for atoms with a relatively

A. Sarsa; E. Buendía; F. J. Gálvez; P. Maldonado

2008-01-01

94

The Electronic Structure of an Icosahedron of Boron Atoms  

Microsoft Academic Search

The electronic structure of a regular icosahedron of boron atoms is investigated theoretically by the method of molecular orbitals. It is found that thirteen bonding orbitals are available for holding the icosahedron together, besides the twelve outward-pointing equivalent orbitals of the separate atoms. The results are used to interpret the stability of boron carbide, to question a recently proposed crystal

H. C. Longuet-Higgins; M. De V. Roberts

1955-01-01

95

Renyi complexities and information planes: Atomic structure in conjugated spaces  

NASA Astrophysics Data System (ADS)

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

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

2009-05-01

96

Nanoscale structure and transport : from atoms to devices  

E-print Network

Nanoscale structures present both unique physics and unique theoretical challenges. Atomic-scale simulations can find novel nanostructures with desirable properties, but the search can be difficult if the wide range of ...

Evans, Matthew Hiram

2005-01-01

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 highly-charged ions. Final report  

SciTech Connect

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

Livingston, A. Eugene

2002-05-23

99

The atomic structure of niobium and tantalum containing borophosphate glasses  

Microsoft Academic Search

A complete structural study has been carried out on sodium borophosphate glass containing increasing amounts of either niobium or tantalum. A combination of high energy x-ray diffraction, neutron diffraction, extended x-ray absorption fine structure, nuclear magnetic resonance, and infrared and Raman spectroscopy has been used to discern the local atomic structure of each component and the changes with M content,

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

2009-01-01

100

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.  

PubMed

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently. PMID:19552480

Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

2009-07-01

101

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 and D) program is meeting the need for a fundamental, molecular-level understanding by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and (3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

Colson, Steve D; McDowell, Rod S

2001-04-15

102

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

103

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

104

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

105

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

106

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

107

Gas atomized chemical reservoir ODS ferritic stainless steels  

SciTech Connect

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

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

2010-06-27

108

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

109

Real topography, atomic relaxations, and short-range chemical interactions in atomic force microscopy: The case of the ?-Sn/Si(111)-(3×3)R30° surface  

NASA Astrophysics Data System (ADS)

We have investigated the phases of the Sn/Si(111)-(3×3)R30° surface below (1)/(3) ML coverage at room temperature by means of atomic force microscopy (AFM) and density functional theory based first-principles calculations. By tuning the Sn concentration at the surface we have been able to discriminate between Sn and Si adatoms, and to assure that the AFM topography for the different phases resembles the one reported using scanning tunneling microscopy. In the mosaic and the intermediate phases, a dependence of the topographic height of the Si adatoms on the number of surrounding Sn adatoms has been identified. In the pure phase, however, variations in the measured height difference between the Sn adatoms and the substitutional Si defects, which are intrinsic to the AFM observation, are reported. Reliable room-temperature force spectroscopic measurements using the atom-tracking technique and first-principles calculations provide an explanation for these striking induced height variations on the pure phase in terms of both the different strength of the short-range chemical interaction and tip-induced atomic relaxations. Our results suggest that the corrugation measured with true atomic resolution AFM operated at low interaction forces and close to the onset of significant short-range chemical interactions provides direct access to the real structure of heterogeneous semiconductor surfaces.

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

2006-05-01

110

Role of fluorine atoms in the oxidation-hydrolysis process of plasma assisted chemical vapor deposition fluorinated silicon nitride film  

Microsoft Academic Search

The oxidation and\\/or hydrolysis of a plasma assisted chemical vapor deposition fluorinated silicon nitride film in a moisture atmosphere has been studied. The film presents fluorine atoms incorporated as -SiF, -SiF[sub 2], -SiF[sub 3], and [-SiF[sub 2]-][sub n] groups. The open structure of the film, due to the high fluorine content as [-SiF[sub 2]-][sub n], favors the penetration of oxygen

O. Sanchez; C. Gomez-Aleixandre; C. Palacio

2009-01-01

111

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

ERIC Educational Resources Information Center

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

Izquierdo-Aymerich, Merce; Aduriz-Bravo, Agustin

2009-01-01

112

Solitonic fullerene structures in light atomic nuclei  

E-print Network

The Skyrme model is a classical field theory which has topological soliton solutions. These solitons are candidates for describing nuclei, with an identification between the numbers of solitons and nucleons. We have computed numerically, using two different minimization algorithms, minimum energy configurations for up to 22 solitons. We find, remarkably, that the solutions for seven or more solitons have nucleon density isosurfaces in the form of polyhedra made of hexagons and pentagons. Precisely these structures arise, though at the much larger molecular scale, in the chemistry of carbon shells, where they are known as fullerenes.

R. A. Battye; P. M. Sutcliffe

2000-12-21

113

Chemical Structure and Dynamics annual report 1997  

SciTech Connect

The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

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

1998-03-01

114

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. PMID:16147526

Oldfield, Eric

2004-01-01

115

Parity-time symmetric Bragg structure in atomic vapor.  

PubMed

We propose an efficient scheme in helium or alkaline earth atomic vapor to achieve a parity-time symmetric Bragg structure using coherent lights. Unidirectional invisibility can be realized in this scheme, i.e., the atomic vapor shows total transparency for probe light incident from one particular direction, but exhibits enhanced Bragg reflection for probe from the opposite side. By changing the relative phase between the coherent lights, this direction can easily be manipulated, providing a convenient way for investigating special properties of -symmetric Bragg structures. PMID:25401544

Chen, Zhongjie; Wang, Haidong; Luo, Bin; Guo, Hong

2014-10-20

116

Vortex-ring-fractal Structure of Atom and Molecule  

SciTech Connect

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

Osmera, Pavel [European Polytechnical Institute Kunovice, Osvobozeni 699, 686 04 Kunovice (Czech Republic)

2010-06-17

117

Control structure design for complete chemical plants Sigurd Skogestad +  

E-print Network

Control structure design for complete chemical plants Sigurd Skogestad + Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway Abstract Control structure design deals with the structural decisions of the control system, including what to control

Skogestad, Sigurd

118

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

SciTech Connect

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

Andreeva, Tamara L; Kuznetsova, S V; Maslov, A I; Sorokin, Vadim N [P.N. Lebedev Physics Institute, Russian Academy of Sciences, Moscow (Russian Federation)

2004-11-30

119

Annual Report 1998: Chemical Structure and Dynamics  

SciTech Connect

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

SD Colson; RS McDowell

1999-05-10

120

Chemical structure and dynamics. Annual report 1994  

SciTech Connect

The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

Colson, S.D.

1995-07-01

121

Atomic and electronic structure of Ni-Nb metallic glasses  

SciTech Connect

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

Yuan, C. C.; Yang, Y.-F., E-mail: yifeng@iphy.ac.cn; Xi, X. K., E-mail: xi@iphy.ac.cn [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

2013-12-07

122

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

123

DNA structures from phosphate chemical shifts  

Microsoft Academic Search

For B-DNA, the strong linear correlation observed by nuclear magnetic resonance (NMR) between the 31P chemical shifts (dP) and three recurrent internucleotide distances demonstrates the tight coupling between phosphate motions and helicoidal parameters. It allows to translate dP into distance restraints directly exploitable in structural refine- ment. It even provides a new method for refining DNA oligomers with restraints exclusively

Josephine Abi-Ghanem; Brahim Heddi; Nicolas Foloppe; Brigitte Hartmann

2010-01-01

124

THE STRUCTURE AND MECHANICS OF ATOMICALLY-THIN GRAPHENE MEMBRANES  

E-print Network

20-850, but showed no reproducibility. In order to produce predictable and reproducible graphene, temperature and electrostatic tensioning. We found that the CVD graphene produces ten- sioned, electricallyTHE STRUCTURE AND MECHANICS OF ATOMICALLY-THIN GRAPHENE MEMBRANES A Dissertation Presented

McEuen, Paul L.

125

Atomic Structure of Intracellular Amorphous Calcium Phosphate Deposits  

Microsoft Academic Search

The radial distribution function calculated from x-ray diffraction of mineralized cytoplasmic structures isolated from the hepatopancreas of the blue crab (Callinectes sapidus) is very similar to that previously found for synthetic amorphous calcium phosphate. Both types of mineral apparently have only short-range atomic order, represented as a neutral ion cluster of about 10 angstrom in longest dimension, whose probable composition

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

1975-01-01

126

Aquaporin water channels - from atomic structure to clinical medicine  

Microsoft Academic Search

The water permeability of biological membranes has been a longstanding problem in physiology, but the proteins responsible for this remained unknown until discovery of the aquaporin 1 (AQP1) water channel protein. AQP1 is selectively permeated by water driven by osmotic gradients. The atomic structure of human AQP1 has recently been defined. Each subunit of the tetramer contains an individual aqueous

Peter Agre; Landon S. King; Masato Yasui; Wm B. Guggino; Ole Petter Ottersen; Yoshinori Fujiyoshi; Andreas Engel; Søren Nielsen

2002-01-01

127

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

128

A Structure Model for Black Holes: Atomic-like Structure, Quantization and the Minimum Schwarzschild Radius  

E-print Network

A structure model for black holes is proposed by mean field approximation of gravity. The model, which consists of a charged singularity at the center and quantum fluctuation of fields around the singularity, is similar to the atomic structure. The model naturally quantizes the black hole. Especially we find the minimum black hole, whose structure is similar to the hydrogen atom and whose Schwarzschild radius becomes about 1.1287 of the Planck length.

Yukinori Nagatani

2005-01-04

129

Atomic structure and electronic properties of c-Si /a-Si:H heterointerfaces  

NASA Astrophysics Data System (ADS)

The atomic structure and electronic properties of crystalline-amorphous interfaces in silicon heterojunction solar cells are investigated by high-resolution transmission electron microscopy, atomic-resolution Z-contrast imaging, and electron energy-loss spectroscopy. With these combined techniques, we directly observe abrupt and flat transition from crystalline Si to hydrogenated amorphous Si at the interface of Si heterojunction solar cells. We find that high-quality hydrogenated amorphous Si layers can be grown abruptly by hot-wire chemical vapor deposition on 200°C (100) Si substrates after a two-step pretreatment of the substrate, comprised of exposure to hot-wire decomposed H2-diluted NH3 followed by atomic H etching.

Yan, Yanfa; Page, M.; Wang, T. H.; Al-Jassim, M. M.; Branz, Howard M.; Wang, Qi

2006-03-01

130

The atomic structure of the bluetongue virus core.  

PubMed

The structure of the core particle of bluetongue virus has been determined by X-ray crystallography at a resolution approaching 3.5 A. This transcriptionally active compartment, 700 A in diameter, represents the largest molecular structure determined in such detail. The atomic structure indicates how approximately 1,000 protein components self-assemble, using both the classical mechanism of quasi-equivalent contacts, which are achieved through triangulation, and a different method, which we term geometrical quasi-equivalence. PMID:9774103

Grimes, J M; Burroughs, J N; Gouet, P; Diprose, J M; Malby, R; Ziéntara, S; Mertens, P P; Stuart, D I

1998-10-01

131

Stable atomic structure of NiTi austenite  

NASA Astrophysics Data System (ADS)

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

Zarkevich, Nikolai A.; Johnson, Duane D.

2014-08-01

132

Atomic disorder and amorphization of B2-structure CoZr by ball milling  

SciTech Connect

For a considerable number of intermetallic compounds it has been found that ball milling introduces atomic (chemical) disorder. Disorder due to milling was demonstrated by x-ray diffraction in AlRu, crystallizing in the B2 structure (ordered b.c.c.) by a decrease of the intensity of superlattice reflections relative to fundamental reflections. The same technique was used to investigate disordering by milling in Ni{sub 3}Al, crystallizing in the L1{sub 2} structure (ordered f.c.c.). In both cases the disorder is anti-site disorder of both components, i.e. both atomic species substitute on the wrong sublattices. Besides x-ray diffraction measurements of magnetic properties turned out to be useful in monitoring structural changes due to milling. The change in the superconducting transition temperature, measured by magnetic a.c. susceptibility, was used to demonstrate atomic disordering by milling in Nb{sub 3}Sn and Nb{sub 3}Au. The type of disorder turned out to be anti-site disorder. Such a type of disorder occurs in the same materials also at high temperatures or after irradiation by neutrons. The disordering was accompanied by an increase of the lattice parameter. An increase in high-field magnetization accompanied by a decrease of the lattice parameter during milling was found in B2 CoGa and B2 CoAl. In principle in the completely ordered state both compounds are non-magnetic, because the CO atoms are shielded from one another by Ga and Al atoms, respectively. However, when a Co atom is transferred to the wrong sublattice, it is surrounded by Co atoms as nearest neighbors and bears a magnetic moment. This explains the strong increase of the magnetization due to milling.

Zhou, G.F.; Bakker, H. [Univ. van Amsterdam (Netherlands). Van der Waals-Zeeman Lab.] [Univ. van Amsterdam (Netherlands). Van der Waals-Zeeman Lab.

1996-01-01

133

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. PMID:18838681

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

2008-01-01

134

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

135

Ab initio nanoplasmonics: The impact of atomic structure  

NASA Astrophysics Data System (ADS)

We present an ab initio study of the hybridization of localized surface plasmons in a metal nanoparticle dimer. The atomic structure, which is often neglected in theoretical studies of quantum nanoplasmonics, has a strong impact on the optical absorption properties when subnanometric gaps between the nanoparticles are considered. We demonstrate that this influences the hybridization of optical resonances of the dimer, and leads to significantly smaller electric field enhancements as compared to the standard jellium model. In addition, we show that the corrugation of the metal surface at a microscopic scale becomes as important as other well-known quantum corrections to the plasmonic response, implying that the atomic structure has to be taken into account to obtain quantitative predictions for realistic nanoplasmonic devices.

Zhang, Pu; Feist, Johannes; Rubio, Angel; García-González, Pablo; García-Vidal, F. J.

2014-10-01

136

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

137

Atomic resolution crystal structure of hydroxynitrile lyase from Hevea brasiliensis.  

PubMed

The X-ray crystal structure of native hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL) has been determined at 1.1 A resolution. It refined to a final R of 11.5% for all data and an Rfree of 14.4%. The favorable data-to-parameter ratio at atomic resolution made the refinement of individual anisotropic displacement parameters possible. The data also allowed a clear distinction of the alternate orientations of all histidine and the majority of asparagine and glutamine side chains. A number of hydrogen atoms, including one on the imidazole of the mechanistically important His-235, became visible as peaks in a difference electron density map. The structure revealed a discretely disordered sidechain of Ser-80, which is part of the putative catalytic triad. Analysis of the anisotropy indicated an increased mobility of residues near the entrance to the active site and within the active site. PMID:10494852

Gruber, K; Gugganig, M; Wagner, U G; Kratky, C

1999-01-01

138

DNA structures from phosphate chemical shifts  

PubMed Central

For B-DNA, the strong linear correlation observed by nuclear magnetic resonance (NMR) between the 31P chemical shifts (?P) and three recurrent internucleotide distances demonstrates the tight coupling between phosphate motions and helicoidal parameters. It allows to translate ?P into distance restraints directly exploitable in structural refinement. It even provides a new method for refining DNA oligomers with restraints exclusively inferred from ?P. Combined with molecular dynamics in explicit solvent, these restraints lead to a structural and dynamical view of the DNA as detailed as that obtained with conventional and more extensive restraints. Tests with the Jun-Fos oligomer show that this ?P-based strategy can provide a simple and straightforward method to capture DNA properties in solution, from routine NMR experiments on unlabeled samples. PMID:19942687

Abi-Ghanem, Josephine; Heddi, Brahim; Foloppe, Nicolas; Hartmann, Brigitte

2010-01-01

139

Magnetism and surface structure of atomically controlled ultrathin metal films  

NASA Astrophysics Data System (ADS)

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, Masahiko; Bader, S. D.

140

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

141

OPTIMIZED SYNTHESIS BY CHEMICAL VAPOR DEPOSITION OF ATOMIC LAYER HEXAGONAL BORON NITRIDE  

E-print Network

also produces high quality h-BN films that are thin, uniform, and continuous. Although h-BN films synthesis of monolayer h-BN films using CVD, which can produce h-BN in large quantities at low costs, hasOPTIMIZED SYNTHESIS BY CHEMICAL VAPOR DEPOSITION OF ATOMIC LAYER HEXAGONAL BORON NITRIDE R. Chen 1

Mellor-Crummey, John

142

Influence of Chemical Modifiers on Ag, Cu, and Si Atomic Absorption Signals  

NASA Astrophysics Data System (ADS)

The influence of tungsten, zirconium, and palladium compounds used as chemical modifiers on the configuration of Ag, Cu, and Si analytical signals was studied. It was suggested that the analyte atomization curve parameters change as a result of matrix effects of the selected modifiers. The prospects of using these modifiers in work with Ag, Cu, and Si were discussed

Kulik, A. N.; Buhay, A. N.; Illiashenko, V. Yu.

2014-03-01

143

Collagen structure deciphered CAMBRIDGE, Mass.--For the first time, an MIT researcher's atom-by-atom study of the  

E-print Network

Collagen structure deciphered CAMBRIDGE, Mass.--For the first time, an MIT researcher's atom-by-atom study of the deformation and fracture of collagen explains Nature's design of its most abundant protein material. It is due to the basis of the collagen structure that leads to its high strength and ability

Buehler, Markus J.

144

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

145

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

Microsoft Academic Search

The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the

T. F. Veremeichik

2006-01-01

146

Atomic structures of multi-walled boron nitride nanohorns.  

PubMed

Boron nitride (BN) nanohorns were synthesized by an arc-melting method, and atomic structure models for BN nanohorns with tetragonal BN rings were proposed from high-resolution electron microscopy and image calculation. Stability and electronic structures of the BN nanohorns were investigated by molecular orbital calculations, comparing with carbon nanohorns. The calculation showed that multi-walled BN nanohorns would be stabilized by the stacking of BN nanohorns. An energy gap of BN nanohorn was calculated to be 0.80 eV, which is lower compared to those of BN clusters and nanotubes. PMID:16157650

Nishiwaki, Atsushi; Oku, Takeo

2005-01-01

147

Structural and morphological characterization of chemically deposited silver films  

NASA Astrophysics Data System (ADS)

Silver thin films were deposited on glass slide substrates at room temperature by the chemical bath deposition (CBD) technique, using silver nitrate (AgNO3) as Ag+1 source and triethanolamine [(N(CH2CH2OH)3)] as the complex reductor agent. We determined the conditions of the CBD process to obtain homogeneous, opaque silver films with good adhesion to the substrate and white coloration. The silver films were studied by X-ray diffraction, scanning electron microscopy, and atomic force microscopy. The results show that the films are composed of several layers with different morphology depending on the deposition time. In all the cases, the crystalline structure of the films was the face cubic centered phase with a moderate [111] texture. Strains and stresses were calculated by the Vook Witt grain interaction model.

Estrada-Raygoza, I. C.; Sotelo-Lerma, M.; Ramírez-Bon, R.

2006-04-01

148

Chemical structures and electrical properties of atomic layer deposited HfO2 thin films grown at an extremely low temperature (?100 °C) using O3 as an oxygen source  

NASA Astrophysics Data System (ADS)

The properties of atomic layer deposited (ALD) HfO2 films grown at low temperatures (?100 °C) were examined for potential applications in flexible display and bioelectronics. A saturated ALD growth behavior was observed even at an extremely low temperature (30 °C) due to the strong oxidizing potential of O3. However, HfO2 films grown at low temperatures showed a low film density and high impurity concentration, because the thermal energy during film growth was insufficient to remove ligands completely from Hf ions in precursor molecule. This resulted in low dielectric constant and high leakage current density of the films. Nevertheless, HfO2 film grown at 100 °C using O3 gas with a high concentration (390 g/Nm3) showed a tolerable impurity concentration with the dielectric constant of ˜16 and breakdown field of ˜4 MV/cm, which are approximately two-thirds of those of HfO2 film grown at 250 °C.

Kim, Jeong Hwan; Park, Tae Joo; Kim, Seong Keun; Cho, Deok-Yong; Jung, Hyung-Suk; Lee, Sang Young; Hwang, Cheol Seong

2014-02-01

149

Comparing quantum-chemical calculation methods for structural investigation of zeolite crystal structures by solid-state NMR spectroscopy.  

