Note: This page contains sample records for the topic atomic structure chemical from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: November 12, 2013.
1

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

Microsoft Academic Search

Direct imaging and chemical identification of all the atoms in a material with unknown three-dimensional structure would constitute a very powerful general analysis tool. Transmission electron microscopy should in principle be able to fulfil this role, as many scientists including Feynman realized early on. It images matter with electrons that scatter strongly from individual atoms and whose wavelengths are about

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

2010-01-01

2

Deducing chemical structure from crystallographically determined atomic coordinates  

PubMed Central

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

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

2011-01-01

3

Atomic Structure  

NSDL National Science Digital Library

In this activity students explore the structure and properties of atoms. They construct models of atoms with properties of particular mass and charge; create models of atoms with different stabilities by adding or subtracting neutrons, protons, and electrons to a model atom; and determine that the same element may have varying number of neutrons and these form isotopes.Students will be able to:

Consortium, The C.

2011-12-11

4

Predicting the chemical composition and structure of Aspergillus nidulans hyphal wall surface by atomic force microscopy  

Microsoft Academic Search

In fungi, cell wall plays an important role in growth and development. Major macromolecular constituents of the aspergilli\\u000a cell wall are glucan, chitin, and protein. We examined the chemical composition and structure of the Aspergillus nidulans hyphal wall surface by an atomic force microscope (AFM). To determine the composition of the cell wall surface, the adhesion\\u000a forces of commercially available

Hyun-uk Lee; Jong Bae Park; Haeseong Lee; Keon-Sang Chae; Dong-Min Han; Kwang-Yeop Jahng

2010-01-01

5

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

PubMed

We use scanning tunneling microscopy and X-ray spectroscopy to characterize the atomic and electronic structure of boron-doped and nitrogen-doped graphene created by chemical vapor deposition on copper substrates. Microscopic measurements show that boron, like nitrogen, incorporates into the carbon lattice primarily in the graphitic form and contributes ?0.5 carriers into the graphene sheet per dopant. Density functional theory calculations indicate that boron dopants interact strongly with the underlying copper substrate while nitrogen dopants do not. The local bonding differences between graphitic boron and nitrogen dopants lead to large scale differences in dopant distribution. The distribution of dopants is observed to be completely random in the case of boron, while nitrogen displays strong sublattice clustering. Structurally, nitrogen-doped graphene is relatively defect-free while boron-doped graphene films show a large number of Stone-Wales defects. These defects create local electronic resonances and cause electronic scattering, but do not electronically dope the graphene film. PMID:24032458

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

2013-09-16

6

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

ERIC Educational Resources Information Center

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

Tsaparlis, Georgios

1997-01-01

7

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

8

Atomic Structure: Energy in 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 third of three Science Objects in the Atomic Structure SciPack. It investigates

National Science Teachers Association (NSTA)

2010-05-24

9

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

SciTech Connect

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

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

2012-09-12

10

New surface atomic structures for III-V(110)-p(1 times 1)-Sb(1ML): Chemical bonding and electronic structure  

SciTech Connect

Tight-binding total energy computations are used to examine the chemical bonding and electronic structure for two new minimum-energy surface atomic structures for p(1{times}1) overlayers of Sb on III-V(110) surfaces. The bonding in each of these structures is unique, having no analog in either the bulk or small molecule coordination chemistry of these materials, and is a phenomena uniquely associated with the constrained epitaxical growth of the Sb overlayer. 13 refs., 2 figs., 2 tabs.

LaFemina, J.P. (Pacific Northwest Lab., Richland, WA (USA)); Duke, C.B. (Xerox Corp., Webster, NY (USA). Webster Research Center); Mailhiot, C. (Lawrence Livermore National Lab., CA (USA))

1990-04-01

11

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

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

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.

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

2007-01-01

14

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

15

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

16

Enhanced Dielectric Properties in SrTiO3\\/BaTiO3 Strained Superlattice Structures Prepared by Atomic-Layer Metalorganic Chemical Vapor Deposition  

Microsoft Academic Search

We describe the investigation of epitaxial SrTiO3\\/BaTiO3 strained superlattice films prepared by an atomic-layer metalorganic chemical vapor deposition (ALMOCVD) method. Transmission electron microscopy (TEM) observation shows that the multilayered structure is globally uniform and that the interfaces formed between the different layers are of low roughness. X-ray diffraction (XRD) analysis reveals a series of satellite peaks on both sides of

Zaiyang Wang; Tomohiko Yasuda; Shigeo Hatatani; Shunri Oda

1999-01-01

17

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

Microsoft Academic Search

A significant BN-to-graphene charge donation is evident in the electronic structure of a graphene\\/h-BN(0001) heterojunction grown by chemical vapor deposition and atomic layer deposition directly on Ru(0001), consistent with density functional theory. This filling of the lowest unoccupied state near the Brillouin zone center has been characterized by combined photoemission\\/k vector resolved inverse photoemission spectroscopies, and Raman and scanning tunneling

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

2010-01-01

18

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

NASA Astrophysics Data System (ADS)

A significant BN-to-graphene charge donation is evident in the electronic structure of a graphene/h-BN(0001) heterojunction grown by chemical vapor deposition and atomic layer deposition directly on Ru(0001), consistent with density functional theory. This filling of the lowest unoccupied state near the Brillouin zone center has been characterized by combined photoemission/k vector resolved inverse photoemission spectroscopies, and Raman and scanning tunneling microscopy/spectroscopy. The unoccupied ?*(?1 +) band dispersion yields an effective mass of 0.05 me for graphene in the graphene/h-BN(0001) heterostructure, in spite of strong perturbations to the graphene conduction band edge placement.

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

2010-08-01

19

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

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…

Wang, Chia-Yu; Barrow, Lloyd H.

2013-01-01

21

Atom probe characterization of an AlN interlayer within HEMT structures grown by molecular beam epitaxy and metal-organic chemical vapor deposition  

NASA Astrophysics Data System (ADS)

An AlN interlayer is introduced in a conventional AlGaN/GaN HEMT to enhance the density and mobility of the two dimensional electron gas (2DEG). MBE and MOCVD are two competitive and proven techniques to grow high quality AlN, but a chemical characterization technique is desired to investigate the purity of the AlN interlayer. Amongst nanoanalyzing techniques, atom probe tomography (APT) is unique for its spatial resolution and 3-D compositional images (0.2nm) with analytical sensitivity (10appm). In this work, plasma assisted MBE(PAMBE) and MOCVD techniques were employed to grow AlGaN/AlN/GaN heterostructures. Detailed compositional data from atom probe shows that a pure AlN layer was grown by PAMBE. From Hall measurements, the carrier density (sheet resistance) was found to be 1.65 x 10^13cm-3(188?/sq). The MOCVD structures do not form a pure AlN layer but that of Al0.45Ga0.55N layer. The carrier density was found to be 1.15 x 10^13cm-3 (425 ?/sq). This work showed that MBE technique is more suitable than MOCVD for growing pure AlN interlayers and that APT can provide valuable nano scale information for further optimization of growth structures, thereby improving device performance.

Mazumder, Baishakhi; Kaun, Stephen W.; Lu, Jing; Keller, Stacia; Mishra, Umesh K.; Speck, James S.

2013-03-01

22

Hydrogen atoms and gas phase chemical dynamics  

SciTech Connect

This thesis describes the applications of Doppler spectroscopy of hydrogen atoms to gas phase chemical dynamics. Hydrogen atoms are generated in the electronic ground state (1s) either from photodissociation or from chemical reactions. They are then excited to the 2p state by 121.6 nm light. The fluorescence intensity (2p [yields] 1s) of the H atoms is monitored by a photomultiplier tube. The measurement of the H atom velocity helps us to follow chemical reactions in the gas phase occurring in a very short time. There are three experimental works described here. The first one shows how the Walden inversion, previously observed indirectly by organic chemists, is followed in the reaction of H atoms with CD[sub 4]. The reactions of electronically excited Xe and Kr atoms with H[sub 2] is illustrated in the next work. The indirect evidence for the formation of XeD and KrD is presented. In the third work, the photodissociation dynamics of small molecules like HCl, HCN and C[sub 2]H[sub 2] is discussed.

Chattopadhyay, A.

1992-01-01

23

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

NASA Astrophysics Data System (ADS)

We report on visualizing the chemical and structural order of double perovskite Sr2-xGdxMnTiO6. The antisite disorder of Mn and Ti is detected even at atomic scale at all x, resulting in Mn-rich and Ti-rich regions. For x ?0.75, the majority of manganese ions are in Mn3+ state and are centered in Jahn-Teller distorted MnO6octahedra. The Fourier transformation of atomic resolution images along the [110] zone axis reveals a superstructure that corresponds to the tilting of oxygen octahedra and that doubles the unit cell along [001]c. This superstructure is spatially inhomogeneous and coincides with the regions where B-site ion (Mn/Ti) is displaced along the [110] direction. We discuss these findings in the frame of possible local ferroelectricity and in the light of strong electroresistance observed in Sr1.25Gd0.75MnTiO6.

Alvarez, Inmaculada; Biskup, Neven; Lopez, Maria; Garcia-Hernandez, Mar; Veiga, Luisa; Varela, Maria

2013-03-01

24

Making inert polypropylene fibers chemically responsive by combining atomic layer deposition and vapor phase chemical grafting  

NASA Astrophysics Data System (ADS)

Uniformly grafting organic reactive molecular species, e.g. -NH2, onto substrates that have three-dimensional complex structures and are chemically inert is challenging. The vapor phase chemical grafting of organic molecules enabled by low temperature metal oxide atomic layer deposition (ALD) is presented as a general and promising solution to functionalize inert matrices with complex morphology, such as nonwoven polypropylene mats, through the controllable self-limited molecular assembly mechanism in a combined ALD and vapor phase chemical grafting process.

Peng, Qing; Gong, Bo; Parsons, Gregory N.

2011-04-01

25

BBB - Brevetoxin Chemical Structure  

Center for Food Safety and Applied Nutrition (CFSAN)

... Print; Share; E-mail. Home; Food; Foodborne Illness & Contaminants; Causes of Foodborne Illness: Bad Bug ... BBB - Brevetoxin Chemical Structure. ... More results from www.fda.gov/food/foodborneillnesscontaminants/causesofillnessbadbugbook

26

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

27

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.

28

X-ray-absorption fine structure in embedded atoms  

Microsoft Academic Search

Oscillatory structure is found in the atomic background absorption in x-ray-absorption fine-structure (XAFS) measurements. This atomic XAFS (AXAFS) arises from scattering within an embedded atom, and is analogous to the Ramsauer-Townsend effect. Calculations and measurements confirm the existence of AXAFS and show that it can dominate contributions such as multielectron excitations. The structure is sensitive to chemical effects and thus

J. J. Rehr; C. H. Booth; F. Bridges; S. I. Zabinsky

1994-01-01

29

ELECTRONIC STRUCTURE OF SUPERHEAVY ATOMS  

Microsoft Academic Search

We describe the status of the problem of the electron structure of superheavy atoms with nuclear charge Z > Zc ; here Zc?170 is the critical value of the nuclear charge, at which the energy of the ground state of the 1S1\\/2 electron reaches the limit of the lower continuum of the solutions of the Dirac equation (? = -

Ya B Zeldovich; Valentin S Popov

1972-01-01

30

Atomic structure of titania nanosheet with vacancies  

PubMed Central

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

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

2013-01-01

31

Atomic structure of titania nanosheet with vacancies.  

PubMed

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

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

2013-09-30

32

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

33

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

34

Chemical Structural Aging Effects.  

National Technical Information Service (NTIS)

This program is determining the individual chemical rate processes that govern the aging of ANB-3066 propellant, and it is attempting to establish the effect of chemical (compositional) changes upon the system's mechanical response to enable better utiliz...

G. E. Myers A. B. Tipton

1972-01-01

35

Atomic structures and compositions of interfaces  

SciTech Connect

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

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

1990-09-01

36

Electrical properties of Al2O3/4H-SiC structures grown by atomic layer chemical vapor deposition  

NASA Astrophysics Data System (ADS)

Al2O3 films have been deposited on n-type and p-type 4H-SiC by atomic layer chemical vapor deposition using trimethylaluminum as a precursor for aluminum and both H2O and O3 as an oxidant. After oxide deposition, annealing at different temperatures (800, 900, 1000 °C) in argon atmosphere for different durations (1, 2, 3 h) was performed. Bulk and interface properties of the oxide films were studied by capacitance-voltage, current-voltage, deep level transient spectroscopy, and thermally dielectric relaxation current (TDRC) measurements. The results reveal a decreasing flatband voltage with increasing annealing time, suggesting decrease of oxide charges and deep interface traps. After 3 h annealing at 1000 °C of the n-type samples, the flatband voltage is reduced to 6 V compared to a value in excess of 40 V for as-deposited samples. The TDRC measurements on annealed Al2O3/SiC (n-type) capacitors showed substantially different spectra relative to conventional SiO2/4H-SiC control samples; in the former ones no signal was recorded at temperatures less than 100 K, demonstrating a low density of shallow electron traps below the conduction band edge of 4H-SiC and hence a prospect of obtaining a high electron channel mobility in 4H-SiC metal-oxide-semiconductor field-effect devices with Al2O3 as gate dielectric.

Avice, Marc; Grossner, Ulrike; Pintilie, Ioana; Svensson, Bengt G.; Servidori, Marco; Nipoti, Roberta; Nilsen, Ola; Fjellva?G, Helmer

2007-09-01

37

The Structure of the Atom  

Microsoft Academic Search

IN a letter to this journal last week, Mr. Soddy has discussed the bearing of my theory of the nucleus atom on radio-active phenomena, and seems to be under the impression that I hold the view that the nucleus must consist entirely of positive electricity. As a matter of fact, I have not discussed in any detail the question of

E. Rutherford

1913-01-01

38

Digital Resource Package for Teaching Atomic Structure  

NSDL National Science Digital Library

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

Moin, Laura

39

Chemical Resolution at Ionic Crystal Surfaces Using Dynamic Atomic Force Microscopy with Metallic Tips  

NASA Astrophysics Data System (ADS)

We demonstrate that well prepared and characterized Cr tips can provide atomic resolution on the bulk NaCl(001) surface with dynamic atomic force microscopy in the noncontact regime at relatively large tip-sample separations. At these conditions, the surface chemical structure can be resolved yet tip-surface instabilities are absent. Our calculations demonstrate that chemical identification is unambiguous, because the interaction is always largest above the anions. This conclusion is generally valid for other polar surfaces, and can thus provide a new practical route for straightforward interpretation of atomically resolved images.

Teobaldi, G.; Lämmle, K.; Trevethan, T.; Watkins, M.; Schwarz, A.; Wiesendanger, R.; Shluger, A. L.

2011-05-01

40

Unraveling the Atomic Structure of Ultrafine Iron Clusters  

PubMed Central

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

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

2012-01-01

41

New hexagonal structure for silicon atoms  

NASA Astrophysics Data System (ADS)

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

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

2012-11-01

42

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

SciTech Connect

To analyze the local structure and/or chemical states of boron atoms in boron-doped diamond, which can be synthesized by the microwave plasma-assisted chemical vapor deposition method (CVD-B-diamond) and the temperature gradient method at high pressure and high temperature (HPT-B-diamond), we measured the soft X-ray emission spectra in the CK and BK regions of B-diamonds using synchrotron radiation at the Advanced Light Source (ALS). X-ray spectral analyses using the fingerprint method and molecular orbital calculations confirm that boron atoms in CVD-B-diamond substitute for carbon atoms in the diamond lattice to form covalent B-C bonds, while boron atoms in HPT-B-diamond react with the impurity nitrogen atoms to form hexagonal boron nitride. This suggests that the high purity diamond without nitrogen impurities is necessary to synthesize p-type B-diamond semiconductors.

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

2008-03-29

43

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

44

Proton Structure and Atomic Physics  

SciTech Connect

We discuss a precise determination of the polarizability and other proton structure dependent contributions to the hydrogen hyperfine splitting, based heavily on the most recent published data on proton spin dependent structure functions from the EG1 experiment at the Jefferson Laboratory. As a result, the total calculated hyperfine splitting now has a standard deviation slightly under 1 part-per-million, and is about 1 standard deviation away from the measured value.

Carlson, Carl E. [Physics Department, College of William and Mary, Williamsburg, VA 23187-8795 (United States)

2009-07-27

45

Interferometer-Type Structures for Guided Atoms  

Microsoft Academic Search

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

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

2002-01-01

46

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

47

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

48

An Atom-Specific Look at the Surface Chemical Bond  

Microsoft Academic Search

High resolution x-ray emission spectroscopy is shown to reveal unprecedented details of the chemical bond formed between a molecule and a transition metal surface. An atom and symmetry projected view of the bonding orbitals is obtained. We find that all outer and inner valence orbitals of the molecule change due to the surface interaction. New types of molecular states are

Anders Nilsson; Martin G. Weinelt; Tomas Wiell; Peter Bennich; O. Karis; Nial Wassdahl; J. Stöhr; Mahesh G. Samant

1997-01-01

49

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

Microsoft Academic Search

Ion\\/molecule reactions are described which facilitate exchange of hydrogens for deuteriums in a variety of different chemical environments. Aromatic hydrogens in alkylbenzenes, oxygenated benzenes, m-toluidine, m-phenylenediamine, thiophene, and several polycyclic aromatic hydrocarbons and metallocenes are exchanged under positive ion CI conditions by using either DâO, EtOD, or NDâ as the reagent gas. Aromatic hydrogens, benzylic hydrogens, and hydrogens on carbon

Donald F. Hunt; Satinder K. Sethi

1980-01-01

50

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

PubMed

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

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

2009-01-01

51

Atomic structure of Tb(11 2 0)  

SciTech Connect

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

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

1992-08-15

52

Molecular Conductance: Effects of Contact Atomic Structure and Anchoring Group  

NASA Astrophysics Data System (ADS)

The nature of the molecule-lead contact is of crucial importance in molecular transport. As an example, we study the molecular conductance of benzene connected to two Au leads through three different anchoring groups (S, Se, and Te). Our calculations proceed from first-principles by using a density functional theory calculation for the electronic structure and a Green function method for the electron transport. We analyze systematically the effects of contact atomic relaxation, lead orientation, absorption site, chemical trends in the anchoring group, and atomic structure around the contact. Different lead orientations, absorption sites, and anchoring groups can cause a change of several times in conductance. Most significantly, adding an additional Au atom at each contact can increase the conductance by two orders of magnitude because of a LUMO-like resonance peak around the Fermi energy. This also leads to a large negative differential conductance. Finally, the equilibrium conductance decreases with increasing atomic number of the anchoring group. This is opposite to the conclusion of previous work using the jellium model for the leads in which the contact atomic structure cannot be taken into account. Supported in part by the NSF (DMR-0103003).

Ke, S.-H.; Baranger, H. U.; Yang, Weitao

2004-03-01

53

Numerical MC SCF Procedures for the Study of Atomic Structures.  

National Technical Information Service (NTIS)

An atomic structure package based on the numerical MC SCF procedure is outlined. The main objective of the package is the determination of energy levels and wave functions for atomic systems from which other atomic properties can be predicted. Particular ...

C. F. Fischer

1988-01-01

54

Energy expression of the chemical bond between atoms in metal oxides  

Microsoft Academic Search

The chemical bond between atoms in metal oxides is expressed in an energy scale. Total energy is partitioned into the atomic energy densities of constituent elements in the metal oxide, using energy density analysis. The atomization energies, ?EM for metal atom and ?EO for O atom, are then evaluated by subtracting the atomic energy densities from the energy of the

Yoshifumi Shinzato; Yuki Saito; Masahito Yoshino; Hiroshi Yukawa; Masahiko Morinaga; Takeshi Baba; Hiromi Nakai

2011-01-01

55

Atomically smooth and single crystalline Ge(111)/cubic-Pr{sub 2}O{sub 3}(111)/Si(111) heterostructures: Structural and chemical composition study  

SciTech Connect

Engineered wafer systems are an important materials science approach to achieve the global integration of single crystalline Ge layers on the Si platform. Here, we report the formation of single crystalline, fully relaxed Ge(111) films by molecular beam epitaxial overgrowth of cubic Pr oxide buffers on Si(111) substrates. Reflection high-energy electron diffraction, scanning electron microscopy, and x-ray reflectivity show that the Ge epilayer is closed, flat, and has a sharp interface with the underlying oxide template. Synchrotron radiation grazing incidence x-ray diffraction and transmission electron microscopy reveal the type-A/B/A epitaxial relationship of the Ge(111)/cubic Pr{sub 2}O{sub 3}(111)/Si(111) heterostructure, a result also corroborated by theoretical ab initio structure calculations. Secondary ion mass spectroscopy confirms the absence of Pr and Si impurities in the Ge(111) epilayer, even after an annealing at 825 deg. C.

Giussani, A.; Rodenbach, P.; Zaumseil, P.; Dabrowski, J.; Kurps, R.; Weidner, G.; Muessig, H.-J.; Schroeder, T. [IHP, Im Technologiepark 25, 15236 Frankfurt (Oder) (Germany); Storck, P. [SILTRONIC AG, Hanns-Seidel-Platz 4, 81737 Muenchen (Germany); Wollschlaeger, J. [University of Osnabrueck, Barbarastrasse 7, 49076 Osnabrueck (Germany)

2009-02-01

56

Structural cluster analysis of chemical reactions in solution  

NASA Astrophysics Data System (ADS)

We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.

Gallet, Grégoire A.; Pietrucci, Fabio

2013-08-01

57

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

58

Contrast Reversal in Atomic-Resolution Chemical Mapping  

SciTech Connect

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

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

2008-12-05

59

Antiprotonic Radioactive Atom for Nuclear Structure Studies  

SciTech Connect

A future experiment to synthesize antiprotonic radioactive nuclear ions is proposed for nuclear structure studies. Antiprotonic radioactive nuclear atom can be synthesized in a nested Penning trap where a cloud of antiprotons is prestored and slow radioactive nuclear ions are bunch-injected into the trap. By observing of the ratio of {pi}+ and {pi}- produced in the annihilation process, we can deduce the different abundance of protons and neutrons at the surface of the nuclei. The proposed method would provide a unique probe for investigating the nuclear structure of unstable nuclei.

Wada, M. [Atomic Physics Laboratory, RIKEN 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Yamazaki, Y. [Atomic Physics Laboratory, RIKEN 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Institute of Physics, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1, Komaba, Meguro, Tokyo 153-8902 (Japan)

2005-10-19

60

Atom probe analysis of planar multilayer structures  

Microsoft Academic Search

Atom probe field ion microscopy has been used to analyze a planar-deposited layered structure in plan view. The specimens were prepared with a newly developed method that involves a combination of photolithography and focused ion-beam milling. A multilayer structure consisting of {Ta\\/CoFe\\/(Cu\\/CoFe)15\\/Ru\\/(CoFe\\/Ru)5\\/Ru\\/NiFe} was sputter deposited for use as a test stack. The corresponding thicknesses of these layers were 7\\/13(3\\/3)\\/50\\/(3\\/1)\\/50\\/150 nm.

D. J. Larson; R. L. Martens; T. F. Kelly; M. K. Miller; N. Tabat

2000-01-01

61

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

NASA Astrophysics Data System (ADS)

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

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

62

Local Atomic Structure of Piperidyl Nd Dithiocarbamate  

NASA Astrophysics Data System (ADS)

The atomic structure of a novel rare earth complex consisting of Nd and the sulfur-containing ligand pipdtc (C5H10NCS2-) has been studied with extended x-ray absorption fine structure (EXAFS) and x-ray diffraction techniques. The complex of formula Nd(pipdtc)4N(CH3)4 crystallizes in the monoclinic space group P21/n with the following lattice parameters, a = 22.685(2), b = 20.332(2), c = 17.1270(10)Å, ? = 100.570(10)°, Z = 8. The calculated density is 1.47 g/cm3. A new derivative method is used to remove the post-edge absorption background including the multielectron excitation effect. The EXAFS results demonstrate that there are about eight S and four O atoms around Nd with the Nd-S bond length of 2.916 Å and the Nd-O bond length of 2.415 Å, respectively. This implies that the powder of this complex is not stable and is easy to oxidize in air. The possible change of structure before and after oxidation is discussed.

Wu, Zhong-hua; Guo, Lin; Ju, Xin; Hu, Tian-dou; Li, Qian-shu; Zhu, He-sun

1999-08-01

63

Putting atoms and molecules into chemically opened fullerenes.  

PubMed

We studied Ar, Kr, CO, and N(2) going into and out of a chemically opened fullerene, 1. We measured the equilibrium constant, K(eq), for the formation of X@1. K(eq) is particularly large for Ar, probably due to the large van der Waals attraction between the Ar atom and the fullerene cage. We measured rate constants and activation energies for the unimolecular reaction X@1-->X + 1 (X = Ar, CO, N(2)). The reactions show an unusually small pre-exponential factor, probably due to the loose binding of X inside the cage. PMID:19209931

Stanisky, Christopher M; Cross, R James; Saunders, Martin

2009-03-11

64

Studying atomic structures by aberration-corrected transmission electron microscopy.  

