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1

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

E-print Network

LETTERS Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy identification of all the atoms in a material with unknown three-dimensional structure would con- stitute a very. The results demon- strate that atom-by-atom structural and chemical analysis of all radiation

Pennycook, Steve

2

Atom structures  

E-print Network

The atom structure of an atomic boolean algebra with operators is some canonically defined frame or relational structure that is based on the set of atoms of the algebra. We discuss the relation between varieties of boolean algebras with operators and the induced class of atom structures. Our main result states that for a variety V of boolean algebras with conjugated operators, the corresponding class At V of atom structures is elementary; moreover, an (infinite) axiomatization of At V can be generated from the equations defining V. 1

Yde Venema

1997-01-01

3

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

NASA Technical Reports Server (NTRS)

A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

Kahn, L. R.

1981-01-01

4

Atomic Structure  

Microsoft Academic Search

Data obtained from the Rutherford scattering experiment are used to present a simple picture of the structure of the atom. This picture is shown to be in agreement with the experimental findings on the electrical nature of matter. On the assumption that the particles which make up the nucleus (neucleons) are neutrons and protons, a \\

R. E. Lapp; H. L. Andrews

1948-01-01

5

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

E-print Network

Probing Atomic and Electronic Structure of Catalysts by Combination of In Situ and Ex Situ Chemical Karim, Robert Dagle, Ja Hun Kwak, Janos Szanyi, Charles Peden Purpose Understand the structural capabilities that enable this understanding Directly relate structural information with the catalytic

6

The atomic structure of a bare buffer layer on SiC(0001) chemically resolved.  

PubMed

A chemical-specific photoelectron diffraction structure determination of a carbon rich buffer layer on SiC is reported. In addition to the long-range ripple of this surface, a local buckling in the hexagonal sublattice, which breaks the local range order symmetry, was unraveled. PMID:25245167

de Lima, Luis Henrique; Handschak, Dominique; Schönbohm, Frank; Landers, Richard; Westphal, Carsten; de Siervo, Abner

2014-11-14

7

Atomic-Scale Chemical Imaging and Quantification of Metallic Alloy Structures by Energy-Dispersive X-Ray Spectroscopy  

SciTech Connect

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

Lu, Ping [Sandia National Laboratories; Zhou, Lin [Ames Laboratory; Kramer, Matthew J. [Ames Laboratory; Smith, David J. [Arizona State University

2014-02-04

8

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

PubMed Central

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

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

2014-01-01

9

Pressure and chemical substitution effects in the local atomic structure of BaFe2As2  

NASA Astrophysics Data System (ADS)

The effects of K and Co substitutions and quasihydrostatic applied pressure (P<9 GPa) in the local atomic structure of BaFe2As2, Ba(Fe0.937Co0.063)2As2 and Ba0.85K0.15Fe2As2 superconductors were investigated by extended x-ray absorption fine structure (EXAFS) measurements in the As K absorption edge. The As-Fe bond length is found to be slightly reduced (?0.01 Å) by both Co and K substitutions, without any observable increment in the corresponding Debye-Waller factor. Also, this bond is shown to be compressible [?=3.3(3)×10-3 GPa-1]. The observed contractions of As-Fe bond under pressure and chemical substitutions are likely related with a reduction of the local Fe magnetic moments, and should be an important tuning parameter in the phase diagrams of the Fe-based superconductors.

Granado, E.; Mendonça-Ferreira, L.; Garcia, F.; Azevedo, G. De M.; Fabbris, G.; Bittar, E. M.; Adriano, C.; Garitezi, T. M.; Rosa, P. F. S.; Bufaiçal, L. F.; Avila, M. A.; Terashita, H.; Pagliuso, P. G.

2011-05-01

10

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

NASA Technical Reports Server (NTRS)

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

Kahn, L. R.