PubMed

Combining quantum-chemical calculations and ultrahigh-field NMR measurements of (29)Si chemical shielding (CS) tensors has provided a powerful approach for probing the fine details of zeolite crystal structures. In previous work, the quantum-chemical calculations have been performed on 'molecular fragments' extracted from the zeolite crystal structure using Hartree-Fock methods (as implemented in Gaussian). Using recently acquired ultrahigh-field (29) Si NMR data for the pure silica zeolite ITQ-4, we report the results of calculations using recently developed quantum-chemical calculation methods for periodic crystalline solids (as implemented in CAmbridge Serial Total Energy Package (CASTEP) and compare these calculations to those calculated with Gaussian. Furthermore, in the context of NMR crystallography of zeolites, we report the completion of the NMR crystallography of the zeolite ITQ-4, which was previously solved from NMR data. We compare three options for the 'refinement' of zeolite crystal structures from 'NMR-solved' structures: (i) a simple target-distance based geometry optimization, (ii) refinement of atomic coordinates in which the differences between experimental and calculated (29)Si CS tensors are minimized, and (iii) refinement of atomic coordinates to minimize the total energy of the lattice using CASTEP quantum-chemical calculations. All three refinement approaches give structures that are in remarkably good agreement with the single-crystal X-ray diffraction structure of ITQ-4. PMID:20623826

Brouwer, Darren H; Moudrakovski, Igor L; Darton, Richard J; Morris, Russell E

2010-12-01

150

InChI - the worldwide chemical structure identifier standard  

PubMed Central

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

2013-01-01

151

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

PubMed

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

Berns, Veronica M; Fredrickson, Daniel C

2014-10-01

152

Delta-doping of boron atoms by photoexcited chemical vapor deposition  

SciTech Connect

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

Akazawa, Housei [NTT Microsystem Integration Laboratories, 3-1 Morinosato Wakamiya, Atsugi, Kanagawa 243-0198 (Japan)

2012-03-15

153

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

154

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures  

E-print Network

Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer...

Li, Yunqi; Roy, Ambrish; Zhang, Yang

2009-08-20

155

Structural Transition in Atomic Chains Driven by Transient Doping  

NASA Astrophysics Data System (ADS)

A reversible structural transition is observed on Si(553)-Au by scanning tunneling microscopy, triggered by electrons injected from the tip into the surface. The periodicity of atomic chains near the step edges changes from the 1×3 ground state to a 1×2 excited state with increasing tunneling current. The threshold current for this transition is reduced at lower temperatures. In conjunction with first-principles density-functional calculations it is shown that the 1×2 phase is created by temporary doping of the atom chains. Random telegraph fluctuations between two levels of the tunneling current provide direct access to the dynamics of the phase transition, revealing lifetimes in the millisecond range.

Polei, S.; Snijders, P. C.; Erwin, S. C.; Himpsel, F. J.; Meiwes-Broer, K.-H.; Barke, I.

2013-10-01

156

Quantum structural methods for atoms and molecules 1907 Quantum structural methods for atoms and molecules  

E-print Network

that the electrons move so quickly that they can adjust their motions essentially instantaneously with respect to any the nuclei about once every 10-15 s (the inner-shell electrons move even faster), while the bonds vibrate and molecules Jack Simons B3.1.1 What does quantum chemistry try to do? Electronic structure theory describes

Simons, Jack

157

Atomic-resolution structures of prion AGAAAAGA amyloid fibrils  

E-print Network

To the best of the author's knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, although many experimental studies have shown that this region has amyloid fibril forming properties and plays an important role in prion diseases. In view of this, the present study is devoted to address this problem from computational approaches such as local optimization steepest descent, conjugate gradient, discrete gradient and Newton methods, global optimization simulated annealing and genetic algorithms, canonical dual optimization theory, and structural bioinformatics. The optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils reported in this Chapter have a value to the scientific community in its drive to find treatments for prion diseases or at least be useful for the goals of medicinal chemistry.

Zhang, Jiapu

2011-01-01

158

Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii  

E-print Network

The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the bond lengths are close to the sums of the corresponding atomic covalent radii of carbon, nitrogen, oxygen, hydrogen and phosphorus. Thus, the conventional molecular structures have been resolved here, for the first time, into probable atomic structures.

Raji Heyrovska

2007-08-09

159

Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii  

E-print Network

The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the bond lengths are close to the sums of the corresponding atomic covalent radii of carbon, nitrogen, oxygen, hydrogen and phosphorus. Thus, the conventional molecular structures have been resolved here, for the first time, into probable atomic structures.

Heyrovska, Raji

2007-01-01

160

Formal Nuclear and Atomic Structure of the Elements  

NASA Astrophysics Data System (ADS)

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

Nduka, Amagh

2004-05-01

161

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

PubMed Central

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

2014-01-01

162

Conservation-dissipation structure of chemical reaction systems.  

PubMed

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

Yong, Wen-An

2012-12-01

163

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

164

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

E-print Network

Atomically precise self-assembly of one-dimensional structures on silicon I. Barke, T.K. Ru atomically precise nanostructures at surfaces, particularly nanowires consisting of atom chains; (2) explore the behavior of one-dimensional electrons in atomic chains; (3) find the fundamental limits of data storage

Himpsel, Franz J.

165

Band structure and Fermi surface of atomically uniform lead films  

NASA Astrophysics Data System (ADS)

Atomically uniform lead films are prepared on Si(111)-(7×7) substrates by the molecular beam epitaxy method, and their electronic structures are investigated by high-resolution angle-resolved photoemission spectroscopy and first-principles density functional theory calculations. We have observed the six-fold symmetric Fermi surfaces of Pb/Si(111)-(7×7) films. Their topology and size are almost the same regardless of the difference of film thicknesses (17, 21, 24 and 25 monolayers). The comparison between the measured and calculated thin-film Fermi surfaces suggests that the as-prepared Pb/Si(111)-(7×7) films are dominated by the hexagonal-close-packed stacking films instead of the face-centered-cubic ones. The theoretical calculations also indicate that spin-orbit coupling plays an important role in the band structures and Fermi surface topologies of Pb films.

He, Shaolong; Zeng, Zhenhua; Arita, Masashi; Sawada, Masahiro; Shimada, Kenya; Qiao, Shan; Li, Guoling; Li, Wei-Xue; Zhang, Yan-Feng; Zhang, Yi; Ma, Xucun; Jia, Jinfeng; Xue, Qi-Kun; Namatame, Hirofumi; Taniguchi, Masaki

2010-11-01

166

Correlation between muonic levels and nuclear structure in muonic atoms  

E-print Network

A method that deals with the nucleons and the muon unitedly is employed to investigate the muonic lead, with which the correlation between the muon and nucleus can be studied distinctly. A "kink" appears in the muonic isotope shift at a neutron magic number where the nuclear shell structure plays a key role. This behavior may have very important implications for the experimentally probing the shell structure of the nuclei far away from the $\\beta$-stable line. We investigate the variations of the nuclear structure due to the interaction with the muon in the muonic atom and find that the nuclear structure remains basically unaltered. Therefore, the muon is a clean and reliable probe for studying the nuclear structure. In addition, a correction that the muon-induced slight change in the proton density distribution in turn shifts the muonic levels is investigated. This correction to muonic level is as important as the Lamb shift and high order vacuum polarization correction, but is larger than anomalous magnetic moment and electron shielding correction.

J. M. Dong; W. Zuo; H. F. Zhang; W. Scheid; J. Z. Gu; Y. Z. Wang

2011-11-02

167

Correlation between muonic levels and nuclear structure in muonic atoms  

E-print Network

A method that deals with the nucleons and the muon unitedly is employed to investigate the muonic lead, with which the correlation between the muon and nucleus can be studied distinctly. A "kink" appears in the muonic isotope shift at a neutron magic number where the nuclear shell structure plays a key role. This behavior may have very important implications for the experimentally probing the shell structure of the nuclei far away from the $\\beta$-stable line. We investigate the variations of the nuclear structure due to the interaction with the muon in the muonic atom and find that the nuclear structure remains basically unaltered. Therefore, the muon is a clean and reliable probe for studying the nuclear structure. In addition, a correction that the muon-induced slight change in the proton density distribution in turn shifts the muonic levels is investigated. This correction to muonic level is as important as the Lamb shift and high order vacuum polarization correction, but is larger than anomalous magnetic...

Dong, J M; Zhang, H F; Scheid, W; Gu, J Z; Wang, Y Z; 10.1016/j.physletb.2011.09.057

2011-01-01

168

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

169

Partial Atomic Charge Derivation of small molecule Partial atomic charge is very crucial for computing physical, chemical and biological  

E-print Network

Partial Atomic Charge Derivation of small molecule Partial atomic charge is very crucial of the atomic charge in a given species, it is possible to predict the stability, solvation energetics atomic charges from experiment. Also, there is no universally agreed upon best procedure for computing

Jayaram, Bhyravabotla

170

T~ STRUCTURE OF T~ ATOM Comparison between the classical continuum theory and the  

E-print Network

SERIESI T~ STRUCTURE OF T~ ATOM LECTURE 1 Comparison between the classical continuum theory and the quantum theory- Chief experimentalresults on the structure of the atom - General principles of the quantum theory - Examples. Physics today is everywhere based on the theory of atoms . Through experimental

171

Atomic structure of nanoclusters in oxide-dispersion-strengthened steels  

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

172

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

173

Study of the atomic structure and morphology of the Pt3Co nanocatalyst  

NASA Astrophysics Data System (ADS)

It has been shown that Pt3Co nanoparticles used as a catalyst for cathode of Proton Exchange Membrane Fuel Cells (PEMFC) enhance oxygen reduction reaction (ORR) activity even by a factor of two compared to pure Pt nanoparticles. The local structure and chemical disorder of a commercially available Pt3Co nanocatalyst supported on high surface area carbon were investigated. High-quality XAFS spectra were collected at the ELETTRA synchrotron XAFS 11.1 beamline. XAFS spectra analysis have been performed accounting for the reduction of the coordination number and degeneracy of three-body configurations, resulting from transmission electron microscopy (TEM) and x-ray diffraction (XRD) extracted mean particles diameter, size distribution and expected surface atom contributions. The presence of a Co-Co first neighbour EXAFS signal is shown to be related to the degree of the alloy's chemical disorder. This is a good starting point for analyzing the atomic structure of Pt3Co nanocrystalline system and their changes as a function of alloy preparation or working conditions when they operate as a catalyst in PEMFC.

Greco, G.; Witkowska, A.; Soldo, Y.; Larquet, E.; Menguy, N.; Cognigni, A.; Minicucci, M.; Principi, E.; Di Cicco, A.

2009-11-01

174

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

PubMed Central

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

2014-01-01

175

STRAIN-INDUCED STRUCTURAL CHANGES AND CHEMICAL REACTIONSI. THERMOMECHANICAL AND  

E-print Network

STRAIN-INDUCED STRUCTURAL CHANGES AND CHEMICAL REACTIONSÐI. THERMOMECHANICAL AND KINETIC MODELS V.S.A. (Received 29 December 1997; accepted 29 April 1998) AbstractÐStrain-induced chemical reactions were observed there are possible macroscopic mechanisms of mechanical intensi®cation of the above and other chemical reactions due

Meyers, Marc A.

176

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Structural origins of pH-dependent chemical  

E-print Network

chemical shifts remain too complex for detailed structural analysis, changes in chemical shifts can provide and can often be meaningfully interpreted.7,8 We have there- fore focused on changes in chemical shift and their relationship to structure. pH-dependent changes in chemical shift can provide a lot of informa- tion

Williamson, Mike P.

177

A Chemical Approach to Understanding Oxide Surface Structure and Reactivity  

NASA Astrophysics Data System (ADS)

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

Enterkin, James Andrew

178

Polarization from aligned atoms as a diagnostics of circumstellar, AGN and interstellar magnetic fields: II. Atoms with Hyperfine Structure  

E-print Network

We show that atomic alignment presents a reliable way to study topology of astrophysical magnetic fields. The effect of atomic alignment arises from modulation of the relative population of the sublevels of atomic ground state pumped by anisotropic radiation flux. As such aligned atoms precess in the external magnetic field and this affects the properties of the polarized radiation arising from both scattering and absorption by the atoms. As the result the polarizations of emission and absorption lines depend on the 3D geometry of the magnetic field as well as the direction and anisotropy of incident radiation. We consider a subset of astrophysically important atoms with hyperfine structure. For emission lines we obtain the dependencies of the direction of linear polarization on the directions of magnetic field and the incident pumping radiation. For absorption lines we establish when the polarization is perpendicular and parallel to magnetic field. For both emission and absorption lines we find the dependence on the degree of polarization on the 3D geometry of magnetic field. We claim that atomic alignment provides a unique tool to study magnetic fields in circumstellar regions, AGN, interplanetary and interstellar medium. This tool allows studying of 3D topology of magnetic fields and establish other important astrophysical parameters. We consider polarization arising from both atoms in the steady state and also as they undergo individual scattering of photons. We exemplify the utility of atomic alignment for studies of astrophysical magnetic fields by considering a case of Na alignment in a comet wake.

Huirong Yan; A. Lazarian

2006-11-09

179

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. PMID:23248746

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

2012-01-01

180

The Nuclear Physics of Hyperfine Structure in Hydrogenic Atoms  

E-print Network

The theory of QED corrections to hyperfine structure in light hydrogenic atoms and ions has recently advanced to the point that the uncertainty of these corrections is much smaller than 1 part per million (ppm), while the experiments are even more accurate. The difference of the experimental results and the corresponding QED theory is due to nuclear effects, which are primarily the result of the finite nuclear charge and magnetization distributions. This difference varies from tens to hundreds of ppm. We have calculated the dominant nuclear component of the 1s hyperfine interval for deuterium, tritium and singly ionized helium, using a unified approach with modern second-generation potentials. The calculated nuclear corrections are within 3% of the experimental values for deuterium and tritium, but are roughly 20% discrepant for helium. The nuclear corrections for the trinucleon systems can be qualitatively understood by invoking SU(4) symmetry.

J. L. Friar; G. L. Payne

2005-02-01

181

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

182

The atomic structure of niobium and tantalum containing borophosphate glasses  

NASA Astrophysics Data System (ADS)

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

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

2009-09-01

183

The atomic structure of niobium and tantalum containing borophosphate glasses.  

PubMed

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

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

2009-09-16

184

First Optical Hyperfine Structure Measurement in an Atomic Anion  

SciTech Connect

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

Fischer, A.; Canali, C.; Warring, U.; Kellerbauer, A.; Fritzsche, S. [Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, 69117 Heidelberg (Germany); GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Planckstrasse 1, 64291 Darmstadt (Germany)

2010-02-19

185

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils  

E-print Network

To date, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins, although many experimental studies have shown that this region has amyloid fibril forming properties. This region belongs to the N-terminal unstructured region (1-123) of prions, the structure of which has proved hard to determine using NMR or X-ray crystallography. Computational optimization approaches, however, allow us to obtain a description of prion 113-120 peptide at a microscopic level. Zhang (J. Mol. Model., 2010, DOI: 10.1007/s00894-010-0691-y) using the traditional local optimization search steepest descent and conjugate gradient methods hybridized with the standard global optimization search simulated annealing method successfully constructed three atomic-resolution structures of prion AGAAAAGA amyloid fibrils. Zhang pointed out, basing on the NNQNTF peptide of elk prion 173--178 (3FVA.pdb released on 30-JUN-2009 in the Protein Data Bank), new models for prion AGAAAAG...

Zhang, Jiapu

2010-01-01

186

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

187

Key ingredients of the alkali atom - metal surface interaction: Chemical bonding versus spectral properties  

NASA Astrophysics Data System (ADS)

The interaction of alkali atoms with metal surfaces is reviewed. The peculiar electronic configuration of such atoms, with only one valence electron participating in the bond formation, suggested simple pictures to describe their interaction with a metal surface. But it was early evident that the adsorption properties depend on many aspects, related to the electronic structure of constituents, leading, for example, to different degrees of ionicity/covalency of the alkali atom-metal bond. Sophisticated theoretical modeling tried to shed light on this aspect. The spectral properties are the ultimate features in determining how the systems interact with each other. In this review the electronic and spectral properties are discussed focusing on different theoretical representations of the physical system and on their consequences. Surface projected energy gaps of the substrate as well as the substrate continuous spectrum are key aspects in determining the nature of the interaction and bonding with alkali adsorbates.

Trioni, M. I.; Achilli, S.; Chulkov, E. V.

2013-05-01

188

Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures  

E-print Network

We propose and analyze a scheme to interface individual neutral atoms with nanoscale solid-state systems. The interface is enabled by optically trapping the atom via the strong near-field generated by a sharp metallic ...

Chang, D. E.

189

Using Machine Learning to Accelerate Complex Atomic Structure Elucidation  

NASA Astrophysics Data System (ADS)

Workers in various scientific disciplines seek to develop chemical models for extended and molecular systems. The modeling process revolves around the gradual refinement of model assumptions, through comparison of experimental and computational results. Solid state Nuclear Magnetic Resonance (NMR) is one such experimental technique, providing great insight into chemical order over Angstrom length scales. However, interpretation of spectra for complex materials is difficult, often requiring intensive simulations. Similarly, working forward from the model in order to produce experimental quantities via ab initio is computationally demanding. The work involved in these two significant steps, compounded by the need to iterate back and forth, drastically slows the discovery process for new materials. There is thus great motivation for the derivation of structural models directly from complex experimental data, the subject of this work. Using solid state NMR experimental datasets, in conjunction with ab initio calculations of measurable NMR parameters, a network of machine learning kernels are trained to rapidly yield structural details, on the basis of input NMR spectra. Results for an environmentally relevant material will be presented, and directions for future work.

Brouwer, William; Calderin, Lazaro; Sofo, Jorge

2012-02-01

190

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

SciTech Connect

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

Veremeichik, T. F. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)], E-mail: tomver@online.ru

2006-07-15

191

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures  

PubMed Central

CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity. PMID:21214931

2011-01-01

192

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

193

Temperature Dependence in Atom-Surface Scattering Chemical Physics Department, Weizmann Institute of Science, 76100 Rehovoth, Israel  

E-print Network

Temperature Dependence in Atom-Surface Scattering Eli Pollak Chemical Physics Department, Weizmann measure of the temperature dependence of energy resolved atom-surface scattering spectra measured under conditions of higher translational energies, larger surface temperatures and partic- ularly for heavier mass

Manson, Joseph R.

194

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

Microsoft Academic Search

The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization\\u000a of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates\\u000a the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the

T. F. Vereme?chik

2006-01-01

195

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

SciTech Connect

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

Drummond, T.J.

1998-12-22

196

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

PubMed

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. PMID:23206110

Kuznetsov, V; Papastavrou, G

2012-11-01

197

Effect of nonequilibrium chemical reactions on the concentration distribution of alkali atoms in the boundary layer  

SciTech Connect

The distribution of alkali metal atoms (potassium) in the boundary layer of combustion products in a laboratory setup with a Mekker burner was studied. It was found that the experimentally determined and computed concentrations are in good agreement with one another and substantially exceed the values corresponding to the limiting cases of both equilibrium and frozen chemical reactions. A qualitative explanation of this effect, which, generally speaking, can occur in large-scale setups, is given based on an analysis of the computational results.

Benilov, M.S.; Vasil'eva, I.A.; Kovbasyuk, V.I.; Kosov, V.F.; Kosova, R.V.; Rogov, B.V.; Sinel'shchikov, V.A.; Sokolova, I.A.; Tirskii, G.A.

1986-05-01

198

Trapping and manipulation of isolated atoms using nanoscale plasmonic structures  

E-print Network

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

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

2009-05-22

199

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

200

GIAO DFT 13C/15N chemical shifts in regioisomeric structure determination of fused pyrazoles.  