PubMed

Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy-loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli-electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations. PMID:18653874

Urban, Knut W

2008-07-25

65

Characteristics of n+ polycrystalline-Si/Al2O3/Si metal-oxide- semiconductor structures prepared by atomic layer chemical vapor deposition using Al(CH3)3 and H2O vapor  

NASA Astrophysics Data System (ADS)

We report interface and dielectric reliability characteristics of n+ polycrystalline-silicon (poly-Si)/Al2O3/Si metal-oxide-semiconductor (MOS) capacitors. Al2O3 films were prepared by atomic layer chemical vapor deposition using Al(CH3)3 and H2O vapor. Interface state density (Dit) and dielectric reliability properties of n+ poly-Si/Al2O3/Si MOS structures were examined by capacitance-voltage, conductance, current-voltage, and time-dependent dielectric breakdown measurements. The Dit of the n+ poly-Si/Al2O3/Si MOS system near the Si midgap is approximately 8×1010 eV-1 cm-2 as determined by the conductance method. Frequency dispersion as small as ~20 mV and hysteresis of ~15 mV were attained under the electric field of +/-8 MV/cm. The gate leakage current of ~36 Å effective thickness Al2O3 dielectric measured at the gate voltage of -2.5 V is ~-5 nA/cm2, which is approximately three orders of magnitude lower than that of a controlled oxide (SiO2). Time-dependent dielectric breakdown data of Al2O3/Si MOS capacitors under the constant current/voltage stress reveal excellent charge-to-breakdown characteristics over controlled oxide. Reliable gate oxide integrity of Al2O3 gate dielectric is manifested by the excellent distribution of gate oxide breakdown voltage on 128 million MOS capacitors having isolation edges. Extracted time constant and capture cross section of the Al2O3/Si junction are discussed.

Park, Dae-Gyu; Cho, Heung-Jae; Lim, Kwan-Yong; Lim, Chan; Yeo, In-Seok; Roh, Jae-Sung; Park, Jin Won

2001-06-01

66

Structure and stability of semiconductor tip apexes for atomic force microscopy  

NASA Astrophysics Data System (ADS)

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

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

2009-07-01

67

Chemical Structures of Native Oxides Formed during Wet Chemical Treatments  

Microsoft Academic Search

The chemical structures of the native oxides formed during various wet chemical treatments were measured nondestructively by changing the effective electron escape depth. The structures of the native oxides can be characterized by the distribution of suboxide Si3+ in the native oxide films. If Si3+ is correlated with Si-H bonds, the formation rate of the native oxide during the wet

Takeo Hattori; Kazuhiko Takase; Hiroaki Yamagishi; Rinshi Sugino; Yasuo Nara; Takashi Ito

1989-01-01

68

Chemical Structure and Molecular Switches.  

NASA Astrophysics Data System (ADS)

The future of molecular electronics depends on designing molecules to exhibit specific nonlinear properties such as rectification or bistable switching. In pursuit of this goal, two distinct types of switching were observed in matrix isolated and complete monolayers of bipyridyl-dinitro-oligophenylene-ethynylene (BPDN). Several groups have observed conductance state switching in this molecule. However, the mechanism of switching between the two conductance states is still not understood. Using BPDN as a starting point, chemically related structures such as bipyridyl- oligophenylene-ethynylene, dinitro-oligophenylene-ethynylene, and biphenyl- oligophenylene-ethynylene were measured in matrix isolated monolayers. By means of such comparisons to related molecules, we determine the key functional groups leading to switching in BPDN.

Blum, Amy; Long, David; Moore, Martin; Kushmerick, James; Tour, James; Ratna, Banahalli

2008-03-01

69

Chemical etiology of nucleic acid structure  

Microsoft Academic Search

The synthesis of potentially natural nucleic acid alternatives and comparison of some of their chemical properties with those of RNA and DNA have led to findings that we consider to be relevant in the context of a chemical etiology of nucleic acid structure. Chemical etiology of nucleic acid structure refers to systematic experimental studies aimed at narrowing the diversity of

A. Eschenmoser; R. Krishnamurthy

2000-01-01

70

Structure feature selection for chemical compound classification  

Microsoft Academic Search

With the development of highly efficient chemin- formatics data collection technology, classification of chemical structure data emerges as an important topic in cheminfor- matics. Towards building highly accurate predictive models for chemical data, here we present an efficient feature selection method. In our method, we first represent a chemical structure by its 2D connectivity map. We then use frequent subgraph

Hongliang Fei; Jun Huan

2008-01-01

71

Automated extraction of chemical structure information from digital raster images  

PubMed Central

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

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

2009-01-01

72

Resolving Complex Atomic-Scale Spin Structures by Spin-Polarized Scanning Tunneling Microscopy  

Microsoft Academic Search

The spin-polarized scanning tunneling microscope (SP-STM) operated in the constant current mode is proposed as a powerful tool to investigate complex atomic-scale magnetic structures of otherwise chemically equivalent atoms. The potential of this approach is demonstrated by successfully resolving the magnetic structure of Cr\\/Ag(111), which is predicted on the basis of ab initio vector spin-density calculations to be a coplanar

D. Wortmann; S. Heinze; Ph. Kurz; G. Bihlmayer; S. Blügel

2001-01-01

73

Chapter 12 New Expression of the Chemical Bond in Hydrides Using Atomization Energies  

Microsoft Academic Search

Atomization energy diagram is proposed for analyzing the chemical bond in the hydrides including perovskite-type hydrides, metal hydrides and complex hydrides. The atomization energies of hydrogen and metal atoms in them are evaluated theoretically by the energy density analysis (EDA) of the total energy, and used for the construction of the atomization energy diagram. Every hydride can be located on

Yoshifumi Shinzato; Hiroshi Yukawa; Masahiko Morinaga; Takeshi Baba; Hiromi Nakai

2008-01-01

74

Structural and electronic properties for atomic clusters  

NASA Astrophysics Data System (ADS)

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

Sun, Yan

75

The PubChem chemical structure sketcher  

Microsoft Academic Search

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex

Wolf D Ihlenfeldt; Evan E Bolton; Stephen H Bryant

2009-01-01

76

Direct atom-by-atom chemical identification of nanostructures and defects of topological insulators.  

PubMed

We present a direct atom-by-atom chemical identification of the nanostructures and defects of topological insulators (TIs) with a state-of-the-art atomic mapping technology. Combining this technique and density function theory calculations, we identify and explain the layer chemistry evolution of Bi(2)Te(3–x)Se(x) ternary TIs. We also reveal a long neglected but crucially important extended defect found to be universally present in Bi(2)Te(3) films, the seven-layer Bi(3)Te(4) nanolamella acceptors. Intriguingly, this defect is found to locally pull down the conduction band, leading to local n-type conductivity, despite being an acceptor which pins the Fermi energy near the valence band maximum. This nanolamella may explain inconsistencies in measured conduction type as well as open up a new route to manipulate bulk carrier concentration. Our work may pave the way to more thoroughly understand and tailor the nature of the bulk, as well as secure controllable bulk states for future applications in quantum computing and dissipationless devices. PMID:23713705

Jiang, Ying; Wang, Yong; Sagendorf, Jared; West, Damien; Kou, Xufeng; Wei, Xiao; He, Liang; Wang, Kang L; Zhang, Shengbai; Zhang, Ze

2013-06-12

77

The electronic structure and chemical bonding of vitamin B12  

NASA Astrophysics Data System (ADS)

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

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

2003-05-01

78

The signature of chemical valence in the electrical conduction through a single-atom contact  

Microsoft Academic Search

Fabrication of structures at the atomic scale is now possible using state-of-the-art techniques for manipulating individual atoms, and it may become possible to design electrical circuits atom by atom. A prerequisite for successful design is a knowledge of the relationship between the macroscopic electrical characteristics of such circuits and the quantum properties of the individual atoms used as building blocks.

Elke Scheer; Nicolás Agraït; Juan Carlos Cuevas; Alfredo Levy Yeyati; Bas Ludoph; Alvaro Martín-Rodero; Gabino Rubio Bollinger; Jan M. van Ruitenbeek; Cristián Urbina

1998-01-01

79

Chemical oxygen-iodine laser with atomic iodine generated in a separate reactor  

NASA Astrophysics Data System (ADS)

The chemical oxygen-iodine laser (COIL) with a chemical method of atomic iodine generation was studied. Two methods of atomic iodine generation were proposed and developed. They are based on fast reactions of gaseous hydrogen iodide with chemically produced chlorine or fluorine atoms. Atomic iodine formation via Cl atoms we studied earlier by mixing of reaction gases directly in the primary O2(1?g) flow in COIL. A revealed oxidation of HI by singlet oxygen and the O2(1?g) quenching by some reaction product, however, reduced the attainable laser gain. This problem could be avoided by atomic iodine generation in separate reactors with following injection of atomic iodine into the primary O2(1?g) flow. Gain measurements using this arrangement are presented in this paper. New experimental results on atomic iodine production via F atoms are also summarized. Using of reactive gases commercially available in pressure cylinders is the main advantage of this method.

Špalek, Otomar; Jirásek, Vít; ?enský, Miroslav; Kodymova, Jarmila; Pickova, Irena; Jakubec, Ivo

2006-05-01

80

MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES  

SciTech Connect

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

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

2000-09-01

81

Atomic diversity, molecular diversity, and chemical diversity: the concept of chemodiversity.  

PubMed

This minireview is meant as an introduction to the following paper. To this end, it presents the general background against which the joint paper should be understood. The first objective of the present paper is thus to clarify some concepts and related terminology, drawing a clear distinction between i) atomic diversity (i.e., atomic-property space), ii) molecular or macromolecular diversity (i.e., molecular- or macromolecular-property spaces), and iii) chemical diversity (i.e., chemical-diversity space). The first refers to the various electronic states an atom can occupy. The second encompasses the conformational and property spaces of a given (macro)molecule. The third pertains to the diversity in structure and properties exhibited by a library or a supramolecular assembly of different chemical compounds. The ground is thus laid for the content of the joint paper, which pertains to case ii, to be placed in its broader chemodiversity context. The second objective of this paper is to point to the concepts of chemodiversity and biodiversity as forming a continuum. Chemodiversity is indeed the material substratum of organisms. In other words, chemodiversity is the material condition for life to emerge and exist. Increasing our knowledge of chemodiversity is thus a condition for a better understanding of life as a process. PMID:19697332

Testa, Bernard; Vistoli, Giulio; Pedretti, Alessandro; Bojarski, Andrzej J

2009-08-01

82

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

83

Chemical Structure and Dynamics annual report 1997  

Microsoft Academic Search

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

S. D. Colson; R. S. McDowell

1998-01-01

84

StructureActivity Relationships Derived by Machine Learning: The Use of Atoms and their Bond Connectivities to Predict Mutagenicity by Inductive Logic Programming  

Microsoft Academic Search

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

Ross D. King; Stephen H. Muggleton; Ashwin Srinivasan; Michael J. E. Sternberg

1996-01-01

85

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

Microsoft Academic Search

Amorphous hydrogenated silicon nitride (SiNH) materials prepared by plasma-enhanced chemical vapor deposition (PECVD) are of high interest because of their suitability for diverse applications including optical coatings, gas\\/vapor permeation barriers, corrosion resistant, and protective coatings and numerous others. In addition, they are very suitable for structurally graded systems such as those with a graded refractive index. In parallel, modeling the

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

2010-01-01

86

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

87

A Variational Monte Carlo Approach to Atomic Structure  

ERIC Educational Resources Information Center

|The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.|

Davis, Stephen L.

2007-01-01

88

Electronic structure and chemical bonding in half-Heusler phases  

Microsoft Academic Search

The electronic structure and chemical bonding in half-Heusler phases have been systematically investigated using first-principles, self-consistent tight-binding linear-muffin-tin-orbital calculations within the atomic-sphere approximation (TB-LMTO-ASA). The density-of-states profiles for the mainstream half-Heusler phases exhibit very similar features originating from the cubic, positional-parameter-free AlLiSi-type structural arrangement and resemblances in composition. The electronic structures of these half-Heusler phases are accordingly very suitable for

Laila Offernes; P. Ravindran; A. Kjekshus

2007-01-01

89

Metal-atom Structures Fabricated on the Si(100) Surface  

NASA Astrophysics Data System (ADS)

We have demonstrated a method of fabricating metal-atom structures on the Si(100)-2x1-H surface by scanning-tunneling-microscopy (STM). Dangling-bond lines are formed by extracting hydrogen atoms using the STM tunneling current. Adsorption of Ga atoms on this surface are observed preferentially on the dangling bonds. By utilizing the selective adsorption of Ga atoms on the dangling-bond patterns, we have thermally deposited Ga atoms and fabricated Ga-atom structures on the Si surface [1]. Connecting the atomic structures to the bulk electrodes is another important key issue for actually measuring the property of those atom structures and evaluate the performance of the atomic devices. We have used micron-order metal mask and have formed metal wires as well as bonding pads on the Si(100)-2x1-H surface by thermally evaporating Au/Ti in-situ. We have found that Ti atoms do not migrate on the hydrogen terminated Si surface and adsorb randomly and stably on the surface, thus it is effectively used as a glue material between Au wire and the Si(100)-2x1-H surface. [1]T. Hashizume, S. Heike, M. I. Lutwyche, S. Watanabe, K. Nakajima, T. Nishi and Y. Wada, Jpn. J. Appl. Phys. 35, L1085 (1996).

Hashizume, Tomihiro; Heike, S.; Lutwyche, M. I.; Watanabe, S.; Wada, Y.

1997-03-01

90

Measurement of Young's modulus of nanocrystalline ferrites with spinel structures by atomic force acoustic microscopy  

Microsoft Academic Search

Using Atomic Force Acoustic Microscopy, the Young's moduli of two thin films of nanocrystalline ferrites with spinel structures have been measured as a function of the oxidation temperature on a nanoscale. There is an overall decrease of the Young's moduli as a function of the oxidation temperature with an intermediate minimum and maximum. These measurements corroborate the existence of chemical

E. Kester; U. Rabe; L. Presmanes; Ph. Tailhades; W. Arnold

2000-01-01

91

Energy density analysis of the chemical bond between atoms in perovskite-type hydrides  

Microsoft Academic Search

Atomization energy diagram is proposed for analyzing the chemical bond in the perovskite-type hydrides such as M1MgH3 (M1=Na, K, Rb), RbCaH3, CaNiH3 and SrPdH3. The atomization energies of hydrogen and metal atoms in the hydrides are evaluated theoretically by the energy density analysis (EDA) of the total energy, and used for the construction of the atomization energy diagram. Every hydride

Yoshifumi Shinzato; Hiroshi Yukawa; Masahiko Morinaga; Takeshi Baba; Hiromi Nakai

2007-01-01

92

Atomic contributions from spin-orbit coupling to 29Si NMR chemical shifts in metallasilatrane complexes.  

PubMed

New members of a novel class of metallasilatrane complexes [X-Si-(?-mt)(4)-M-Y], with M=Ni, Pd, Pt, X=F, Cl, Y=Cl, Br, I, and mt=2-mercapto-1-methylimidazolide, have been synthesized and characterized structurally by X-ray diffraction and by (29)Si solid-state NMR. Spin-orbit (SO) effects on the (29)Si chemical shifts induced by the metal, by the sulfur atoms in the ligand, and by heavy halide ligands Y=Cl, Br, I were investigated with the help of relativistic density functional calculations. Operators used in the calculations were constructed such that SO coupling can selectively be switched off for certain atoms. The unexpectedly large SO effects on the (29)Si shielding in the Ni complex with X=Y=Cl reported recently originate directly from the Ni atom, not from other moderately heavy atoms in the complex. With respect to Pd, SO effects are amplified for Ni owing to its smaller ligand-field splitting, despite the smaller nuclear charge. In the X=Cl, Y=Cl, Br, I series of complexes the Y ligand strongly modulates the (29)Si shift by amplifying or suppressing the metal SO effects. The pronounced delocalization of the partially covalent M?Y bond plays an important role in modulating the (29)Si shielding. We also demonstrate an influence from the X ligand on the (29)Si SO shielding contributions originating at Y. The NMR spectra for [X-Si-(?-mt)(4)-M-Y] must be interpreted mainly based on electronic and relativistic effects, rather than structural differences between the complexes. The results highlight the sometimes unintuitive role of SO coupling in NMR spectra of complexes containing heavy atoms. PMID:22930544

Autschbach, Jochen; Sutter, Kiplangat; Truflandier, Lionel A; Brendler, Erica; Wagler, Jörg

2012-08-28

93

Atomic force microscopy of supercoiled DNA structure on mica  

Microsoft Academic Search

Atomic force microscopy (AFM) has been used to investigate supercoiled DNA structure. In AFM imaging, the deformation of DNA structure in the adsorption process onto the mica surface is a serious problem. To investigate the structure of supercoiled DNA in solution by AFM, the method by which DNA is fixed on the substrate without any deformation of the structure should

Masato Tanigawa; Takao Okada

1998-01-01

94

Annual Report 1998: Chemical Structure and Dynamics  

Microsoft Academic Search

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

RS McDowell

1999-01-01

95

Annual Report 1998: Chemical Structure and Dynamics  

Microsoft Academic Search

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

SD Colson; RS McDowell

1999-01-01

96

Chemical structure and dynamics: Annual report 1996  

Microsoft Academic Search

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important

S. D. Colson; R. S. McDowell

1997-01-01

97

Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures  

USGS Publications Warehouse

New crystal-structure refinements of Pca21 boracite, Mg3ClB7O13, and R??{lunate}c ericaite, Fe2.4Mg0.6ClB7O13, show that some boron and oxygen atoms are involved in the 'ferro' transitions as well as the metal and halogen atoms. The atomic displacements associated with the polarity changes are as large as 0.6A??. ?? 1972.

Dowty, E.; Clark, J. R.

1972-01-01

98

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

99

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

100

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

101

Crystal Structure, Chemical Binding, and Lattice Properties  

NASA Astrophysics Data System (ADS)

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

Geurts, J.

102

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

103

Radio Frequency Study of Atomic Structure and Spectra.  

National Technical Information Service (NTIS)

We have investigated the possibility of using radio-frequency techniques for the study of the spectra and structure of free atomic ions. After consideration of various methods of producing polarized ions and detecting their polarization we concluded that ...

L. W. Anderson

1969-01-01

104

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

Microsoft Academic Search

We report combined first-principle and tight-binding (TB) calculations to simulate the effects of chemical edge modifications on structural and electronic properties. The C-C bond lengths and bond angles near the graphene nanoribbon (GNR) edge have considerable changes when edge carbon atoms are bounded to different atoms. By introducing a phenomenological hopping parameter t1 for nearest-neighbor hopping to represent various chemical

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

2007-01-01

105

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

106

Hyperspectral imaging of structure and composition in atomically thin heterostructures.  

PubMed

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

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

2013-07-12

107

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

108

Atomic Structure of Graphene on SiO 2  

Microsoft Academic Search

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

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

2007-01-01

109

Electrical and structural properties of chemically modified graphene sheets  

NASA Astrophysics Data System (ADS)

The chemical exfoliation of graphite through oxidation and then dispersion in a solvent is one of the methods of achieving scalable production of single graphene sheets. We use this method for making chemically modified graphene (CMG) sheets with tunable electronic properties, which can be placed flat on any surface or dispersed in various matrices. CMG sheets share some similarities with pristine graphene and with carbon nanotubes, e.g. tunable electron- and hole-type conductivity is observed in single CMG sheets just above the percolation threshold. CMGs may also be considered as a template for a bottom up development of a new class of materials. We have performed electrical measurements of individual CMG sheets and will discuss their electronic properties and the possible mechanisms of the charge transport in relation to their atomic structure and chemical composition.

Dikin, Dmitriy A.; Jung, Inhwa; Ruoff, Rodney S.

2009-03-01

110

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

111

Chemical structure and dynamics. Annual report 1995  

SciTech Connect

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

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

1996-05-01

112

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

113

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

114

Chemical Short-Range-Ordering Effect on Structural Relaxation in Metallic Glasses  

NASA Astrophysics Data System (ADS)

A model is proposed to address chemical effects on structural relaxation in metallic glasses. The atomic short range ordering (SRO) is described under the quasi-chemical approximation (QCA). Local chemical deviations from the ideal SRO are considered as an excess enthalpy. The simplified analysis of a disordered region’s evolution is based on the notion of the collective bond exchange between neighboring atoms. The approach suggests a bimolecular mechanism with possibly large apparent activation energy for structural relaxation near the glass transitions.

Zhu, Aiwu; Shiflet, G. J.; Poon, S. J.

2008-08-01

115

Protein structure determination from NMR chemical shifts  

PubMed Central

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

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

2007-01-01

116

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

117

Atomic structure of icosahedral Al6Mg4Cu  

NASA Astrophysics Data System (ADS)

An atomic structural model (quasiperiodic configuration of icosahedral clusters , or QCIC, model) for icosahedral Al6Mg4Cu was developed under the following assumptions: (1) The structural framework of the icosahedral phase is a three-dimensional (3D) Penrose tiling (PT). (2) The atomic arrangement is divided into two structural elements; those are the (Al,Cu)25Mg20 icosahedral cluster which is located at the twelvefold vertex in 3D PT, and the glue atoms between the icosahedral clusters. For a test of the validity of the QCIC model, the x-ray structure factor S(q) and the pair distribution function ?(r) of the model were compared with those determined experimentally. The ?(r) of the QCIC model is found to be in better agreement with the experimental ?(r) than that of the Henley-Elser model. The S(q) of the QCIC model is also found to agree satisfactorily with the experimental S(q).

Sakurai, Yoshiharu; Tanaka, Yoshikazu; Watanabe, Yasuhiro; Nanao, Susumu

1990-04-01

118

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

119

Crystal structure solution from experimentally determined atomic pair distribution functions  

Microsoft Academic Search

The paper describes an extension of the Liga algorithm for structure solution from atomic pair distribution function (PDF), to handle periodic crystal structures with multiple elements in the unit cell. The procedure is performed in 2 separate steps - at first the Liga algorithm is used to find unit cell sites consistent with pair distances extracted from the experimental PDF.

Pavol Juhas; Luke Granlund; Saurabh R. Gujarathi; Phillip M. Duxbury; Simon J. L. Billinge

2010-01-01

120

Atomic structures at a Si-nitride/Si(001) interface  

NASA Astrophysics Data System (ADS)

We used high-resolution transmission electron microscopy to show that the atomic structures at a Si3N4/Si interface are clearly different from those at a SiO2/Si interface. Using first-principles calculations, we also found that, in one of the observed N-induced interfacial geometries, a dangling bond was produced on a Si atom adjacent to a N atom. We thus argue that such N-induced interfacial dangling bonds can cause degradation in the performance of metal-oxide-semiconductor transistors with Si-oxynitride (SiON) gate dielectrics when the N concentration is increased at the SiON/Si interfaces. We also argue that the difference in flatness between Si3N4 and SiON/Si interfaces and SiO2/Si interfaces is the result of the difference between their atomic structures.

Ikarashi, Nobuyuki; Watanabe, Koji; Miyamoto, Yoshiyuki

2001-09-01

121

Structure and chemical bond characteristics of LaB6  

NASA Astrophysics Data System (ADS)

The structure and chemical bond characteristics of LaB6 have been achieved by means of the density functional theory using the state-of-the-art full-potential linearized augmented plane wave (FPLAPW) method, which are implemented within the EXCITING code. The results show our optimized lattice constant a (4.158 Å), parameter z (0.1981) and bulk modulus B (170.4 GPa) are in good agreement with the corresponding experimental data. Electron localization function (ELF) shows the La-La bond mainly is ionic bond, La-B bond is between ionic and covalent bond while the covalent bond between the nearest neighbor B atoms (B2 and B3) is a little stronger than that between the nearer neighbor B atoms (B1 and B4).

Bai, Lina; Ma, Ning; Liu, Fengli

2009-11-01

122

Steric Structuring of Polyolefins by Chemical Methods  

NASA Astrophysics Data System (ADS)

The present state of the problem of the steric structuring of polyolefins by chemical cross-linking agents (organic peroxides, azo-compounds, and organo-silanes) is examined. The structure formation mechanisms, the process conditions, the requirements which must be met by cross-linking agents, the factors determining the properties of cross-linked polymers, as well as the prospects for the development of the method are discussed. The bibliography includes 28 references.

Konoval, I. V.; Konovalenko, N. G.; Ivanchev, Sergei S.

1988-01-01

123

The effect of doping three Al and N atoms on the chemical shielding tensor parameters of the boron phosphide nanotubes: A DFT study  

NASA Astrophysics Data System (ADS)

In this work, an armchair model of the (4,4) boron phosphide nanotubes (BPNTs) with a 1-nm length and consisting of 32 B and 32 P atoms is considered to study the influence of doping three atoms of aluminum in sites of boron (B3AlPNTs) and three atoms of nitrogen in sites of phosphors (BP3NNTs) on the electrostatic structure properties. The mouths of nanotubes are capped by hydrogen atoms in order to saturate the dangling bonds of the boundaries and to decrease the calculation time. The structures of BPNTs, B3AlPNTs and BP3NNTs are optimized by performing the level of density functional theory (DFT) using 6-31G* basis set. The optimized structures are used for calculating the chemical shielding (CS) tensors and nuclear magnetic resonance parameters such as isotropic chemical shielding (CSI) and anisotropic chemical shielding (CSA). The results reveal that in both models of B3AlPNTs and BP3NNTs by doping N atoms the chemical shielding parameters of P and B atoms, which are directly connected to the Al and N atoms decreased and the other sites significantly changed.