1982-01-01

11

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

NASA Technical Reports Server (NTRS)

The application of ab initio quantum mechanical approaches in the study of metal atom clusters requires simplifying techniques that do not compromise the reliability of the calculations. Various aspects of the implementation of the effective core potential (ECP) technique for the removal of the metal atom core electrons from the calculation were examined. The ECP molecular integral formulae were modified to bring out the shell characteristics as a first step towards fulfilling the increasing need to speed up the computation of the ECP integrals. Work on the relationships among the derivatives of the molecular integrals that extends some of the techniques pioneered by Komornicki for the calculation of the gradients of the electronic energy was completed and a formulation of the ECP approach that quite naturally unifies the various state-of-the-art "shape- and Hamiltonian-consistent" techniques was discovered.

Kahn, L. R.

1981-01-01

12

Atomic Structure Timeline  

NSDL National Science Digital Library

Lee Buescher is a microbiology and chemistry instructor at Watertown High School in Watertown, WI. He maintains the Atomic Structure Timeline page. The timeline follows major discoveries and advancements throughout history related to atomic structure. From Democritus to Bohr to modern day scientists, the descriptions and links explain the individual and what they accomplished.

Buescher, Lee.

13

Atomic Structure Webquest  

NSDL National Science Digital Library

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

Stefaniak, Linda

2007-10-02

14

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

15

Atom Probe Tomography Frontiers in Chemical Imaging  

E-print Network

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

16

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

PubMed

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

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

2014-01-01

17

Influence of krypton atoms on the structure of hydrogenated amorphous carbon deposited by plasma enhanced chemical vapor deposition  

SciTech Connect

Hydrogenated amorphous carbon (a-C:H) films were prepared by plasma enhanced chemical vapor deposition using methane (CH{sub 4}) plus krypton (Kr) mixed atmosphere. The depositions were performed as function of the bias voltage and krypton partial pressure. The goal of this work was to study the influence of krypton gas on the physical properties of a-C:H films deposited on the cathode electrode. Krypton concentration up to 1.6 at. %, determined by Rutherford Back-Scattering, was obtained at high Kr partial pressure and bias of -120 V. The structure of the films was analyzed by means of optical transmission spectroscopy, multi-wavelength Raman scattering and Fourier Transform Infrared spectroscopy. It was verified that the structure of the films remains unchanged up to a concentration of Kr of about 1.0 at. %. A slight graphitization of the films occurs for higher concentration. The observed variation in the film structure, optical band gap, stress, and hydrogen concentration were associated mainly with the subplantation process of hydrocarbons radicals, rather than the krypton ion energy.

Oliveira, M. H. Jr. [Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas-UNICAMP, C. P. 6165, Campinas, Sao Paulo 13083-970 (Brazil); Institut de Ciencia dels Materials, Universitat de Valencia, E-46071 Valencia (Spain); Viana, G. A.; Marques, F. C. [Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas-UNICAMP, C. P. 6165, Campinas, Sao Paulo 13083-970 (Brazil); Lima, M. M. Jr. de; Cros, A.; Cantarero, A. [Institut de Ciencia dels Materials, Universitat de Valencia, E-46071 Valencia (Spain)

2010-12-15

18

Influence of krypton atoms on the structure of hydrogenated amorphous carbon deposited by plasma enhanced chemical vapor deposition  

NASA Astrophysics Data System (ADS)

Hydrogenated amorphous carbon (a-C:H) films were prepared by plasma enhanced chemical vapor deposition using methane (CH4) plus krypton (Kr) mixed atmosphere. The depositions were performed as function of the bias voltage and krypton partial pressure. The goal of this work was to study the influence of krypton gas on the physical properties of a-C:H films deposited on the cathode electrode. Krypton concentration up to 1.6 at. %, determined by Rutherford Back-Scattering, was obtained at high Kr partial pressure and bias of -120 V. The structure of the films was analyzed by means of optical transmission spectroscopy, multi-wavelength Raman scattering and Fourier Transform Infrared spectroscopy. It was verified that the structure of the films remains unchanged up to a concentration of Kr of about 1.0 at. %. A slight graphitization of the films occurs for higher concentration. The observed variation in the film structure, optical band gap, stress, and hydrogen concentration were associated mainly with the subplantation process of hydrocarbons radicals, rather than the krypton ion energy.