PubMed

The combined use of two-dimensional NMR correlation experiments and gauge including atomic orbital density functional theory in (13)C NMR chemical shift (CS) calculations allowed reliable and simple structural determination of regioisomeric heterocyclic systems that originate from the reactions of acylquinolinones with substituted hydrazines. Moreover, the results of differential analysis between the calculated (15)N NMR CSs for hypothetical structures and the experimental data of the title azaheterocyclic systems were even more advantageous with respect to (13)C because there was no need for correlational analysis: structures of the regioisomeric compounds could be determined just by direct comparison. PMID:20589725

Chimichi, Stefano; Boccalini, Marco; Matteucci, Alessandra; Kharlamov, Sergey V; Latypov, Shamil K; Sinyashin, Oleg G

2010-08-01

201

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

202

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?g mL(-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

203

Measurement of fluorine atom concentrations and reaction rates in chemical laser systems  

Microsoft Academic Search

The line positions of all three components of the fluorine atom ground state fine structure transition have been measured by diode laser absorption spectroscopy, using a water vapor pure rotational line at 404.077\\/cm as a wavelength reference. These results imply a spin orbit splitting for fluorine of 404.142 + or - 0.005\\/cm. The results for the line positions are in

A. C. Stanton; J. C. Wormhoudt; J. W. Duff

1982-01-01

204

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

ERIC Educational Resources Information Center

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

Inner London Education Authority (England).

205

221A Lecture Notes Fine and Hyperfine Structures of the Hydrogen Atom  

E-print Network

221A Lecture Notes Fine and Hyperfine Structures of the Hydrogen Atom 1 Introduction With the usual Hamiltonian for the hydrogen-like atom (in the Gaussian unit), H0 = p2 2m - Ze2 r , (1) we have the n2 -fold that the electron in the hydrogen atom is non- relativistic, v c, but not that slow. The expectation value

Murayama, Hitoshi

206

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

207

Atomic-scale kinetic Monte Carlo simulations of diamond chemical vapor deposition  

NASA Astrophysics Data System (ADS)

Diamond's superb mechanical, thermal, optical, and electronic properties are ideally suited for use in protective coatings, thermal management components, cold cathode emitters, and high-performance electronic devices, among others. Diamond can be chemically vapor deposited (CVD) to produce coatings and thin films, but this technique is currently expensive and difficult to control, and the details of the molecular processes that lead to diamond deposition remain unclear. The goal of this work is to construct a tool by which the nano-scale processes that lead to diamond growth, and their effects on film properties, can be examined. This is accomplished through the development of a kinetic Monte Carlo simulation method that treats diamond deposition on the atomic length scale using established chemical reaction rate data as input, while addressing deposition time scales that correspond directly to real growth experiments. The impact of the atomic-scale surface reaction processes on the growth kinetics, surface morphologies, and defect densities of single crystal CVD diamond are examined. In this way, a clearer understanding of the connection between atomic-scale deposition processes and CVD diamond film properties can be obtained. The growth kinetics and surface morphologies that develop during deposition are found to depend primarily on the details of the atomic surface features and their effects on bonding during deposition. The (110) and (111) surfaces facet under certain growth conditions. The (100) surface grows fastest and roughens, in contradiction to experimental observations. This can be rectified by the introduction of a mechanism for the preferential etching of monatomic islands on (100) facets, whereby the simulations predict slow-growing smooth (100) faces in accord with experimental observations. The trapping of H atoms is enhanced at higher substrate temperatures where the flux of larger Csb2Hsb2 molecules to the surface is high. Incorporation of spsp2 defects is highest for high-CHsb4 feeds which generate less H, since H is required to convert sp2-bonded C on the surface to spsp3-bonded material. Vacancy incorporation is not substantial. The ratio of simulated growth rate to defect concentration is maximized around 800-950sp°C and 1% inlet CHsb4, for which experiments also produce the best quality CVD diamond.

Battaile, Corbett Chandler

208

Dehydration of phenylboronic acid to boroxine catalyzed by Au(n) nanoclusters with atom packing core-shell structure.  

PubMed

Atomically precise Au(n) nanoclusters (n = number of gold atom in cluster) ideally composed of an exact number of gold atoms have unique core-shell structure and non-metallic electronic properties. The extremely small size of Au25 and Au38 nanoclusters induces a large energy gap in their electronic structures, which gives rise to unprecedented catalytic activity in some chemical reactions. Here we report dehydration of phenylboronic acid to boroxine with small Au25 and Au38 nanocluster catalysts, respectively. Especially, Au25 nanocluster is arranged with Au13 icosahedral core capped by twelve gold atoms as an exterior shell. Au38 nanocluster is a face-fused biicosahedral Au23 core encapsulated by a shell comprised of fifteen gold atoms. Au38 nanoclusters exhibit higher activity than Au25 nanoclusters. This study is an attempt to provide a powerful tool for the catalyst design and to gain a further insight into the correlation of structural properties with catalytic properties. PMID:23901534

Huang, Ping; Jiang, Zhi; Chen, Guoxiang; Zhu, Yan; Sun, Yuhan

2013-07-01

209

Revealing electronic structure in atomically-engineered manganite thin films  

NASA Astrophysics Data System (ADS)

Semiconductor technology is based on tuning the properties of devices by manipulating thin films and interfaces. Recently, this approach has been extended to complex oxides, where quantum many-body interactions give rise to emergent ground states not present in the parent materials. Rationally controlling and engineering correlated electronic phases has the potential to revolutionize modern electronics, but is hindered by the inability of current theory to account for the effects of many-body interactions on the underlying electronic structure. Manganites provide a particularly model system for studying many-body effects due to their complex electronic and magnetic phase diagrams, which give rise to many potentially useful properties. Despite extensive work on manganite films demonstrating numerous electronic phase transitions, little is directly known about how the electronic structure responds to the 'control parameters' accessible in thin films. This dissertation presents direct measurements of the electronic structure in La1-- xSrxMnO3 based thin films and interfaces through several phase transitions using a unique integrated oxide molecular-beam epitaxy and angle-resolved photoemission spectroscopy system. We observe the full Fermi surface and near-EF electronic structure of the ferromagnetic and A-type antiferromagnetic metallic phases, reconciling first-principles calculations with experiment for the first time. Furthermore, our results provide key insights into the polaronic nature of the metallic charge carriers. We then explore the mechanism underlying the insulating ground state for La2/3Sr1/3MnO3 under strong tensile strain. Our measurements rule out the scenarios of bandwidth or localization-driven metal-insulator transitions, and reveal an instability of the strongly interacting metal towards an ordered insulating phase that can be accessed through epitaxial strain. By next studying atomically precise interfaces in (LaMnO3)2n/(SrMnO 3)n superlattices, we directly see how the interplay between dimensionality and strong many-body interactions drives large period superlattices into a pseudogapped insulating phase. Our results provide new insights into the physics of perovskite manganites, and illustrate in detail the nature and importance of phase competition in controlling the electronic properties of correlated thin films. These results should be applicable to correlated materials in general, and can help develop predictive models capable of realizing the full potential of oxide electronics.

Monkman, Eric Justin

210

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

NASA Astrophysics Data System (ADS)

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

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

2008-04-01

211

Modeling chemical flame structure and combustion dynamics in LES  

Microsoft Academic Search

In turbulent premixed combustion, the instantaneous flame thickness is typically thinner that the grid size usually retained in Large Eddy Simulations (LES), requiring adapted models. Two alternatives to couple chemical databases with LES balance equations, the Thickened Flame (TFLES) and the Filtered Tabulated Chemistry (F-TACLES) models, are investigated here and compared in terms of chemical flame structure and dynamics. To

P. Auzillon; B. Fiorina; R. Vicquelin; N. Darabiha; O. Gicquel; D. Veynante

2011-01-01

212

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

213

The Carbon Atom Model and the Structure of Diamond  

Microsoft Academic Search

Electron orbits in the neutral carbon atom.-The atomic model of carbon used is assumed to have four 21 orbits. The dimensions of these orbits are computed by a method outlined in a previous paper using various assumptions as to screening, viz.: (a) spherical distribution of charge about the nucleus; (b) orientation in orbital planes with random phase relations; (c) orientation

R. B. Lindsay

1927-01-01

214

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

215

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

216

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...

217

The B-spline R-matrix method for atomic processes: application to atomic structure, electron collisions and photoionization  

NASA Astrophysics Data System (ADS)

The basic ideas of the B-spline R-matrix (BSR) approach are reviewed, and the use of the method is illustrated with a variety of applications to atomic structure, electron-atom collisions and photo-induced processes. Special emphasis is placed on complex, open-shell targets, for which the method has proven very successful in reproducing, for example, a wealth of near-threshold resonance structures. Recent extensions to a fully relativistic framework and intermediate energies have allowed for an accurate treatment of heavy targets as well as a fully nonperturbative scheme for electron-impact ionization. Finally, field-free BSR Hamiltonian and electric dipole matrices can be employed in the time-dependent treatment of intense short-pulse laser-atom interactions.

Zatsarinny, Oleg; Bartschat, Klaus

2013-06-01

218

Structural biology: Origins of chemical biodefence  

Microsoft Academic Search

The idea that complex biological systems can evolve through a series of simple, random events is not universally accepted. The structure of a vital immune protein shows how such evolution can occur at a molecular level.

Robert Liddington; Laurie Bankston

2005-01-01

219

Atomic and electronic structures of interfaces in dye-sensitized, nanostructured solar cells.  

PubMed

Key processes in nanostructured dye-sensitized solar cells occur at material interfaces containing, for example, oxides, dye molecules, and hole conductors. A detailed understanding of interfacial properties is therefore important for new developments and device optimization. The implementation of X-ray-based spectroscopic methods for atomic-level understanding of such properties is reviewed. Specifically, the use of the chemical and element sensitivity of photoelectron spectroscopy, hard X-ray photoelectron spectroscopy, and resonant photoelectron spectroscopy for investigating interfacial molecular and electronic properties are described; examples include energy matching, binding configurations, and molecular orbital composition. Finally, results from the complete oxide/dye/hole-conductor systems are shown and demonstrate how the assembly itself can affect the molecular and electronic structure of the materials. PMID:24692317

Johansson, Erik M J; Lindblad, Rebecka; Siegbahn, Hans; Hagfeldt, Anders; Rensmo, Håkan

2014-04-14

220

Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis.  

PubMed

Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins. PMID:18524775

Schmidt, Andrea; Gruber, Karl; Kratky, Christoph; Lamzin, Victor S

2008-08-01

221

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

SciTech Connect

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

Paesler, M.; Sayers, D.

1988-12-01

222

Structural transformations in chemically modified graphene  

NASA Astrophysics Data System (ADS)

In this article, we review our efforts to continuously tune mechanical and thermal properties in multilayer chemically modified graphene (CMG) films. An alteration of the graphene lattice by functional groups, by defects created during reduction, or by defect re-crystallization is used to control CMG mechanical and thermal properties. We attribute a notable increase in Young's modulus and film strength to an emerging network of sp2-sp3 crosslinks established between graphene layers. Control over the film stress and strength enabled us to dramatically improve the performance of radio frequency CMG resonators by fine tuning the fabrication process.

Robinson, Jeremy T.; Zalalutdinov, Maxim K.; Junkermeier, Chad E.; Culbertson, James C.; Reinecke, Thomas L.; Stine, Rory; Sheehan, Paul E.; Houston, Brian H.; Snow, Eric S.

2012-11-01

223

Atomic and electronic structure of acetic acid on Ge(100) Do Hwan Kim a,b  

E-print Network

Atomic and electronic structure of acetic acid on Ge(100) Do Hwan Kim a,b , Eunkyung Hwang to investigate the atomic and electronic structure of acetic acid adsorbed on Ge(100) surface. Due to its acidity, acetic acid dissociates and the resulting electron-rich acetate group reacts with the electron

Kim, Sehun

224

Fabrication of nano-structural arrays by channeling pulsed atomic beams through an intensity-modulated  

E-print Network

Fabrication of nano-structural arrays by channeling pulsed atomic beams through an intensity-dimensional nano-structure arrays by passing a pulsed atomic beam through an intensity-modulated continuous of ``cooling'' along the longitudinal direction. This enables fabrication of vertically heterogeneous nano

Zhu, Xiangdong

225

Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii  

Microsoft Academic Search

The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the

Raji Heyrovska

2007-01-01

226

Structural study of Al-1. 4 at pct Fe powder produced by atomization  

SciTech Connect

The Al[sub 1-x]Fe[sub x] alloys with small Fe content which have been studied in the past decades were mainly obtained by rapid solidification. These techniques noticeably increase the solubility of iron solute in the f.c.c. aluminium matrix, thereby reducing the formation of intermetallic compounds: depending on the quenching rate, the iron atoms may associate into clusters. It follows that the solid solution structure may look different from an ideally disordered one. For low rates of solidification, intermetallic compounds are formed and they modify the workability and chemical properties of the material. The small angle X-ray scattering technique would appear to be the most suitable to study the Fe dispersion. However, it seems that the electronic density of the obtained species is very close to that of Al so that no recent developments over the last years have been performed on this subject by that technique. Moessbauer Spectroscopy has not been extensively used to specify the various expected entities. An analysis of the microstructure of atomized powder has been carried out by electronic microscopy for an Al-4 at Pct Fe composition with powder particle size in the range lower than 50 [mu]m. Even if the structures were carefully studied versus the particle diameter, no information was elicited about the Fe distribution in the Al matrix. In the present work, results are given from X-ray diffraction, X-ray photoelectron spectrometry and Moessbauer Spectroscopy about the various iron combinations found in an Al-1.4 at Pct Fe powder prepared by atomization in air from the liquid alloy.

Djega-Meriadassou, C.; Chekroud, S.; Cizeron, G. (Univ. Paris Sud, Orsay (France))

1993-08-15

227

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

228

Precision physics of simple atoms: QED tests, nuclear structure and fundamental constants  

E-print Network

Quantum electrodynamics is the first successful and still the most successful quantum field theory. Simple atoms, being essentially QED systems, allow highly accurate theoretical predictions. Because of their simple spectra, such atoms have been also efficiently studied experimentally frequently offering the most precisely measured quantities. Our review is devoted to comparison of theory and experiment in the field of precision physics of light simple atoms. In particular, we consider the Lamb shift in the hydrogen atom, the hyperfine structure in hydrogen, deuterium, helium-3 ion, muonium and positronium, as well as a number of other transitions in positronium. Additionally to a spectrum of unperturbed atoms, we consider annihilation decay of positronium and the g factor of bound particles in various two-body atoms. Special attention is paid to the uncertainty of the QED calculations due to the uncalculated higher-order corrections and effects of the nuclear structure. We also discuss applications of simple atoms to determination of several fundamental constants.

Savely G. Karshenboim

2005-09-01

229

A neural network structure for prediction of chemical agent fate  

NASA Astrophysics Data System (ADS)

This work presents the development of a multi-input, multi-output neural network structure to predict the time dependent concentration of chemical agents as they participate in chemical reaction with environmental substrates or moisture content within these substrates. The neural network prediction is based on a computationally or experimentally produced database that includes the concentration of all chemicals presents (reactants and products) as a function of the chemical agent droplet size, wind speed, temperature, and turbulence. The utilization of this prediction structure is made userfriendly via an easy-to-use graphical user interface. Furthermore, upon the knowledge of the time-varying environmental parameters (wind speed and temperature that are usually recorded and available), the time varying concentration of all chemicals can be predicted almost instantaneously by recalling the previously trained network. The network prediction was compared with actual open air test data and the results were found to match.

Navaz, H. K.; Kehtarnavaz, N.; Jovic, Zoran

2014-05-01

230

Static and Dynamic Structural Modeling Analysis of Atomic Force Microscope  

NASA Astrophysics Data System (ADS)

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

Zhang, Yin; Murphy, Kevin D.

231

Atomic Ordering in Self-assembled Epitaxial and Endotaxial Compound and Element Semiconductor Quantum Dot Structures: The First Review  

E-print Network

Atomic Ordering in Self-assembled Epitaxial and Endotaxial Compound and Element Semiconductor alloy quantum dots, the suggestion is made that atomically ordered quantum dots which are grown superior long term structural stability. Such atomically ordered quantum dots should, therefore

Moeck, Peter

232

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

SciTech Connect

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

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

1984-01-01

233

Smallest Nanoelectronic with Atomic Devices with Precise Structures  

NASA Technical Reports Server (NTRS)

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

Yamada, Toshishige

2000-01-01

234

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

SciTech Connect

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

Nilsson, A.; Wassdahl, N.; Weinelt, M. [Uppsala Univ. (Sweden)] [and others

1997-04-01

235

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

236

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

237

Atomic hydrogen-induced chemical vapor deposition of aSi:C:H thin-film materials from alkylsilane precursors  

Microsoft Academic Search

Amorphous hydrogenated silicon-carbon films (a-Si:C:H) were produced by atomic hydrogen-induced chemical vapor deposition (CVD) using hexamethyldisilane (HMDS) and tetrakis(trimethylsilyl)silane (TMSS) as a single-source compounds. The CVD process has been examined in terms of the mechanism of the activation step. The susceptibility of particular bonds in the source compounds towards reaction with atomic hydrogen is characterized. The effect of substrate temperature

A. M. Wróbel; S. Wickramanayaka; Y. Nakanishi; Y. Hatanaka; S. Paw?owski; W. Olejniczak

1997-01-01

238

Chemically-selective imaging of brain structures with CARS microscopy  

E-print Network

Chemically-selective imaging of brain structures with CARS microscopy Conor L. Evans1§ , Xiaoyin Xu anti-Stokes Raman scattering (CARS) microscopy to image brain structure and pathology ex vivo. Although. Definitive diagnosis still requires brain biopsy in a significant number of cases. CARS microscopy

Xie, Xiaoliang Sunney

239

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

PubMed

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

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

2012-10-19

240

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. PMID:23025278

Andujar-De Sanctis, Ivonne L.

2012-01-01

241

Miniature photoacoustic chemical sensor using microelectromechanical structures  

NASA Astrophysics Data System (ADS)

Photoacoustic spectroscopy is a useful monitoring technique that is well suited for trace gas detection. The technique also possesses favorable detection characteristics when the system dimensions are scaled to a micro-system design. The objective of present work is to incorporate two strengths of the Army Research Laboratory (ARL), piezoelectric microelectromechanical systems (MEMS) and chemical and biological sensing into a monolithic MEMS photoacoustic trace gas sensor. A miniaturized macro-cell design was studied as a means to examine performance and design issues as the photoacoustics is scaled to a dimension approaching the MEMS level. Performance of the macro-cell was tested using standard organo-phosphate nerve gas simulants, Dimethyl methyl phosphonate (DMMP) and Diisoprpyl methyl phosphonate (DIMP). Current MEMS work centered on fabrication of a multi-layer cell subsystem to be incorporated in the full photoacoustic device. Preliminary results were very positive for the macro-cell sensitivity (ppb levels) and specificity indicating that the scaled cell maintains sensitivity. Several bonding schemes for a three-dimension MEMS photoacoustic cavity were investigated with initial results of a low temperature AuSn bond proving most feasible.

Pellegrino, Paul M.; Polcawich, Ronald G.; Firebaugh, Samara L.

2004-08-01

242

Chemical composition in relation with biomass ash structure  

NASA Astrophysics Data System (ADS)

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

Holubcik, Michal; Jandacka, Jozef

2014-08-01

243

Report on the Tenerife Workshop on Uncertainties in Atomic Data and How They Propagate in Chemical Abundances  

NASA Astrophysics Data System (ADS)

In 2010, we organised a workshop in Tenerife with the aim of bringing together scientists concerned with the completeness and accuracy of atomic data for astrophysical applications. Participants included atomic physicists, theoretical astrophysicists and astronomers, and the workshop covered topics such as the evaluation of uncertainties in atomic data, the propagation of such uncertainties in chemical abundances, and the feedback between observations and calculations. Communication issues were also discussed, including questions such as: How can it be ensured that atomic data are correctly understood and used? Which forum is the best one for a fluid interaction between all communities involved in the production and use of atomic data? This contribution lays out the main issues raised during the workshop and some of the solutions proposed.

Luridiana, Valentina; García-Rojas, Jorge

2012-08-01

244

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

245

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

246

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

NASA Astrophysics Data System (ADS)

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.

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

2013-11-01

247

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

SciTech Connect

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

Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: stella.offner@yale.edu [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)

2013-06-10

248

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

PubMed Central

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

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

2013-01-01

249

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

PubMed

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

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

2014-11-10

250

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

PubMed Central

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

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

2014-01-01

251

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

NASA Astrophysics Data System (ADS)

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

Heyrovska, Raji; Narayan, Sara

2009-04-01

252

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

253

Atomic Structure Schrdinger equation has approximate solutions for multi-  

E-print Network

in the previous noble gas ! outer electrons: after that highest energy levels ! valence electrons: same as outer of the following electron configurations represent an atom in an excited state. Identify the element and write its) Si or P I or Se? Practice Problems Sample 8.6. Using condensed electron configurations, write

Zakarian, Armen

254

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

PubMed Central

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.; Bednarcik, J.; Gao, Y. L.; Zhai, Q. J.; Mattern, N.; Eckert, J.