Rezaei-Sameti, Mahdi

2012-01-01

124

Atomic and Electronic Structures of Submonolayer In on Cu(111)  

Microsoft Academic Search

We have studied the atomic and electronic structures of submonolayer In on Cu(111) using synchrotron radiation photoemission and scanning tunnelling microscopy. At very low coverage, In atoms were favourable to occupy substitutional sites and to be distributed evenly on the Cu(111) surface. At a higher coverage of 0.33 and 0.50 ML, two ordered reconstructed phases of ((3)1\\/2×(3)1\\/2)R30o and (2×1) have

Peng Wang; Kun Xun; Jin-Feng Jia; Xing Gao; Hai-Jie Qian; Feng-Qin Liu; Kurash Ibrahim; Yu-Mei Zhou; Qi-Kun Xue; Si-Cheng Wu

2002-01-01

125

Electronic structure of atomically resolved carbon nanotubes  

NASA Astrophysics Data System (ADS)

Carbon nanotubes can be considered as single graphene sheets wrapped up into cylinders. Theoretical studies have shown that nanotubes can be either metallic or semiconducting, depending on minor differences in wrapping angle and diameter. We have obtained scanning tunneling microscopy and spectroscopy results on individual nanotubes which verify this prediction( J.W.G.Wildöer, L.C. Venema, A.G. Rinzler, R.E. Smalley, and C. Dekker, Nature, aimed for publication in Januari 1998). The combination of spectroscopy measurements and atomically resolved images allow to relate the electronic spectra to the wrapping angle and diameter. Tubes with various wrapping angles appear to be either metallic or semiconducting. Carbon nanotubes are expected to be one-dimensional conductors. Sharp peaks in the tunneling density of states that can be associated with the onsets of one-dimensional subbands are indeed observed. Furthermore, we are able to control the length of carbon nanotubes by STM nanostructuring( L.C. Venema, J.W.G. Wildöer, H.J. Temminck Tuinstra, A.G. Rinzler, R.E. Smalley and C. Dekker, Appl. Phys. Lett. (1997)). By applying voltage pulses to the STM tip above a nanotube, the tube can cut into a shorter section. In this way the electronic properties of nanotubes of various lengths can be investigated. footnotetext[0] email: venema@qt.tn.tudelft.nl Work done in collaboration with J.W.G. Wildöer, A.G. Rinzler, R.E. Smalley and C. Dekker.

Venema, Liesbeth

1998-03-01

126

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

SciTech Connect

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

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

1992-09-01

127

Structure and atomic motions in liquid sodium.  

National Technical Information Service (NTIS)

The microscopic structure function for liquid Na in the temperature range T=100 deg C - 600 deg C from the hard sphere approach and neutron diffraction data at the low momentum transfer measurements are obtained. These data are used within the mean field,...

I. Padureanu G. Rotarescu I. Popescu O. E. Kudryashov I. E. Ovchinnikov

1992-01-01

128

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

Microsoft Academic Search

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

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

2010-01-01

129

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

Microsoft Academic Search

Processes for depositing thin films with various electronic, optical, mechanical, and chemical properties are indispensable in many industries today. Of the many deposition methods available, chemical vapor deposition (CVD) has proved over time to be one of the most flexible, efficient, and cost-effective. Atomic layer deposition (ALD) is a newer process that is gaining favor as a method for depositing

Jeffrey Thomas Barton

2003-01-01

130

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

131

Structure–Activity Model of Chemicals That Cause Human Respiratory Sensitization  

Microsoft Academic Search

We report a structure–activity model of chemicals with the potential to cause respiratory allergy developed through the CASE\\/MultiCASE systems. Chemicals documented to elicit a decrease in FEV1of ?20% within 24 h of inhalation provocation challenge were used to form a learning set. Additional requirements for inclusion in the learning set were that chemicals had at least two contiguous nonhydrogen atoms

Cynthia Graham; Herbert S. Rosenkranz; Meryl H. Karol

1997-01-01

132

Applications of atomic magnetometry in chemical and biological imaging  

NASA Astrophysics Data System (ADS)

Atomic magnetometry has been recently developed as the most sensitive technique for detecting magnetic field, especially low-frequency magnetic signal. However, its applications in chemistry and biomedicine have not been extensively explored. In addition, the applications are often limited by the bulky size and high operating temperature of the magnetometers. We report a sensitive and compact atomic magnetometer that has an optimal operating temperature of 37 degree. The small size of the atomic sensors significantly improves the coupling between the sample and the detectors. Using this magnetometer in a scanning detection scheme, we show high-resolution, quantitative imaging of magnetically-labeled antibody binding to targeted molecules. We also show applications of this technique in nuclear magnetic resonance and magnetic resonance imaging in the Earth's magnetic field: a pH-sensitive gadolinium chelate for low magnetic field is revealed, which can be potentially used for minimum-invasive pH mapping; fluid flow in porous metallic materials is measured, which overcomes the penetration problem associated with conventional magnetic resonance imaging. Further improvement for the magnetometer and new detection schemes will be discussed.

Xu, Shoujun; Yao, Li; Garcia, Nissa; Yu, Dindi

2010-03-01

133

Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy.  

PubMed

The effect of tip chemical reactivity on the lateral manipulation of intrinsic Si adatoms toward a vacancy site on a Si(111)-(7 × 7) surface has been investigated by noncontact atomic force microscopy at room temperature. Here we measure the atom-hopping probabilities associated with different manipulation processes as a function of the tip-surface distance by means of constant height scans with chemically different types of tips. The interactions between different tips and Si atoms are evaluated by force spectroscopic measurements. Our results demonstrate that the ability to manipulate Si adatoms depends extremely on the chemical nature of the tip apex and is correlated with the maximal attractive force measured over Si adatoms. We rationalize the observed dependence of the atom manipulation process on tip-apex chemical reactivity by means of density functional theory calculations. The results of these calculations suggest that the ability to reduce the energy barrier associated with the Si adatom movement depends profoundly on tip chemical reactivity and that the level of energy barrier reduction is higher with tips that exhibit high chemical reactivity with Si adatoms. The results of this study provide a better way to control the efficiency of the atomic manipulation process for chemisorption systems. PMID:23906095

Sugimoto, Yoshiaki; Yurtsever, Ayhan; Abe, Masayuki; Morita, Seizo; Ondrá?ek, Martin; Pou, Pablo; Pérez, Ruben; Jelínek, Pavel

2013-08-01

134

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

135

Static and Dynamic Structural Modeling Analysis of Atomic Force Microscope  

Microsoft Academic Search

As a cantilever structure, atomic force microscope (AFM) can be either modeled as a beam, plate or a simple one degree-of-freedom\\u000a (DOF) system depending on its geometry and application scenario. The AFM structure can experience the deformation shapes of\\u000a vertical bending, lateral bending, torsion, extension and couplings between these four deformations depending on the excitation\\u000a mode. As a small structure

Yin Zhang; Kevin D Murphy

2010-01-01

136

Chemical Composition of Polymer Surfaces Imaged by Atomic Force Microscopy and Complementary Approaches  

Microsoft Academic Search

In this article we review the recent developments in the field of high resolution lateral mapping\\u000a of the surface chemical composition of polymers by atomic force microscopy (AFM) and other complementary\\u000a imaging techniques. The different AFM approaches toward nanometer scale mapping with chemical sensitivity\\u000a based on chemical force microscopy (CFM) are discussed as a means to unravel, for instance, the\\u000a lateral

G. Julius Vancso; Henrik Hillborg; Holger Schönherr

2005-01-01

137

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

138

Relativistic many-body theory of atomic structures  

NASA Astrophysics Data System (ADS)

The effect of relativity and electron correlations on atomic processes were studied. Current efforts include hyperfine structure (hfs) studies using the multiconfiguration Dirac-Fock (MCDF) techniques. Atomic hfs are known to be sensitive to relativity and electron correlations, and provide important tests of relativistic atomic many-body theories. Preliminary results on the hfs of the 4f(12) (3)H ground state of 68Fr(167) are shown and are in good agreement with experiment. The MCDF technique is an efficient and powerful method for atomic hfs studies. Further tests of this method are in progress. The absorption spectra for Xe-like ions in the region of 4d (FEMALE) nf, epsilonf transitions is being studied.

Cheng, K. T.

139

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

140

Surface atomic and electronic structure of ZnO polymorphs  

SciTech Connect

The surface atomic and electronic structures of the zinc-blende-, wurtzite-, and rocksalt-structure polymorphs of ZnO are investigated within a unified tight-binding (TB) model. For the fourfold-coordinated wurtzite and zinc-blende structures, large relaxations ({similar to}0.54 A) of the surface atoms are observed as a consequence of their ability to undergo approximately bond-length-conserving motions. For the sixfold-coordinated rocksalt structure, these motions are prohibited by the close-packed surface topology. Thus, only small movements of the cation and anion are expected in the direction normal to the surface. Within the resolution of this TB model ({similar to}0.01 A), we observe no surface relaxation of the rocksalt structure.

Skinner, A.J.; LaFemina, J.P. (Molecular Science Research Center, Pacific Northwest Laboratory, P.O. Box 999, Richland, Washington 99352 (United States))

1992-02-15

141

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

PubMed

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

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

2013-09-01

142

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

143

Chemical mapping of mammalian cells by atom probe tomography  

PubMed Central

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

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

2012-01-01

144

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

145

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

146

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

SciTech Connect

An adaptation of R.D. Cowan's Atomic Structure program, CATS, has been developed as part of the Theoretical Atomic Physics (TAPS) code development effort at Los Alamos. CATS has been designed to be easy to run and to produce data files that can interface with other programs easily. The CATS produced data files currently include wave functions, energy levels, oscillator strengths, plane-wave-Born electron-ion collision strengths, photoionization cross sections, and a variety of other quantities. This paper describes the use of CATS. 10 refs.

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

1988-12-01

147

Crambin: a direct solution for a 400-atom structure.  

PubMed

The crystal structure of crambin, a 46-residue protein containing the equivalent of approximately 400 fully occupied non-H-atom positions, was originally solved at 1.5 A by exploiting the anomalous scattering of its six S atoms at a single wavelength far removed from the absorption edge of sulfur. The crambin structure has now been resolved without the use of any anomalous-dispersion measurements. The technique employed was an ab initio 'shake-and-bake' method, consisting of a phase-refinement procedure based on the minimal function alternated with Fourier refinement. This method has successfully yielded solutions for a smaller molecule (28 atoms) using 1.2 A data, and a crambin solution was obtained at 1.1 A. PMID:15299333

Weeks, C M; Hauptman, H A; Smith, G D; Blessing, R H; Teeter, M M; Miller R

1995-01-01

148

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

149

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

150

Quantitative metallography of structural materials with the atomic force microscope  

Microsoft Academic Search

The atomic force microscopy (AFM) is now a well-established technique for imaging surface topography with high resolution and can be used to study the microstructure of structural materials in a nanometer range. On multiphase materials a contrast in the topographic AFM images is obtained from small height differences between the different phases. Accordingly investigations of microstructures that are prepared to

M. Goeken; H. Vehoff

1996-01-01

151

The physical structure of atoms: a new model  

Microsoft Academic Search

Purpose – The purpose of this paper is to establish a systemic yoyo model-based explanation for the internal structure of atoms, which is totally different of the conventional ones. Design\\/methodology\\/approach – The spin fields of systemic yoyos are used to explain the interactions between electric and magnetic fields and between elementary particles. Findings – The concepts of potential pits (traps)

Yi Lin; Xiaoya He

2010-01-01

152

Polymerase Activities and RNA Structures in the Atomic Force Microscope  

Microsoft Academic Search

The structures of the reaction products are the basis for novel polymerase assays using the atomic force microscope (AFM). Polymerases are the enzymes involved in transcription and replication of DNA. Rapid semiquantitative estimates of the activity of DNA polymerases such as Sequenase, Taq polymerase, and AMV reverse transcriptase and RNA polymerases (RNAP) such as Escherichia coli RNAP were obtained from

Helen G. Hansma; Roxana Golan; Wan Hsieh; Sarah L. Daubendiek; Eric T. Kool

1999-01-01

153

Visualization of hemiknot DNA structure with an atomic force microscope  

Microsoft Academic Search

The hemiknot, a novel type of DNA structure in which a loop is stabilized by threading one end of the duplex through another, has been studied in this paper. The hemiknot was obtained by reasso- ciation of a DNA fragment with (CA\\/TG)n inserts of different lengths. Slow and fast migrating products were purified by gel electrophoresis and imaged by atomic

Yuri L. Lyubchenko; Luda S. Shlyakhtenko; Melinda Binus; Claire Gaillard; Francois Strauss

2002-01-01

154

Angular coefficients in large-scale atomic structure calculations  

Microsoft Academic Search

Recent calculations on atomic structure and properties have used sets of configurational states (CSFs) of dimension O(10), much larger than was envisaged in the 1970s when programs such as MCHF and GRASP were designed. Current algorithms for reducing matrix elements between open shell CSFs to a sum of Slater integrals account for a substantial part of the computational cost of

Ian P. Grant

2004-01-01

155

Atomic structure calculations on the CRAY X-MP  

Microsoft Academic Search

Atomic structure calculations require both radial and angular integrations, where the latter are often based on Racah algebra. With relatively minor modifications, good performance is obtained on vector machines for radial integrations. Angular integrations, however, present the bottleneck. Some recent improvements in the algorithms for angular integrations are described, as well as some multitasking experiments on the CRAY X-MP and

1988-01-01

156

Atomic Structure of the Silicon/Silicon Dioxide Interface.  

National Technical Information Service (NTIS)

The atomic structure of the Si-SiO sub 2 interfaces obtained by thermal oxidation of singular and vicinal surfaces of silicon in dry O sub 2 at temperatures above 960 deg C has been studied in cross-section by high resolution electron microscopy (HREM). T...

J. H. Mazur

1985-01-01

157

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

158

Workshop on foundations of the relativistic theory of atomic structure  

SciTech Connect

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

Not Available

1981-03-01

159

MCHF atomic-structure package: support libraries and utilities  

NASA Astrophysics Data System (ADS)

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

Fischer, Charlotte Froese

1991-06-01

160

On the fine-structure splitting inbar p atoms  

NASA Astrophysics Data System (ADS)

Recent measurements of fine-structure splitting inbar p atoms of174Yb are analysed. Effects of nuclear deformation are calculated. The strength of nuclear spin-orbit coupling is determined and its implications on the N bar N potential are discussed.

Wycech, S.; Poth, H.; Rook, J. R.

1990-09-01

161

Atomic structure of Si-SiO(sub 2) interface.  

National Technical Information Service (NTIS)

Investigations of the atomic structure of Si-SiO(sub 2) interfaces have mostly been performed with high resolution transmission electron microscopy. However, the interpretation of the phase contrast in the amorphous phase at the interface is not unique. T...

G. Duscher S. J. Pennycook F. Banhart

1997-01-01

162

Atomic structure of (110) tilt grain boundaries in FCC materials.  

National Technical Information Service (NTIS)

High-resolution electron microscopy (HREM) has been used to study the atomic-scale structure and localized relaxations at grain boundaries (GBs) in Au, Al, and MgO. The (110) tilt GBs play an important role in polycrystalline fcc metals since among all of...

K. L. Merkle L. J. Thompson

1997-01-01

163

Theoretical studies of atomic structure and electronic structure in ternary amorphous Al - Cu - Y and Mg - Cu - Y alloys  

NASA Astrophysics Data System (ADS)

The atomic structure for the amorphous 0953-8984/9/46/013/img6 and 0953-8984/9/46/013/img7 (x = 30 and 80) alloys has been calculated in molecular dynamics simulations with the use of the Hausleitner - Hafner approach for the construction of the interatomic potentials. The parameters are adjusted so as to reconcile the resulting radial distribution function (RDF) spectrum with the measured one as closely as possible. Using the atomic structure thus obtained, the valence band structure is calculated in the LMTO recursion method. We show in this way the development of different chemical bonding states, depending on whether the third element introduced into the amorphous Cu - Y matrix is Al or Mg, and can successfully explain the Al and Mg concentration dependence of various physical properties.

Takeichi, N.; Sato, H.; Mizutani, U.

1997-11-01

164

Structure and dynamics in two-electron atoms  

NASA Astrophysics Data System (ADS)

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

Shuman, Edward Somerville

165

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

SciTech Connect

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

Alloyeau, D.; Nelayah, J.; Wang, G.; Ricolleau, C. [Laboratoire Materiaux et Phenomenes Quantiques, Universite Paris Diderot/CNRS, UMR 7162, Batiment Condorcet, 4 rue Elsa Morante, 75205 Paris Cedex 13 (France); Oikawa, T. [Laboratoire Materiaux et Phenomenes Quantiques, Universite Paris Diderot/CNRS, UMR 7162, Batiment Condorcet, 4 rue Elsa Morante, 75205 Paris Cedex 13 (France); JEOL Ltd, 1-2 Musashino 3-Chome, Akishima, Tokyo 196-8558 (Japan)

2012-09-17

166

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

NASA Astrophysics Data System (ADS)

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

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

2012-09-01

167

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

NASA Astrophysics Data System (ADS)

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

Hosono, Hideo; Matsunami, Noriaki

1993-11-01

168

Atomic structure of [110] tilt grain boundaries in FCC materials  

SciTech Connect

High-resolution electron microscopy (HREM) has been used to study the atomic-scale structure and localized relaxations at grain boundaries (GBs) in Au, Al, and MgO. The [110] tilt GBs play an important role in polycrystalline fcc metals since among all of the possible GB geometries this series of misorientations as a whole contains the lowest energies, including among others the two lowest energy GBs, the (111) and (113) twins. Therefore, studies of the atomic-scale structure of [110] tilt GBs in fcc metals and systematic investigations of their dependence on misorientation and GB plane is of considerable importance to materials science. [110] tilt GBs in ceramic oxides of the fcc structure are also of considerable interest, since in this misorientation range polar GBs exist, i.e. GBs in which crystallographic planes that are made up of complete layers of cations or anions can join to form a GB.

Merkle, K.L.; Thompson, L.J. [Argonne National Lab., IL (United States). Materials Science Div.

1997-04-01

169

Atomic structure variations of mechanically stable fcc-bcc interfaces  

NASA Astrophysics Data System (ADS)

It has recently been shown that under severe plastic deformation processing bi-metal fcc/bcc composites develop a mechanically stable heterophase interface that joins the {112}fcc//{112}bcc planes in the Kurdjumov-Sachs orientation relationship. In this article, we study variations in the relaxed equilibrium atomic structure of this interface with changes in fcc stacking fault energy (SFE) and lattice mismatch between the two crystals. Using molecular statics/dynamics simulations for three fcc/bcc systems, Cu-Nb, Al-Fe, and Al-Nb, we find that the number of distinct sets of intrinsic interfacial dislocations and their core structures vary significantly among these three systems. The impact of these atomic-scale structural differences on interfacial properties is demonstrated through their interactions with point defects. The interfaces studied here are shown to exhibit a wide variation in ability, ranging from being a poor to an excellent sink for vacancies.

Kang, K.; Wang, J.; Beyerlein, I. J.

2012-03-01

170

Finding the Atomic Configuration with a Required Physical Property in Multi-Atom Structures  

SciTech Connect

In many problems in molecular and solid state structures one seeks to determine the energy-minimizing decoration of sites with different atom types. In other problems, one is interested in finding a decoration with a target physical property (e.g. alloy band gap) within a certain range. In both cases, the sheer size of the configurational space can be horrendous. We present two approaches which identify either the minimum-energy configuration or configurations with a target property for a fixed underlying Bravais lattice. We compare their efficiency at locating the deepest minimum energy configuration of face centered cubic Au-Pd alloy. We show that a global-search genetic-algorithm approach with diversity-enhancing constraints and reciprocal-space mating can efficiently find the global optimum, whereas the local-search virtual-atom approach presented here is more efficient at finding structures with a target property.

d'Avezac, M.; Zunger, A.

2007-01-01

171

Atomic structure affects the directional dependence of friction.  

PubMed

Friction between two objects can be understood by the making, stretching, and breaking of thousands of atomic-scale asperities. We have probed single atoms in a nonisotropic surface [the H-terminated Si(100) surface] with a lateral force microscope operating in noncontact mode. We show that these forces are measurably different, depending upon the direction. Experimentally, these differences are observable in both the line profiles and the maximum stiffnesses. Density functional theory calculations show a concerted motion of the whole Si dimer during the tip-sample interaction. These results demonstrate that on an asperity-by-asperity basis, the surface atomic structure plays a strong role in the directional dependence of friction. PMID:24093279

Weymouth, A J; Meuer, D; Mutombo, P; Wutscher, T; Ondracek, M; Jelinek, P; Giessibl, F J

2013-09-18

172

Atomic Structure Affects the Directional Dependence of Friction  

NASA Astrophysics Data System (ADS)

Friction between two objects can be understood by the making, stretching, and breaking of thousands of atomic-scale asperities. We have probed single atoms in a nonisotropic surface [the H-terminated Si(100) surface] with a lateral force microscope operating in noncontact mode. We show that these forces are measurably different, depending upon the direction. Experimentally, these differences are observable in both the line profiles and the maximum stiffnesses. Density functional theory calculations show a concerted motion of the whole Si dimer during the tip-sample interaction. These results demonstrate that on an asperity-by-asperity basis, the surface atomic structure plays a strong role in the directional dependence of friction.

Weymouth, A. J.; Meuer, D.; Mutombo, P.; Wutscher, T.; Ondracek, M.; Jelinek, P.; Giessibl, F. J.

2013-09-01

173

Atomic structures and compositions of internal interfaces. [Produced by internal oxidation of alloys  

SciTech Connect

This research program addresses fundamental questions concerning the relations between atomic structures and compositions of homophase and heterophase interfaces. Metal/ceramic heterophase interfaces are created via the process of internal oxidation of metallic alloys. The interfaces are studied via a combination of conventional transmission electron microscopy, high resolution electron microscopy, field-ion microscopy and atom probe microscopy. The latter technique is employed to chemically sequence the interfacial region, and to show that the terminating (222) plane of MgO and CdO consists solely of oxygen atoms forthe Cu/MgO (111) and Ag/CdO (111) heterophase interfaces, respectively; this is achieved with no deconvolution of the experimental data. The evolution of metal/ceramic heterophase interfaces is studied by following the process of internal oxidation on an atomic scale from its very earliest stages. It is demonstrated that during the early stages of internal oxidation that metal atom clusters as well as hypo and hyperstoichiometric metal-oxygen clusters are present. Solute-atom segregation to grain boundaries is studied in binary metal alloys employing the free energy simulations and the overlapping distribution Monte Carlo methodologies for dilute Pt(Au), Cu(Ni) and Pd(Ni) alloys for both twist and tilt boundaries.

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

1993-05-10

174

Atomic structures and compositions of internal interfaces. Progress report, September 1, 1992--August 31, 1993  

SciTech Connect

This research program addresses fundamental questions concerning the relations between atomic structures and compositions of homophase and heterophase interfaces. Metal/ceramic heterophase interfaces are created via the process of internal oxidation of metallic alloys. The interfaces are studied via a combination of conventional transmission electron microscopy, high resolution electron microscopy, field-ion microscopy and atom probe microscopy. The latter technique is employed to chemically sequence the interfacial region, and to show that the terminating (222) plane of MgO and CdO consists solely of oxygen atoms forthe Cu/MgO (111) and Ag/CdO (111) heterophase interfaces, respectively; this is achieved with no deconvolution of the experimental data. The evolution of metal/ceramic heterophase interfaces is studied by following the process of internal oxidation on an atomic scale from its very earliest stages. It is demonstrated that during the early stages of internal oxidation that metal atom clusters as well as hypo and hyperstoichiometric metal-oxygen clusters are present. Solute-atom segregation to grain boundaries is studied in binary metal alloys employing the free energy simulations and the overlapping distribution Monte Carlo methodologies for dilute Pt(Au), Cu(Ni) and Pd(Ni) alloys for both twist and tilt boundaries.

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

1993-05-10

175

Contact atomic structure and electron transport through molecules  

NASA Astrophysics Data System (ADS)

Using benzene sandwiched between two Au leads as a model system, we investigate from first principles the change in molecular conductance caused by different atomic structures around the metal-molecule contact. Our motivation is the variable situations that may arise in break junction experiments; our approach is a combined density functional theory and Green function technique. We focus on effects caused by (1) the presence of an additional Au atom at the contact and (2) possible changes in the molecule-lead separation. The effects of contact atomic relaxation and two different lead orientations are fully considered. We find that the presence of an additional Au atom at each of the two contacts will increase the equilibrium conductance by up to two orders of magnitude regardless of either the lead orientation or different group-VI anchoring atoms. This is due to a resonance peak near the Fermi energy from the lowest energy unoccupied molecular orbital. In the nonequilibrium properties, the resonance peak manifests itself in a negative differential conductance. We find that the dependence of the equilibrium conductance on the molecule-lead separation can be quite subtle: either very weak or very strong depending on the separation regime.

Ke, San-Huang; Baranger, Harold U.; Yang, Weitao

2005-02-01

176

Atomic Force Microscopy Study on the Dissolution Processes of Chemically Amplified Resists for KrF Excimer Laser Lithography  

NASA Astrophysics Data System (ADS)

The surface images of chemically amplified KrF excimer laser resists after development were measured by atomic force microscopy (AFM). From the AFM images at various exposure doses, the dissolution behavior of the polyvinylphenol-based KrF resists differed from that of novolak-diazonaphthoquinone (DNQ) resists. An explanation for the different dissolution behavior has been proposed by considering the difference in the mechanisms of formation of soluble sites between chemically amplified resists and novolak-DNQ resists (non-chemically amplified resists). In addition, AFM topographic images of the resists dissolving layer by layer were observed clearly in the resist spin-coated on a Si wafer. The step heights of the layered structure observed by AFM are in good agreement with the computed value of the distance between two adjacent nodes of standing waves formed by KrF excimer laser exposure. The layered dissolution may be applied to the processing of thin polymer films.

Kanzaki, Kenichi; Ohfuji, Takeshi; Sasago, Masaru; Tagawa, Seiichi

1999-05-01

177

Modeling Protein Structure at Near Atomic Resolutions With Gorgon  

PubMed Central

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

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

2011-01-01

178

Dependence of oxide surface structure on surface topology and local chemical bonding  

Microsoft Academic Search

The atomic geometries of the charge neutral surfaces of several oxides exhibiting different crystal structures and varying participation of O(2{ital p}) electrons in the chemical bonding have been calculated using tight-binding total energy models. Surface structures have been computed for exemplary cubic (MgO), wurtzite (ZnO), β-tridymite, and ideal β-cristobalite (SiOâ) oxides. The cubic oxide exhibits a minimum energy structure involving

John P. LaFemina; C. B. Duke

1991-01-01

179

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

PubMed Central

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

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

2008-01-01

180

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

PubMed

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 MoS(2) 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 WS(2) 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

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

2008-10-06

181

Atomic and electronic structures of novel silicon surface structures.  

National Technical Information Service (NTIS)

The modification of silicon surfaces is presently of great interest to the semiconductor device community. Three distinct areas are the subject of inquiry: first, modification of the silicon electronic structure; second, passivation of the silicon surface...

J. H. Terry

1997-01-01

182

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

183

Chemical Bonds and Valence States of Atoms in Monocarbides and Mononitrides of D-Transition Metals.  

National Technical Information Service (NTIS)

On the basis of the metallic bond model described earlier, the chemical bond and atomic valency in these phases are considered. It is shown that the character of the interatomic bond in nitrides and carbides is identical. Electron transfer between the com...

P. P. Kuz'menko

1975-01-01

184

Electronic structure and effective chemical and magnetic exchange interactions in bcc Fe-Cr alloys  

Microsoft Academic Search

Electronic structure calculations are employed in order to investigate the cohesive properties (lattice parameter, enthalpy of formation, and bulk modulus) of random Fe-Cr alloys as a function of composition and magnetic state, as well as to derive the chemical and magnetic exchange interactions of the constituent atoms. The calculations predict certain anomalies in the cohesive properties of ferromagnetic alloys at

P. A. Korzhavyi; A. V. Ruban; J. Odqvist; J.-O. Nilsson; B. Johansson

2009-01-01

185

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

186

Quantum Degeneracy in Atomic Point Contacts Revealed by Chemical Force and Conductance  

NASA Astrophysics Data System (ADS)

Quantum degeneracy is an important concept in quantum mechanics with large implications to many processes in condensed matter. Here, we show the consequences of electron energy level degeneracy on the conductance and the chemical force between two bodies at the atomic scale. We propose a novel way in which a scanning probe microscope can detect the presence of degenerate states in atomic-sized contacts even at room temperature. The tunneling conductance G and chemical binding force F between two bodies both tend to decay exponentially with distance in a certain distance range, usually maintaining direct proportionality G?F. However, we show that a square relation G?F2 arises as a consequence of quantum degeneracy between the interacting frontier states of the scanning tip and a surface atom. We demonstrate this phenomenon on the Si(111)-(7×7) surface reconstruction where the Si adatom possesses a strongly localized dangling-bond state at the Fermi level.

Sugimoto, Yoshiaki; Ondrá?ek, Martin; Abe, Masayuki; Pou, Pablo; Morita, Seizo; Perez, Ruben; Flores, Fernando; Jelínek, Pavel

2013-09-01

187

The Creation and Characterization of Chemically Created Atomic Population Inversions for the Development of a Visible Chemical Laser  

NASA Astrophysics Data System (ADS)

The possibility of developing a chemically pumped laser in the visible region has been investigated. First, the history and the recent developments of short wavelength chemical lasers (SWCL) were reviewed. The energy transfer pumped thallium self-terminating visible chemical laser and the chemically pumped sodium dimer laser amplifier developed previously in the Georgia Tech chemical physics laboratory were discussed in detail. Combining the basic knowledge of laser physics, gas dynamics, reaction chemistry and the experience accumulated by other researchers in the past quarter century, a mode of energy transfer pumping of an atomic laser medium is adopted. Efficient near-resonant energy transfer involving metastable excited states of SiO* (or GeO*) and ground state alkali (Na and K) or copper atoms have been realized. The energy donors, SiO* (or GeO*) in rm a^3 Sigma^+ and rm b^3 {bfPi} states, were generated in high yield from rm Si+N_2O (or rm Ge+O_3) reactions. The energy stored in these triplet states is transferred in a near resonant process to excite sodium to its rm 3d^2D, 4d^2D and rm 5s^2S states. rm(5d ^2D, 6s^2S.. in potassium and rm 4p^2p^0 in copper.). An electronically inverted atomic configuration in sodium atoms is formed from highly efficient near resonant intermolecular energy transfer using a newly developed chemical laser apparatus. Evidence was shown that the Si-N_2O-Na system satisfies the basic requirements for a visible chemical laser and has the potential to lase at a few hundred milliwatts at 569nm in the current laboratory scale apparatus. Gains were measured in the Si-N_2 O-Na system using three different methods. With an amplified spontaneous emission (ASE) method, gains at lambda = 569,616 and 819nm, corresponding to the rm 4d^2D, 5s^2S and rm 3d^2D to rm 3p^2P transitions, were detected. Gain at 569nm was also measured with a sodium discharge lamp and with a single mode dye laser. Efforts are also made to oscillate the sodium rm 4d^2D -rm 3p^2P transition at 569nm. Evidence from full optical cavity experiments demonstrated that the output intensity has exceeded the chemiluminescent intensity, indicating light amplification and initial oscillation.

Shen, Kang-Kang

188

Fine Structure of DNA Bundles: Atomic Force Microscopy Study  

Microsoft Academic Search

Direct observations of fine structure of DNA bundles were presented in this paper. These DNA bundles existed originally in lambda-DNA solution with a high concentration of 480 ng\\/mu l. When this solution was diluted, DNA bundles finally split into individual DNA molecules. DNA bundles were stretched on mica treated with 3-aminopropyl triethoxysilane (APS) and observed by an atomic force microscope

Guanglai Li; Yi Zhang; Bin Li; Jun Hu; Minqian Li

2001-01-01

189

Band structure and Fermi surface of atomically uniform lead films  

Microsoft Academic Search

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,

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

2010-01-01

190

The grasp2K relativistic atomic structure package  

Microsoft Academic Search

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

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

2007-01-01

191

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

192

Eremomycin--new glycopeptide antibiotic: chemical properties and structure.  

PubMed

By a combination of chemical and spectroscopic (1H and 13C NMR) studies the structure of a glycopeptide antibiotic eremomycin has been elucidated. It is closely related to vancomycin, but differs in sugar and chlorine content. The eremomycin aglycone contains monodechlorovancomycinic acid; the only chlorine atom is situated in the second amino acid after the N-terminal amino acid residue of the peptide. The sugar part is composed of glucose and two residues of an amino sugar shown to be 2,3,6-trideoxy-3-amino-C-3-methyl-L-arabino-hexopyranose (4-epi-vancosamine). One of the amino sugar residues is a component of the disaccharide 2-O-(alpha-L-4-epi-vancosaminyl)-beta-D-glucopyranose, attached to a triphenyl ether moiety; the position of another one is at the serine oxygen in the C-terminal region of the aglycone. PMID:2621162

Gause, G F; Brazhnikova, M G; Lomakina, N N; Berdnikova, T F; Fedorova, G B; Tokareva, N L; Borisova, V N; Batta, G Y

1989-12-01

193

Theory of the ac Stark effect on the atomic hyperfine structure and applications to microwave atomic clocks  

NASA Astrophysics Data System (ADS)

Microwave atomic clocks are based on the intrinsic hyperfine energy interval in the ground state of an atom. In the presence of an oscillating electric field, the atomic system---namely, the hyperfine interval---becomes perturbed (the ac Stark effect). For the atomic sample in a clock, such a perturbation leads to an undesired shift in the clock frequency and, ultimately, to an inaccuracy in the measurement of time. Here a consistent perturbation formalism is presented for the theory of the ac Stark effect on the atomic hyperfine structure. By further implementing relativistic atomic many-body theory, this formalism is then utilized for two specific microwave atomic clock applications: a high-accuracy calculation of the blackbody radiation shift in the 133Cs primary frequency standard and a proposal for microwave clocks based on atoms in an engineered optical lattice.

Beloy, Kyle

194

Features of the chemical models of a nonideal atomic plasma at high temperatures  

SciTech Connect

The equation of state for a hydrogen plasma at high temperatures is considered in a physical and a chemical model. A simple expression is obtained that relates the pressure correction in chemical models to the high-temperature limit of the atom partition function. This expression ensures a correct asymptotic behavior of the equation of state in the high-temperature limit. It is explained why the familiar astrophysical model of Hummer, Mihalas, and Daeppen, as applied to helioseismology, yields worse results than a physical model. A modification of the astrophysical model is proposed that makes it possible to use the nearest neighbor approximation to calculate the atom partition function in chemical models in solving astrophysical problems and problems concerning low-temperature plasmas.

Khomkin, A. L.; Shumikhin, A. S. [Russian Academy of Sciences, Joint Institute for High Temperatures (Russian Federation)

2008-03-15

195

Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations  

Microsoft Academic Search

The structural comparison of proteins has become increasingly important as a means to identify protein motifs and fold families. In this paper we present a new algorithm for the comparison of proteins based on a hierarchy of structural representations, from the secondary structure level to the atomic level. Our technique represents ?-helices and ?-strands as vectors and uses a set

Amit Pal Singh; Douglas L. Brutlag

1997-01-01

196

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

NASA Astrophysics Data System (ADS)

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

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

2000-07-01

197

InChI - the worldwide chemical structure identifier standard.  

PubMed

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

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

2013-01-24

198

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.

2013-01-01

199

Structure of a Quantized Vortex in Fermi Atom Gas  

SciTech Connect

In atomic Fermi gases, the pairing character changes from BCS-like to BEC-like when one decreases the threshold energy of the Feshbach resonance. With this crossover, the system enters the strong-coupling regime through the population enhancement of diatom molecules, and the vortex structure becomes much different from well-known core structures in BCS superfluid since the superfluid order parameter is given by a sum of BCS pairs and BEC molecular condensates. In this paper, we study the structure of a vortex by numerically solving the generalized Bogoliubov-de Gennes equation derived from the fermion-boson model and clarify how the vortex structure changes with the threshold energy of the Feshbach resonance. We find that the diatom boson condensate enhances the matter density depletion inside the vortex core and the discreteness of localized quasi-particle spectrum.

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

2006-09-07

200

AFM-IR: combining atomic force microscopy and infrared spectroscopy for nanoscale chemical characterization.  

PubMed

Polymer and life science applications of a technique that combines atomic force microscopy (AFM) and infrared (IR) spectroscopy to obtain nanoscale IR spectra and images are reviewed. The AFM-IR spectra generated from this technique contain the same information with respect to molecular structure as conventional IR spectroscopy measurements, allowing significant leverage of existing expertise in IR spectroscopy. The AFM-IR technique can be used to acquire IR absorption spectra and absorption images with spatial resolution on the 50 to 100 nm scale, versus the scale of many micrometers or more for conventional IR spectroscopy. In the life sciences, experiments have demonstrated the capacity to perform chemical spectroscopy at the sub-cellular level. Specifically, the AFM-IR technique provides a label-free method for mapping IR-absorbing species in biological materials. On the polymer side, AFM-IR was used to map the IR absorption properties of polymer blends, multilayer films, thin films for active devices such as organic photovoltaics, microdomains in a semicrystalline polyhydroxyalkanoate copolymer, as well as model pharmaceutical blend systems. The ability to obtain spatially resolved IR spectra as well as high-resolution chemical images collected at specific IR wavenumbers was demonstrated. Complementary measurements mapping variations in sample stiffness were also obtained by tracking changes in the cantilever contact resonance frequency. Finally, it was shown that by taking advantage of the ability to arbitrarily control the polarization direction of the IR excitation laser, it is possible to obtain important information regarding molecular orientation in electrospun nanofibers. PMID:23231899

Dazzi, Alexandre; Prater, Craig B; Hu, Qichi; Chase, D Bruce; Rabolt, John F; Marcott, Curtis

2012-12-01

201

Improved Performance of On-line Atom Trapping in Flame Furnace Atomic Absorption Spectrometry by Chemical Vapor Generation: Determination of Cadmium in High-Salinity Water Samples  

Microsoft Academic Search

On-line atom trapping inside a nickel flame furnace using chemical vapor generation for sample introduction was proposed for the determination of trace cadmium by flame atomic absorption spectrometry (AAS). Cadmium volatile species was generated upon reaction with potassium borohydride and then flushed into a flame furnace for on-line trapping by a flow of nitrogen carrier gas. The middle part of

Xi Wu; Peng Wu; Shaopang He; Wenshu Yang; Xiandeng Hou

2009-01-01

202

Quantitative metallography of structural materials with the atomic force microscope  

SciTech Connect

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

Goeken, M.; Vehoff, H. [Max-Planck-Inst. fuer Eisenforschung GmbH, Duesseldorf (Germany)

1996-10-15

203

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

204

Chemical state of carbon atoms on the surface of nanodiamond particles  

Microsoft Academic Search

Auger electron spectroscopy study of the chemical state of carbon atoms on the surface of nanodiamond particles is performed.\\u000a Auger spectra of nanodiamond particles indicate that carbon atoms in nanodiamond are in the same state as those in graphite,\\u000a i.e., in the ?\\u000a s\\u000a 1\\u000a ?\\u000a p\\u000a 2\\u000a ?1 state, but the ? band is displaced 1 eV in energy

A. P. Dement’ev; K. I. Maslakov

2004-01-01

205

Structural trends and chemical bonding in Te-doped silicon clathrates.  

PubMed

The recently discovered tellurium-doped silicon clathrates, Te7+xSi20-x and Te16Si38, both low- and high-temperature forms (cubic and rhombohedral, respectively), exhibit original structures that are all derived from the parent type I clathrate G8Si46 (G = guest atom). The similarities and differences between the structures of these compounds and that of the parent one are analyzed and discussed on the basis of charge distribution and chemical bonding considerations. Because of the particular character of the Te atom, these compounds appear to be at the border between the clathrate and polytelluride families. PMID:15792455

Jaussaud, Nicolas; Pouchard, Michel; Gravereau, Pierre; Pechev, Stanislas; Goglio, Graziella; Cros, Christian; San Miguel, Alfonso; Toulemonde, Pierre

2005-04-01

206

Formation, atomic structural optimization and electronic structures of tetrahedral carbon onion  

Microsoft Academic Search

The carbon onion with a tetrahedral structure was produced by electron-beam irradiation on amorphous carbon synthesized from polyvinyl alcohol. Atomic structure analysis and structural optimization of the onion were carried out by high-resolution electron microscopy, image simulation, molecular mechanics and molecular orbital calculations. A structure model of C84@C276 was proposed at the center of the tetrahedral carbon onion.

Takeo Oku; Ichihito Narita; Atsushi Nishiwaki

2004-01-01

207

Understanding the structure of the first atomic contact in gold  

PubMed Central

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

2013-01-01

208

Understanding the structure of the first atomic contact in gold  

NASA Astrophysics Data System (ADS)

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

Sabater, Carlos; Caturla, María José; Palacios, Juan José; Untiedt, Carlos

2013-05-01

209

Understanding the structure of the first atomic contact in gold.  

PubMed

: We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics. PMID:23718316

Sabater, Carlos; Caturla, María José; Palacios, Juan José; Untiedt, Carlos

2013-05-29

210

Molecular dynamic simulations and atomic structures of amorphous materials  

NASA Astrophysics Data System (ADS)

A long-standing issue of using molecular dynamics (MD) to simulate local atomic structures in nonequilibrium metals and alloys is the huge difference in cooling rates used in experimental studies and theoretical calculations. In this study, a unique approach was introduced to correct the fast time steps involved in the MD calculations. This approach has demonstrated various medium-range ordered zones with imperfect ordered packing, which are verified experimentally by high-resolution transmission electron microscopy and its selected simulation imaging of Zr2Ni glass.

Chen, G. L.; Liu, X. J.; Hui, X. D.; Hou, H. Y.; Yao, K. F.; Liu, C. T.; Wadsworth, J.

2006-05-01

211

Fine Structure of DNA Bundles: Atomic Force Microscopy Study  

NASA Astrophysics Data System (ADS)

Direct observations of fine structure of DNA bundles were presented in this paper. These DNA bundles existed originally in ?-DNA solution with a high concentration of 480 ng/? l. When this solution was diluted, DNA bundles finally split into individual DNA molecules. DNA bundles were stretched on mica treated with 3-aminopropyl triethoxysilane (APS) and observed by an atomic force microscope (AFM). A method was developed to avoid the possible artifacts during the drying process in sample preparation. It was found that in a bundle composed of two individual DNA molecules, these two molecules wound around each other in a helical path.

Li, Guanglai; Zhang, Yi; Li, Bin; Hu, Jun; Li, Minqian

2001-12-01

212

Atomic structure calculations on the CRAY X-MP  

SciTech Connect

Atomic structure calculations require both radial and angular integrations, where the latter are often based on Racah algebra. With relatively minor modifications, good performance is obtained on vector machines for radial integrations. Angular integrations, however, present the bottleneck. Some recent improvements in the algorithms for angular integrations are described, as well as some multitasking experiments on the CRAY X-MP and CRAY 2. These show that the workload can easily be distributed evenly among available processors with dynamic scheduling. 18 refs., 1 fig., 3 tabs.

Fischer, C.F.

1988-01-01

213

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

214

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

NASA Astrophysics Data System (ADS)

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

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

2011-11-01

215

Synthesis of large-area MoS2 atomic layers with chemical vapor deposition.  

PubMed

Large-area MoS(2) atomic layers are synthesized on SiO(2) substrates by chemical vapor deposition using MoO(3) and S powders as the reactants. Optical, microscopic and electrical measurements suggest that the synthetic process leads to the growth of MoS(2) monolayer. The TEM images verify that the synthesized MoS(2) sheets are highly crystalline. PMID:22467187

Lee, Yi-Hsien; Zhang, Xin-Quan; Zhang, Wenjing; Chang, Mu-Tung; Lin, Cheng-Te; Chang, Kai-Di; Yu, Ya-Chu; Wang, Jacob Tse-Wei; Chang, Chia-Seng; Li, Lain-Jong; Lin, Tsung-Wu

2012-03-30

216

Photo-induced chemical-vapor generation for sample introduction in atomic spectrometry  

Microsoft Academic Search

Chemical-vapor generation (CVG) is widely used as a sample-introduction technique for atomic spectrometry, with the advantages of efficient matrix separation, high analyte-transport efficiency, and high selectivity and sensitivity. Recently, photo-induced CVG (photo-CVG) was demonstrated to be a powerful alternative to conventional CVG. In photo-CVG, volatile species (including hydrides, elemental, carbonylated and alkylated analytes) are generated from non-volatile precursors by ultraviolet

Yongguang Yin; Jingfu Liu; Guibin Jiang

2011-01-01

217

Atom probe analysis of roughness and chemical intermixing in CoFe\\/Cu films (invited)  

Microsoft Academic Search

Three-dimensional atom probe analyses of the interfaces between CoFe and Cu layers has shown that both roughness and chemical intermixing can occur independently. Interfaces formed by the deposition of Cu onto CoFe mimic the roughness present in previously deposited interfaces, but have a very small amount of interfacial mixing. In contrast, interfaces formed by the deposition of CoFe onto Cu

D. J. Larson; A. Cerezo; P. H. Clifton; A. K. Petford-Long; R. L. Martens; T. F. Kelly; N. Tabat

2001-01-01

218

Chemical generation of a population inversion between the spin-orbit states of atomic iodine  

Microsoft Academic Search

An experiment is described in which metastable O2 was produced chemically by the reaction between chlorine fluorosulfate and hydrogen peroxide. Molecular iodine was then injected into a flowing stream of this oxygen, and the resulting population inversion between ground-state and excited iodine atoms was monitored by means of an optical double-resonance technique. Experimental data are presented which indicate that a

A. T. Pritt Jr.; R. D. Coombe; D. Pilipovich; R. I. Wagner; D. Benard; C. Dymek

1977-01-01

219

AMO Database in KAERI and Atomic Structure Studies  

NASA Astrophysics Data System (ADS)

Atomic spectroscopy studies carried out at the Laboratory for Quantum Optics in Korea Atomic Energy Research Institute are introduced together with the AMO (Atomic, Molecular, and Optical) database established based upon those studies.

Rhee, Yongjoo; Park, H. M.; Kwon, D. H.

2005-05-01

220

Data Mining of Toxic Chemicals: Structure Patterns and QSAR  

Microsoft Academic Search

We take a two-step strategy to explore noncongeneric toxic chemicals from the database RTECS: the screening of structure patterns and the generation of a detailed relationship between structure and activity. An efficient similarity comparison is proposed to screen chemical patterns for further QSAR analysis. Then CoMFA study is carried out on one structure pattern as an example of the implementation,

Jiansuo Wang; Luhua Lai; Youqi Tang

1999-01-01

221

Conservation-dissipation structure of chemical reaction systems  

NASA Astrophysics Data System (ADS)

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.

Yong, Wen-An

2012-12-01

222

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

223

Atomic structure of amorphous shear bands in boron carbide.  

PubMed

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

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

2013-09-20

224

Atomic structure of amorphous shear bands in boron carbide  

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

225

Quantum structural phase transition in chains of interacting atoms  

SciTech Connect

A quasi-one-dimensional system of trapped, repulsively interacting atoms (e.g., an ion chain) exhibits a structural phase transition from a linear chain to a zigzag structure, tuned by reducing the transverse trap potential or increasing the particle density. Since it is a one-dimensional transition, it takes place at zero temperature and therefore quantum fluctuations dominate. In Fishman et al.[Phys. Rev. B 77, 064111 (2008)] it was shown that the system close to the linear-zigzag instability is described by a {phi}{sup 4} model. We propose a mapping of the {phi}{sup 4} field theory to the well-known Ising chain in a transverse field, which exhibits a quantum critical point. Based on this mapping, we estimate the quantum critical point in terms of the system parameters. This estimate gives the critical value of the transverse trap frequency for which the quantum phase transition occurs and which has a finite, measurable deviation from the critical point evaluated within the classical theory. A measurement is suggested for atomic systems which can probe the critical trap frequency at sufficiently low temperatures T. We focus in particular on a trapped-ion system and estimate the implied limitations on T and on the interparticle distance. We conclude that the experimental observation of the quantum critical behavior is, in principle, accessible.

Shimshoni, Efrat [Department of Physics, Bar-Ilan University, Ramat-Gan IL-52900 (Israel); Morigi, Giovanna [Theoretische Physik, Universitaet des Saarlandes, D-66041 Saarbruecken (Germany); Department de Fisica, Universitat Autonoma de Barcelona, E-08193 Bellaterra (Spain); Fishman, Shmuel [Department of Physics, Technion, Haifa IL-32000 (Israel)

2011-03-15

226

Magnetic and atomic structure parameters of Sc-doped barium hexagonal ferrites  

NASA Astrophysics Data System (ADS)

Scandium-doped M-type barium hexagonal ferrites of the composition BaFe12-xScxO19 are well suited for low frequency microwave device applications such as isolators and circulators. A series of Sc-doped M-type barium hexagonal ferrite powders (x=0-1.2) were prepared by conventional ceramic processing techniques. The resulting powders were verified to be pure phase and maintain the nominal chemical stoichiometry by x-ray diffraction and energy dispersive x-ray spectroscopy, respectively. Static magnetic measurements indicated that both saturation magnetization and uniaxial magnetocrystalline anisotropy field decreased with increasing concentration of scandium. Extended x-ray absorption fine structure measurements were carried out to clarify the correlation between the magnetic and atomic structure properties. It is found that the substituted Sc has a strong preference for the bipyramidal site. Nevertheless, the substitution did not introduce additional atomic structural disorder into the barium hexagonal structure. The structural study provided important evidence to quantitatively explain the change in dc and microwave magnetic properties due to Sc ion doping.