2014-01-01

255

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

NASA Astrophysics Data System (ADS)

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.

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

2014-01-01

256

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

257

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. PMID:23618056

2013-01-01

258

Atomic Structures of all the Twenty Essential Amino Acids and a Tripeptide, with Bond Lengths as Sums of Atomic Covalent Radii  

E-print Network

Recently, the bond lengths of the molecular components of nucleic acids and of caffeine and related molecules were shown to be sums of the appropriate covalent radii of the adjacent atoms. Thus, each atom was shown to have its specific contribution to the bond length. This enabled establishing their atomic structures for the first time. In this work, the known bond lengths for amino acids and the peptide bond are similarly shown to be sums of the atomic covalent radii. Based on this result, the atomic structures of all the twenty essential amino acids and a tripeptide have been presented.

Raji Heyrovska

2008-04-15

259

Magneto-structural relationships for radical cation and neutral pyridinophane structures with intrabridgehead nitrogen atoms. An integrated experimental and quantum mechanical study.  

PubMed

An integrated experimental and computational approach was used to compare the properties of representative molecules containing intrabridgehead nitrogen atoms with those of the corresponding radical cations issuing from one-electron oxidation with the aim of unraveling the characteristics of the three-electron sigma-bonds formed in the open-shell species. From a quantitative point of view, last-generation density functional methods coupled with proper basis sets and, when needed, continuum models for describing bulk solvent effects confirm their reliability for the computation of structures and magnetic properties of organic free radicals. From an interpretative point of view, different hybridizations of nitrogen atoms tuned by their chemical environment lead to markedly different magnetic properties that represent reliable and sensitive probes of structural and electronic characteristics. PMID:19507811

Williams, Ffrancon; Chen, Guo-Fei; Mattar, Saba M; Scudder, Paul H; Trieber, Dwight A; Saven, Jeffery G; Whritenour, David C; Cimino, Paola; Barone, Vincenzo

2009-07-01

260

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

ERIC Educational Resources Information Center

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

Park, Eun Jung; Light, Gregory

2009-01-01

261

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

262

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

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

263

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. PMID:23928998

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

2013-01-01

264

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

PubMed

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

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

2013-01-01

265

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

266

The atomic structure of extended defects in GaN  

SciTech Connect

GaN layers contain large densities (10{sup 10} cm{sup {minus}2}) of threading dislocations, nanopipes, (0001) and {l_brace}11{bar 2}0{r_brace} stacking faults, and {l_brace}10{bar 1}0{r_brace} inversion domains. Three configurations have been found for pure edge dislocations, mainly inside high angle grain boundaries where the 4 atom ring cores can be stabilized. Two atomic configurations, related by a 1/6<10{bar 1}0>stair rod dislocation, have been observed for the {l_brace}11{bar 2}0{r_brace} stacking fault in (Ga-Al)N layers. For the {l_brace}10{bar 1}0{r_brace} inversion domain boundaries, a configuration corresponding to the Holt model was observed, as well as another with no N-N or Ga-Ga bonds.

Ruterana, P.; Nouet, G.

2000-07-01

267

Atomic structure calculations for F-like tungsten  

NASA Astrophysics Data System (ADS)

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

Sunny, Aggarwal

2014-09-01

268

Characterization of chemically and enzymatically treated hemp fibres using atomic force microscopy and spectroscopy  

NASA Astrophysics Data System (ADS)

The mechanical and moisture resistance properties of natural fibre reinforced composites are dependent on the adhesion between the matrix of choice and the fibre. The main goal of this study was to investigate the effect of NaOH swelling of hemp fibres prior to enzymatic treatment and a novel chemical sulfonic acid method on the physical properties of hemp fibres. The colloidal properties of treated hemp fibres were studied exclusively using an atomic force microscope. AFM imaging in tapping mode revealed that each treatment rendered the surface topography of the hemp fibres clean and exposed the individual fibre bundles. Hemp fibres treated with laccase had no effect on the surface adhesion forces measured. Interestingly, mercerization prior to xylanase + cellulase and laccase treatments resulted in greater enzyme access evident in the increased adhesion force measurements. Hemp fibres treated with sulfonic acid showed an increase in surface de-fibrillation and smoothness. A decrease in adhesion forces for 4-aminotoulene-3-sulfonic acid (AT3S) treated fibres suggested a reduction in surface polarity. This work demonstrated that AFM can be used as a tool to estimate the surface forces and roughness for modified fibres and that enzymatic coupled with chemical methods can be used to improve the surface properties of natural fibres for composite applications. Further, this work is one of the first that offers some insight into the effect of mercerization prior to enzymes and the effect on the surface topography. AFM will be used to selectively screen treated fibres for composite applications based on the adhesion forces associated with the colloidal interface between the AFM tip and the fibre surfaces.

George, Michael; Mussone, Paolo G.; Abboud, Zeinab; Bressler, David C.

2014-09-01

269

Laser-Induced Continuum Structure and Third Harmonic Generation in - and Two-Valence Atoms.  

NASA Astrophysics Data System (ADS)

A model for calculating third harmonic generation (THG) in a near-resonantly coupled 4-level atomic system in the presence of laser-induced continuum structure (LICS) is formulated in terms of the time dependent density matrix elements which can be obtained by solving the time dependent density matrix equations for the atomic system interacting with laser pulses. The theory is applied to a single-valence -electron atom, sodium, as well as to a two-valence-electron atom, calcium. Analysis of the existing experimental data in sodium is given applying our theoretical model. It is found that the spatio-temporal overlap of the two laser pulses is a very sensitive factor for the experimental observation. Calculations of atomic parameters for a two -valence-electron atom (calcium) using multiconfiguration Hartree-Fock method with finite B spline basis is also presented. (Copies available exclusively from Micrographics Department, Doheny Library, USC, Los Angeles, CA 90089 -0182.).

Zhang, Jian

1991-05-01

270

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

271

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

SciTech Connect

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

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

1997-04-01

272

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

PubMed

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

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

2011-02-01

273

Comparative study of chemical modifiers for the determination of molybdenum in milk by electrothermal atomisation atomic absorption spectrometry.  

PubMed

A comparative study of various chemical modifiers for the determination of molybdenum in milk by electrothermal atomisation atomic absorption spectrometry was carried out. Methods with nitric acid or barium difluoride as the chemical modifier and in the absence of a chemical modifier were studied by introducing the milk samples directly into the graphite furnace with octyl alcohol. The graphite furnace programme, amount of modifier and the calibration and additions graphs were studied in all instances. The characteristic masses were 17.82, 18.64 and 12.08 pg of molybdenum in the absence of a chemical modifier and with nitric acid or barium difluoride as the chemical modifier, respectively. The precision, accuracy and interferences of the method were also investigated. PMID:2168685

Bermejo-Barrera, P; Calvo, C P; Bermejo-Martinez, F

1990-05-01

274

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

275

Atomic structure of silicene nanoribbons on Ag(110)  

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

276

Unexpected Symmetry in the Nodal Structure of the He Atom  

SciTech Connect

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

Bressanini, Dario [Dipartimento di Scienze Chimiche e Ambientali, Universita dell'Insubria, via Lucini 3, 22100 Como (Italy); Reynolds, Peter J. [Physics Division, Army Research Office, Research Triangle Park, North Carolina 27709 (United States)

2005-09-09

277

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

PubMed Central

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

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

2008-01-01

278

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

279

Influences of halogen atoms on indole-3-acetonitrile (IAN): Crystal structure and Hirshfeld surfaces analysis  

NASA Astrophysics Data System (ADS)

Crystal structural investigations and Hirshfeld surface analysis of three halogen atoms (4-Cl, 6-Cl and 4-Br) substituted indole-3-acetonitrile (IAN) were reported in this work. The structures of the present three compounds were characterized by Infrared spectra, Elemental analyses, NMR spectra, differential scanning calorimetry (DSC), thermogravimetric analyses (TGA) and hot stage microscopy (HSM). The Hirshfeld surfaces analysis in terms of crystal structure, intermolecular interactions and ?⋯? stacking motifs were performed. We found that the different kinds of halogen atoms and the different substituted positions have a significant effect on the crystal structures, molecular ?⋯? stacking motifs, melting points, and the nature of intermolecular interactions for IANs.

Luo, Yang-Hui; Yang, Li-Jing; Han, Guangjun; Liu, Qing-Ling; Wang, Wei; Ling, Yang; Sun, Bai-Wang

2014-11-01

280

Controlling atomic structures and photoabsorption processes by an infrared laser  

SciTech Connect

We propose a theoretical method to calculate the infrared (IR) laser-assisted photoabsorption cross sections over a broad energy range by a single calculation. In this method we define an initial wave function as the product of the dipole operator and the atomic ground state, propagate the initial wave function in the IR laser field with different initial phases, then calculate the generalized autocorrelation function, which is defined as the averaged value of the autocorrelation function over the initial phase from 0 to 2{pi} (or one IR optical cycle). The IR laser-assisted photoabsorption cross sections are obtained by the Fourier transform of the generalized autocorrelation function. We apply this method to study the IR laser-assisted photoabsorption of He atoms. From the simulation results, we see that the IR laser field affects not only the resonant position but also the lifetime or the width of the bound states. This photoabsorption cross section is an important quantity to analyze the IR-laser-assisted dynamical processes by an attosecond pulse, a pulse train, or a free-electron laser.

Tong, X. M. [Institute of Materials Science, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573 (Japan); Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 (Japan); Toshima, N. [Institute of Materials Science, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573 (Japan)

2010-06-15

281

Nuclear Corrections to Hyperfine Structure in Light Hydrogenic Atoms  

E-print Network

Hyperfine intervals in light hydrogenic atoms and ions are among the most accurately measured quantities in physics. The theory of QED corrections has recently advanced to the point that uncalculated terms for hydrogenic atoms and ions are probably smaller than 0.1 parts per million (ppm), and the experiments are even more accurate. The difference of the experiments and QED theory is interpreted as the effect on the hyperfine interaction of the (finite) nuclear charge and magnetization distributions, and this difference varies from tens to hundreds of ppm. We have calculated the dominant component of the 1s hyperfine interval for deuterium, tritium and singly ionized helium, using modern second-generation potentials to compute the nuclear component of the hyperfine splitting for the deuteron and the trinucleon systems. The calculated nuclear corrections are within 3% of the experimental values for deuterium and tritium, but are about 20% discrepant for singly ionized helium. The nuclear corrections for the trinucleon systems can be qualitatively understood by invoking SU(4) symmetry.

J. L. Friar; G. L. Payne

2005-04-04

282

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

283

Semiflexible polymer rings on topographically and chemically structured surfaces  

E-print Network

We investigate morphologies of semiflexible polymer rings, such as circular DNA, which are adsorbed onto topographically or chemically structured substrate surfaces. We classify all equilibrium morphologies for two striped surface structures, (i) topographical surface grooves and (ii) chemically structured surface domains. For both types of stripes, we find four equilibrium shapes: a round toroidal and a confined elongated shape as well as two shapes containing bulges. We determine the complete bifurcation diagram of these morphologies as a function of their contour length and the ratio of adhesive strength to bending rigidity. For more complex geometries consisting of several stripes we find a cascade of transitions between elongated shapes. Finally, we compare our findings to ring condensation by attractive interactions.

Petra Gutjahr; Reinhard Lipowsky; Jan Kierfeld

2014-05-25

284

Functionalization of BN honeycomb structure by adsorption and substitution of foreign atoms  

NASA Astrophysics Data System (ADS)

We carried out first-principles calculations within density-functional theory to investigate the structural, electronic, and magnetic properties of boron-nitride (BN) honeycomb structure functionalized by adatom adsorption, as well as by the substitution of foreign atoms for B and N atoms. For periodic high-density coverage, most of 3d transition metal atoms and some of group 3A, 4A, and 6A elements are adsorbed with significant binding energy and modify the electronic structure of bare BN monolayer. While bare BN monolayer is nonmagnetic, wide band-gap semiconductor, at high coverage of specific adatoms it can achieve magnetic metallic, even half-metallic ground states. At low coverage, the bands associated with adsorbed atoms are flat and the band structure of parent BN is not affected significantly. Therefore, adatoms and substitution of foreign atoms at low coverage are taken to be the representative of impurity atoms yielding localized states in the band gap and resonance states in the band continua. Notably, the substitution of C for B and N yield donorlike and acceptorlike magnetic states in the band gap. Localized impurity states occurring in the gap give rise to interesting properties for electronic and optical application of the single-layer BN honeycomb structure.

Ataca, C.; Ciraci, S.

2010-10-01

285

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

286

Structure activity relationships to assess new chemicals under TSCA  

SciTech Connect

Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

1990-12-31

287

Chemical Bonding and Electronic Structure of Buckminsterfullerene As is well-known C60 resembles an American soccerball, containing 12 pentagons and  

E-print Network

with one of the adjacent carbon atoms. To summarize, each carbon forms three q-bonds with its Sp2 hybrid than one correct Lewis structure. C60 is such a molecule and, as a matter of fact, it has 12Chemical Bonding and Electronic Structure of Buckminsterfullerene As is well-known C60 resembles

Rioux, Frank

288

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

289

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

PubMed

Materials with reduced dimensionality have attracted much interest in various fields of fundamental and applied science. True one-dimensional (1D) crystals with single-atom thickness have been realized only for few elemental metals (Au, Ag) or carbon, all of which showed very short lifetimes under ambient conditions. We demonstrate here a successful synthesis of stable 1D ionic crystals in which two chemical elements, one being a cation and the other an anion, align alternately inside carbon nanotubes. Unusual dynamical behaviours for different atoms in the 1D lattice are experimentally corroborated and suggest substantial interactions of the atoms with the nanotube sheath. Our theoretical studies indicate that the 1D ionic crystals have optical properties distinct from those of their bulk counterparts and that the properties can be engineered by introducing atomic defects into the chains. PMID:25218060

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

2014-11-01

290

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

291

Structural and chemical properties of gold rare earth disilicide core-shell nanowires.  

PubMed

Clear understanding of the relationship between electronic structure and chemical activity will aid in the rational design of nanocatalysts. Core-shell Au-coated dysprosium and yttrium disilicide nanowires provide a model atomic scale system to understand how charges that transfer across interfaces affect other electronic properties and in turn surface activities toward adsorbates. Scanning tunneling microscopy data demonstrate self-organized growth of Au-coated DySi? nanowires with a nanometer feature size on Si(001), and Kelvin probe force microscopy data measure a reduction of work function that is explained in terms of charge transfer. Density functional theory calculations predict the preferential adsorption site and segregation path of Au adatoms on Si(001) and YSi?. The chemical properties of Au-YSi? nanowires are then discussed in light of charge density, density of states, and adsorption energy of CO molecules. PMID:21142188

Ouyang, Wenjie; Shinde, Aniketa; Zhang, Yanning; Cao, Juxian; Ragan, Regina; Wu, Ruqian

2011-01-25

292

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

293

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. PMID:20877495

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

2010-01-01

294

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. PMID:18754631

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

2009-01-01

295

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

NASA Astrophysics Data System (ADS)

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

Ünlü, Pervin

2010-07-01

296

Evolution of atomic collision cascades in vanadium crystal with internal structure  

NASA Astrophysics Data System (ADS)

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

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

2009-11-01

297

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

SciTech Connect

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

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

2008-06-30

298

Chemical identification of point defects and adsorbates on a metal oxide surface by atomic force microscopy  

Microsoft Academic Search

Atomic force microscopy in the non-contact mode (nc-AFM) can provide atom-resolved images of the surface of, in principle, any material independent of its conductivity. Due to the complex mechanisms involved in the contrast formation in nc-AFM imaging, it is, however, far from trivial to identify individual surface atoms or adsorbates from AFM images. In this work, we successfully demonstrate how

Jeppe V. Lauritsen; Adam S. Foster; Georg H. Olesen; Mona C. Christensen; Angelika Kühnle; Stig Helveg; Jens R. Rostrup-Nielsen; Bjerne S. Clausen; Michael Reichling; Flemming Besenbacher

2006-01-01

299

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

PubMed Central

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

1999-01-01

300

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

301

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

SciTech Connect

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.

Debela, T. T. [Zhejiang University; Wang, X. D. [Zhejiang University; Cao, Q. P. [Zhejiang University; Zhang, D. X. [Zhejiang University; Wang, S. Y. [Fudan University; Wang, Cai-Zhuang [Ames Laboratory; Jiang, J. Z. [Zhejiang University

2013-12-12

302

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

PubMed Central

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

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

1996-01-01

303

Atomic Resolution Structures of Rieske Iron-Sulfur Protein: Role of Hydrogen Bonds in Tuning  

E-print Network

Structure Article Atomic Resolution Structures of Rieske Iron-Sulfur Protein: Role of Hydrogen, Urbana, IL 61801, USA 3 Northwestern University Center for Synchrotron Research, Life Sciences a molecular frame- work for understanding the role hydrogen bonds to the cluster play in tuning thermody

Crofts, Antony R.

304

Atomic and electronic structure of styrene on Ge(100) Do Hwan Kim a  

E-print Network

Atomic and electronic structure of styrene on Ge(100) Do Hwan Kim a , Yun Jeong Hwang b , Junga: Styrene Ge(100) Adsorption DFT calculations STM Coverage-dependent adsorption structures of styrene favorable configuration at room temperature is that the two styrene molecules are bound to two Ge dimers

Kim, Sehun

305

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

SciTech Connect

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

Browning, N.D.; McGibbon, M.M.; McGibbon, A.J.; 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

1994-03-01

306

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation  

E-print Network

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP, we show that the entropy compo- nent of our free energy estimates can be useful in distinguishing

Langmead, Christopher James

307

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation  

E-print Network

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP, we show that the entropy component of our free energy estimates can useful in distinguishing native

Langmead, Christopher James

308

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief  

E-print Network

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation H Detection, Free Energy, Probabilistic Graphical Models #12;Abstract We present a technique for approximating the free energy of protein structures using Generalized Belief Propagation (GBP). The accuracy and utility

Langmead, Christopher James

309

Atomic-scale Structural Characterizations of Functional Epitaxial Thin Films  

E-print Network

................................................................ 10 1.3.1 Superconducting FeSe0.5Te0.5 epitaxial films........................................ 10 1.3.2 YBa2Cu3O7-x(YBCO) epitaxial thin films and flux-pinning effects ...... 14 1.3.3 Perovskite oxide epitaxial thin films... ...................................... 22 Figure 1.9. (a) Schematic illustration of ABO3 perovskite structure. (b) The corner -sharing oxygen octahedra in perovskite structure. . ................................... 23 Figure 1.10. (a) A HRTEM micrograph,67 (b) a Cs-corrected HRTEM image...

Zhu, Yuanyuan

2013-06-03

310

Atomic Force Microscopy Investigation of Vaccinia Virus Structure?  

PubMed Central

Vaccinia virus was treated in a controlled manner with various combinations of nonionic detergents, reducing agents, and proteolytic enzymes, and successive products of the reactions were visualized using atomic force microscopy (AFM). Following removal of the outer lipid/protein membrane, a layer 20 to 40 nm in thickness was encountered that was composed of fibrous elements which, under reducing conditions, rapidly decomposed into individual monomers on the substrate. Beneath this layer was the virus core and its prominent lateral bodies, which could be dissociated or degraded with proteases. The core, in addition to the lateral bodies, was composed of a thick, multilayered shell of proteins of diverse sizes and shapes. The shell, which was readily etched with proteases, was thoroughly permeated with pores, or channels. Prolonged exposure to proteases and reductants produced disgorgement of the viral DNA from the remainders of the cores and also left residual, flattened, protease-resistant sacs on the imaging substrate. The DNA was readily visualized by AFM, which revealed some regions to be “soldered” by proteins, others to be heavily complexed with protein, and yet other parts to apparently exist as bundled, naked DNA. Prolonged exposure to proteases deproteinized the DNA, leaving masses of extended, free DNA. Estimates of the interior core volume suggest moderate but not extreme compaction of the genome. PMID:18508898

Kuznetsov, Y.; Gershon, P. D.; McPherson, A.