Yang, Aria; Chen, Yajie; Chen, Zhaohui; Vittoria, Carmine; Harris, V. G.

2008-04-01

227

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

SciTech Connect

Scandium-doped M-type barium hexagonal ferrites of the composition BaFe12?xScxO19 are well suited for low frequency microwave device applications such as isolators and circulators. A series of Sc-doped M-type barium hexagonal ferrite powders (x = 0-1.2) were prepared by conventional ceramic processing techniques. The resulting powders were verified to be pure phase and maintain the nominal chemical stoichiometry by x-ray diffraction and energy dispersive x-ray spectroscopy, respectively. Static magnetic measurements indicated that both saturation magnetization and uniaxial magnetocrystalline anisotropy field decreased with increasing concentration of scandium. Extended x-ray absorption fine structure measurements were carried out to clarify the correlation between the magnetic and atomic structure properties. It is found that the substituted Sc has a strong preference for the bipyramidal site. Nevertheless, the substitution did not introduce additional atomic structural disorder into the barium hexagonal structure. The structural study provided important evidence to quantitatively explain the change in dc and microwave magnetic properties due to Sc ion doping.

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

2008-01-01

228

Visualization of hemiknot DNA structure with an atomic force microscope.  

PubMed

The hemiknot, a novel type of DNA structure in which a loop is stabilized by threading one end of the duplex through another, has been studied in this paper. The hemiknot was obtained by reassociation of a DNA fragment with (CA/TG)n inserts of different lengths. Slow and fast migrating products were purified by gel electrophoresis and imaged by atomic force microscopy (AFM) using the aminopropylsilatrane-mica technique for sample preparation. Slow migrating product was characterized by the formation of small blobs for the short insert (60 bp) and clear loops and other morphologies for the long insert (188 bp). These structural features were found in almost 100% of the molecules of the slow migrating sample and were not present in the control sample. Measurements showed that the location of the blobs coincided with the positions of the inserts. The sample with the 188 bp insert in the 573 bp fragment had large structural irregularities. The majority of the molecules (77%) had asymmetrically located loops. The location of the loop in the molecules correlated well with the position of the insert in the fragment. The measured sizes of the loops were in agreement with the insert size. Altogether, these data support the hypothesis for hemiknot formation suggested earlier. In addition to looped structures, other morphologies of the hemiknot were identified in AFM images. Possible models for hemiknot formation and structure are discussed. PMID:12433993

Lyubchenko, Yuri L; Shlyakhtenko, Luda S; Binus, Melinda; Gaillard, Claire; Strauss, François

2002-11-15

229

Nanometer scale atomic structure of zirconium based bulk metallic glass  

NASA Astrophysics Data System (ADS)

We have studied the nanometer scale structure of bulk metallic glass (BMG) using fluctuation electron microscopy (FEM). The nanometer scale medium range order (MRO) in BMG is of significant interest because of its possible relationship to the properties, but the experimental study of the MRO is difficult because conventional diffraction techniques are not sensitive to the MRO scale. FEM is a quantitative transmission electron microscopy technique which measures the nanoscale structural fluctuation associated with MRO in amorphous materials, and provides information about the size, distribution, and internal structure of MRO. In this work, we developed an improved method for FEM using energy-filtered STEM nanodiffraction with highly coherent probes with size up to 11nm in a state-of-the-art Cs- corrected STEM. We also developed an effective way to eliminate the effect of sample thickness variation to the FEM data by using Z-contrast images as references. To study the detailed structure of MRO, we developed a hybrid reverse Monte Carlo (H-RMC) simulation which combines an empirical atomic potential and the FEM data. H-RMC generated model structures that match the experimental data at short and medium range. In addition, the subtle rotational symmetries in the FEM nanodiffraction patterns were analyzed by angular correlation function to reveal more details of the internal structure of MRO. Our experiments and simulations show that Zr-based BMG contains pseudo-planar, crystal-like MRO as well as icosahedral clusters in its nanoscale structure. We found that some icosahedral clusters may be connected, and that structural relaxation by annealing increases the population of icosahedral clusters.

Hwang, Jinwoo

230

Interface Structure and Atomic Bonding Characteristics in Silicon Nitride Ceramics  

Microsoft Academic Search

Direct atomic resolution images have been obtained that illustrate how a range of rare-earth atoms bond to the interface between the intergranular phase and the matrix grains in an advanced silicon nitride ceramic. It has been found that each rare-earth atom bonds to the interface at a different location, depending on atom size, electronic configuration, and the presence of oxygen

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

2004-01-01

231

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

232

Nanoscale investigation of the structural and chemical changes induced by oxidation on carbon black surfaces: A scanning probe microscopy approach  

Microsoft Academic Search

Scanning tunneling microscopy (STM) and noncontact tapping mode atomic force microscopy (AFM) have been employed to study on a local scale the structural and, for the first time, the chemical changes of carbon black (CB) particles following plasma oxidation. STM imaging of the pristine, untreated particles revealed a relatively ordered structure of tiny crystallites with a few amorphous regions. After

J. I. Paredes; M. Gracia; A. Martínez-Alonso; J. M. D. Tascón

2005-01-01

233

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

SciTech Connect

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

An, Nguyen Ba; Kim, Jaewan; Kim, Kisik [Center for Theoretical Physics, Institute of Physics, 10 Dao Tan, Hanoi (Viet Nam) and School of Computational Sciences, Korea Institute for Advanced Study, 207-43 Cheongryangni 2-dong, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of); Department of Physics, Inha University, 253 Yonghyun-Dong, Nam-Gu, Incheon 402-751 (Korea, Republic of)

2011-08-15

234

Atomic layer deposition on fiber forming polymers and nonwoven fiber structures  

NASA Astrophysics Data System (ADS)

Recent advances in fiber processing technology have allowed the formation of fibers with sub-micron and nanoscale dimensions. Such fibers have received much recent attention due to their potential in wide ranging applications including but not limited to tissue scaffolds, affinity membranes, and other advanced filtration applications. This is due to their ability to provide high surface area, high porosity and good mechanical properties. However, in order to expand the range of applications and improve chemical and physical functionality, the ability to uniformly and predictably modify the surface of fibers in highly dense and tortuous nonwoven structures, in an environmentally friendly manor, is required. A variety of different techniques are currently used to modify the surface of planar polymers as well as nonwoven fiber structures. In this study, a vapor phase film deposition technique called atomic layer deposition (ALD) has been used to modify the surface of planar films of fiber forming polymers as well as nonwoven fiber structures. In-situ gravimetric and chemical analyses have been employed to investigate film precursor and polymer chemical and physical interaction, as well as the effect of process variables such as temperature on the nucleation and growth of ALD films on polymer materials.

Spagnola, Joseph Charles

235

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

Microsoft Academic Search

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

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

2010-01-01

236

Chemical reactions of atomic hydrogen at SiC surface and heterogeneous chemiluminescence  

NASA Astrophysics Data System (ADS)

In studies of the surface properties of SiC polytypes and chemical reactions of hydrogen atoms at SiC surfaces the surface (chemi)luminescence of SiC has been applied excited in the reaction of hydrogen atoms due to chemical energy released (heterogeneous chemiluminescence, HCL). The bulk photoluminescence (PL) have also been used for comparison with surface HCL. All the samples showed HCL, but only ?-SiC (6H, 15R), technologically or specially doped (predominantly by N, B, Al), exhibited PL (?ex=365 nm). Cubic polycrystalline ?-SiC (or 3C SiC) did not show PL. The general luminescence band of ?-SiC (6H, 15R) and B and Al doped SiC (6H) was a broad yellow band with ?max ranged from 620 to 650 nm for PL (110 K). Another less intensive luminescence band is a blue one, which has been observed only at low temperatures for ?-SiC (6H,15R) and B and Al doped SiC (6H) in PL spectra and as a shoulder in HCL spectra (?max=477 nm at 110 K for 15R SiC). The green band near 540 nm was also observed sometimes in PL spectra for ?-SiC. The heat of adsorption of hydrogen atoms at polycrystalline ?-SiC estimated from HCL data was found to be in the range from 2 to 3 eV.

Styrov, V. V.; Tyutyunnikov, V. I.; Sergeev, O. T.; Oya, Y.; Okuno, K.

2005-02-01

237

Defects in p-GaN and their atomic structure  

SciTech Connect

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

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

2004-10-08

238

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

239

Chemical Compound Classification with Automatically Mined Structure Patterns  

Microsoft Academic Search

In this paper we propose new methods of chemical structure classification based on the integration of graph database mining from data mining and graph kernel functions from machine learning. In our method, we first identify a set of general graph patterns in chemical structure data. These patterns are then used to augment a graph kernel function that calculates the pairwise

Aaron M. Smalter; J. Huan; Gerald H. Lushington

2008-01-01

240

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

241

Atomic structure of Si-SiO{sub 2} interface  

SciTech Connect

Investigations of the atomic structure of Si-SiO{sub 2} interfaces have mostly been performed with high resolution transmission electron microscopy. However, the interpretation of the phase contrast in the amorphous phase at the interface is not unique. The authors investigated the Si-SiO{sub 2} interface by studying the ELNES of the O-K edge with the spatial difference technique with a dedicated STEM with 100kV. Also the interface was studied by Z-contrast imaging with a 300 kV dedicated STEM. Silicon wafers (110) were first thermally oxidised to produce a SiO{sub 2} layer. The thermally grown oxide was used as a substrate for liquid phase epitaxy of silicon.

Duscher, G.; Pennycook, S.J. [Oak Ridge National Lab., TN (United States); Banhart, F. [MPI fuer Metallforschung, Stuttgart (Germany)] [and others

1997-04-01

242

Probing interface structure and bonding at atomic resolution by STEM  

SciTech Connect

Advantage of STEM is that no model structures are required to interpret the images to first order, so that unexpected interfacial phenomena will be immediately apparent, such as in CoSi{sub 2}/Si(100) interface made by Co implantation/annealing. By depositing two monolayer Ge marker layers during growth of Si{sub 0. 5}Ge{sub 0.5} alloy layer, a misfit dislocation was found to nucleate to relieve the strain. Hole concentration profiles can be measured in YBCO superconductor, using the pre-edge of the oxygen K EELS spectrum. Future directions of this combination of atomic-resolution imaging and analysis on a single microscope are discussed briefly.

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

1993-06-01

243

Atomic structure of the actin: DNase I complex  

NASA Astrophysics Data System (ADS)

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

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

1990-09-01

244

Physical and chemical structure of the IC 63 nebula. II. Chemical models  

Microsoft Academic Search

Chemical models are presented for the photon dominated region (PDR) IC 63, a small isolated molecular cloud located close to the B0.5 IVpe star gamma Cas for which we have presented observations of various molecular species in an earlier paper, and for which observations of ionized and neutral atomic carbon, as well as additional CO observations, are available. The models

D. J. Jansen; E. F. van Dishoeck; J. H. Black; M. Spaans; C. Sosin

1995-01-01

245

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

246

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

247

Chemical Sputtering of graphite surfaces by slow H and D Atomic and Molecular projectiles  

NASA Astrophysics Data System (ADS)

Because of its high thermal conductivity, excellent shock resistance, absence of melting, low activation, and low atomic number, there is significant technological interest in using graphite as a plasma-facing component on present and future fusion devices, despite its poor chemical erosion and sputtering properties. As divertor designs evolve, the interest in the erosion characteristics of the carbon surfaces is shifting to progressively lower impact energies. Results are presented of chemical sputtering yields for ATJ graphite and HOPG impacted by H^+(D^+), H2^+(D2^+)and H3^+(D3^+) in the energy range 5-250 eV/amu. The measurements serve as benchmarks for in house MD simulations [Physica Scripta T128, 50 (2007)] of the chemical sputtering process that seek to incorporate more realistic many-body potentials and to expand the reaction pathway to include vibrational and/or electronic excited states. Comparison between same velocity atomic and molecular ion impact at energies as low as 5 eV/amu will be described [J. Nucl. Mater. 357, 9(2006)]. In addition, the isotope effect in methane production by H and D incident ions will be discussed.

Meyer, F. W.; Zhang, H.; Krause, H. F.

2007-11-01

248

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

SciTech Connect

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

Brown, William Michael (Sandia National Laboratories, Albuquerque, NM); Martin, Shawn Bryan (Sandia National Laboratories, Albuquerque, NM); Faulon, Jean-Loup Michel

2005-06-01

249

Determination of bismuth, indium and lead in spiked sea water by electrothermal atomic absorption spectrometry using tungsten containing chemical modifiers  

Microsoft Academic Search

The determination of bismuth, indium and lead in spiked synthetic and natural sea water by electrothermal atomic absorption spectrometry (ETAAS) with Zeeman-effect background correction was investigated using tungsten containing chemical modifiers and tartaric acid (TA) as a reducing agent. Maximum pyrolysis and optimum atomization temperatures for the analyte elements were determined in the presence and absence of various modifiers. The

Orhan Acar; Ziya Kiliç

2000-01-01

250

Atomic-level 2-dimensional chemical mapping and imaging of individual dopants in a phosphor crystal.  

PubMed

The ability to visualize and identify individual dopants, as well as measure their local physical and chemical environments in a bulk, provides deep insight for designing new functional materials and predicting their properties. However, a full understanding of dopants inside a solid has been limited by currently available characterization techniques. We demonstrate the first atomic-level 2-dimensional elemental maps of Pr dopants using the electron energy-loss spectroscopy (EELS) technique and we image Al dopants located in a lattice. Based on spectroscopic and imaging evidence we provide plausible local defect configurations of implanted Pr(+) and Al(+) ions within SrTiO3 single crystals. Our results demonstrate the detection of single Pr atoms and the formation of Al-rich nanoscale clusters ranging from 1 to 3 nm in size randomly distributed in the implanted lattice. These results provide insight into the mechanism of red light emission in doped SrTiO3. PMID:23744110

Zhu, Guo-zhen; Lazar, Sorin; Knights, Andrew P; Botton, Gianluigi A

2013-06-07

251

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

SciTech Connect

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

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

1993-12-01

252

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

Microsoft Academic Search

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

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

2002-01-01

253

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

NASA Astrophysics Data System (ADS)

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

Kuznetsov, V.; Papastavrou, G.

2012-11-01

254

Atomic Oxygen Recombination and Chemical Energy Accommodation on Alumina at High Temperature  

SciTech Connect

To develop heat shields for space vehicles, materials must be characterized in simulation conditions close to those in space environments. The most important conditions for simulating the Earth re-entry phase of space vehicles are achieved through the MESOX set-up associating a 6 kW solar radiation concentrator and a 2450 MHz microwave plasma generator. This paper presents some experimental results for the recombination coefficient {gamma} and the chemical energy accommodation coefficient {beta} in the surface-catalyzed oxygen atom recombination based on experiments performed on the MESOX set-up. This set-up allows both the experimental measurements of the recombination coefficient {gamma} using Optical Emission Spectroscopy and the chemical energy accommodation coefficient {beta} using calorimetry according to a defined protocol. Experimental results are presented for three types of alumina in the temperature range 900-2400 K, for 200 Pa total air pressure. These three alumina differ essentially from their content of sintering additives.

Balat-Pichelin, Marianne J.H.; Bedra, L.; Badie, J.-M. [Laboratoire Procedes, Materiaux et Energie Solaire, PROMES-CNRS (ex IMP-CNRS), BP5, 66125 Odeillo, Font-Romeu (France); Boubert, P. [Institut Universitaire des Systemes Thermiques Industriels, IUSTI-CNRS, 5 rue E. Fermi, 13453 Marseille (France)

2005-05-16

255

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

PubMed

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

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

2009-05-01

256

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields  

PubMed Central

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

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

2012-01-01

257

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

258

Wear minimization through utilization of atomic-scale functional surface structure  

NASA Astrophysics Data System (ADS)

A method for wear minimization through utilization of an atomic-scale functional surface structure is proposed. The basic idea is to effectively dissipate the frictional energy generated during contact sliding so that its contribution to permanent displacement of atoms is minimized. This may be achieved by using a surface structure with optimum compliance that can accommodate the contact stresses through elastic, rather than permanent, deformation of the structure. This method was verified through molecular dynamics simulation of atomic-scale wear of a tip sliding against a hard coating layer that is supported by an atomic-scale functional surface structure.

Kim, Hyun-Joon; Kim, Dae-Eun

2013-10-01

259

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…

Inner London Education Authority (England).

260

The efficient cluster packing model – An atomic structural model for metallic glasses  

Microsoft Academic Search

A structural model is described for metallic glasses based on a new sphere packing scheme – the efficient filling of space by solute-centered clusters. This model combines random positioning of solvent atoms with atomic order of solutes. It shows that metallic glasses contain ?4 topologically distinct species and that solutes possess specific sizes relative to solvent atoms to produce efficient

D. B. Miracle

2006-01-01

261

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

SciTech Connect

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

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

1991-12-31

262

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

SciTech Connect

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

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

1991-01-01

263

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

264

Effect of interstitial lithium atom on crystal and electronic structure of silicon oxynitride  

Microsoft Academic Search

Plane-wave pseudopotential total energy method was used to calculate the effects of impurity Li atom on crystal structure,\\u000a electronic and dielectric properties of Si2N2O. It is proved that Li atom prefers to occupy interstitial site than to substitute the Si atomic site. In addition, the presence\\u000a of interstitial Li atom leads to relaxation of internal coordinates of Si, N, and

Bin Liu; Jingyang Wang; Fangzhi Li; Hongqiang Nian; Yanchun Zhou

2009-01-01

265

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

PubMed Central

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

Hay, Mark E.

2012-01-01

266

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

SciTech Connect

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

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

1990-09-01

267

Entangling Strings of Neutral Atoms in 1D Atomic Pipeline Structures  

NASA Astrophysics Data System (ADS)

We study a string of neutral atoms with nearest neighbor interaction in a 1D beam splitter configuration, where the longitudinal motion is controlled by a moving optical lattice potential. The dynamics of the atoms crossing the beam splitter maps to a 1D spin model with controllable time dependent parameters, which allows the creation of maximally entangled states of atoms by crossing a quantum phase transition. Furthermore, we show that this system realizes protected quantum memory, and we discuss the implementation of one- and two-qubit gates in this setup.

Dorner, U.; Fedichev, P.; Jaksch, D.; Lewenstein, M.; Zoller, P.

2003-08-01

268

Evolution of carbon structure in chemically activated wood  

Microsoft Academic Search

13C NMR and FTIR analyses have been employed to follow the evolution of chemical structure in relation to porosity development, as a function of heat treatment temperature (HTT), for activated carbons produced from white oak by phosphoric acid activation. The chemical changes effected by acid treatment at low HTT are: by 50 °C there is significant alteration of the lignin

M. S. Solum; R. J. Pugmire; M. Jagtoyen; F. Derbyshire

1995-01-01

269

Predicting Modes of Toxic Action from Chemical Structure: An Overview.  

National Technical Information Service (NTIS)

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 not empirical data a...

S. P. Bradbury

1994-01-01

270

Structural Features Associated with Degradable and Persistent Chemicals.  

National Technical Information Service (NTIS)

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

G. J. Niemi G. D. Veith R. R. Regal D. D. Vaishnav

1987-01-01

271

Intra-atomic noncollinear magnetism and the magnetic structures of antiferromagnetic FeMn  

NASA Astrophysics Data System (ADS)

Both collinear and noncollinear magnetic structures of FeMn with L10 atomic ordering were determined from total-energy full-potential linearized augmented plane-wave calculations incorporating noncollinear magnetism with no shape approximation for the magnetization density. Different spin-density orientations for the different band states are observed on a smaller length scale inside an atom. The presence of the intra-atomic noncollinear magnetism enhances the stability of the 3Q noncollinear magnetic structure, in which the magnetic moments align toward the center of the cell of four atoms, thus becoming the lowest-energy state of the structures considered.

Nakamura, Kohji; Ito, Tomonori; Freeman, A. J.; Zhong, Lieping; Fernandez-de-Castro, Juan

2003-01-01

272

Magnetic field structures in chemically peculiar stars  

NASA Astrophysics Data System (ADS)

We report the results of magnetic field modelling of around 50 CP stars, performed using the "magnetic charges" technique. The modelling shows that the sample reveals four main types of magnetic configurations: 1) a central dipole, 2) a dipole, shifted along the axis, 3) a dipole, shifted across the axis, and 4) complex structures. The vast majority of stars has the field structure of a dipole, shifted from the center of the star. This shift can have any direction, both along and across the axis. A small percentage of stars possess field structures, formed by two or more dipoles.

Glagolevskij, Yu. V.

2011-04-01

273

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

274

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

275

Mining Chemical Compound Structure Data Using Inductive Logic Programming  

Microsoft Academic Search

\\u000a Discovering knowledge from chemical compound structure data is a challenge task in KDD. It aims to generate hypotheses describing\\u000a activities or characteristics of chemical compounds from their own structures. Since each compound composes of several parts\\u000a with complicated relations among them, traditional mining algorithms cannot handle this kind of data efficiently. In this\\u000a research, we apply Inductive Logic Programming (ILP)

Cholwich Nattee; Sukree Sinthupinyo; Masayuki Numao; Takashi Okada

2003-01-01

276

Atomic structure calculations of KLL Auger spectra from highly charged ion-solid-surface collisions  

Microsoft Academic Search

Systematic atomic structure calculations of KLL Auger electron spectra from ``hollow'' atom configurations 1s2l23lZ-3 are performed for atomic numbers 6<=Z<=10. In comparison with the corresponding 1s2l2 Li-like configurations it is shown that the additional Z-3 M electrons, apart from taking part in LLM Coster-Kronig transitions, can be regarded basically as mere spectator electrons, neither severely influencing the peak structure due

S. Schippers; J. Limburg; J. Das; R. Hoekstra; R. Morgenstern

1994-01-01

277

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

PubMed

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

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

2013-03-05

278

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

279

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

SciTech Connect

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

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

1991-08-05

280

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

Microsoft Academic Search

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

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

1997-01-01

281

Gyration-radius dynamics in structural transitions of atomic clusters  

NASA Astrophysics Data System (ADS)

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating ``bath'' modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

Yanao, Tomohiro; Koon, Wang S.; Marsden, Jerrold E.; Kevrekidis, Ioannis G.

2007-03-01

282

Gyration-radius dynamics in structural transitions of atomic clusters.  

PubMed

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum. PMID:17411103

Yanao, Tomohiro; Koon, Wang S; Marsden, Jerrold E; Kevrekidis, Ioannis G

2007-03-28

283

Structure, stability and catalytic activity of chemically synthesized Pt, Au, and Au-Pt nanoparticles.  

PubMed

Small (1-5 nm) metallic nanoparticles of Pt, Au, and Au/Pt of different nominal compositions in colloidal form were synthesized by a chemical reduction method using polymer (PVP) as protecting agent. Analytical techniques like HREM and UV-vis spectroscopy have been used to characterize the morphology and structural properties of these small particles. Theoretical simulations based on molecular dynamical have been used to interpret the experimental structural results and analyze the macroscopic properties like stability and catalytic selectivity of these nanoparticles based on the morphology and atomic distribution in the clusters. PMID:16004132

Esparza, R; Ascencio, J A; Rosas, G; Sánchez Ramírez, J F; Pal, U; Perez, R

2005-04-01

284

New Insight into Cellulose Structure by Atomic Force Microscopy Shows the I ? Crystal Phase at Near-Atomic Resolution  

Microsoft Academic Search

The organization of the surface of cellulose is important in cell structure, as well as in industrial processing and modification. Using atomic force microscopy, we show that the I? phase of native cellulose first proposed in 1984 and subsequently characterized by a triclinic unit cell exists over large areas of the surface of microcrystals from Valonia, one of the most

A. A. Baker; W. Helbert; J. Sugiyama; M. J. Miles

2000-01-01

285

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

286

Characteristics of n{sup +} polycrystalline-Si/Al{sub 2}O{sub 3}/Si metal{endash}oxide{endash} semiconductor structures prepared by atomic layer chemical vapor deposition using Al(CH{sub 3}){sub 3} and H{sub 2}O vapor  

SciTech Connect

We report interface and dielectric reliability characteristics of n{sup +} polycrystalline-silicon (poly-Si)/Al{sub 2}O{sub 3}/Si metal{endash}oxide{endash}semiconductor (MOS) capacitors. Al{sub 2}O{sub 3} films were prepared by atomic layer chemical vapor deposition using Al(CH{sub 3}){sub 3} and H{sub 2}O vapor. Interface state density (D{sub it}) and dielectric reliability properties of n{sup +} poly-Si/Al{sub 2}O{sub 3}/Si MOS structures were examined by capacitance{endash}voltage, conductance, current{endash}voltage, and time-dependent dielectric breakdown measurements. The D{sub it} of the n{sup +} poly-Si/Al{sub 2}O{sub 3}/Si MOS system near the Si midgap is approximately 8{times}10{sup 10}eV{sup {minus}1}cm{sup {minus}2} as determined by the conductance method. Frequency dispersion as small as {similar_to}20 mV and hysteresis of {similar_to}15 mV were attained under the electric field of {+-}8 MV/cm. The gate leakage current of {similar_to}36 Aa effective thickness Al{sub 2}O{sub 3} dielectric measured at the gate voltage of {minus}2.5 V is {similar_to}{minus}5 nA/cm2, which is approximately three orders of magnitude lower than that of a controlled oxide (SiO{sub 2}). Time-dependent dielectric breakdown data of Al{sub 2}O{sub 3}/Si MOS capacitors under the constant current/voltage stress reveal excellent charge-to-breakdown characteristics over controlled oxide. Reliable gate oxide integrity of Al{sub 2}O{sub 3} gate dielectric is manifested by the excellent distribution of gate oxide breakdown voltage on 128 million MOS capacitors having isolation edges. Extracted time constant and capture cross section of the Al{sub 2}O{sub 3}/Si junction are discussed. {copyright} 2001 American Institute of Physics.