2008-01-01

311

Mechanism of pulse discharge production of iodine atoms from CF3I molecules for a chemical oxygen-iodine laser  

NASA Astrophysics Data System (ADS)

The pulsed chemical oxygen-iodine laser (COIL) development is aimed at many new applications. Pulsed electric discharge is most effective in turning COIL operation into the pulse mode by instant production of iodine atoms. A numerical model is developed for simulations of the pulsed COIL initiated by an electric discharge. The model comprises a system of kinetic equations for neutral and charged species, electric circuit equation, gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are found by solving the electron Boltzmann equation, which is re-calculated in a course of computations when plasma parameters changed. The processes accounted for in the Boltzmann equation include excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions, second-kind collisions and stepwise excitation of molecules. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. Results of numerical simulations are compared with experimental laser pulse waveforms. It is concluded that there is satisfactory agreement between theory and the experiment. The prevailing mechanism of iodine atom formation from the CF3I donor in a very complex kinetic system of the COIL medium under pulse discharge conditions, based on their detailed numerical modelling and by comparing these results both with experimental results of other authors and their own experiments, is established. The dominant iodine atom production mechanism for conditions under study is the electron-impact dissociation of CF3I molecules. It was proved that in the conditions of the experiment the secondary chemical reactions with O atoms play an insignificant role.

Kochetov, I. V.; Napartovich, A. P.; Vagin, N. P.; Yuryshev, N. N.

2009-03-01

312

Chemical and structural properties of polymorphous silicon thin films grown from dichlorosilane  

NASA Astrophysics Data System (ADS)

We have examined the effects of hydrogen dilution (RH) and deposition pressure on the morphological, structural and chemical properties of polymorphous silicon thin films (pm-Si:H), using dichlorosilane as silicon precursor in the plasma enhanced chemical vapor deposition (PECVD) process. The use of silicon chlorinated precursors enhances the crystallization process in as grown pm-Si:H samples, obtaining crystalline fractions from Raman spectra in the range of 65-95%. Atomic Force Microscopy results show the morphological differences obtained when the chlorine chemistry dominates the growth process and when the plasma-surface interactions become more prominent. Augmenting RH causes a considerable reduction in both roughness and topography, demonstrating an enhancement of ion bombardment and attack of the growing surface. X-ray Photoelectron Spectroscopy results show that, after ambient exposure, there is low concentration of oxygen inside the films grown at low RH, present in the form of SiO, which can be considered as structural defects. Instead, oxidation increases with deposition pressure and dilution, along with film porosity, generating a secondary SiOx phase. For higher pressure and dilution, the amount of chlorine incorporated to the film decreases congruently with HCl chlorine extraction processes involving atomic hydrogen interactions with the surface. In all cases, weak silicon hydride (SiH) bonds were not detected by infrared spectroscopy, while bonding configurations associated to the silicon nanocrystal surface were clearly observed. Since these films are generally used in photovoltaic devices, analyzing their chemical and structural properties such as oxygen incorporation to the films, along with chlorine and hydrogen, is fundamental in order to understand and optimize their electrical and optical properties.

Álvarez-Macías, C.; Monroy, B. M.; Huerta, L.; Canseco-Martínez, M. A.; Picquart, M.; Santoyo-Salazar, J.; Sánchez, M. F. García; Santana, G.

2013-11-01

313

Measurements of chemical species in flame at temperatures above 2000°C — X-ray atomic absorption spectroscopy  

Microsoft Academic Search

XANES spectra of chemical species in high temperature flame were measured for the first time utilizing apparatus of atomic absorption spectroscopy and synchrotron radiation. Metal nitrate solution [1 M] was introduced into an air-acetylene flame (ca. 2000°C) through nebulizer. Small monochromated X-ray beam was passed through the flame so that its XANES spectra were successfully measured in fluorescence mode. XANES

Izumi Nakai; Yasuko Terada; Masaharu Nomura; Tetsuo Uchida

1995-01-01

314

Electronic structure of Eu atomic wires encapsulated inside single-wall carbon nanotubes  

NASA Astrophysics Data System (ADS)

X-ray absorption (resonant) photoelectron spectroscopy has been employed to investigate electronic structure of Eu atomic wires encapsulated in single-wall carbon nanotubes (SWCNTs). The measurements reveal that there is a substantial electron transfer of +1.79 ± 0.11 from a Eu atom to the surrounding SWCNT. The shape of the observed Fermi edge is different from that of a three-dimensional metal, suggesting that electrons in this one-dimensional system form a Tomonaga-Luttinger liquid.

Nakanishi, Ryo; Kitaura, Ryo; Ayala, Paola; Shiozawa, Hidetsugu; de Blauwe, Kathrin; Hoffmann, Patrick; Choi, Daeheon; Miyata, Yasumitsu; Pichler, Thomas; Shinohara, Hisanori

2012-09-01

315

How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.  

SciTech Connect

Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

Friesner, Richard A.(Columbia University) [Columbia University; Baik, Mu-Hyun (Columbia University) [Columbia University; Gherman, Benjamin F.(Columbia University) [Columbia University; Guallar, Victor (Washington University) [Washington University; Wirstam, Maria E.(1836) [1836; Murphy, Robert B.(Schrodinger Inc) [Schrodinger Inc; Lippard, Stephen J.(Massachusetts Institute of Technology) [Massachusetts Institute of Technology

2003-03-01

316

Quantitative Structure-Properties Relationship Study of the 29Si-NMR Chemical Shifts of Some Silicate Species  

Microsoft Academic Search

In this work, the quantitative structure–properties relationship (QSPR) was applied to modeling and predicting the Si-NMR chemical shifts of a series of silicate species (on Q sites). The descriptors that were selected by stepwise multiple linear regression technique were square of alpha polarizability, Moran autocorrelation–lag3\\/unweighted by atomic Sanderson electronegativities, square of asphericity, and topological path\\/walk 2-Randic shape index. These descriptors

Nasser Goudarzi; M. H. Fatemi; A. Samadi-Maybodi

2009-01-01

317

Atomic Physics  

NSDL National Science Digital Library

This collection provides a basic introduction to Atomic Physics. It reviews the building blocks of atomic structure, explores atomic isotopes, explains Einstein's famous equation E = mc2, and introduces the various types of radiation.

Griffith, Christopher

318

Analysis of Atomic and Electronic Structures of Cu2ZnSnS4 Based on First-Principle Calculation  

Microsoft Academic Search

Atomic and electronic structures of Cu2ZnSnS4 (CZTS) are discussed on the basis of the first-principle pseudopotential method. CZTS is usually assumed to have the stannite or kesterite structure, but one can consider three other structures under the condition that a S atom is bonded to two Cu, one Zn, and one Sn atom. For each of the five structures, the

Masaya Ichimura; Yuki Nakashima

2009-01-01

319

Characterization of asphaltene structure using atomic force microscopy.  

PubMed

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

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

2008-09-01

320

Femtosecond electrons probing currents and atomic structure in nanomaterials  

NASA Astrophysics Data System (ADS)

The investigation of ultrafast electronic and structural dynamics in low-dimensional systems such as nanowires and two-dimensional materials requires femtosecond probes providing high spatial resolution and strong interaction with small volume samples. Low-energy electrons exhibit large scattering cross-sections and high sensitivity to electric fields, but their pronounced dispersion during propagation in vacuum so far prevented their use as femtosecond probe pulses in time-resolved experiments. Here, employing a laser-triggered point-like source of either divergent or collimated electron wave packets, we developed a hybrid approach for femtosecond point projection microscopy and femtosecond low-energy electron diffraction. We investigate ultrafast electric currents in nanowires with sub-100 femtosecond temporal and few 10?nm spatial resolutions, and demonstrate the potential of our approach for studying structural dynamics in crystalline single-layer materials.

Müller, Melanie; Paarmann, Alexander; Ernstorfer, Ralph

2014-10-01

321

Femtosecond electrons probing currents and atomic structure in nanomaterials.  

PubMed

The investigation of ultrafast electronic and structural dynamics in low-dimensional systems such as nanowires and two-dimensional materials requires femtosecond probes providing high spatial resolution and strong interaction with small volume samples. Low-energy electrons exhibit large scattering cross-sections and high sensitivity to electric fields, but their pronounced dispersion during propagation in vacuum so far prevented their use as femtosecond probe pulses in time-resolved experiments. Here, employing a laser-triggered point-like source of either divergent or collimated electron wave packets, we developed a hybrid approach for femtosecond point projection microscopy and femtosecond low-energy electron diffraction. We investigate ultrafast electric currents in nanowires with sub-100 femtosecond temporal and few 10?nm spatial resolutions, and demonstrate the potential of our approach for studying structural dynamics in crystalline single-layer materials. PMID:25358554

Müller, Melanie; Paarmann, Alexander; Ernstorfer, Ralph

2014-01-01

322

Functional Nano-Structures Using Atomic Layer Deposition  

E-print Network

with the help of numerous people, and thanks to the finanical support provided by the UK Engineering and Physical Sciences Research Council and Trinity College. I would like to start by thanking my supervisor Prof. Dr. Ullrich Steiner for giving me... are not well- adapted for the fabrication of complicated, for example three-dimensional, structures. Recently bottom-up fabrication protocols have been developed which overcome the problems outline above. In general these protocols rely on self-assembly, which...

Salgård Cunha, Pedro

2014-05-27

323

Organohelium compounds: structures, stabilities and chemical bonding analyses.  

PubMed

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

Fourré, Isabelle; Alvarez, Elsa; Chaquin, Patrick

2014-02-24

324

Structures of quasi-freestanding ultra-thin silicon films deposited on chemically inert surfaces  

NASA Astrophysics Data System (ADS)

Silicon thin films were deposited on a sapphire and a highly oriented pyrolytic graphite (HOPG), which have atomically flat and chemically inert surfaces. The electronic and geometrical structures of the films were analyzed by X-ray photoelectron spectroscopy (XPS) and polarization-dependent X-ray absorption fine structure (XAFS). It was found that the silicon K-edge XAFS spectra for ultra-thin silicon films thinner than 0.2 monolayer exhibited two distinct resonance peaks which were not observed for bulk silicon. The peaks were assigned to the resonance excitations from the Si 1s into the valence unoccupied orbitals with ?? and ?? characters. The average tilted angle of the ?? orbitals was determined by the polarization dependencies of the peak intensities. It was demonstrated that direction of a part of the ?? orbitals in silicon film is perpendicular to the surface. These results support the existence of quasi-freestanding single-layered silicon films with sp2 configuration.

Baba, Y.; Shimoyama, I.; Hirao, N.; Sekiguchi, T.

2014-11-01

325

Hydrogen Atoms under Magnification: Direct Observation of the Nodal Structure of Stark States  

NASA Astrophysics Data System (ADS)

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

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

2013-05-01

326

The atomic structure of the $\\sqrt{3} \\times \\sqrt{3}$ phase of silicene on Ag(111)  

E-print Network

The growth of the $\\sqrt{3} \\times \\sqrt{3}$ reconstructed silicene on Ag substrate has been frequently observed in experiments while its atomic structure and formation mechanism is poorly understood. Here by first-principles calculations we show that $\\sqrt{3} \\times \\sqrt{3}$ reconstructed silicene is constituted by dumbbell units of Si atoms arranged in a honeycomb pattern. Our model shows excellent agreement with the experimentally reported lattice constant and STM image. We propose a new mechanism for explaining the spontaneous and consequential formation of $\\sqrt{3} \\times \\sqrt{3}$ structures from $3 \\times 3$ structures on Ag substrate. We show that the $\\sqrt{3} \\times \\sqrt{3}$ reconstruction is mainly determined by the interaction between Si atoms and have weak influence from Ag substrate. The proposed mechanism opens the path to understanding of multilayer silicon.

Cahangirov, Seymur; Xian, Lede; Avila, Jose; Cho, Suyeon; Asensio, María C; Ciraci, Salim; Rubio, Angel

2014-01-01

327

Atomic structure of the ?3 ×?3 phase of silicene on Ag(111)  

NASA Astrophysics Data System (ADS)

The growth of the ?3 ×?3 reconstructed silicene on Ag substrate has been frequently observed in experiments while its atomic structure and formation mechanism is poorly understood. Here, by first-principles calculations, we show that ?3 ×?3 reconstructed silicene is constituted by dumbbell units of Si atoms arranged in a honeycomb pattern. Our model shows excellent agreement with the experimentally reported lattice constant and STM image. We propose a new mechanism for explaining the spontaneous and consequential formation of ?3 ×?3 structures from 3×3 structures on Ag substrate. We show that the ?3 ×?3 reconstruction is mainly determined by the interaction between Si atoms and have weak influence from Ag substrate. The proposed mechanism opens the path to understanding of multilayer silicon.

Cahangirov, Seymur; Özçelik, Veli Ongun; Xian, Lede; Avila, Jose; Cho, Suyeon; Asensio, María C.; Ciraci, Salim; Rubio, Angel

2014-07-01

328

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

NASA Astrophysics Data System (ADS)

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

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

1997-03-01

329

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

330

Probing atomic structure in magnetic core\\/shell nanoparticles using synchrotron radiation  

Microsoft Academic Search

Core\\/shell Fe\\/Cu and Fe\\/Au nanoparticles were prepared directly by deposition from the gas phase. A detailed study of the atomic structure in both the cores and shells of the nanoparticles was undertaken by means of extended absorption fine structure (EXAFS) measurements. For Fe\\/Cu nanoparticles, a Cu shell ~ 20 monolayers thick appears similar in structure to bulk Cu and is

S. H. Baker; M. Roy; S. C. Thornton; M. Qureshi; C. Binns

2010-01-01

331

Tiny-Scale Atomic Structure and the Cold Neutral Medium--Review and Recap  

E-print Network

Almost a decade ago I wrote an article with the same title as this. It focused on the physical properties of the Tiny-Scale Atomic Structure (TSAS) as discrete structures of the Cold Neutral Medium (CNM). To be observable, tiny discrete structures that don't grossly violate pressure equilibrium need two attributes: low temperatures and geometrical anisotropy. Here I update that article. I discuss thermal and pressure equilibrium, ionization, optical lines, H_2 abundance, and evaporation.

Carl Heiles

2007-01-22

332

Hydrogen Atom and Time Variation of Fine-Structure Constant  

E-print Network

In this paper, we have solved the de Sitter special relativistic ($\\mathcal{SR}_{cR}$-) Dirac equation of hydrogen in the earth-QSO(quasar) framework reference by means of the adiabatic approach. The aspects of geometry effects of de Sitter space-time described by Beltrami metric are explored and taken into account. It is found that the $\\mathcal{SR}_{cR}$-Dirac equation of hydrogen is a time dependent quantum Hamiltonian system. We provide an explicit calculation to justify the adiabatic approach in dealing with this time-dependent system. Since the radius of de Sitter sphere $R$ is cosmologically large, the evolution of the system is very slow so that the adiabatic approximation legitimately works with high accuracy. We conclude that the electromagnetic fine-structure constant, the electron mass and the Planck constant are time variations. This prediction of fine-structure constant is consistent with the presently available observation data. For confirming it further, experiments/observations are required.

Mu-Lin Yan

2009-09-26

333

Chemical and physical structures of proteinoids and related polyamino acids  

NASA Astrophysics Data System (ADS)

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

Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

334

The effect of different chemical agents on human enamel: an atomic force and scanning electron microscopy study  

NASA Astrophysics Data System (ADS)

PURPOSE: The goal of our study was to investigate the changes in enamel surface roughess induced by the application of different chemical substances by atomic force microscopy and scanning electron microscopy. METHOD: Five sound human first upper premolar teeth were chosen for the study. The buccal surface of each tooth was treated with a different chemical agent as follows: Sample 1 - 38% phosphoric acid etching (30s) , sample 2 - no surface treatment (control sample), 3 - bleaching with 37.5 % hydrogen peroxide (according to the manufacturer's instructions), 4 - conditioning with a self-etching primer (15 s), 5 - 9.6 % hydrofluoric acid etching (30s). All samples were investigated by atomic force microscopy in a non-contact mode and by scanning electron microscopy. Several images were obtained for each sample, showing evident differences regarding enamel surface morphology. The mean surface roughness and the mean square roughness were calculated and compared. RESULTS: All chemical substances led to an increased surface roughness. Phosphoric acid led to the highest roughness while the control sample showed the lowest. Hydrofluoric acid also led to an increase in surface roughness but its effects have yet to be investigated due to its potential toxicity. CONCLUSIONS: By treating the human enamel with the above mentioned chemical compounds a negative microretentive surface is obtained, with a morphology depending on the applied substance.

Rominu, Roxana O.; Rominu, Mihai; Negrutiu, Meda Lavinia; Sinescu, Cosmin; Pop, Daniela; Petrescu, Emanuela

2010-12-01

335

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

336

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. PMID:18957132

Makino, Yoshihide; Itoh, Nobuya

2008-01-01

337

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

338

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

E-print Network

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 ...

Griffin, Robert Guy

339

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

340

Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process  

PubMed Central

Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate's application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein.

Lee, H. V.; Hamid, S. B. A.; Zain, S. K.

2014-01-01

341

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

342

Importance of the structural zinc atom for the stability of yeast alcohol dehydrogenase.  

PubMed Central

Yeast alcohol dehydrogenase is a tetrameric enzyme containing zinc. Initially we confirmed the presence of two zinc atoms per subunit. Incubation of the enzyme with increasing concentrations of dithiothreitol, a method for partial chelation, allowed first the reduction of four disulphide bridges per enzyme, but eventually was sufficient to chelate the structural zinc atom without having any effect on the zinc located in the active site. The enzyme activity was not affected but the enzyme became very sensitive to heat denaturation. Chelation by EDTA was also performed. Given its location at an external position in the globular protein, protected in each subunit by one disulphide bridge, the results establish that the second zinc atom present on each enzymic subunit plays a prominent conformational role, probably by stabilizing the tertiary structure of yeast alcohol dehydrogenase. Recovery experiments were performed by incubation of the native enzyme, or the dithiothreitol-treated enzyme, with a small amount of Zn2+. A stabilization effect was found when the structural zinc was re-incorporated after its removal by dithiothreitol. In all cases a large increase in activity was also observed, which was much greater than that expected based on the amount of re-incorporated zinc atom, suggesting the re-activation of some inactive commercial enzyme which had lost some of its original catalytic zinc atoms. PMID:1445195

Magonet, E; Hayen, P; Delforge, D; Delaive, E; Remacle, J

1992-01-01

343

Extraction of chemical structures and reactions from the literature  

E-print Network

................................................................................................................................ 193 Appendix C ................................................................................................................................ 194 XIII Glossary AST = Abstract Syntax Tree CAS = Chemical Abstracts Service ChEBI = Chemical...

Lowe, Daniel Mark

2012-10-09

344

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

PubMed

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

Wong, Keith T; Lewis, Nathan S

2014-10-21

345

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

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

346

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

347

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

SciTech Connect

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

Huang, L.; Zingaro, R.A.; Meyers, E.A. (Texas A and M Univ., College Station, TX (United States). Dept. of Chemistry); Nair, P.K.; Nair, M.T.S. (Univ. Nacional Autonoma de Mexico, Morelos (Mexico). Lab. de Energia Solar)

1994-09-01

348

Privileged Structures: Efficient Chemical "Navigators" toward Unexplored Biologically Relevant Chemical Spaces.  

PubMed

In the search for new therapeutic agents for currently incurable diseases, attention has turned to traditionally "undruggable" targets, and collections of drug-like small molecules with high diversity and quality have become a prerequisite for new breakthroughs. To generate such collections, the diversity-oriented synthesis (DOS) strategy was developed, which aims to populate new chemical space with drug-like compounds containing a high degree of molecular diversity. The resulting DOS-derived libraries have been of great value for the discovery of various bioactive small molecules and therapeutic agents, and thus DOS has emerged as an essential tool in chemical biology and drug discovery. However, the key challenge has become how to design and synthesize drug-like small-molecule libraries with improved biological relevancy as well as maximum molecular diversity. This Perspective presents the development of privileged substructure-based DOS (pDOS), an efficient strategy for the construction of polyheterocyclic compound libraries with high biological relevancy. We envisioned the specific interaction of drug-like small molecules with certain biopolymers via the incorporation of privileged substructures into polyheterocyclic core skeletons. The importance of privileged substructures such as benzopyran, pyrimidine, and oxopiperazine in rigid skeletons was clearly demonstrated through the discovery of bioactive small molecules and the subsequent identification of appropriate target biomolecule using a method called "fluorescence difference in two-dimensional gel electrophoresis". Focusing on examples of pDOS-derived bioactive compounds with exceptional specificity, we discuss the capability of privileged structures to serve as chemical "navigators" toward biologically relevant chemical spaces. We also provide an outlook on chemical biology research and drug discovery using biologically relevant compound libraries constructed by pDOS, biology-oriented synthesis, or natural product-inspired DOS. PMID:25310802

Kim, Jonghoon; Kim, Heejun; Park, Seung Bum

2014-10-22

349

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

350

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

NASA Astrophysics Data System (ADS)

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

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

1992-07-01

351

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

NASA Astrophysics Data System (ADS)

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

Han, Ming

2000-10-01

352

J. Phys. Chem. 1995, 99, 15557-15564 15557 Confined Clusters of Rare Gas Atoms: Structures and Phases  

E-print Network

J. Phys. Chem. 1995, 99, 15557-15564 15557 Confined Clusters of Rare Gas Atoms: Structures Classical-mechanicalisoenergetic molecular dynamics simulations model Xe atoms and XeN clusters trapped in a cage of atomic dimensions, a homogeneous spherical cavity with Morse interaction between its walls

Berry, R. Stephen

353

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

SciTech Connect

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

Saito, M. [School of Health Science, Faculty of Medicine, Niigata University, Niigata 951-8518 (Japan); Suzuki, S. [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577 (Japan)]. E-mail: ssuzuki@tagen.tohoku.ac.jp; Kimura, M. [Technical Development Bureau, Nippon Steel Corporation, Futtsu 293-8511 (Japan); Suzuki, T. [Technical Development Bureau, Nippon Steel Corporation, Futtsu 293-8511 (Japan); Kihira, H. [Technical Development Bureau, Nippon Steel Corporation, Futtsu 293-8511 (Japan); Waseda, Y. [School of Health Science, Faculty of Medicine, Niigata University, Niigata 951-8518 (Japan)

2005-11-15

354

Characterization of iron ferromagnetism by the local atomic volume: from three-dimensional structures to isolated atoms.  

PubMed

We present a comprehensive study of the relationship between the ferromagnetism and the structural properties of Fe systems from three-dimensional ones to isolated atoms based on the spin-density functional theory. We have found a relation between the magnetic moment and the volume of the Voronoi polyhedron, determining, in most cases, the value of the total magnetic moment as a function of this volume with an average accuracy of ±0.28 ?(B) and of the 3d magnetic moment with an average accuracy of ±0.07 ?(B) when the atomic volume is larger than 22 ų. It is demonstrated that this approach is applicable for many three-dimensional systems, including high-symmetry structures of perfect body-centered cubic (bcc), face-centered cubic (fcc), hexagonal close-packed (hcp), double hexagonal close-packed (dhcp), and simple cubic (sc) crystals, as well as for lower-symmetry ones, for example atoms near a grain boundary (GB) or a surface, around a vacancy or in a linear chain (for low-dimensional cases, we provide a generalized definition of the Voronoi polyhedron). Also, we extend the validity of the Stoner model to low-dimensional structures, such as atomic chains, free-standing monolayers and surfaces, determining the Stoner parameter for these systems. The ratio of the 3d-exchange splitting to the magnetic moment, corresponding to the Stoner parameter, is found to be I(3d) = (0.998 ± 0.006) eV /?(B) for magnetic moments up to 3.0 ?(B). Further, the 3d exchange splitting changes nearly linearly in the region of higher magnetic moments (3.0-4.0 ?(B)) and the corresponding Stoner exchange parameter equals I(h)(3d) = (0.272 ± 0.006) eV /?(B). The existence of these two regions reflects the fact that, with increasing Voronoi volume, the 3d bands separate first and, consequently, the 3d magnetic moment increases. When the Voronoi volume is sufficiently large (?22 ų), the separation of the 3d bands is complete and the magnetic moment reaches a value of 3.0 ?(B). Then, when the volume further increases, the 4s bands start to separate, increasing thus the 4s magnetic moment. Surprisingly, in the region of higher magnetic moments (?3.0 ?(B)), there is also a linear relationship between the 4s exchange splitting and the total magnetic moment with a slope of I(h)(4s) = (1.053 ± 0.016) eV /?(B), which is nearly identical to I(3d) for magnetic moments up to 3.0 ?B. These linear relations can be considered as an extension of the Stoner model for low-dimensional systems. PMID:24501204

Zhang, Lei; Sob, M; Wu, Zhe; Zhang, Ying; Lu, Guang-Hong

2014-02-26

355

Role of N2 molecules in pulse discharge production of I atoms for a pulsed chemical oxygen-iodine laser  

NASA Astrophysics Data System (ADS)

A pulsed electric discharge is the most effective means to turn chemical oxygen-iodine laser (COIL) operation into the pulse mode by fast production of iodine atoms. Experimental studies and numerical simulations are performed on a pulsed COIL initiated by an electric discharge in a mixture CF3I : N2 : O2(3X) : O2(a 1?g) flowing out of a chemical singlet oxygen generator. A transverse pulsed discharge is realized at various iodide pressures. The model comprises a system of kinetic equations for neutral and charged species, the electric circuit equation, the gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are repeatedly re-calculated by the electron Boltzmann equation solver when the plasma parameters are changed. The processes accounted for in the Boltzmann equation include direct and stepwise excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions and second-kind collisions. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. A conclusion is drawn about satisfactory agreement between the theory and the experiment.

Kochetov, I. V.; Napartovich, A. P.; Vagin, N. P.; Yuryshev, N. N.

2011-09-01

356

Predicting Physical-Chemical Properties of Compounds from Molecular Structures by Recursive Neural Networks  

E-print Network

Predicting Physical-Chemical Properties of Compounds from Molecular Structures by Recursive Neural of a recently developed neural network for structures applied to the prediction of physical chemical properties. INTRODUCTION To predict the physical-chemical properties of com- pounds, starting from the molecular structure

Sperduti, Alessandro

357

Atomic structures and electronic properties of 2H-NbSe2: The impact of Ti doping  

NASA Astrophysics Data System (ADS)

Layered transition metal dichalcogenides have aroused renewed interest as electronic materials, yet their electronic performances could be modified by chemical doping. Here, we perform a systematic first-principles calculation to investigate the effect of Ti doping on atomic structure and electronic properties of the 2H-NbSe2. We consider a total of three possible Ti-doping models and find that both the substitution and intercalated models are chemically preferred with the intercalation model being more favorable than the substitution one. Structural analyses reveal a slight lattice distortion triggered by Ti doping, but the original structure of 2H-NbSe2 is maintained. We also observe an expansion of c axis in the substituted model, which is attributed to the reduced van der Waals interaction arising from the increased Se-Se bond length. Our calculations also predict that the electron transport properties can be enhanced by the Ti doping, especially for the Ti-intercalated 2H-NbSe2, which should be beneficial for the realization of superconductivity. Furthermore, the covalence element is found in the Ti-Se bonds, which is ascribed to the hybridization of Ti 3d and Se 4p orbitals. The findings indicate that doping of transition metals can be regarded as a useful way to tailor electronic states so as to improve electron transport properties of 2H-NbSe2.

Li, Hongping; Chen, Lin; Zhang, Kun; Liang, Jiaqing; Tang, Hua; Li, Changsheng; Liu, Xiaojuan; Meng, Jian; Wang, Zhongchang

2014-09-01

358

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

PubMed

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

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

2009-06-17

359

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

ERIC Educational Resources Information Center

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

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

2013-01-01

360

Ab initio studies on atomic and electronic structures of black phosphorus  

Microsoft Academic Search

The atomic and electronic properties of black phosphorus (BP), which has been recently shown to have potential application as anode material for lithium ion batteries, are studied via ab initio calculations. The calculations reveal that the interlayer interaction in BP is Van der Waals Keesom force, which is critical to the formation of the layered structure. Interestingly, we also found

Yanlan Du; Chuying Ouyang; Siqi Shi; Minsheng Lei

2010-01-01

361

One-hundred-million-atom electronic structure calculations on the K computer  

E-print Network

One-hundred-million-atom electronic structure calculations on the K computer Takeo HOSHI1,2 1,toappearinISSPSupercomputerActivityReport(2014). (http://www.damp.tottori-u.ac.jp/~hoshi/info/hoshi_2014_invited_review_ISSP_SC_v1.pdf) 1 #12

Hoshi, Takeo

362

Nodal structures of intrashell states of three-valence-electron atoms  

Microsoft Academic Search

The nodal structures of intrashell states of a three-valence-electron atom are investigated. We expand the wave function in the body frame of the three electrons and show that the effect of symmetry such as rotation, space inversion, and permutation is to impose nodal surfaces on the components of the wave function. The equilibrium configuration is deduced to be a coplanar

C. G. Bao; Xiazhou Yang; C. D. Lin

1997-01-01

363

Photodissociation of HI and DI: Testing models for electronic structure via polarization of atomic photofragments  

E-print Network

Photodissociation of HI and DI: Testing models for electronic structure via polarization of atomic The photodissociation dynamics of HI and DI are examined using time-dependent wave-packet techniques. The orientation would be able to distinguish between the available models for the HI potential-energy curves

Brown, Alex

364

Three-Dimensional Structure of Nanocomposites from Atomic Pair Distribution Function Analysis: Study of Polyaniline and  

E-print Network

the 3D periodicity and translational order of conventional crystals and exhibit very diffuse diffraction from the fact that materials constructed at the nanoscale, such as nanocomposites and polymers, lack and diffuse scattering and yields the atomic structure in terms of a small set of parameters such as a unit

Trikalitis, Pantelis N.

365

AGB and Post-AGB Evolution: Structural and Chemical Changes  

E-print Network

Structural and chemical changes during the AGB and post-AGB evolution are discussed with respect to two recent observational and theoretical findings. On the one hand, high-resolution infrared observations revealed details of the dynamical evolution of the fragmented, bipolar dust shell around the far-evolved carbon star IRC+10216 giving evidence for rapid changes of an already PPN-like structure during the very end of the AGB evolution. On the other hand, stellar evolution calculations considering convective overshoot have shown how thermal pulses during the post-AGB stage lead to the formation of hydrogen-deficient post-AGB stars with abundance patterns consistent with those observed for Wolf-Rayet central stars.

T. Bloecker; R. Osterbart; G. Weigelt; Y. Balega; A. Men'shchikov

2001-02-22

366

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

PubMed

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

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

2005-07-15

367

Long range ordered magnetic and atomic structures of the quasicrystal approximant in the Tb-Au-Si system.  

PubMed

The atomic and magnetic structure of the 1/1 Tb(14)Au(70)Si(16) quasicrystal approximant has been solved by combining x-ray and neutron diffraction data. The atomic structure is classified as a Tsai-type 1/1 approximant with certain structural deviations from the prototype structures; there are additional atomic positions in the so-called cubic interstices as well as in the cluster centers. The magnetic property and neutron diffraction measurements indicate the magnetic structure to be ferrimagnetic-like below 9 K in contrast to the related Gd(14)Au(70)Si(16) structure that is reported to be purely ferromagnetic. PMID:25055216

Gebresenbut, Girma; Andersson, Mikael Svante; Beran, P?emysl; Manuel, Pascal; Nordblad, Per; Sahlberg, Martin; Gomez, Cesar Pay

2014-08-13

368

Long range ordered magnetic and atomic structures of the quasicrystal approximant in the Tb-Au-Si system  

NASA Astrophysics Data System (ADS)

The atomic and magnetic structure of the 1/1 Tb(14)Au(70)Si(16) quasicrystal approximant has been solved by combining x-ray and neutron diffraction data. The atomic structure is classified as a Tsai-type 1/1 approximant with certain structural deviations from the prototype structures; there are additional atomic positions in the so-called cubic interstices as well as in the cluster centers. The magnetic property and neutron diffraction measurements indicate the magnetic structure to be ferrimagnetic-like below 9 K in contrast to the related Gd(14)Au(70)Si(16) structure that is reported to be purely ferromagnetic.

Gebresenbut, Girma; Svante Andersson, Mikael; Beran, P?emysl; Manuel, Pascal; Nordblad, Per; Sahlberg, Martin; Pay Gomez, Cesar

2014-08-01

369

Nitrogen and carbon in austenitic and martensitic steels: atomic interactions and structural stability  

SciTech Connect

The effect of nitrogen and carbon on the structure of austenitic and martensitic steels is discussed. A correlation is shown between the electronic structure, atomic distribution and thermodynamic stability of Fe-based alloys. An increase in stability of solid solutions and a delay of precipitation is observed in the order of alloying with carbonRTnitrogenRTcarbon+nitrogen. Experimental data are presented for C, N and C+N steels.

Gavriljuk, V (Institute for Metals, Kiev, Ukraine); Rawers, James C.; Shanina, B (Institute for Semiconductor Physics, Kiev, Ukraine); Berns, H. (Ruhr University, Germany)

2003-01-01

370

Finite-temperature atomic structure of 180° ferroelectric domain walls in PbTiO3  

Microsoft Academic Search

In this letter we obtain the finite-temperature structure of 180° domain walls in PbTiO3 using a quasi-harmonic-lattice dynamics approach. We obtain the temperature dependence of the atomic structure of domain walls from 0 K up to room temperature. We also show that both Pb-centered and Ti-centered 180° domain walls are thicker at room temperature; domain wall thickness at T=300 K

Arzhang Angoshtari; Arash Yavari

2010-01-01

371

Correlation between atomic structure and localized gap states in silicon grain boundaries  

Microsoft Academic Search

Tight-binding molecular-dynamics simulations of a typical high-energy grain boundary in silicon show that its equilibrium atomic structure is similar to that of bulk amorphous silicon and contains coordination defects. The corresponding electronic structure is also amorphouslike, displaying gap states mainly localized around the coordination defects, where large changes in the bond-hybridization character are observed. It is proposed that such coordination

Fabrizio Cleri; Pawel Keblinski; Luciano Colombo; Simon R. Phillpot; Dieter Wolf

1998-01-01

372

Spontaneous emission of a photon: wave packet structures and atom-photon entanglement  

E-print Network

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

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

2004-12-14

373

Improved Sodium Lifetime and Hyperfine Structure Measurements Using Novel Precision Laser Spectroscopic Techniques with Laser Cooled\\/trapped Atoms  

Microsoft Academic Search

Laser cooling\\/trapping techniques can now produce cold atomic samples which offer new spectroscopic possibilities. This dissertation presents two atomic structure measurements which required development of precision laser spectroscopic techniques for use with laser-cooled atomic samples. This work also reports measurements on the first Na magneto -optic vapor cell trap and its corresponding cold ( ~40muK) atom velocity distribution. The first

Christopher Wallace Oates

1995-01-01

374

Surface atomic geometry and electronic structure of II--VI cleavage faces  

SciTech Connect

Recent models of the electronic structure and surface atomic geometries on wurtzite-structure CdS and CdSe have been extended to encompass zinc-blende structure CdTe. The driving force for the surface reconstruction of the cleavage faces of all these materials is the lowering in energy of a band of anion dangling bond surface states accompanied by their acquisition of back-bonding character. The resulting reconstructed surface is characterized by the eigenvalue spectrum associated with this band of states as well as the atomic geometries. The predicted geometries for CdTe(110), CdSe(101-bar0), and CdSe(112-bar0) are in good correspondence with low-energy electron diffraction (LEED) and low-energy positron diffraction intensity analyses. The calculated surface state eigenvalue spectra are compared with recent angle-resolved photoemission spectra (ARPES) for CdTe(110) and CdSe(101-bar0). The main features of the ARPES measurements are reproduced by the calculated eigenvalue spectra. The predicted atomic geometry for CdTe(110) corresponds well both with prior predictions for ZnSe(110) and ZnS(110), and with LEED experimental surface structures indicating that these surfaces exhibit a universal structure in which the independent surface structural parameters scale linearly with the bulk lattice constant.

Duke, C.B.; Wang, Y.R.

1989-05-01

375

Towards atomic resolution structural determination by single-particle cryo-electron microscopy  

PubMed Central

Recent advances in cryo-electron microscopy and single-particle reconstruction (collectively referred to as “cryoEM”) have made it possible to determine the three-dimensional (3D) structures of several macromolecular complexes at near-atomic resolution (~3.8 – 4.5 Å). These achievements were accomplished by overcoming challenges in sample handling, instrumentation, image processing, and model building. At near-atomic resolution, many detailed structural features can be resolved, such as the turns and deep grooves of helices, strand separation in ? sheets, and densities for loops and bulky amino acid side chains. Such structural data of the cytoplasmic polyhedrosis virus (CPV), the Epsilon 15 bacteriophage and the GroEL complex have provided valuable constraints for atomic model building using integrative tools, thus significantly enhancing the value of the cryoEM structures. The CPV structure revealed a drastic conformational change from a helix to a ? hairpin associated with RNA packaging and replication, coupling of RNA processing and release, and the long sought-after polyhedrin-binding domain. These latest advances in single-particle cryoEM provide exciting opportunities for the 3D structural determination of viruses and macromolecular complexes that are either too large or too heterogeneous to be investigated by conventional X-ray crystallography or nuclear magnetic resonance (NMR) methods. PMID:18403197

Zhou, Z. Hong

2009-01-01

376

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

377

Tuning the electronic structure and transport properties of graphene by noncovalent functionalization: effects of organic donor, acceptor and metal atoms.  

PubMed

Using density functional theory and nonequilibrium Green's function (NEGF) formalism, we have theoretically investigated the binding of organic donor, acceptor and metal atoms on graphene sheets, and revealed the effects of the different noncovalent functionalizations on the electronic structure and transport properties of graphene. The adsorptions of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and tetrathiafulvalene (TTF) induce hybridization between the molecular levels and the graphene valence bands, and transform the zero-gap semiconducting graphene into a metallic graphene. However, the current versus voltage (I-V) simulation indicates that the noncovalent modifications by organic molecules are not sufficient to significantly alter the transport property of the graphene for sensing applications. We found that the molecule/graphene interaction could be dramatically enhanced by introducing metal atoms to construct molecule/metal/graphene sandwich structures. A chemical sensor based on iron modified graphene shows a sensitivity two orders of magnitude higher than that of pristine graphene. The results of this work could help to design novel graphene-based sensing or switching devices. PMID:20057033

Zhang, Yong-Hui; Zhou, Kai-Ge; Xie, Ke-Feng; Zeng, Jing; Zhang, Hao-Li; Peng, Yong

2010-02-10

378

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

NASA Astrophysics Data System (ADS)

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

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

2014-02-01

379

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

380

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

381

Atomic Structure  

NSDL National Science Digital Library

SciPacks are self-directed online learning experiences for teachers to enhance their understanding of a particular scientific concept and its related pedagogical implications for student learning. Unlimited expert content help via email and a final assess

National Science Teachers Association (NSTA)

2010-05-24

382

Quantum spacetime fluctuations: Lamb Shift and hyperfine structure of the hydrogen atom  

E-print Network

We consider the consequences of the presence of metric fluctuations upon the properties of a hydrogen atom. Particularly, we introduce these metric fluctuations in the corresponding effective Schroedinger equation and deduce the modifications that they entail upon the hyperfine structure related to a hydrogen atom. We will find the change that these effects imply for the ground state energy of the system and obtain a bound for its size comparing our theoretical predictions against the experimental uncertainty reported in the literature. In addition, we analyze the corresponding Lamb shift effect emerging from these fluctuations of spacetime. Once again, we will set a bound to these oscillations resorting to the current experimental outcomes

Juan Israel Rivas; Abel Camacho; Ertan Goeklue

2011-05-31

383

Atomic-Scale Structure of Single-Layer MoS2 Nanoclusters  

NASA Astrophysics Data System (ADS)

We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide ( MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2 nanoparticles synthesized on Au(111), and establishes a new picture of the active edge sites of the nanoclusters. The results demonstrate a way to get detailed atomic-scale information on catalysts in general.

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

2000-01-01

384

Understanding the Properties and Structure of Metallic Glasses at the Atomic Level  

SciTech Connect

Liquids and glasses have been well known to human kind for millennia. And yet major mysteries remain in the behavior of glasses and liquids at the atomic level, and identifying the microscopic mechanisms that control the properties of glasses is one of the most challenging unsolved problems in physical sciences. For this reason, applying simplistic approaches to explain the behavior of metallic glasses can lead to serious errors. On the other hand because metallic glasses are atomic glasses with relatively simple structure, they may offer better opportunities to advance our fundamental understanding on the nature of the glass. The difficulties inherent to the problem and some recent advances are reviewed here.