Park, Dae-Gyu; Cho, Heung-Jae; Lim, Kwan-Yong; Lim, Chan; Yeo, In-Seok; Roh, Jae-Sung; Park, Jin Won

2001-06-01

287

Atomic size and chemical effects on the local order of Zr2M ( M=Co , Ni, Cu, and Ag) binary liquids  

NASA Astrophysics Data System (ADS)

First-principles molecular dynamics simulations are performed to investigate the atomic size and chemical effects on the short-range order (SRO) in superheated and undercooled Zr-based metallic liquids, Zr2M ( M=Co , Ni, Cu, and Ag). We demonstrate that the local atomic structures in liquids are quite sensitive to the atomic size ratio and the electronic interactions between component elements. The large negative heats of mixing for Zr-M do not favor icosahedral SRO in these binary liquids, contrary to the common belief. Full icosahedral structure units are few in the superheated liquids, although the number of icosahedral clusters increases upon undercooling. Comparing Zr2Co , Zr2Ni , and Zr2Cu , all of which have very similar atomic size ratios, we find that the degree of local icosahedral order increases with decreasing interaction strength between the d electrons in Zr-Co, Zr-Ni, and Zr-Cu. A comparison of Zr2Cu and Zr2Ag alloys shows that the degree of icosahedral order increases much more in Zr2Ag than in Zr2Cu with decreasing temperature. The difference in atomic sizes of Cu and Ag may account for the subtle discrepancy in the evolution of short-range ordering in undercooled Zr2Cu and Zr2Ag liquids.

Huang, Li; Wang, C. Z.; Hao, S. G.; Kramer, M. J.; Ho, K. M.

2010-01-01

288

Interpreting protein structural dynamics from NMR chemical shifts.  

PubMed

In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static X-ray structures. Improved chemical shift predictions result from population-weighted sampling of multiple conformational states and from sampling smaller fluctuations within conformational basins. Improved chemical shift predictions also result from discrete changes to conformations observed in X-ray structures, which may result from crystal contacts, and are not always reflective of conformational dynamics in solution. Chemical shifts are sensitive reporters of fluctuations in backbone and side chain torsional angles, and averaged (1)H chemical shifts are particularly sensitive reporters of fluctuations in aromatic ring positions and geometries of hydrogen bonds. In addition, poor predictions of MD-averaged chemical shifts can identify spurious conformations and motions observed in MD simulations that may result from force field deficiencies or insufficient sampling and can also suggest subsets of conformational space that are more consistent with experimental data. These results suggest that the analysis of dynamically averaged NMR chemical shifts from MD simulations can serve as a powerful approach for characterizing protein motions in atomistic detail. PMID:22381384

Robustelli, Paul; Stafford, Kate A; Palmer, Arthur G

2012-03-28

289

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

PubMed

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

Helmich, Benjamin; Sierka, Marek

2011-10-14

290

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.

291

Chemically synthesised atomically precise gold clusters deposited and activated on titania. Part II.  

PubMed

Synchrotron XPS was used to investigate a series of chemically synthesised, atomically precise gold clusters Au(n)(PPh3)y (n = 8, 9 and 101, y depending on the cluster size) immobilized on anatase (titania) nanoparticles. Effects of post-deposition treatments were investigated by comparison of untreated samples with analogues that have been heat treated at 200 °C in O2, or in O2 followed by H2 atmosphere. XPS data shows that the phosphine ligands are oxidised upon heat treatment in O2. From the position of the Au 4f(7/2) peak it can be concluded that the clusters partially agglomerate immediately upon deposition. Heating in oxygen, and subsequently in hydrogen, leads to further agglomeration of the gold clusters. It is found that the pre-treatment plays a crucial role in the removal of ligands and agglomeration of the clusters. PMID:23907108

Anderson, David P; Adnan, Rohul H; Alvino, Jason F; Shipper, Oliver; Donoeva, Baira; Ruzicka, Jan-Yves; Al Qahtani, Hassan; Harris, Hugh H; Cowie, Bruce; Aitken, Jade B; Golovko, Vladimir B; Metha, Gregory F; Andersson, Gunther G

2013-09-21

292

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

PubMed

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

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

2008-10-22

293

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

PubMed Central

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

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

2008-01-01

294

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

295

Visual Chemistry: Three-Dimensional Perception of Chemical Structures  

NASA Astrophysics Data System (ADS)

Chemical structures are being modeled by formulas which in turn may be viewed as graphs. They have to be represented pictorially in two (constitutional formulas) or three dimensions (stereochemical formulas). How to present the latter formulas is the topic of the present paper. First, however, a discussion of isomerism is necessary. Then, for quantitative structure-activity relationships (QSAR) one has to find a correspondence between chemical formulas (or the shape of chemical compounds) and numerical molecular descriptors (also called topological indices). The various types of conventions for translating three-dimensional objects into two-dimensional representations are presented and discussed. It is hoped that stereo-drawings and colored images will facilitate the task of molecular modelers in search for new medicinal drugs. The ultimate goal, the production of holograms for chemical structures, needs the development of specialized software.

Balaban, Alexandru T.

1999-12-01

296

Structural, Nanomechanical and Nanotribological Characterization of Human Hair Using Atomic Force Microscopy and Nanoindentation  

NASA Astrophysics Data System (ADS)

Human hair is a nanocomposite biological fiber. Healthy, soft hair with good feel, shine, color and overall aesthetics is generally highly desirable. It is important to study hair care products such as shampoos and conditioners as well as damaging processes such as chemical dyeing and permanent wave treatments because they affect the maintenance and grooming process and therefore alter many hair properties. Nanoscale characterization of the cellular structure, the mechanical properties, as well as the morphological, frictional and adhesive properties (tribological properties) of hair is essential if we wish to evaluate and develop better cosmetic products, and crucial to advancing the understanding of biological and cosmetic science. The atomic/friction force microscope (AFM/FFM) and nanoindenter have recently become important tools for studying the micro/nanoscale properties of human hair. In this chapter, we present a comprehensive review of structural, mechanical, and tribological properties of various hair and skin as a function of ethnicity, damage, conditioning treatment, and various environments. Various cellular structures of human hair and fine sublamellar structures of the cuticle are identified and studied. Nanomechanical properties such as hardness, elastic modulus, creep and scratch resistance are discussed. Nanotribological properties such as roughness, friction, and adhesion are presented, as well as investigations of conditioner distribution, thickness and binding interactions.

Bhushan, Bharat; Latorre, Carmen; Wei, Guohua

297

Atomic structure of Au-nanoparticles on silica support by X-ray PDF study  

SciTech Connect

We investigated the atomic structure of gold nanoparticles with an average size of 5 nm in diameter, supported by silica. We used high-energy X-ray diffraction and the atomic pair distribution function (PDF) to probe the local atomic structure. Measurements were performed from 25 to 950 C. The structure is approximately fcc in average but exhibits small distortions. The structural distortion increases with the temperature and could be related to the catalytic activity of gold nanoparticles. Above 425 C, rapid particle growth and coalescence were observed.

Dmowski, W. [University of Tennessee, Knoxville (UTK); Yin, Hongfeng [ORNL; Dai, Sheng [ORNL; Overbury, Steven {Steve} H [ORNL; Egami, T. [University of Tennessee, Knoxville (UTK)

2010-01-01

298

Atomic Structure of Au Nanoparticles on a Silica Support by an X-ray PDF Study  

SciTech Connect

We investigated the atomic structure of gold nanoparticles with an average size of {approx}5 nm in diameter, supported by silica. We used high-energy X-ray diffraction and the atomic pair distribution function (PDF) to probe the local atomic structure. Measurements were performed from 25 to 950 C. The structure is approximately fcc in average but exhibits small distortions. The structural distortion increases with the temperature and could be related to the catalytic activity of gold nanoparticles. Above 425 C, rapid particle growth and coalescence were observed.

Dmowski, Wojtek; Yin, Hongfeng; Dai, Sheng; Overbury, Steven H.; Egami, Takeshi (Tennessee-K); (ORNL)

2010-05-04

299

Direct structure analysis of W(110)-(1×1)-O by full solid-angle X-ray photoelectron diffraction with chemical-state resolution  

Microsoft Academic Search

The atomic structure of the W(110)-(1×1)-O surface with an additional (1×12) periodicity has been determined using full solid-angle X-ray photoelectron diffraction (XPD) patterns with chemical-state resolution. The W4f binding energy of atoms directly bonded to oxygen is 0.73eV higher than that of “bulk” W atoms. The full solid-angle XPD data for this shifted peak show strong forward focusing peaks, making

Hiroshi Daimon; Ramon Ynzunza; Javier Palomares; H Takabi; Charles S Fadley

1998-01-01

300

LogCHEM: Interactive Discriminative Mining of Chemical Structure  

Microsoft Academic Search

One of the most well known successes of Inductive Logic Programming (ILP) is on Structure-Activity Relationship (SAR) problems. In such problems, ILP has proved several times to be capable of constructing expert comprehensible models that help to explain the activity of chemical compounds based on their structure and properties. However, despite its successes on SAR problems, ILP has severe scalability

Vítor Santos Costa; Nuno A. Fonseca; Rui Camacho

2008-01-01

301

Recent Strategies for Retrieving Chemical Structure Information on the Web.  

ERIC Educational Resources Information Center

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

Lo, Mei Ling

1997-01-01

302

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

303

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

NASA Astrophysics Data System (ADS)

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 spectra of free atoms were detected for the nitrate solutions of Cu and Ni, but not for those of Sr and Rb, which have low ionization potentials and low atomization efficiency and may exist as ionized species such as free ions, oxides, etc. in the flame.

Nakai, Izumi; Terada, Yasuko; Nomura, Masaharu; Uchida, Tetsuo

1995-02-01

304

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

2012-10-01

305

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

NASA Astrophysics Data System (ADS)

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

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

2013-05-01

306

Heavy atom tunneling in chemical reactions: Study of H+LiF collisions  

NASA Astrophysics Data System (ADS)

The H+LiF(X 1?+,?=0-2,j=0)-->HF(X 1?+,?',j')+Li(2S) bimolecular process is investigated by means of quantum scattering calculations on the chemically accurate X 2A' LiHF potential energy surface of Aguado et al. [A. Aguado, M. Paniagua, C. Sanz, and J. Roncero, J. Chem. Phys. 119, 10088 (2003)]. Calculations have been performed for zero total angular momentum for translational energies from 10-7 to 10-1 eV. Initial-state selected reaction probabilities and cross sections are characterized by resonances originating from the decay of metastable states of the H...F-Li and Li...F-H van der Waals complexes. Extensive assignment of the resonances has been carried out by performing quasibound states calculations in the entrance and exit channel wells. Chemical reactivity is found to be significantly enhanced by vibrational excitation at low temperatures, although reactivity appears much less favorable than nonreactive processes due to the inefficient tunneling of the relatively heavy fluorine atom strongly bound in van der Waals complexes.

Weck, P. F.; Balakrishnan, N.

2005-06-01

307

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

308

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

2013-10-10

309

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

SciTech Connect

This paper presents a full account of the EXAFS measurements and reverse Monte Carlo (RMC) modeling of the atomic arrangements and short-to-medium range structure in an amorphous Ni-P alloy, expanding on the description included in our recent publication. The atomic packing is analyzed from the standpoint of solute atoms. The short-to-medium range structure is discussed based on single-solute-centered quasi-equivalent clusters that form due to strong chemical short-range ordering, and the topological order is described in terms of both intra-cluster and inter-cluster dense packing for efficient filling of space. This analysis is also conducted for amorphous Ni80P20 prepared via different processing routes, to observe if the polyamorphism suggested in literature for amorphous Ni-P can be confirmed from the local structure perspective. The structural differences between the proposed polymorphs are apparently subtle and a full resolution of this issue is found to be beyond the capabilities of our EXAFS/RMC modeling approach. The amorphous structural features uncovered are also compared briefly with those observed before in amorphous alloy systems with positive heat of mixing.

Luo,W.; Ma, E.

2008-01-01

310

Frequent Sub-Structure-Based Approaches for Classifying Chemical Compounds  

Microsoft Academic Search

In this paper we study the problem of classifying chemical com- pound datasets. We present a sub-structure-based classifica- tion algorithm that decouples the sub-structure discovery pro- cess from the classification model construction and uses frequent subgraph discovery algorithms to find all topological and geo- metric sub-structures present in the dataset. The advantage of our approach is that during classification model

Mukund Deshpande; Michihiro Kuramochi; George Karypis

2003-01-01

311

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

Microsoft Academic Search

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

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

2001-01-01

312

Chemical and structural characterization of carbon nanotube surfaces.  

PubMed

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

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

2010-01-06

313

A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures  

NASA Astrophysics Data System (ADS)

High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or ``best,'' estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.

Feller, David; Peterson, Kirk A.; Dixon, David A.

2008-11-01

314

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

PubMed Central

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

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

2012-01-01

315

Dynamical strain at semiconductor interfaces: Structure and surface-atom vibrations of GaAs(110) and GaAs(110)-- p (1 times 1)--Sb  

SciTech Connect

The dynamical force fields of the clean GaAs(110) surface, an isolated Sb chain, and the GaAs(110)--{ital p}(1{times}1)--Sb(1-ML) interface have been computed utilizing tight-binding total energy models that have been used successfully to describe the atomic and electronic structure of the clean and adsorbed cleavage faces of the tetrahedrally coordinated compound semiconductors. Since the main consequences of the different chemical bonding in these two cases are manifested in changes in the force field associated with the dynamics of the top-layer atoms, we explore these consequences using a restricted dynamical model in which only the top-layer atoms are allowed to vibrate. The resulting vibrational energies are in remarkably good agreement with experimental measurements, and hence afford a vehicle to obtain quantitative relationships between the nature of the surface chemical bonds and the vibrational energies of the surface atomic species.

Godin, T.J.; LaFemina, J.P. (Pacific Northwest Laboratory Molecular Science Research Center, Richland, WA (USA)); Duke, C.B. (Xerox Webster Research Center, 0114-38D, Webster, NY (USA))

1991-07-01

316

Chemical, structural, and chemical-structural varieties of minerals and once again on ways to rationalize mineralogical nomenclature  

NASA Astrophysics Data System (ADS)

The names of minerals are mostly irrational with respect to their chemical composition and crystal structure. The division of mineral species into structural and chemical-structural subspecies or varieties is proposed to simplify and rationalize mineral nomenclature. Special modifiers could be used and written after the root name of an initial mineral. For example, the eudialyte-group minerals could be divided into eudialyte-(CaMn), -(CaFe), -(MnCa), -(CaSr), and -(CaH) and alluaivite. The format of such modifiers should be a matter of discussion and approval.

Bulakh, A. G.

2008-12-01

317

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

NASA Astrophysics Data System (ADS)

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

Lopatin, Sergei

318

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

319

Mechanics driven Chemical Reactions in Structural Energetic Materials  

Microsoft Academic Search

Fundamental mechanisms that are responsible for shock-initiation of chemical reactions, are dominated by non-equilibrium processes including changes in reactant particle configurations caused by plastic deformation or by fracture, mixing of constituents in and around the voids, and rapid increases in temperature from mechanical work. Mechanics driven chemical reactions occur in structural energetic mixtures, during the high-pressure shock state in time

Vindhya Narayanan; Derek Redding; Sathya Hanagud

2007-01-01

320

Connecting Atomic Structures with Continuum Mechanics in Cytoskeletal Polymers  

NASA Astrophysics Data System (ADS)

The mechanics of the cytoskeleton, namely actin filaments and microtubules, are key to many of their cellular functions. These polymers have been extensively studied using a wide range of biophysical techniques, and we have sought to connect the dynamics we observe in all-atom molecular dynamics simulations with continuum mechanics properties. We have developed coarse-graining techniques that allow us calculate mechanical properties of these polymers using a simple mesoscopic description. Our findings match very well with experimental measurements and allow us to probe how the atomic level effects of small molecules and/or point mutations manifest themselves at the level of the polymer.

Sept, David

2011-03-01

321

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

322

Dependence of oxide surface structure on surface topology and local chemical bonding  

SciTech Connect

The atomic geometries of the charge neutral surfaces of several oxides exhibiting different crystal structures and varying participation of O(2{ital p}) electrons in the chemical bonding have been calculated using tight-binding total energy models. Surface structures have been computed for exemplary cubic (MgO), wurtzite (ZnO), {beta}-tridymite, and ideal {beta}-cristobalite (SiO{sub 2}) oxides. The cubic oxide exhibits a minimum energy structure involving small outward relaxations of the oxygens and inward relaxations of the cations. For the cleavage faces of wurtzite ZnO, large bond-length-conserving relaxations occur because the surface atoms can relax without appreciable distortion of the local bond lengths. The charge neutral faces of {beta}-tridymite and ideal {beta}-cristobalite SiO{sub 2} also undergo bond-length-conserving relaxations. Thus the mechanism for the surface relaxation of tetrahedrally coordinated oxides is significantly different from that of the cubic oxides as is the role of the oxygen {ital p} electrons in the surface chemical bonding. Most importantly, the surface structural chemistry of charge neutral oxide surfaces reflects the interplay of both surface topology (via the ability to undergo bond-length-conserving relaxations) and local coordination chemistry (via the participation of {ital p} electrons in bonding versus nonbonding surface state bands).

LaFemina, J.P. (Molecular Science Research Center, Pacific Northwest Laboratory, P.O. Box 999, Richland, Washington 99352 (USA)); Duke, C.B. (Xerox Webster Research Center, 800 Phillips Road 0114-38D, Webster, New York 14580 (USA))

1991-05-01

323

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

NASA Astrophysics Data System (ADS)

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

Suewattana, Malliga

324

Structural Analysis for Water Absorption of SiOF Films Prepared by High-Density-Plasma Chemical Vapor Deposition  

Microsoft Academic Search

Fluorine-doped silicon oxide (SiOF) films, prepared by high-density-plasma chemical vapor deposition, are investigated as to the effect of bond structure on water absorption. In this investigation, two kinds of SiOF films, containing 12% and 8% fluorine atoms, were compared with regard to the change in their bond structure before and after accelerated water absorption. Fourier transform infrared (FT-IR) spectra, thermal

Takahiro Tamura; Junro Sakai; Yoichi Inoue; Makoto Satoh; Hikaru Yoshitaka

1998-01-01

325

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

PubMed Central

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

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

2012-01-01

326

Atomic structure and magnetic properties of Fe1-xCox alloys  

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

327

Electronic structure of atoms in laser plasmas: a Debye shielding approach  

Microsoft Academic Search

Spectral properties of the low-lying singlet states of a helium atom and those of the low-lying doublet states of a lithium atom in laser plasmas are calculated using a quantum chemical configuration interaction method with a Debye shielding model Hamiltonian. A large spherical Gaussian basis set is adopted to describe the wavefunctions of electrons bound in a non-Coulombic Yukawa-type potential

Hiroshi Okutsu; Tokuei Sako; Kaoru Yamanouchi; Geerd H. F. Diercksen

2005-01-01

328

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

PubMed Central

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 prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.

Li, Yunqi; Roy, Ambrish; Zhang, Yang

2009-01-01

329

Analyzing focal adhesion structure by atomic force microscopy  

Microsoft Academic Search

Atomic force microscopy (AFM) can produce high- resolution topographic images of biological samples in physiologically relevant environments and is therefore well suited for the imaging of cellular surfaces. In this work we have investigated focal adhesion complexes by combined fluorescence microscopy and AFM. To generate high- resolution AFM topographs of focal adhesions, REF52 (rat embryo fibroblast) cells expressing YFP-paxillin as

Clemens M. Franz; Daniel J. Müller

2005-01-01

330

Atomic structure of the SnO2 (110) surface.  

National Technical Information Service (NTIS)

Using a tight-binding, total-energy model, we examine atomic relaxations of the ideal stoichiometric and reduced tin oxide (11) surfaces. In both cases we find a nearly bond-length conserving rumple of the top layer, and a smaller counter-relaxation of th...

T. J. Godin J. P. LaFemina

1991-01-01

331

Atomic structure and energy of threading screw dislocations in wurtzite GaN  

Microsoft Academic Search

Atomic structure and energy of the screw dislocation b = in the full core configuration has been investigated with a self-consistent density functional tight binding calculation. A 288-atom cluster was used and the dangling bonds saturated with pseudo-hydrogen. The line energy is comparable to the values obtained using a supercell.

I. Belabbas; M. Akli Belkhir; Y. H. Lee; A. Béré; P. Ruterana; J. Chen; G. Nouet

2005-01-01

332

Optical properties and band structure of atomically thin MoS2  

Microsoft Academic Search

Atomically thin layers of materials can be expected to exhibit distinct electronic structure and novel properties compared to their bulk counterparts. Layered compounds, for which stable atomically thin samples can be produced, are ideal candidates for such studies. Graphene, a monolayer slice of the graphite crystal, is an illustrative example of both the stability and of the interest and importance

Jie Shan; Kin Fai Mak; Changgu Lee; James Hone; Tony Heinz

2010-01-01

333

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

334

The structure and characterization of air-assisted swirl atomizer sprays  

Microsoft Academic Search

The detailed aerodynamic structure of air-assisted swirl atomizer sprays is investigated in this paper. In contrast to previously published papers on spray characterization, special emphasis is placed on the region near the atomizer exit where significant variation of the mean drop size and drop velocity occurs. Simple correlations are found for the spray mean drop size and some initial input

C.-P. Mao; G. Wang; N. Chigier

1985-01-01

335

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

336

Effect of Nuclear Structure on Hyperfine Level Splitting in Muonic Atoms.  

National Technical Information Service (NTIS)

The effect of nuclear structure on hyperfine level splitting in muonic atoms is considered. The analytical analysis has been carried out which allows one to describe spectra of muonic atoms with even-even nuclei possessing a static non-axial deformation. ...

V. I. Bagaev I. N. Mikhailov

1977-01-01

337

Multiple electron loss by structured heavy ions in fast collisions with complex atoms  

SciTech Connect

A nonperturbative theory of multiple ionization of heavy structured ions in fast collisions with complex neutral atoms is developed. Cross sections are calculated for multiple loss of electrons (up to 15) in collisions of U{sup 10+} and U{sup 28+} with argon atoms and nitrogen molecules. The results are compared with experimental data.

Matveev, V. I. [Pomor State University, Lomonosov (Russian Federation)], E-mail: matveev.victor@pomorsu.ru; Matrasulov, D. U. [Uzbek Academy of Sciences, Heat Physics Department (Uzbekistan); Ryabchenko, S. V. [Arkhangelsk State Technical University (Russian Federation)

2006-01-15

338

Correlation Between the Atomic and Bulk Chemical Potentials of Low work Function Metals;Journal of Applied Physics.  

National Technical Information Service (NTIS)

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 sa...

T. J. Drummond

1998-01-01

339

Correlation of shock initiated and thermally initiated chemical reactions in a 1:1 atomic ratio nickel-silicon mixture  

Microsoft Academic Search

Shock initiated chemical reaction experiments have been performed on a 1:1 atomic ratio mixture of 20- to 45-?m nickel and ?325 mesh crystalline silicon powders. It has been observed that no detectable or only minor surface reactions occur between the constituents until a thermal energy threshold is reached, above which the reaction goes to completion. The experiments show the energy

Barry R. Krueger; Andrew H. Mutz; Thad Vreeland

1991-01-01

340

Measuring the Effect of Fuel Chemical Structure on Particulate and Gaseous Emissions using Isotope Tracing  

SciTech Connect

Using accelerator mass spectrometry (AMS), a technique initially developed for radiocarbon dating and recently applied to internal combustion engines, carbon atoms within specific fuel molecules can be labeled and followed in particulate or gaseous emissions. In addition to examining the effect of fuel chemical structure on emissions, the specific source of carbon for PM can be identified if an isotope label exists in the appropriate fuel source. Existing work has focused on diesel engines, but the samples (soot collected on quartz filters or combustion gases captured in bombs or bags) are readily collected from large industrial combustors as well.