Egami, T. [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL)

2010-01-01

385

CHEMICAL STRUCTURES IN COAL: GEOCHEMICAL EVIDENCE FOR THE PRESENCE OF MIXED STRUCTURAL COMPONENTS.  

USGS Publications Warehouse

The purpose of this paper is to summarize work on the chemical structural components of coal, comparing them with their possible plant precursors in modern peat. Solid-state **1**3C nuclear magnetic resonance (NMR), infrared spectroscopy (IR), elemental analysis and, in some cases, individual compound analyses formed the bases for these comparisons.

Hatcher, P.G.; Breger, I.A.; Maciel, G.E.; Szeverenyi, N.M.

1983-01-01

386

Simultaneous mapping of chemical abundances and magnetic field structure in Ap stars  

NASA Astrophysics Data System (ADS)

Magnetic A stars represent about 5 highly ordered, very stable and often very strong magnetic fields. They frequently show variations in both brightness and spectral line profiles that are synchronised to stellar rotation. Those variations are believed to be produced by atomic diffusion operating in the stellar atmospheres which have become stabilized by multi-kG magnetic fields. In recent years, with the development and application of the Doppler and magnetic-Doppler imaging techniques and the availability of high-precision spectroscopic and spectropolarimetric data, it has became possible to map the chemical abundances and magnetic field structures of Ap stars simultaneously and in increasing detail, based on full Stokes vector observations. I review the state-of-the-art understanding pf Ap star spots and their relation to magnetic fields, the development of Doppler and magnetic-Doppler imaging into one of the most powerful remote sensing methods for astrophysics, and the physics of Ap stars atmospheres that we can deduce from simultaneous mapping of magnetic field structure and chemical abundances.

Lueftinger, T.

2014-11-01

387

Conductivity of DNA probed by conducting-atomic force microscopy: Effects of contact electrode, DNA structure, and surface interactions  

Microsoft Academic Search

We studied the electrical conductivity of DNA molecules with conducting-atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a few molecules to ropes and large fibers containing up to ~106 molecules). Independent of the chemical nature of the surface (hydrophobic or hydrophilic,

Thomas Heim; Dominique Deresmes; Dominique Vuillaume

2004-01-01

388

Changes in the Atomic Structure through Glass Transition Observed by X-Ray Scattering  

SciTech Connect

The glass transition involves a minor change in the internal energy, and yet the physical and mechanical properties of a glass change dramatically. In order to determine the evolution of the atomic structure through the glass transition, we employed in-situ synchrotron X-ray scattering measurements as a function of temperature on a model material: Zr-Cu-Al metallic glass. We found that the thermal expansion at the atomic level is smaller than the macroscopic thermal expansion, and significantly increases above the glass transition temperature. The observed changes in the pair-distribution function (PDF) are explained in terms of the fluctuations in the local atomic volume and their change through the glass transition.

Egami, Takeshi [ORNL

2012-01-01

389

Atomic and Electronic Structure of Pyridine on Ge(100) Suklyun Hong,*, Young Eun Cho, Jae Yeol Maeng, and Sehun Kim*,  

E-print Network

Atomic and Electronic Structure of Pyridine on Ge(100) Suklyun Hong,*, Young Eun Cho, Jae Yeol to investigate the atomic and electronic structure of pyridine adsorbed on the Ge(100) surface. A large number of pyridine/Ge(100) adsorption configurations possibly resulting from cycloadditions and Lewis acid

Kim, Sehun

390

An analysis of Taiwanese eighth graders' science achievement, scientific epistemoiogical beliefs and cognitive structure outcomes after learning basic atomic theory  

Microsoft Academic Search

This study explored the interrelationships between students’ general science achievement, scientific epistemoiogical beliefs and their cognitive structure outcomes derived from instruction of basic atomic theory. Research data were mainly gathered from 48 Taiwanese eighth graders’ questionnaire responses and their recalled scientific information about the atomic model, analysed by a flow map technique as evidence of their cognitive structures. This study

1998-01-01

391

Local electronic and chemical structure of oligo-acetylene derivatives formed through radical cyclizations at a surface.  

PubMed

Semiconducting ?-conjugated polymers have attracted significant interest for applications in light-emitting diodes, field-effect transistors, photovoltaics, and nonlinear optoelectronic devices. Central to the success of these functional organic materials is the facile tunability of their electrical, optical, and magnetic properties along with easy processability and the outstanding mechanical properties associated with polymeric structures. In this work we characterize the chemical and electronic structure of individual chains of oligo-(E)-1,1'-bi(indenylidene), a polyacetylene derivative that we have obtained through cooperative C1-C5 thermal enediyne cyclizations on Au(111) surfaces followed by a step-growth polymerization of the (E)-1,1'-bi(indenylidene) diradical intermediates. We have determined the combined structural and electronic properties of this class of oligomers by characterizing the atomically precise chemical structure of individual monomer building blocks and oligomer chains (via noncontact atomic force microscopy (nc-AFM)), as well as by imaging their localized and extended molecular orbitals (via scanning tunneling microscopy and spectroscopy (STM/STS)). Our combined structural and electronic measurements reveal that the energy associated with extended ?-conjugated states in these oligomers is significantly lower than the energy of the corresponding localized monomer orbitals, consistent with theoretical predictions. PMID:24387223

Riss, Alexander; Wickenburg, Sebastian; Gorman, Patrick; Tan, Liang Z; Tsai, Hsin-Zon; de Oteyza, Dimas G; Chen, Yen-Chia; Bradley, Aaron J; Ugeda, Miguel M; Etkin, Grisha; Louie, Steven G; Fischer, Felix R; Crommie, Michael F

2014-05-14

392

Light-assisted cold chemical reactions of barium ions with rubidium atoms  

NASA Astrophysics Data System (ADS)

Light-assisted reactive collisions between laser-cooled Ba+ ions and Rb atoms were studied in an ion-atom hybrid trap. The reaction rate was found to strongly depend on the electronic state of the reaction partners with the largest rate constant (7(2) x 10^-11 cm^3 s^-1) obtained for the excited Ba+(6s)+Rb(5p) reaction channel. Similar to the previously studied Ca+ + Rb system, charge transfer and radiative association were found to be the dominant reactive processes. The generation of molecular ions by radiative association could directly be observed by their sympathetic cooling into a Coulomb crystal. Potential energy curves up to the Ba+(6s)+Rb(5p) asymptote and reactive-scattering cross sections for the radiative processes were calculated. The theoretical rate constant obtained for the lowest reaction channel Ba+(6s)+Rb(5s) is compatible with the experimental estimates obtained thus far.

Hall, Felix H. J.; Aymar, Mireille; Raoult, Maurice; Dulieu, Olivier; Willitsch, Stefan

2013-07-01

393

Atomic domain magnetic nanoalloys: interplay between molecular structure and temperature dependent magnetic and dielectric properties in manganese doped tin clusters.  

PubMed

We present extensive temperature dependent (16-70 K) magnetic and electric molecular beam deflection measurements on neutral manganese doped tin clusters Mn/SnN (N = 9-18). Cluster geometries are identified by comparison of electric deflection profiles and quantum chemical data obtained from DFT calculations. Most clusters adopt endohedral cage structures and all clusters exhibit non-vanishing magnetic dipole moments. In the high temperature regime all species show exclusively high field seeking magnetic response and the magnetic dipole moments are extracted from the shift of the molecular beam. At low nozzle temperatures, some of the clusters show considerably broadened beam profiles due to non-uniform deflection in the magnetic field. The results reflect the influence of the chemical environment on the magnetic properties of the transition metal in atomic domain magnetic nanoalloys. Different ground state spin multiplicities and coupling of rotational and vibrational degrees of freedom with the spin angular momentum of isolated clusters of different size apparently cause these variations of spin orientation. This is discussed by taking electronic and molecular structure data into account. PMID:25283162

Rohrmann, Urban; Schwerdtfeger, Peter; Schäfer, Rolf

2014-11-21

394

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

NASA Technical Reports Server (NTRS)

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

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

1990-01-01

395

Evolution of polymer photovoltaic performances from subtle chemical structure variations.  

PubMed

Conjugated polymers are promising replacements for their inorganic counterparts in photovoltaics due to their low cost, ease of processing, and straightforward thin film formation. New materials have been able to improve the power conversion efficiency of photovoltaic cells up to 8%. However, rules for rational material design are still lacking, and subtle chemical structure variations usually result in large performance discrepancies. The present paper reports a detailed study on the crystalline structure, morphology, and in situ optoelectronic properties of blend films of polythiophene derivatives and [6,6]-phenyl C61-butyric acid methyl ester by changing the alkyl side chain length and position of polythiophene. The correlation among the molecular structure, mesoscopic morphology, mesoscopic optoelectronic property and macroscopic device performance (highest efficiency above 4%) was directly established. Both solubility and intermolecular interactions should be considered in rational molecular design. Knowledge obtained from this study can aid the selection of appropriate processing conditions that improve blend film morphology, charge transport property, and overall solar cell efficiency. PMID:23042235

Yan, Han; Li, Denghua; Lu, Kun; Zhu, Xiangwei; Zhang, Yajie; Yang, Yanlian; Wei, Zhixiang

2012-11-21

396

On the structures of 55-atom transition-metal clusters and their relationship to the crystalline bulk.  

PubMed

Correlation of cluster and bulk structure: Electron-diffraction measurements of homonuclear 55-atom transition-metal cluster anions covering essentially all 3d and 4d elements show only four main structure families. Elements with the same bulk lattice morphology generally have a common cluster structure type. The cluster structure types differ in maximum atomic coordination numbers in analogy to the coordination numbers in the corresponding bulk lattices. PMID:23657978

Rapps, Thomas; Ahlrichs, Reinhart; Waldt, Eugen; Kappes, Manfred M; Schooss, Detlef

2013-06-01

397

Determination of bismuth in environmental samples by slurry sampling graphite furnace atomic absorption spectrometry using combined chemical modifiers.  

PubMed

Slurry sampling graphite furnace atomic absorption spectrometry technique was applied for the determination of Bi in environmental samples. The study focused on the effect of Zr, Ti, Nb and W carbides, as permanent modifiers, on the Bi signal. Because of its highest thermal and chemical stability and ability to substantially increase Bi signal, NbC was chosen as the most effective modifier. The temperature programme applied for Bi determination was optimized based on the pyrolysis and atomization curves obtained for slurries prepared from certified reference materials (CRMs) of the soil and sediments. To overcome interferences caused by sulfur compounds, Ba(NO3)2 was used as a chemical modifier. Calibration was performed using the aqueous standard solutions. The analysis of the CRMs confirmed the reliability of the proposed analytical method. The characteristic mass for Bi was determined to be 16 pg with the detection limit of 50 ng/g for the optimized procedure at the 5 % (w/v) slurry concentration. PMID:25384374

Dobrowolski, Ryszard; Dobrzy?ska, Joanna; Gawro?ska, Barbara

2015-01-01

398

Asymptotic Structure in the Classically Forbidden Region of the Hooke's Atoms  

NASA Astrophysics Data System (ADS)

The two-electron Hooke's atom — a quantum mechanical system with two electrons bound in a harmonic potential — is well known for its exact analytical properties at certain oscillator strengths. The Hooke's atoms with more than two electrons offer more scope for valuable practical applications. In this work, we study the asymptotic structure of these Hooke's atoms in the classically forbidden region. The leading-order term of the long-range expression for the KS exchange-correlation potential vxc(r) is shown to be -1/r. The second and third higher order terms are also exactly obtained. Various components of vxc(r) are also studied. It is shown that the leading term of O(1/r) in vxc(r) is due to the pure Pauli correlation, while the leading contribution of the Coulomb correlation is of O(1/r3). Neither of them makes contribution to the term of O(1/r2), which is shown to be solely due to the kinetic correlation effect. Results for the two-electron Hooke's atom were obtained before in the literature. Our results reduce to those of the two-electron Hooke's atom as a special case.

Wang, Xue-Mei

2013-05-01

399

Structural and Optical Study of Chemical Bath Deposited Nano-Structured CdS Thin Films  

NASA Astrophysics Data System (ADS)

CdS is commonly used as window layer in polycrystalline solar cells. The paper presents a structural and optical study of CdS nano-structured thin films. High quality CdS thin films are grown on commercial glass by means of chemical bath deposition. It involves an alkaline solution of cadmium salt, a complexant, a chalcogen source and a non-ionic surfactant. The films have been prepared under various process parameters. The chemically deposited films are annealed to estimate its effect on the structural and optical properties of films. These films (as -deposited and annealed) have been characterized by means of XRD, SEM and UV-Visible spectrophotometer. XRD of films show the nano-crystalline nature. The energy gap of films is found to be of direct in nature.

Kumar, Suresh; Sharma, Dheeraj; Sharma, Pankaj; Sharma, Vineet; Barman, P. B.; Katyal, S. C.

2011-12-01

400

Conversion of lignocellulosic biomass to nanocellulose: structure and chemical process.  

PubMed

Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate's application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein. PMID:25247208

Lee, H V; Hamid, S B A; Zain, S K

2014-01-01

401

Replication of noise-sustained autocatalytic chemical structures  

NASA Astrophysics Data System (ADS)

Autocatalytic systems in a differential-flow reactor may undergo a differential-flow-induced chemical instability toward a convectively unstable regime, in which noise-sustained structures may appear. This is the case of a system with Gray-Scott kinetics in a packed-bed reactor, as reported in [B. von Haeften and G. Izús, Phys. Rev. E 67, 056207 (2003)]. In this work, two identical copies of such a system are coupled in master-slave configuration and submitted to independent spatiotemporal Gaussian white noise sources. Numerical simulation of two-dimensional reactors with uniform and Poiseuille flows reveals that the slave system replicates to a very high degree of precision and the convective patterns arising in the master one due to the presence of noise. The quality of this synchronization is assessed through several measures. A convective instability in the synchronization manifold is theoretically predicted and numerically confirmed.

Izús, Gonzalo G.; Deza, Roberto R.; Sánchez, Alejandro D.

2010-06-01

402

Atomic Chain Electronics  

NASA Technical Reports Server (NTRS)

Adatom chains, precise structures artificially created on an atomically regulated surface, are the smallest possible candidates for future nanoelectronics. Since all the devices are created by combining adatom chains precisely prepared with atomic precision, device characteristics are predictable, and free from deviations due to accidental structural defects. In this atomic dimension, however, an analogy to the current semiconductor devices may not work. For example, Si structures are not always semiconducting. Adatom states do not always localize at the substrate surface when adatoms form chemical bonds to the substrate atoms. Transport properties are often determined for the entire system of the chain and electrodes, and not for chains only. These fundamental issues are discussed, which will be useful for future device considerations.

Yamada, Toshishige; Saini, Subhash (Technical Monitor)

1998-01-01

403

Local atomic structure of a zirconia-based americium transmutation fuel  

SciTech Connect

(Zr,Y,Am)O{sub 2} with 6 and 19 mol% Am were prepared by infiltration of americium in porous yttria-stabilised zirconia (YSZ) beads. Samples were sintered at 1600 deg. C in Ar/H{sub 2} to yield Am(III). By annealing them at 1000 deg. C in flowing air, the Am is oxidised to Am(IV). Both Am(III) and Am(IV) samples exhibit the presence of a single (Zr,Y,Am)O{sub 2} phase with fluorite structure. The local atomic structure around the Zr, Y, and Am atoms is determined by EXAFS analysis. The Zr-O bond distance decreases from 2.15 to 2.12 A with increasing Am(III) content, whereas the Y-O bond distance is independent of Am content and oxidation state. The Am(III)-O bond distance is 2.37 A for both Am concentrations, while oxidation to Am(IV) decreases the Am(IV)-O distance to 2.28 A, with a simultaneous expansion of the environment around the Zr atoms. The Am-O bond distances are contracted compared with the compounds Am{sub 2}Zr{sub 2}O{sub 7} and AmO{sub 2} and the distances expected from the ionic radii. - Graphical abstract: Local atomic structure in (Zr,Y,Am(III))O{sub 2-x}. The oxygen vacancies induced by Y and Am(III) dopant ions are associated with Zr atoms. Oxidation in air at 1000 deg. C contracts the Am(IV)-O bond, whereas the Zr environment relaxes.

Walter, Marcus [European Commission, Joint Research Centre, Institute for Transuranium Elements, PO. Box 2340, D-76125 Karlsruhe (Germany)], E-mail: marcus.walter@ec.europa.eu; Naestren, Catharina [European Commission, Joint Research Centre, Institute for Transuranium Elements, PO. Box 2340, D-76125 Karlsruhe (Germany); Somers, Joseph [European Commission, Joint Research Centre, Institute for Transuranium Elements, PO. Box 2340, D-76125 Karlsruhe (Germany)], E-mail: joseph.somers@ec.europa.eu; Jardin, Regis [European Commission, Joint Research Centre, Institute for Transuranium Elements, PO. Box 2340, D-76125 Karlsruhe (Germany); Denecke, Melissa A.; Brendebach, Boris [Forschungszentrum Karlsruhe, Institut fuer Nukleare Entsorgung (INE), PO. Box 3640, D-76021 Karlsruhe (Germany)

2007-11-15

404

The atomic and electronic structures of NiO(001)/Au(001) interfaces  

NASA Astrophysics Data System (ADS)

The atomic and electronic structures of NiO(001)/Au(001) interfaces were analyzed by high-resolution medium energy ion scattering (MEIS) and photoelectron spectroscopy using synchrotron-radiation-light. The MEIS analysis clearly showed that O atoms were located above Au atoms at the interface and the inter-planar distance of NiO(001)/Au(001) was derived to be 2.30 ± 0.05 Å, which was consistent with the calculations based on the density functional theory (DFT). We measured the valence band spectra and found metallic features for the NiO thickness up to 3 monolayer (ML). Relevant to the metallic features, electron energy loss analysis revealed that the bandgap for NiO(001)/Au(001) reduced with decreasing the NiO thickness from 10 down to 5 ML. We also observed Au 4f lines consisting of surface, bulk, and interface components and found a significant electronic charge transfer from Au(001) to NiO(001). The present DFT calculations demonstrated the presence of an image charge beneath Ni atoms at the interface just like alkali-halide/metal interface, which may be a key issue to explain the core level shift and band structure.

Visikovskiy, A.; Mitsuhara, K.; Hazama, M.; Kohyama, M.; Kido, Y.

2013-10-01

405

The structure and energetics of $^3$He and $^4$He nanodroplets doped with alkaline earth atoms  

E-print Network

We present systematic results, based on density functional calculations, for the structure and energetics of $^3$He and $^4$He nanodroplets doped with alkaline earth atoms. We predict that alkaline earth atoms from Mg to Ba go to the center of $^3$He drops, whereas Ca, Sr, and Ba reside in a deep dimple at the surface of $^4$He drops, and Mg is at their center. For Ca and Sr, the structure of the dimples is shown to be very sensitive to the He-alkaline earth pair potentials used in the calculations. The $5s5p\\leftarrow5s^2$ transition of strontium atoms attached to helium nanodroplets of either isotope has been probed in absorption experiments. The spectra show that strontium is solvated inside $^3$He nanodroplets, supporting the calculations. In the light of our findings, we emphasize the relevance of the heavier alkaline earth atoms for analyzing mixed $^3$He-$^4$He nanodroplets, and in particular, we suggest their use to experimentally probe the $^3$He-$^4$He interface.

A. Hernando; R. Mayol; M. Pi; M. Barranco; F. Ancilotto; O. B{ü}nermann; F. Stienkemeier

2007-05-08

406

Atomic-scale X-ray structural analysis of self-assembled monolayers on Silicon  

NASA Astrophysics Data System (ADS)

Two related self-assembled monolayers (SAMs), 4-bromostyrene (BrSty) and 4-bromophenylacetylene (BPA), are photochemically grown from solution on to the monohydride-terminated Si(111) surface. The atomic-scale structures of the resulting SAMs are examined by X-ray standing waves (XSW), X-ray reflectivity (XRR), X-ray fluorescence, atomic-force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). The coverage is 0.5 ML. The results show that in each case the molecule covalently bonds to a single Si T1 site and stands up-right with a slight molecular tilt of 17? that leaves the Br terminal end over a neighboring T4 site. The Br height is 8.5 Å (BrSty) and 8.6 Å (BPA) above the top surface Si atom. The combined XSW and XRR results rule-out two alternative bonding models predicted by DFT that have the root of the molecule bonded to two neighboring top Si surface atoms. Based on the XSW 111 and 333 coherent fractions, the BPA/Si(111) has a reduced vertical Br distribution width in comparison to BrSty. This greater rigidity in the molecular structure is correlated to a C=C bond at the root.