Buchholz, B A; Mueller, C J; Martin, G C; Upatnicks, A; Dibble, R W; Cheng, S

2003-09-11

341

[Erytrocyte membrane change due to the chemical treatment studied with atomic force microscopy].  

PubMed

The influence of some selected pharmacological compounds on the structure of human erythrocytes (red blood cells, RBCs) has been studied by means of an atomic force microscopy (AFM). The imaging has been done both in the air environment on the fixed cells, and in the liquid (physiological conditions). It was shown that RBCs are very sensitive to osmotic changes in the solution. Increased NaCl concentration in the solution to a value higher than 0.9% leads to the characteristic changes of the erythrocyte from a discoid-like shape to a very irregular one, the so-called "echinocyte", with a lot of ledges. After exposition on nifedipin the modification of the erythrocyte surface morphology was observed. Based on the contact and non-contact AFMs study the consecutive stages of RBCs surface modification were observed. Scanning electron microscopy pictures of erythrocytes were presented for comparison. PMID:20514900

Targosz-Korecka, Marta; Su?owicz, W?adys?aw; Czuba, Pawe?; Szymo?ski, Marek; Miklaszewska, Monika; Pietrzyk, Jacek A; Rumian, Roman; Krawentek, Lidia

2009-01-01

342

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

PubMed

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

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

2012-11-17

343

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

National Technical Information Service (NTIS)

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

A. S. Davydov G. F. Filippov

1981-01-01

344

Electronic band structure and bonding in transition metal layered dichalcogenides by atomic orbital methods  

Microsoft Academic Search

It is shown that the main features of the electronic structure of transition metal layered dichalcogenides can be calculated in a simple ab initio atomic orbital framework. Examples from Groups IV, V and VI of the transition series are considered.

D. W. Bullett

1978-01-01

345

Local Electronic Structure at Oxide-Oxide Interfaces Probed by Atomic Resolution Electron Energy Loss Spectroscopy  

NASA Astrophysics Data System (ADS)

We report an atomic resolution study of the electronic structure of 12 x 4 LaMnO3-SrMnO3 and 2 x 2 LaMnO3-SrTiO3 superlattices and their interfaces grown on SrTiO3 by EELS. We correlated the interfacial electronic structure with the interfacial atomic structure using atomic resolution Z-contrast STEM using an electron probes of <0.1 nm. The oxide superlattices were synthesized using molecular beam epitaxy. We measured the site-specific unoccupied states of oxygen atoms and transition metals. In the LMO-SMO system we found extra states (holes) near the Fermi level and their dependence on abruptness of interface. In LMO-STO, we will present evidence of site-dependent electronic structure of oxygen and the Mn valence based on the L-edge ratios.

Shah, Amish; Ramasse, Q. M.; May, S. J.; Wen, J. G.; Eckstein, J. N.; Bhattacharya, A.; Zuo, J. M.

2009-03-01

346

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

347

NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.  

PubMed

NMR crystallography-the synergistic combination of X-raydiffraction, solid-state NMR spectroscopy, and computational chemistry-offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of NMR crystallography applied to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the ?-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of l-Trp formation. PMID:23537227

Mueller, Leonard J; Dunn, Michael F

2013-03-28

348

Atomic and Electronic Structure of V\\/MgO Interface  

Microsoft Academic Search

Thin films of vanadium were deposited on the (001) surface of a MgOsubstrate by molecular beam epitaxy (MBE) and the V\\/MgO interface wasinvestigated by cross-sectional high resolution electron microscopy(HREM) and electron energy loss spectroscopy (EELS). In order todetermine the location of atoms at the interface, computersimulations were performed for four possible models, and bestmatching between the experimental and simulated images

Y. Ikuhara; Y. Sugawara; I. Tanaka; P. Pirouz

1997-01-01

349

Electrical properties of metal-molecule-silicon structures with varying molecular backbones, dipoles, and atomic tethers  

NASA Astrophysics Data System (ADS)

We present the results of an extensive experimental investigation of metal-monolayer-silicon junctions. By varying the molecular dipole, the molecular backbone, the Si-molecule linkage, and the Si-doping, we indentified critical features that determine the electrical transport and injection properties of the junctions. Two basic structures were used. One is an enclosed planar structure in which an organic monolayer is directly assembled on silicon and contacted with evaporated silver. The other was made via Flip Chip Lamination, a novel approach that relies on the formation of monolayers on a gold surface first, which enables the study of a wider range of molecular layers on silicon of very high-quality. Two charge transport regimes dominate: (1) a Schottky barrier limited regime where the molecular dipole results in silicon band bending at the junction interface, and (2) a tunneling regime where the molecular dipole creates a small local electric field that screens the electrical transport. Transition Voltage spectroscopy was used to identify electrical differences between ?-conjugated and alkyl backbones attributed to the extended ?-delocalization and variations due to the chemical nature of Si-atom linkage.

Richter, Curt A.; Gergel-Hackett, Nadine; Coll, Mariona; Hacker, Christina A.

2011-03-01

350

Laser machining of CVD diamond: chemical and structural alteration effects  

Microsoft Academic Search

Nd:YAG laser (1064 nm) and ArF laser (193 nm) surface machining of 400 ?m thick, free-standing CVD diamond plates produced photon interaction zones which were chemically and structurally altered. A significant H loss and change in C?C bonding environment were observed in the Nd:YAG laser-processed specimens, while ArF laser processing exhibited less H depletion and structural alteration on a less

Philip M. Fabis

1996-01-01

351

Structural and chemical changes in binary versus ternary tetrahedral semiconductors  

Microsoft Academic Search

The properties of a prototype ternary semiconductor with the chalcopyrite structure-MgSiP2-are studied for the first time as a function of lattice constant, tetragonal distortion, and anion displacement with the use of the ab initio density-functional method. This system is then used as a general model for understanding the chemical and structure differences between a binary tetrahedral semiconductor (e.g., zinc blende)

José Luís Martins; Alex Zunger

1985-01-01

352

Structural fluctuation and atom-permutation in transition-metal clusters  

Microsoft Academic Search

The atomic structure and thermodynamic properties of transition-metal clusters containingN atoms are investigated forN=6 and 7 using the method of molecular dynamics, where Gupta's potential taking into account many-body interaction is employed. The caloric curve (total energy — temperature curve) and the structural fluctuations are studied. The “fluctuating state” is found forN=6 in the region of the temperature near below

S. Sawada; S. Sugano

1989-01-01

353

Cooling rate of thermal electrons by electron impact excitation of fine structure levels of atomic oxygen  

Microsoft Academic Search

The atomic oxygen fine structure cooling rate of thermal electrons based on new effective collision strengths for electron impact excitation of the ground-state 3P fine-structure levels in atomic oxygen have been fitted to an analytical expression which is available to the researcher for quick reference and accurate computer modeling with a minimum of calculations. We found that at the F

A. V. Pavlov; K. A. Berrington

1999-01-01

354

Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy  

Microsoft Academic Search

Acetic acid treatment has been frequently used to remove cellular contaminants from plant chromosome samples for structural analyses by scanning electron microscopy and atomic force microscopy (AFM). We evaluated the effects of various concentrations of acetic acid treatments on barley chromosome structures by using AFM. The long-term 45% acetic acid treatment significantly damaged the chromosome structures, although the treatment effectively

Shigeru Sugiyama; Tomoyuki Yoshino; Hiroko Kanahara; Motoharu Shichiri; Daisuke Fukushi; Toshio Ohtani

2004-01-01

355

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

ERIC Educational Resources Information Center

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

Downs, Geoff M.; Barnard, John M.

1998-01-01

356

STRUCTURAL FEATURES ASSOCIATED WITH DEGRADABLE AND PERSISTENT CHEMICALS  

EPA Science Inventory

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

357

CHEMICAL COMPOUND CLASSIFICATION WITH AUTOMATICALLY MINED STRUCTURE PATTERNS.  

PubMed

In this paper we propose new methods of chemical structure classification based on the integration of graph database mining from data mining and graph kernel functions from machine learning. In our method, we first identify a set of general graph patterns in chemical structure data. These patterns are then used to augment a graph kernel function that calculates the pairwise similarity between molecules. The obtained similarity matrix is used as input to classify chemical compounds via a kernel machines such as the support vector machine (SVM). Our results indicate that the use of a pattern-based approach to graph similarity yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art approaches. In addition, the identification of highly discriminative patterns for activity classification provides evidence that our methods can make generalizations about a compound's function given its chemical structure. While we evaluated our methods on molecular structures, these methods are designed to operate on general graph data and hence could easily be applied to other domains in bioinformatics. PMID:20448828

Smalter, A M; Huan, J; Lushington, G H

2008-01-01

358

Structural features of atomized white cast iron powder  

Microsoft Academic Search

White cast iron powder rapidly quenched from the liquid condition with presence of the same phases and structural components differs markedly in structure from normally cast white iron.2.With an increase in cooling rate vcool during solidification the amount of eutectic decreases. However, with an increase in carbon content this tendency is weakened and with 3.9% the structure of powder cast

A. P. Gulyaev; S. I. Astakhov

1991-01-01

359

Atomic Structure of Highly Strained BiFeO3 Thin Films  

SciTech Connect

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

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

2012-01-01

360

Atomic accuracy in predicting and designing non-canonical RNA structure  

PubMed Central

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

Das, Rhiju; Karanicolas, John; Baker, David

2010-01-01

361

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

NASA Astrophysics Data System (ADS)

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

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

2003-12-01

362

Data quality in predictive toxicology: identification of chemical structures and calculation of chemical properties.  

PubMed Central

Every technique for toxicity prediction and for the detection of structure-activity relationships relies on the accurate estimation and representation of chemical and toxicologic properties. In this paper we discuss the potential sources of errors associated with the identification of compounds, the representation of their structures, and the calculation of chemical descriptors. It is based on a case study where machine learning techniques were applied to data from noncongeneric compounds and a complex toxicologic end point (carcinogenicity). We propose methods applicable to the routine quality control of large chemical datasets, but our main intention is to raise awareness about this topic and to open a discussion about quality assurance in predictive toxicology. The accuracy and reproducibility of toxicity data will be reported in another paper.

Helma, C; Kramer, S; Pfahringer, B; Gottmann, E

2000-01-01

363

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.

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

2008-01-01

364

Calculation of 13C Chemical Shifts in RNA Nucleosides: Structure 13C Chemical Shift Relationships  

Microsoft Academic Search

Isotropic 13C chemical shifts of the ribose sugar in model RNA nucleosides are calculated using SCF and DFT-GIAO ab initio methods for different combinations of ribose sugar pucker, exocyclic torsion angle, and glycosidic torsion angle. Idealized conformations were obtained using structures that were fully optimized by ab initio DFT methods starting with averaged parameters from a collection of crystallographic data.

Paolo Rossi; Gerard S. Harbison

2001-01-01

365

Molecular Structure Effects on Atomic and Nuclear Capture of Mesons  

Microsoft Academic Search

A review is given of the experimental studies in which the effects of ; the chemical nature of matter on the meson capture processes are detected and ; analyzed. Some theoretical ideas currently used for the analysts of the ; experimental results are also given. (JFP);

L. I. Ponomarev

1973-01-01

366

Synthesis-Dependent Atomic Surface Structures of Oxide Nanoparticles  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

367

Synthesis-dependent atomic surface structures of oxide nanoparticles.  

PubMed

Using SrTiO_{3} nanocuboids as a model system, we show with aberration-corrected high resolution electron microscopy at sub-Å resolution that surface relaxations or reconstructions are present on the nanocuboids, depending on the synthetic process. Oleic acid synthesis, acetic acid synthesis, and microwave-assisted acetic acid synthesis result in a SrO termination, TiO_{2}-rich reconstruction, and mixed termination, respectively. The experimental atomic positions are in better agreement with density functional theory calculations using an exact-exchange corrected PBEsol functional than the Perdew-Burke-Ernzerhof (PBE) functional. PMID:24160614

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

2013-10-08

368

Structural Analysis for Water Absorption of SiOF Films Prepared by High-Density-Plasma Chemical Vapor Deposition  

NASA Astrophysics Data System (ADS)

Fluorine-doped silicon oxide (SiOF) films, prepared by high-density-plasma chemical vapor deposition, are investigated as to the effect of bond structure on water absorption. In this investigation, two kinds of SiOF films, containing 12% and 8% fluorine atoms, were compared with regard to the change in their bond structure before and after accelerated water absorption. Fourier transform infrared (FT-IR) spectra, thermal desorption mass spectroscopy (TDS) spectra and Raman spectra studies clarified the following. (1) The SiOF film which contains 12% fluorine atoms has more Si F bonds than that containing 8% fluorine atoms, but it has fewer 3-fold rings. (2) The SiOF film which contains 8% fluorine atoms absorbs little water, and its Si F bond does not change after water absorption. (3) The 3-fold ring of the SiOF film which contains 12% fluorine atoms has an unstable F Si O Si bond structure. (4) The F Si O Si bond structure of the 3-fold ring is easily changed to the F Si OH and Si OH bond structures due to hydration, upon water absorption.

Tamura, Takahiro; Sakai, Junro; Inoue, Yoichi; Satoh, Makoto; Yoshitaka, Hikaru

1998-05-01

369

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

370

Measurements of atomic hydrogen temperature and methyl radical concentration in a diamond chemical vapor deposition reactor  

NASA Astrophysics Data System (ADS)

This investigation covers the development of nonintrusive, laser-based optical diagnostic tools for the measurement of trace amount molecular species in hostile, reactive environments such as plasmas. Two- photon laser induced fluorescence (LIF) spectroscopy is applied to obtain the temperature of atomic hydrogen and Cavity Ring-Down Spectroscopy (CRDS) to measure absolute concentrations of methyl radical in a hot filament diamond chemical vapor deposition (CVD) reactor. Atomic hydrogen (H) and methyl radical (CH3) are two abundant, reactive species in the hot filament diamond CVD process. An equilibrium temperature was deduced from the hydrogen Doppler line width at 20 Torr, which is the diamond deposition pressure in the reactor. The gas phase temperature measurement reached a high precision of 50 K due to a solar blind photo-multiplier tube was used that has the highest detection sensitivity at 121.6 nm of Lyman-? fluorescence and rejects efficiently the incandescent background. Resonant trapping of Lyman- ? raised difficulties in carrying out data analysis. For the condition of unsaturated two-photon absorption this study concluded that the Doppler line width is not related to the extent of re-absorption and re-emission of Lyman-? fluorescence. The dynamic range of the temperature measurement covers 400 K or higher providing no significant thermal ionization occurs. Methyl radical absorption is measured at the wavelength of 213.9 nm by CRDS, a sensitive linear absorption technique. An Abel transformation is required to convert the absorbance to the absolute concentration of methyl radicals based on the knowledge of the absorption cross-section at this wavelength. The spatial profile of the methyl concentration is at the order of 1014 molecules/cm3. A peak occurs 5 mm away from the filament, which indicates that methyl radical generation must involve gas-phase reaction, such as higher dissociation rate of methyl radical near filament, or density variation caused by temperature gradient rather than a direct dissociation process on the hot filament surface. Both measurements were carried out in the vicinity of the hot filament or between the filament and the substrate for diamond deposition with a spatial resolution of 0.2 mm. The results also demonstrated that the presence of a substrate influences on both the temperature and concentration measurements. This work increases our understanding of the hot filament diamond CVD process and demonstrated two reliable, advanced laser-based diagnostic methods that are of general importance for extracting parameters of basic interest in plasma chemistry such as temperature and absolute concentrations of gas-phase species at trace amounts nearby.

Ma, Yeming

371

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

372

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

373

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

NASA Astrophysics Data System (ADS)

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

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

2004-12-01

374

Transition structures for the interchange of hydrogen atoms within the water dimer  

NASA Astrophysics Data System (ADS)

High levels of ab initio molecular orbital theory were used to examine rearrangement processes in the water dimer corresponding to the interchange of various hydrogen atoms. The most reliable calculations involve MP4/6-311 + G(2df,2p) energy evaluations at MP2/6-311 + G(d,p) optimized structures. The lowest energy-rearrangement pathway corresponds to the interchange of hydrogen atoms of the acceptor molecule within the C(s) water dimer structure. This proceeds via a transition structure of C(1) symmetry and requires an energy of 0.59 kcal/mol. The interchange of donor and acceptor molecules can be achieved via a transition structure with C(i) symmetry and requires an energy of 0.87 kcal/mol. Finally, the interchange of hydrogen atoms of the donor molecule, via a C(2v) transition structure, requires 1.88 kcal/mol.

Smith, Brian J.; Swanton, David J.; Pople, John A.; Schaefer, Henry F., III; Radom, Leo

1990-01-01

375

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

NASA Astrophysics Data System (ADS)

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

Hawthorne, Frank C.

2012-11-01

376

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

SciTech Connect

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

2005-03-01

377

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

PubMed

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

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

2013-05-30

378

Atomic Force Microscopy of Physical and Chemical Processes at the Solid-Liquid Interface  

NASA Astrophysics Data System (ADS)

This thesis describes research using atomic force microscopy (AFM) to study dynamics of solid surfaces in contact with liquids. Specifically, three applications are described: electrochemistry (Chapters 1-3), crystal growth (Chapters 4 and 5), and biomineralization (Chapter 6). Chapter 1 shows the feasibility of using AFM to image metal atoms in liquid, which sets the stage for high -resolution electrochemistry. Chapter 2 describes methods to convert the standard AFM liquid cell into an electrochemical cell and shows images of a gold electrode during oxidation/reduction cycling. Chapter 3 follows an electroplating cycle, wherein copper is deposited from electrolyte onto a gold electrode and then stripped off. The surface lattice is shown to change from that of bulk gold to bulk copper during plating, and back to bulk gold after stripping. Moreover, the first monolayer of copper--which deposits at an "underpotential", before the bulk deposition--is shown to have a lattice which differs from the bulk and is electrolyte dependent. Like electrochemistry, the study of crystal growth is also perfectly suited to a surface technique such as AFM. AFM makes it possible to image "elemental steps" (i.e., steps one unit cell thick) on a single crystal and quantify their motion during growth and dissolution. This is illustrated for the inorganic crystal calcite (Chapter 4) and the more fragile organic crystal L-leucine (Chapter 5). In both cases it is shown that step speed is independent of spacing between steps, indicating that motion occurs by direct interaction of the step-site molecules with the solvent. Chapter 5 also describes techniques for growing and imaging organic crystals. Living organisms also use crystal growth, modified by inorganic and organic additives, to grow mineralized structures such as bones, teeth and seashells. In Chapter 6, AFM reveals the three-dimensional structure of the nacreous or pearly layer of mollusc shells by slowly etching away successive mineral layers (in weak acid) while imaging. Etch figures on the mineral (aragonite) are correlated with crystallographic directions, revealing overall crystalline order on large scans. In bivalves, this order is observed both laterally across the layer and vertically between layers, whereas gastropod nacre is observed to be ordered only vertically.

Manne, Srinivas

379

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

2012-10-24

380

Detailed Atomic Structure of Neutral and Near-Neutral Systems  

SciTech Connect

This paper highlights the issues which need to be addressed in undertaking accurate calculations of multi-electron atoms and ions, particularly at or near the neutral end of an isoelectronic sequence. We illustrate the processes through two calculations--of transitions in Cl I and Sn II--and discuss the convergence of our results as well as updating previous work. In particular, in the case of Cl I, we propose new identifications of the levels involved in certain transitions which are important in determining the abundance of chlorine in the inter-stellar medium (ISM), while in singly ionised tin, our calculations suggest a re-evaluation of the the abundance of tin in the ISM. We also confirm recent identification of Sn II lines seen in tokamak plasmas.

Oliver, Paul; Hibbert, Alan [School of Mathematics and Physics, Queen's University, Belfast BT7 1NN, Northern Ireland (United Kingdom)

2011-05-11

381

Near-Origin Structure of the Hooke's Atoms  

NASA Astrophysics Data System (ADS)

The Hooke's atoms with two or more than two electrons give rise to an interesting quantum mechanical model with valuable practical applications. In this work, we study the electronic properties near the origin of the harmonic potential. It is seen that the spherically averaged density, ?¯, exhibits an interesting character — it has only even order terms in its small r expansion. The spherical average of the Hartree potential, v¯H, and the spherical average of the Kohn—Sham exchange-correlation potential, v¯xc, are also shown to have the same property — all odd order terms in their expansions vanish. Furthermore, the analysis and results extend also to the case of two-dimensional models. While only models interacting via. the Coulomb potential are primarily considered in the article, the results also extend to models interacting via. other potentials (viz. Van der Waals potential).

Wang, Xue-Mei

2012-12-01

382

Applications of the Cambridge Structural Database in chemical education1  

PubMed Central

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

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

2010-01-01

383

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

PubMed

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

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

2010-03-29

384

Unraveling the atomic structure of biogenic silica: evidence of the structural association of Al and Si in diatom frustules  

Microsoft Academic Search

We used X-ray absorption spectroscopy at the Al K-edge to investigate the atomic structure of biogenic silica and to assess the effect of Al on its crystal chemistry. Our study provides the first direct evidence for a structural association of Al and Si in biogenic silica. In samples of cultured diatoms, Al is present exclusively in fourfold coordination. The location

M. Gehlen; L. Beck; G. Calas; A.-M. Flank; A. J. Van Bennekom; J. E. E. Van Beusekom

2002-01-01

385

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.

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

1999-01-01

386

ATOMIC AND MOLECULAR PHYSICS: Structures, stabilities and magnetic moment of small copper-nickel clusters  

NASA Astrophysics Data System (ADS)

This paper obtains the lowest-energy geometric structures and the electronic and magnetic properties of small CuNiN clusters by using all-electron density functional theory. The calculated results reveal that the Cu atom prefers to occupy the apical site when N <= 9 and for the clusters with N = 10, the Cu atom starts to encapsulate in the cage. The CuNi7 and CuNi9 are magic clusters. The magnetism correlates closely with the symmetry of the clusters. For these clusters, the charge tends to transfer from the nickel atoms to the copper atoms. It finds that the doping of Cu atom decreases the stability of pure NiN clusters.

Feng, Cui-Ju; Xue, Yong-Hong; Zhang, Xiao-Yan; Zhang, Xiao-Chun

2009-04-01

387

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.

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

1996-01-01

388

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

PubMed

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

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

2003-06-01

389

Atomic Structure of the in on Si(111)(4 × 1) Surface  

NASA Astrophysics Data System (ADS)

The atomic structure of the In on Si(111)(4×1) surface has been determined using direct methods applied to transmission electron diffraction data. It consists of a zigzag chain of In atoms and a region of silicon including a dimer chain. The structure is sufficiently similar to recent models of the Au on Si(111)(5×2) and metal on Si(111)(3×1) structures, that some preliminary generalizations on the linear n×1 and n×2 Si(111) reconstructions can be made.

Collazo-Davila, C.; Marks, L. D.; Nishii, K.; Tanishiro, Y.

390

Atomic structure of nickel phthalocyanine probed by X-ray absorption spectroscopy and density functional simulations  

NASA Astrophysics Data System (ADS)

The local atomic structure of Ni in nickel phthalocyanine was studied by K-edge X-ray absorption fine structure spectroscopy. The obtained inter atomic nickel-nitrogen distance differs from the reference X-ray diffraction data so an additional study was performed within density functional theory framework. The justification of the used theoretical approach was provided by a comparison of theoretical free electron densities of states with experimental Ni K-edge X-ray absorption near edge spectra. The refined Ni local environment retain the reference structure of the molecule except for the length of Ni-N bond which increases to 1.90 Å.

Avakyan, L. A.; Manukyan, A. S.; Mirzakhanyan, A. A.; Sharoyan, E. G.; Zubavichus, Y. V.; Trigub, A. L.; Kolpacheva, N. A.; Bugaev, L. A.

2013-03-01

391

Local atomic structure in equilibrium and supercooled liquid Zr75.5Pd24.5  

NASA Astrophysics Data System (ADS)

Atomic structures were obtained in equilibrium and supercooled eutectic Zr75.5Pd24.5 liquids by in situ high-energy synchrotron diffraction measurements using the beamline electrostatic levitation (BESL) technique, which provides a high-vacuum, containerless, environment. Reverse Monte Carlo fits to the x-ray static structure factors, constrained using partial pair correlation functions obtained from ab initio molecular dynamics simulations, indicate the presence of medium-range order (MRO) in the form of a strong tendency for Pd-Pd (solute-solute) avoidance. This order persists over the entire temperature range studied, from 170 °C above the equilibrium liquidus temperature to 263 °C below it. Further, a quantitative analysis of the atomic structures obtained indicates a modest degree of icosahedral-like local order around Pd atoms, with the clusters showing an increased tendency for face-sharing to form more extended structures with decreasing temperature.

Mauro, N. A.; Fu, W.; Bendert, J. C.; Cheng, Y. Q.; Ma, E.; Kelton, K. F.