Lin, J.-C.; Kellar, J. A.; Kim, J.-H.; Yoder, N. L.; Bevan, K. H.; Nguyen, S. T.; Hersam, M. C.; Bedzyk, M. J.

2009-02-01

407

Atomic-scale X-ray structural analysis of self-assembled monolayers on Silicon  

SciTech Connect

Two related self-assembled monolayers (SAMs), 4-bromostyrene (BrSty) and 4-bromophenylacetylene (BPA), are photochemically grown from solution on to the monohydride-terminated Si(111) surface. The atomic-scale structures of the resulting SAMs are examined by X-ray standing waves (XSW), X-ray reflectivity (XRR), X-ray fluorescence, atomic-force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). The coverage is 0.5 ML. The results show that in each case the molecule covalently bonds to a single Si T{sub 1} site and stands up-right with a slight molecular tilt of 17{sup o} that leaves the Br terminal end over a neighboring T{sub 4} site. The Br height is 8.5 {angstrom} (BrSty) and 8.6 {angstrom} (BPA) above the top surface Si atom. The combined XSW and XRR results rule-out two alternative bonding models predicted by DFT that have the root of the molecule bonded to two neighboring top Si surface atoms. Based on the XSW 111 and 333 coherent fractions, the BPA/Si(111) has a reduced vertical Br distribution width in comparison to BrSty. This greater rigidity in the molecular structure is correlated to a C=C bond at the root.

Lin, J.-C.; Kellar, J.A.; Kim, J.-H.; Yoder, N.L.; Bevan, K.H.; Nguyen, S.T.; Hersam, M.C.; Bedzyk, M.J.; (NWU); (Purdue)

2009-04-02

408

Modeling chemical flame structure and combustion dynamics in LES P. Auzillona,  

E-print Network

Modeling chemical flame structure and combustion dynamics in LES P. Auzillona, , B. Fiorinaa , R and compared in terms of chemical flame structure and dynamics. To avoid the uncertainties related.ecp.fr [3, 5], the chemical subspace of a turbulent premixed flame can be approximated by a collection of 1

Paris-Sud XI, Université de

409

A pseudo-atomic model for the capsid shell of bacteriophage lambda using chemical cross-linking/mass spectrometry and molecular modeling.  

PubMed

Bacteriophage lambda is one of the most exhaustively studied of the double-stranded DNA viruses. Its assembly pathway is highly conserved among the herpesviruses and many of the bacteriophages, making it an excellent model system. Despite extensive genetic and biophysical characterization of many of the lambda proteins and the assembly pathways in which they are implicated, there is a relative dearth of structural information on many of the most critical proteins involved in lambda assembly and maturation, including that of the lambda major capsid protein. Toward this end, we have utilized a combination of chemical cross-linking/mass spectrometry and computational modeling to construct a pseudo-atomic model of the lambda major capsid protein as a monomer, as well as in the context of the assembled procapsid shell. The approach described here is generalizable and can be used to provide structural models for any biological complex of interest. The procapsid structural model is in good agreement with published biochemical data indicating that procapsid expansion exposes hydrophobic surface area and that this serves to nucleate assembly of capsid decoration protein, gpD. The model further implicates additional molecular interactions that may be critical to the assembly of the capsid shell and for the stabilization of the structure by the gpD decoration protein. PMID:23811054

Singh, Pragya; Nakatani, Eri; Goodlett, David R; Catalano, Carlos Enrique

2013-09-23

410

Designing Allosteric Control into Enzymes by Chemical Rescue of Structure  

SciTech Connect

Ligand-dependent activity has been engineered into enzymes for purposes ranging from controlling cell morphology to reprogramming cellular signaling pathways. Where these successes have typically fused a naturally allosteric domain to the enzyme of interest, here we instead demonstrate an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. We present two examples, W33G in a {beta}-glycosidase enzyme ({beta}-gly) and W492G in a {beta}-glucuronidase enzyme ({beta}-gluc), in which we engineer indole-dependent activity into enzymes by removing a buried tryptophan side chain that serves as a buttress for the active site architecture. In both cases, we observe a loss of function, and in both cases we find that the subsequent addition of indole can be used to restore activity. Through a detailed analysis of {beta}-gly W33G kinetics, we demonstrate that this rescued enzyme is fully functionally equivalent to the corresponding wild-type enzyme. We then present the apo and indole-bound crystal structures of {beta}-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate {beta}-glycosidase activity in living cells using indole. Disruption and recovery of protein structure may represent a general technique for introducing allosteric control into enzymes, and thus may serve as a starting point for building a variety of bioswitches and sensors.

Deckert, Katelyn; Budiardjo, S. Jimmy; Brunner, Luke C.; Lovell, Scott; Karanicolas, John (Kansas)

2012-08-07

411

Structure of self-interstitial atom clusters in iron and copper  

NASA Astrophysics Data System (ADS)

The dislocation core structure of self-interstitial atom (SIA) clusters in bcc iron and fcc copper is determined using the hybrid ab initio continuum method of Banerjee [Philos. Mag. 87, 4131 (2007)]. To reduce reliance on empirical potentials and to facilitate predictions of the effects of local chemistry and stress on the structure of defects, we present here a hybrid extension of the Peierls-Nabarro continuum model, with lattice resistance to slip determined separately from ab initio calculations. A method is developed to reconstruct atomic arrangements and geometry of SIA clusters from the hybrid model. The results are shown to compare well with molecular-dynamics simulations. In iron, the core structure does not show dependence on the size of the self-interstitial cluster, and is nearly identical to that of a straight edge dislocation. However, the core structure of SIA clusters in Cu is shown to depend strongly on the cluster size. Small SIA clusters are found to have nondissociated compact dislocation cores, with a strong merging of Shockley partial dislocations and a relatively narrow stacking fault (SF) region. The compact nature of the SIA core in copper is attributed to the strong dependence of the self-energy on the cluster size. As the number of atoms in the SIA cluster increases, Shockley partial dislocations separate and the SF region widens, rendering the SIA core structure to that of an edge dislocation. The separation distance between the two partials widens as the cluster size increases, and tends to the value of a straight edge dislocation for cluster sizes above 400 atoms. The local stress is found to have a significant effect on the atomic arrangements within SIA clusters in copper and the width of the stacking faults. An applied external shear can delocalize the core of an SIA cluster in copper, with positive shear defined to be on the (111) plane along the [1¯1¯2] direction. For an SIA cluster containing 1600 atoms, a positive 1 GPa shear stress delocalizes the cluster and expands the SF to 30b , while a negative shear stress of 2 GPa contracts the core to less than 5b , where b is the Burgers vector magnitude.

Takahashi, Akiyuki; Ghoniem, Nasr M.

2009-11-01

412

STRUCTURAL BASIS OF THE MUTAGENCITY OF CHEMICALS IN SALMONELLA TYPHIMURIUM: THE GENE-TOX DATA BASE  

EPA Science Inventory

The case structure-activity methodology has been applied to a Gene-Tox derived Salmonella mutagenicity data base consisting of 808 chemicals. ased upon qualitative structural features, CASE indentified 29 activating and 3 inactivating structural determinants hich correctly predic...

413

Structure and morphology of aluminium doped Zinc-oxide layers prepared by atomic layer deposition  

Microsoft Academic Search

The aim of this work is to study the effects of deposition temperature and aluminium incorporation on the crystalline properties, orientation and grain size of atomic layer deposited ZnO layers. X-ray diffraction analysis revealed a change in the dominant crystallite orientation with increasing substrate temperature. The most perfect crystal structure and largest grain size was found at 2at.% aluminium content.

Zs. Baji; Z. Lábadi; Z. E. Horváth; I. Bársony

414

Atomic-Scale Structure of Single-Layer MoS2 Nanoclusters  

Microsoft Academic Search

We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide ( MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2 nanoparticles synthesized on Au(111), and establishes a new picture of the active edge sites of

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

2000-01-01

415

Structure and dynamics of interfaces in organic and inorganic materials using atomic level simulation  

Microsoft Academic Search

Interfaces in materials play a key role for industrial applications. The structures and dynamics at various interfaces including ferroelectric domain walls, gas-organic interface, organic-semiconductor interface and metal-gas interface are investigated with different atomic levels of simulation approaches. Ferroelectricity: Due to their unique ferroelectric and nonlinear optical properties, trigonal ferroelectrics such as LiNbO3 and LiTaO 3, are of wide interest for

Donghwa Lee

2010-01-01

416

Atomic Force Microscopy in Microbiology: New Structural and Functional Insights into the Microbial Cell Surface  

PubMed Central

ABSTRACT Microbial cells sense and respond to their environment using their surface constituents. Therefore, understanding the assembly and biophysical properties of cell surface molecules is an important research topic. With its ability to observe living microbial cells at nanometer resolution and to manipulate single-cell surface molecules, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Here, we survey major breakthroughs made in cell surface microbiology using AFM techniques, emphasizing the most recent structural and functional insights. PMID:25053785

2014-01-01

417

Estimation of the adequacy of the fractal model of the atomic structure of amorphous silicon  

SciTech Connect

A method of constructing a fractal model of noncrystalline solid substance is considered using the example of amorphous silicon. In systems of iteration functions, the physical meaning of dihedral and valence angles of the elementary crystallographic cell is assigned to arguments. The model adequacy is estimated by the radial distribution function, the atomic structure density, the distribution of valence and dihedral angles, and the density of dangling interatomic bonds.

Golodenko, A. B., E-mail: sashgol@mail.ru [Voronezh State Technological Academy (Russian Federation)

2010-01-15

418

Local atomic and electronic structure in LaMn O3 across the orbital ordering transition  

NASA Astrophysics Data System (ADS)

The local atomic disorder and electronic structure in the environment of manganese atoms in LaMnO3 has been studied by x-ray absorption spectroscopy over a temperature range (300-870K) covering the orbital ordering transition (˜710K) . The Mn-O distance splitting into short and long bonds (1.95 and 2.15Å ) is kept across the transition temperature, so that the MnO6 octahedra remain locally Jahn-Teller distorted. Discontinuities in the Mn local structure are identified in the extended x-ray fine structure spectra at this temperature, associated with a reduction of the disorder in the superexchange angle and to the removal of the anisotropy in the radial disorder within the coordination shell. Subtle changes in the electronic local structure also take place at the Mn site at the transition temperature. The near-edge spectra show a small drop of the Mn 4p hole count and a small enhancement in the pre-edge structures at the transition temperature. These features are associated with an increase of the covalence of the Mn-O bonds. Our results shed light on the local electronic and structural phenomena in a model of order-disorder transition, where the cooperative distortion is overcome by the thermal disorder.

Souza, Raquel A.; Souza-Neto, Narcizo M.; Ramos, Aline Y.; Tolentino, Hélio C. N.; Granado, Eduardo

2004-12-01

419

Structural analysis of photosystem I polypeptides using chemical crosslinking  

NASA Technical Reports Server (NTRS)

Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

1994-01-01

420

Structure and magnetism of Tm atoms and monolayers on W(110)  

NASA Astrophysics Data System (ADS)

We investigated the growth and magnetic properties of Tm atoms and monolayers deposited on a W(110) surface using scanning tunneling microscopy and x-ray magnetic circular and linear dichroism. The equilibrium structure of Tm monolayer films is found to be a strongly distorted hexagonal lattice with a Moiré pattern due to the overlap with the rectangular W(110) substrate. Monolayer as well as isolated Tm adatoms on W present a trivalent ground-state electronic configuration, contrary to divalent gas phase Tm and weakly coordinated atoms in quench-condensed Tm films. Ligand field multiplet simulations of the x-ray absorption spectra further show that Tm has a |J=6,Jz=±5> electronic ground state separated by a few meV from the next lowest substates |J=6,Jz=±4> and |J=6,Jz=±6>. Accordingly, both the Tm atoms and monolayer films exhibit large spin and orbital moments with out-of-plane uniaxial magnetic anisotropy. X-ray magnetic dichroism measurements as a function of temperature show that the Tm monolayers develop antiferromagnetic correlations at about 50 K. The triangular structure of the Tm lattice suggests the presence of significant magnetic frustration in this system, which may lead to either a noncollinear staggered spin structure or intrinsic disorder.

Nistor, Corneliu; Mugarza, Aitor; Stepanow, Sebastian; Gambardella, Pietro; Kummer, Kurt; Diez-Ferrer, José Luis; Coffey, David; de la Fuente, César; Ciria, Miguel; Arnaudas, José I.

2014-08-01

421

On the emergence of molecular structure from atomic shape in the 1/r2 harmonium model.  

PubMed

The formal similarity of the three-body Hamiltonians for helium and the hydrogen molecule ion is used to demonstrate the unfolding of a rotating dumbbell-like proton distribution from a (1s)2-type electron distribution by smooth variation of the particles' masses in the 1/r2 harmonium model. The 1/r2 harmonium is an exactly solvable modification of the harmonium model (also known as Hooke's law atom) where the attraction between different particles is harmonic and the repulsion between the two equal particles is given by a 1/r2 potential. The dumbbell-like molecular structure appears as an expression of increasing spatial correlation due to increasing mass. It gradually appears in the one-density distribution of the two equal particles if their mass exceeds a critical value depending on the mass of the third particle. For large mass of the equal particles, their one-density distribution approaches an asymptotic form derived from the Born-Oppenheimer treatment of H2+ in the 1/r2 harmonium model. Below the critical value, the one density is a spherical, Gaussian-type atomic density distribution with a maximum at the center of mass. The topological transition at the critical value separates molecular structure and atomic shape as two qualitatively different manifestations of spatial structure. PMID:16409022

Müller-Herold, Ulrich

2006-01-01

422

THEORETICAL AND COMPUTATIONAL APPROACH TO CHEMICAL EVALUATION BASED ON STRUCTURE-ACTIVITY RELATIONSHIPS  

EPA Science Inventory

During the past ten years we have been developing relationships to predict physical, chemical, environmental, and toxicological properties of chemicals directly from structure. he fundamental framework of our approach is to propose a theoretical basis for such relationships, comp...

423

NLP-inspired structural pattern recognition in chemical application q J. Sidorova  

E-print Network

NLP-inspired structural pattern recognition in chemical application q J. Sidorova , M. Anisimova Computational Biochemistry Research Group, Department of Computer Science, Swiss Federal Institute of Technology recognition Grammar inference Natural language processing Chemical descriptors SMILES Activity prediction a b

Anisimova, Maria

424

Effects of chemical kinetics of the performance of the atomic iodine laser system  

SciTech Connect

Model calculations show that chemical reactions which take place in the active medium of a photolytically pumped iodine laser limit the efficiency with which pump photons are utilized and convert significant amounts of the starting material RI to the unwanted by-products R/sub 2/ and I/sub 2/. Laser- and rf-discharge-based methods for regenerating starting materials from by-products are evaluated experimentally. For economical operation of large iodine laser systems, CF/sub 3/I is presently the best starting material, and a pulsed rf-discharge technique is presently the best one for chemical regeneration. The absorbed energy required to regenerate one CF/sub 3/I molecule using pulsed rf-discharge techniques is 5.8 eV.

Fisk, G.A.; Truby, F.K.

1980-01-01

425

The chemical structure of macromolecular fractions of a sulfur-rich oil  

SciTech Connect

A selective stepwise chemical degradation has been developed for structural studies of high-molecular-weight (HMW) fractions of sulfur-rich oils. The degradation steps are: (i) desulfurization; (ii) cleavage of oxygen-carbon bonds; and (iii) oxidation of aromatic structural units. After each step, the remaining macromolecular matter was subjected to the subsequent reaction. This degradation scheme was applied to the asphaltene, the resin, and a macromolecular fraction of low polarity (LPMF) of Rozel Point oil. Total amounts of degraded low-molecular-weight compounds increased progressively in the order asphaltene < resin < LPMF. Desulfurization yielded mainly phytane, steranes, and triterpanes. Oxygen-carbon bond cleavage resulted in hydrocarbon fractions predominated by n-alkanes and acyclic isoprenoids. The oxidation step afforded high amounts of linear carboxylic acids in the range of C[sub 11] to C[sub 33]. The released compounds provide a more complete picture of the molecular structure of the oil fractions than previously available. Labelling experiments with deuterium atoms allowed characterization of the site of bonding and the type of linkage for compounds. Evidence is presented that subunits of the macromolecular network are attached simultaneously by oxygen and sulfur (n-alkanes, hopanes) or by sulfur and aromatic units (n-alkanes, steranes).

Richnow, H.H.; Jenisch, A.; Michaelis, W. (Universitaet Hamburg (Germany))

1993-06-01

426

The chemical structure of macromolecular fractions of a sulfur-rich oil  

NASA Astrophysics Data System (ADS)

A selective stepwise chemical degradation has been developed for structural studies of highmolecularweight (HMW) fractions of sulfur-rich oils. The degradation steps are: (i) desulfurization (ii) cleavage of oxygen-carbon bonds (iii) oxidation of aromatic structural units. After each step, the remaining macromolecular matter was subjected to the subsequent reaction. This degradation scheme was applied to the asphaltene, the resin and a macromolecular fraction of low polarity (LPMF) of the Rozel Point oil. Total amounts of degraded low-molecular-weight compounds increased progressively in the order asphaltene < resin < LPMF. Desulfurization yielded mainly phytane, steranes and triterpanes. Oxygen-carbon bond cleavage resulted in hydrocarbon fractions predominated by n-alkanes and acyclic isoprenoids. The oxidation step afforded high amounts of linear carboxylic acids in the range of C 11 to C 33. The released compounds provide a more complete picture of the molecular structure of the oil fractions than previously available. Labelling experiments with deuterium atoms allowed to characterize the site of bonding and the type of linkage for the released compounds. Evidence is presented that subunits of the macromolecular network are attached simultaneously by oxygen and sulfur (n-alkanes, hopanes) or by sulfur and aromatic units ( n-alkanes, steranes).

Richnow, Hans H.; Jenisch, Angela; Michaelis, Walter

1993-06-01

427

Atomic structure of the cross-[beta] spine of islet amyloid polypeptide (amylin)  

SciTech Connect

Human islet amyloid polypeptide (IAPP or amylin) is a 37-residue hormone found as fibrillar deposits in pancreatic extracts of nearly all type II diabetics. Although the cellular toxicity of IAPP has been established, the structure of the fibrillar form found in these deposits is unknown. Here we have crystallized two segments from IAPP, which themselves form amyloid-like fibrils. The atomic structures of these two segments, NNFGAIL and SSTNVG, were determined, and form the basis of a model for the most commonly observed, full-length IAPP polymorph.

Wiltzius, J.J.; Sievers, S.A.; Sawaya, M.R.; Cascio, D.; Popov, D.; Riekel, C.; Eisenberg, D. (UCLA); (ESRF)

2009-03-27

428

Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin  

NASA Astrophysics Data System (ADS)

We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

2004-04-01

429

Correlation between atomic structure and localized gap states in silicon grain boundaries  

SciTech Connect

Tight-binding molecular-dynamics simulations of a typical high-energy grain boundary in silicon show that its equilibrium atomic structure is similar to that of bulk amorphous silicon and contains coordination defects. The corresponding electronic structure is also amorphouslike, displaying gap states mainly localized around the coordination defects, where large changes in the bond-hybridization character are observed. It is proposed that such coordination defects in disordered high-energy grain boundaries are responsible for the experimentally observed gap states in polycrystalline Si. {copyright} {ital 1998} {ital The American Physical Society}

Cleri, F. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)] [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States); [Divisione Materiali Avanzati, ENEA, Centro Ricerche Casaccia, Casella Postale, 2400, 00100Roma (Italy); Keblinski, P. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)] [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States); Colombo, L. [Dipartimento di Scienza dei Materiali, Universita di Milano, and Istituto Nazionale per la Fisica della Materia, via Emanueli 15, 20126Milano (Italy)] [Dipartimento di Scienza dei Materiali, Universita di Milano, and Istituto Nazionale per la Fisica della Materia, via Emanueli 15, 20126Milano (Italy); Phillpot, S.R.; Wolf, D. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)] [Materials Science Division, Argonne National Laboratory, Argonne, Illinois60439 (United States)

1998-03-01

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