2012-07-01

392

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

NASA Astrophysics Data System (ADS)

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

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

2009-01-01

393

Chromatin Structure in Bands and Interbands of Polytene Chromosomes Imaged by Atomic Force Microscopy  

Microsoft Academic Search

Polytene chromosomes fromDrosophila melanogaster, observed from squash preparations, and chromosomes fromChironomus thummi thummi, investigated under physiological conditions, are imaged using an Atomic Force Microscope. Various chromatin fiber structures can be observed with high detail in fixed chromosomes and correspond to structures which are also observed in chromosomes of diploid cells. Unfixed chromosomes can be imaged in buffer and show less

C. J de Grauw; A. Avogadro; D. J van den Heuvel; K. O vd Werf; C. Otto; Y. Kraan; N. F van Hulst; J. Greve

1998-01-01

394

Correlation of diffusion coefficients with the electronic structure of interacting atoms  

Microsoft Academic Search

spect to the electron-phonon structure of solids, the interaction between the diffusion parameters and the electronic structure of atoms interecting during the diffusion was followed. An analysis of diagrams constructed from experimental data on the activation energy A and the preexponential factor D o of elements diffusing into the matrix shows that both quantities are very sensitive to the electronic

G. V. Samsonov; I. S. Kiva; N. G. Kaidash; E. G. Borisenko

1976-01-01

395

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home  

Microsoft Academic Search

We describe predictions made using the Rosetta structure prediction methodology for both tem- plate-based modeling and free modeling catego- ries in the Seventh Critical Assessment of Tech- niques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@ home distributed computing network.

Rhiju Das; Bin Qian; Srivatsan Raman; Robert Vernon; James Thompson; Philip Bradley; Sagar Khare; Michael D. Tyka; Divya Bhat; Dylan Chivian; David E. Kim; William H. Sheffler; Lars Malmström; Andrew M. Wollacott; Chu Wang; Ingemar Andre; David Baker

2007-01-01

396

Atomic and electronic structure of the corundum ([alpha]-alumina) (0001) surface  

SciTech Connect

Using a tight-binding, total-energy model, we predict the atomic and electronic structure of the relaxed (1[times]1) corundum (0001) surface. The surface shows a large, bond-length-conserving relaxation, which is allowed by the topology of the surface. The relaxation is driven by a rehybridization of the surface Al atoms to [ital sp][sup 2], and an accompanying drop in the energy of occupied surface states, during the relaxation. Displacements of surface atoms from bulk positions are as large as 0.7 A, and should be observable using a low-energy electron diffraction intensity analysis. Full relaxed atomic positions are reported, as well as a wavelength-resolved surface band structure, including orbital characters of surface states.

Godin, T.J.; LaFemina, J.P. (Molecular Science Research Center, Pacific Northwest Laboratory, P.O. Box 999, Richland, Washington 99352 (United States))

1994-03-15

397

Influence of sample surface condition on chemical analysis using laser ablation inductively coupled plasma atomic emission spectroscopy  

Microsoft Academic Search

The influence of sample surface condition on chemical analysis was investigated when using laser ablation sampling with inductively coupled plasma atomic emission spectroscopy (ICP-AES). The ablated mass quantity and composition were found to be significantly different from original vs. pre-ablated surfaces. The ablated mass quantity from original surfaces was much greater than that from pre-ablated surfaces, and the ablation rate

Xianglei Mao; Richard E. Russo; Wing-Tat Chan

1997-01-01

398

Emission actinometric investigations of atomic hydrogen and CH radicals in plasma-enhanced chemical vapour deposition processes of hexamethyldisiloxane  

Microsoft Academic Search

Spectral investigations were carried out in a plasma-enhanced chemical vapour deposition (PECVD) process using hexamethyldisiloxane (HMDSO) thin film deposition. The experiments were performed in a closed reactor with r.f. plasma generation in the pressure range of 20–40 Pa and power range of 10–20 W.It is shown that the emission lines of atomic hydrogen (486 nm) and CH radicals (431 nm)

V. Shogun; A. Tyablikov; St. Schreiter; W. Scharff; T. Wallendorf; S. Marke

1998-01-01

399

Atomic structure of Al88Y7Fe5 metallic glass  

NASA Astrophysics Data System (ADS)

The structure of Al88Y7Fe5 metallic glass has been investigated by differential scanning calorimetry, x-ray powder diffraction, and x-ray absorption fine structure (XAFS) techniques. The amorphous alloy crystallizes according to the following scheme: amorphous -->?-Al+ residual amorphous -->?-Al+Al3Y+AlFeY. The atomic structure of the amorphous alloy was modeled by reverse Monte Carlo methods. The resulting structure indicates that the prepeak (at 1.42 A?-1) in the static structure factor S(Q) is caused by contributions of distinct Y-Y, Y-Fe pairs. From the analysis of our XAFS spectra at the Fe and Y K edge the following characteristics of the local structure are found: The interatomic distance between Fe and coordinated Al atoms in the amorphous state is significantly (8.9%) shorter than the sum of the nominal metallic-state radii. The average coordination number is anomalously 36% reduced compared to the value derived from the dense-random-packing (DRP) model, using again the nominal metallic-state radii. On the other hand, the Y-Al distance as well as the number of Al atoms coordinating Y is close to the values predicted by the DRP model. These anomalous changes around the Fe atoms indicate a strong interaction between Fe and Al, which corroborate a covalent bonding. In connection with the values obtained from the XAFS data analysis, the effective atomic radii in the amorphous phase have been calculated. Consequently, applying them to the calculation of the atomic size factor (?=0.1076) confirms that Al88Y7Fe5 follows the rule of atomic size ratio for glass formation.

Saksl, K.; Jóvári, P.; Franz, H.; Jiang, J. Z.

2005-06-01

400

First-principles studies of BN sheets with absorbed transition metal single atoms or dimers: stabilities, electronic structures, and magnetic properties.  

PubMed

BN sheets with absorbed transition metal (TM) single atoms, including Fe, Co, and Ni, and their dimers have been investigated by using a first-principles method within the generalized gradient approximation. All of the TM atoms studied are found to be chemically adsorbed on BN sheets. Upon adsorption, the binding energies of the Fe and Co single atoms are modest and almost independent of the adsorption sites, indicating the high mobility of the adatoms and isolated particles to be easily formed on the surface. However, Ni atoms are found to bind tightly to BN sheets and may adopt a layer-by-layer growth mode. The Fe, Co, and Ni dimers tend to lie (nearly) perpendicular to the BN plane. Due to the wide band gap of the pure BN sheet, the electronic structures of the BN sheets with TM adatoms are determined primarily by the distribution of TM electronic states around the Fermi level. Very interesting spin gapless semiconductors or half-metals can be obtained in the studied systems. The magnetism of the TM atoms is preserved well on the BN sheet, very close to that of the corresponding free atoms and often weakly dependent on the adsorption sites. The present results indicate that BN sheets with adsorbed TM atoms have potential applications in fields such as spintronics and magnetic data storage due to the special spin-polarized electronic structures and magnetic properties they possess. PMID:22410806

Ma, Dongwei; Lu, Zhansheng; Ju, Weiwei; Tang, Yanan

2012-03-13

401

The structure and conformations of piracetam (2-oxo-1-pyrrolidineacetamide): Gas-phase electron diffraction and quantum chemical calculations  

Microsoft Academic Search

The geometric structure of piracetam was studied by quantum chemical calculations (DFT and ab initio), gas electron diffraction (GED), and FTIR spectroscopy. Two stable mirror symmetric isomers of piracetam were found. The conformation of pyrrolidine ring is an envelope in which the C4 atom deviates from the ring plane, the angle between the planes (C3C4C5) and (C2C3C5) is 154.1°. The

Denis N. Ksenafontov; Natalia F. Moiseeva; Lyudmila V. Khristenko; Nikolai M. Karasev; Igor F. Shishkov; Lev V. Vilkov

2010-01-01

402

Chemical composition, crystallographic structure and impedance spectroscopy of titanium oxynitride TiN xO y thin films  

Microsoft Academic Search

Titanium oxynitride TiNxOy thin films have been deposited by DC-pulsed magnetron sputtering from Ti target in the Ar+N2+O2 reactive atmosphere controlled by plasma emission spectroscopy. Correlation between chemical composition and crystallographic structure of thin films has been determined and presented in the form of the pseudo-equilibrium ternary phase diagram. The atomic N\\/Ti and O\\/Ti ratios have been derived from Rutherford

M. Radecka; E. Pamula; A. Trenczek-Zajac; K. Zakrzewska; A. Brudnik; E. Kusior; N.-T. H. Kim-Ngan; A. G. Balogh

2011-01-01

403

Effect of structural and chemical parameters on magnetic coupling in hydroxo-bridged Cu(II) dimer  

Microsoft Academic Search

The influence of various structural and chemical parameters on magnetic coupling in model hydroxo-bridged Cu(II) dimers has been analyzed using the density functional theory and the broken symmetry approach. These parameters, such as the environment around copper atom, the electro negativity of the nonbridging ligands, the Cu–O–Cu angle, the Cu–O distance, the out-of-plane displacement of hydroxo group and the hinge

Haiquan Hu; Yongjun Liu; Dongju Zhang; Chengbu Liu

2001-01-01

404

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

SciTech Connect

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

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

2010-04-15

405

Atomic and electronic structures of large and small carbon tori  

NASA Astrophysics Data System (ADS)

The stability of large carbon tori is examined within the elasticity theory. Tori of diameter larger than 200 nm obtained by bending a single-wall nanotube and connecting the two ends together are proved to be stable. Molecular mechanics is used for optimizing the structure of a small polygonal torus (C1960) obtained by connecting short portions of (6,6) and (10,0) nanotubes with ten pairs of pentagons and heptagons. The electronic structures of both small and large tori are determined within the framework of a tight-binding Hamiltonian, and their energies are compared. By application of London theory, it is shown that a magnetic field deeply influences the electronic structure of the carbon tori.

Meunier, V.; Lambin, Ph.; Lucas, A. A.

1998-06-01

406

The chemical structure of the pigments in Ara macao plumage.  

PubMed

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

Stradi, R; Pini, E; Celentano, G

2001-08-01

407

Chemical and structural characterization of carbon nanotube surfaces  

Microsoft Academic Search

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

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

2010-01-01

408

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

Microsoft Academic Search

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

Jian Zhang

1991-01-01

409

The electronic structure at the atomic scale of ultrathin gate oxides  

Microsoft Academic Search

The narrowest feature on present-day integrated circuits is the gate oxide-the thin dielectric layer that forms the basis of field-effect device structures. Silicon dioxide is the dielectric of choice and, if present miniaturization trends continue, the projected oxide thickness by 2012 will be less than one nanometre, or about five silicon atoms across. At least two of those five atoms

D. A. Muller; T. Sorsch; S. Moccio; F. H. Baumann; K. Evans-Lutterodt; G. Timp

1999-01-01

410

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

SciTech Connect

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

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

2010-02-15

411

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

Microsoft Academic Search

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

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

2004-01-01

412

Atomic Structure of Interface States in Silicon Heterojunction Solar Cells  

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

413

Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling  

NASA Astrophysics Data System (ADS)

Grain boundaries influence many physical and chemical properties of crystalline materials. Here, we perform molecular dynamics simulations to study the structure of a series of [100] symmetric tilt grain boundaries in Mg2SiO4 forsterite. The present results show that grain boundary energies depend significantly on misorientation angle. For small misorientation angles (up to 22°), grain boundary structures consist of an array of partial edge dislocations with Burgers vector 1/2[001] associated with stacking faults and their energies can be readily fit with a model which adds the Peach-Koehler equation to the Read-Shockley dislocation model for grain boundaries. The core radius of partial dislocations and the spacing between the partials derived from grain boundary energies show that the transition from low- to high-angle grain boundaries occurs for a misorientation angle between 22° and 32°. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Finally, we use a low energy atomic configuration obtained by molecular dynamics for the misorientation of 12.18° as input to simulate a high-resolution transmission electron microscopy (HRTEM) image. The simulated image is in good agreement with an observed HRTEM image, which indicates the power of the present approach to predict realistic atomic structures of grain boundaries in complex silicates.

Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro

2012-10-01

414

Imaging biological structures with the cryo atomic force microscope.  

PubMed Central

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

Zhang, Y; Sheng, S; Shao, Z

1996-01-01

415

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

416

Chemical Vapor Generation with Slurry Sampling: A Review of Atomic Absorption Applications  

Microsoft Academic Search

This review summarizes and discusses the analytical methods and techniques described in the literature for hydride generation as a mode of slurry sample introduction into atomization cells. A brief comparison of detection limits for analytical atomic absorption methods and practical applications to analytical samples that utilize slurry hydride generation is discussed. The current state-of-the-art, including advantages and limitations of this

Henryk Matusiewicz

2003-01-01

417

Atomic Force Microscopy of Physical and Chemical Processes at the Solid-Liquid Interface  

Microsoft Academic Search

This thesis describes research using atomic force microscopy (AFM) to study dynamics of solid surfaces in contact with liquids. Specifically, three applications are described: electrochemistry (Chapters 1-3), crystal growth (Chapters 4 and 5), and biomineralization (Chapter 6). Chapter 1 shows the feasibility of using AFM to image metal atoms in liquid, which sets the stage for high -resolution electrochemistry. Chapter

Srinivas Manne

1994-01-01

418

Quantum chemical 13Calpha chemical shift calculations for protein NMR structure determination, refinement, and validation  

Microsoft Academic Search

A recently determined set of 20 NMR-derived conformations of a 48-residue all-alpha-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Calpha chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Calpha

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

2008-01-01

419

Atomic Structure and Phase Transformations in Pu Alloys  

SciTech Connect

Plutonium and plutonium-based alloys containing Al or Ga exhibit numerous phases with crystal structures ranging from simple monoclinic to face-centered cubic. Only recently, however, has there been increased convergence in the actinides community on the details of the equilibrium form of the phase diagrams. Practically speaking, while the phase diagrams that represent the stability of the fcc {delta}-phase field at room temperature are generally applicable, it is also recognized that Pu and its alloys are never truly in thermodynamic equilibrium because of self-irradiation effects, primarily from the alpha decay of Pu isotopes. This article covers past and current research on several properties of Pu and Pu-(Al or Ga) alloys and their connections to the crystal structure and the microstructure. We review the consequences of radioactive decay, the recent advances in understanding the electronic structure, the current research on phase transformations and their relations to phase diagrams and phase stability, the nature of the isothermal martensitic {delta} {yields} {alpha}{prime} transformation, and the pressure-induced transformations in the {delta}-phase alloys. New data are also presented on the structures and phase transformations observed in these materials following the application of pressure, including the formation of transition phases.

Schwartz, A J; Cynn, H; Blobaum, K M; Wall, M A; Moore, K T; Evans, W J; Farber, D L; Jeffries, J R; Massalski, T B

2008-04-28

420

The Electronic Structure of Oxygen Atom Vacancy and Hydroxyl Impurity Defects on Titanium Dioxide (110) Surface  

SciTech Connect

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

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

2009-03-23

421

Structures of ultra-thin atomic-layer-deposited TaNx films  

NASA Astrophysics Data System (ADS)

Atomic layer deposition (ALD) is an attractive technique in fabrication of microelectronics presently and in the future, for its accurate thickness control in atomic scale, excellent conformality, and uniformity over large areas at low temperature. It has been adapted and used in deposition of ultrathin TaNx films as diffusion barriers for Cu metallization. In this study, composition, structure, and stability of ultra-thin (1.5-10 nm) atomic layer deposited films are characterized by a set of complementary analytical techniques. The results indicate that the N to Ta atomic concentration ratio in the ALD TaNx films is approximately 2, independent of the film thickness and annealing up to 750 °C. Hydrogen, oxygen, and carbon are detected as impurities within the as-deposited films. The as-deposited ALD TaNx films have an fcc NaCl-type nanocrystalline structure even when the film thickness is 1.5 nm. Following thermal anneal at 600 °C and higher, the films do not undergo a structural change except for an increase in grain size and a decrease in the lattice constant. X-ray photoelectron spectra results indicate that all the Ta atoms in the films are bonded ionically with the surrounding N atoms. An ex situ thermal treatment at 600 °C for 1 h removes the O, which penetrated the layers, by a reduction reaction with the residual H and results in densification of the ALD films. Our analysis of the experimental results indicates that the excess of N atoms of the ALD TaNx films is mainly due to Ta vacancies in the fcc NaCl-type structure. The structural and compositional characteristics of the films explain why the films serve as good diffusion barriers to Cu metallization.

Wu, Y. Y.; Kohn, A.; Eizenberg, M.

2004-06-01

422

New version: GRASP2K relativistic atomic structure package  

NASA Astrophysics Data System (ADS)

A revised version of GRASP2K [P. Jönsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] is presented. It supports earlier non-block and block versions of codes as well as a new block version in which the njgraf library module [A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375] has been replaced by the librang angular package developed by Gaigalas based on the theory of [G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747, G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263]. Tests have shown that errors encountered by njgraf do not occur with the new angular package. The three versions are denoted v1, v2, and v3, respectively. In addition, in v3, the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Changes in v2 include minor improvements. For example, the new version of rci2 may be used to compute quantum electrodynamic (QED) corrections only from selected orbitals. In v3, a new program, jj2lsj, reports the percentage composition of the wave function in LSJ and the program rlevels has been modified to report the configuration state function (CSF) with the largest coefficient of an LSJ expansion. The bioscl2 and bioscl3 application programs have been modified to produce a file of transition data with one record for each transition in the same format as in ATSP2K [C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. All versions of the codes have been adapted for 64-bit computer architecture.

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

2013-09-01

423

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

SciTech Connect

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

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

1994-11-01

424

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

425

Electron spectra and structure of atomic and molecular clusters  

SciTech Connect

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

Dehmer, P.M.

1980-01-01

426

Atomic structure of bacteriophage Sf6 tail needle knob.  

PubMed

Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the "tail needle" likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 ? resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 ? resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands. PMID:21705802

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

2011-06-25

427

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

428

Modelling the atomic structure of Al92U8 metallic glass  

NASA Astrophysics Data System (ADS)

The local atomic structure of the glassy Al92U8 alloy was modelled by the reverse Monte Carlo (RMC) method, fitting x-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) signals. The final structural model was analysed by means of partial pair correlation functions, coordination number distributions and Voronoi tessellation. In our study we found that the most probable atomic separations between Al-Al and U-Al pairs in the glassy Al92U8 alloy are 2.7 Å and 3.1 Å with coordination numbers 11.7 and 17.1, respectively. The Voronoi analysis did not support evidence of the existence of well-defined building blocks directly embedded in the amorphous matrix. The dense-random-packing model seems to be adequate for describing the connection between solvent and solute atoms.

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

2010-10-01

429

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

PubMed

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. PMID:23745864

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

2013-05-20

430

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

431

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

432

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

433

Atomic Resolution Crystal Structure of NAD+-Dependent Formate Dehydrogenase from Bacterium Moraxella sp. C-1  

PubMed Central

The crystal structure of the ternary complex of NAD+-dependent formate dehydrogenase from the methylotrophic bacterium Moraxella sp. C-1 with the cofactor (NAD+) and the inhibitor (azide ion) was established at 1.1 A resolution. The complex mimics the structure of the transition state of the enzymatic reaction. The structure was refined with anisotropic displacitalicents parameters for non-hydrogen atoms to a R factor of 13.4%. Most of the nitrogen, oxygen, and carbon atoms were distinguished based on the analysis of the titalicperature factors and electron density peaks, with the result that side-chain rotamers of histidine residues and most of asparagine and glutamine residues were unambiguously determined. A comparative analysis of the structure of the ternary complex determined at the atomic resolution and the structure of this complex at 1.95 A resolution was performed. In the atomic resolution structure, the covalent bonds in the nicotinamide group are somewhat changed in agreitalicent with the results of quantum mechanical calculations, providing evidence that the cofactor acquires a bipolar form in the transition state of the enzymatic reaction.

Shabalin, I.G.; Polyakov, K.M.; Tishkov, V.I.

2009-01-01

434

Structure of Adsorbed Organometallic Rhodium: Model Single Atom Catalysts  

NASA Astrophysics Data System (ADS)

We have determined the structure of a complex rhodium carbonyl chloride [Rh(CO)2Cl] molecule adsorbed on the TiO2(110) surface by the normal incidence x-ray standing wave technique. The data show that the technique is applicable to reducible oxide systems and that the dominant adsorbed species is undissociated with Rh binding atop bridging oxygen and to the Cl found close to the fivefold coordinated Ti ions in the surface. A minority geminal dicarbonyl species, where Rh-Cl bond scission has occurred, is found bridging the bridging oxygen ions forming a high-symmetry site.

Bennett, R. A.; McCavish, N. D.; Basham, M.; Dhanak, V. R.; Newton, M. A.

2007-02-01

435

STRUCTURAL BIOLOGY: A Chloride Pump at Atomic Resolution  

NSDL National Science Digital Library

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

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

2000-05-26

436

Electronic shell structure of group-IIIA metal atomic clusters  

NASA Astrophysics Data System (ADS)

Ionization potentials of Aln and Inn clusters (n<80) in supercooled beams have been measured by photoionization spectroscopy. The abrupt leveling near n=5 of the initial linear increase in ionization potentials and the subsequent gradual approach to the classical metallic sphere model are consistent with a simple picture of s-p band hybridization. For n>6, there is clear evidence of electron shell filling, yet substantial deviations from shell-model predictions remain. Crystal-field effects are considered the most probable source of symmetry breaking and give insight to cluster structure.

Schriver, Kenneth E.; Persson, John L.; Honea, Eric C.; Whetten, Robert L.

1990-05-01

437

Atomic structure-colour relationship in natural diamonds  

NASA Astrophysics Data System (ADS)

Colour is a physical attribute that can be very difficult to characterise in diamond and consequently it receives regular attention from scientists working in the gem industry. In this work we compare natural brown (the most common colour) and colourless type IIa diamonds containing only trace quantities (< 1 at. ppm) of nitrogen. Numerous attempts have been made to trace the origin of brown tints in natural diamond, with the most likely culprits, i.e. dislocations and nitrogen impurities, ruled out through the application of various analytical techniques. Consequently more emphasis has recently been placed on the study of smaller defects in the diamond structure and their influence on colour. The focus of this research work is the analysis of vacancy defects having a size of the order of 1nm using aberration corrected scanning transmission electron microscopy (AC-STEM). The small electron probe size and depth of focus afforded by this technique allows such defect structures together with their position to be resolved far more readily than with conventional HR-TEM. Small-scale contrast variations are apparent in the lattice images of brown and not of colourless diamonds. These features have been compared to simulated phase contrast images of vacancy clusters in diamond. In addition, both experimental and simulated defocus series indicate that such features are not restricted to the surface of the specimen.

Godfrey, I. S.; Bangert, U.

2010-07-01

438

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

SciTech Connect

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

Zhang, Zaoli; Rashkova, B. [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Leoben (Austria); Dehm, G. [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Leoben (Austria); Department Materials Physics, University of Leoben, Leoben (Austria); Lazar, P.; Redinger, J. [Institute of Applied Physics, Vienna University of Technology, Vienna (Austria); Podloucky, R. [Department of Physical Chemistry, Vienna University, Vienna (Austria)

2010-08-01

439

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

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

440

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

SciTech Connect

It is over 100 y since Lord Rayleigh first showed the differences between coherent and incoherent imaging in the light microscope, pointing out the advantages of the latter for resolution and image interpretation. The annular detector in the high-resolution STEM provides the same advantages for electrons, allowing incoherent imaging at atomic resolution, with image contrast strongly dependent on atomic number (Z). Since incoherent imaging has no phase problem, these Z-contrast images may be directly inverted to given the (projected) atomic positions. A maximum entropy method avoids false detail associated with direct deconvolution, and gives atomic coordinates to an accuracy of {+-}0.1{Angstrom}. Electron energy loss spectroscopy can provide valuable complementary information on light element bonding and the presence of impurities in specific atomic planes selected from the image. Together, these techniques have revealed some surprisingly complex interfacial structures. For surface studies, the 1.3{Angstrom} probe of the VG Microscopes HB603U STEM provides sufficient penetration and contrast to image single Pt and Rh atoms on {gamma}-alumina supports. Such images reveal preferred atomic configurations and allow possible surface adsorption sites to be deduced.

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

1996-12-31

441

A framework for the evaluation of chemical structure databases.  

PubMed

Access to desk-top structure and reaction databases through applications such as Chemical Abstracts' SciFinder, MDL's Beilstein CrossFire, and ISIS Reaction Browser has led to changes in information seeking habits of research chemists, the impact of which has implications when database purchasing decisions are made. A semiquantitative assessment is proposed which takes into account key aspects of structure and reaction databases. Assessment criteria are identified which can be weighted according to an organization's information needs. Values are then assigned to criteria for each data source, after which a formula is applied which leads to an indication of the relative value of systems under consideration. The formula takes into account the cost of database products and also the incremental benefit of adding a new system to an existing collection. This work is presented as a generic approach to the evaluation of databases and is not limited in scope to only structure and reactions databases. PMID:11604014

Cooke, F; Schofield, H

442