Oliveira, M. H.; Viana, G. A.; de Lima, M. M.; Cros, A.; Cantarero, A.; Marques, F. C.

2010-12-01

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

Atomic fluorine source for chemical lasers  

NASA Astrophysics Data System (ADS)

We present results from the early development of an F atom source appropriate for HF and AGIL chemical laser research. The system uses high power microwaves to produce a high enthalpy plasma that thermally dissociates molecular species such as SF6 and F2. Results of the characterization of the flow are presented.

Davis, Steven J.; Oakes, David B.; Read, Michael E.; Gelb, Alan H.

2002-05-01

21

How low-excitation, fine-structure atomic lines can help understand the chemical evolution of PPNe and PNe  

NASA Astrophysics Data System (ADS)

The nebular gas composition evolves very strongly during the post-AGB/PPN phase, from the molecule-rich AGB shells to the fully ionized evolved PNe, which has important effects on the thermodynamics and dynamics of nebulae in the intermediates phases and on their observational properties. Before the end of its operational life, Herschel/HIFI+PACS provided us with very high-spectral resolution and sensitivity FIR observations of the C I, C II and O I emission of a sample of 10 C-rich and O-rich PPNe and young PNe, 2 AGB stars and 1 supergiant star. We derive estimates for the mass of the C I- and C II-rich emitting regions (which partly overlap with the molecular and H II regions) of this sample. Results range between ?10^{-3} and ˜0.2 M? for %the C I-emitting region, and between ?10^{-3} and ˜0.5 M? for the C II-emitting region. We also determine the characteristic excitation temperature of the C I-rich region and compare atomic and molecular line profiles in order to determine the spatial distribution of the atomic emission and the origin of dissociation of molecules —which in some young PNe could be due to developing shocks.

Santander-García, M.; Bujarrabal, V.; Alcolea, J.

2014-04-01

22

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.

23

Morphology and atomic structure of hydrogen-terminated Si(110)-(1 × 1) surfaces prepared by a wet chemical process  

NASA Astrophysics Data System (ADS)

We have measured the macroscopic and microscopic surface morphology of hydrogen-terminated Si(110)-(1 × 1) [H:Si(110)-(1 × 1)] surfaces prepared by an improved wet chemical process. The observations were performed by high-resolution electron-energy-loss spectroscopy (HREELS), low-energy-electron diffraction (LEED), and scanning tunneling microscopy (STM). At macroscopic scale, it was found that the surface is a mono-hydride terminated surface with a two-dimensional p2mg space group, thus, being a well-defined H:Si(110)-(1 × 1) surface. At microscopic scale, elongated terraces were observed along the [1 1 bar0] direction reflecting surface anisotropy. The terraces extend in frames with sizes up to a few micrometers. We discussed the macroscopic and microscopic surface morphology by combining our LEED and STM results.

Matsushita, Stephane Yu; Kawamoto, Erina; Haga, Kenya; Yamada, Taro; Suto, Shozo

2015-02-01

24

Chemical evolution STRUCTURE OF GALAXIES  

E-print Network

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

Kruit, Piet van der

25

RADIOACTIVE CHEMICAL ELEMENTS IN THE ATOMIC TABLE.  

SciTech Connect

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

HOLDEN, N.E.

2005-08-13

26

Atomic Structure in Black Hole  

E-print Network

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

Nagatani, Y

2006-01-01

27

Relativistic calculation of atomic structures  

Microsoft Academic Search

The current state of the art in relativistic calculation of atomic structures is surveyed. The theory is modelled on the practice in non-relativistic calculations, using many-particle wave functions built from Dirac central field spinors. The Hamiltonian includes quantum electrodynamic effects in the form of the Breit approximation for the interaction energy of two electrons. Within the limits for which this

I. P. Grant

1970-01-01

28

Atomic Structure in Black Hole  

E-print Network

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

Yukinori Nagatani

2006-11-27

29

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. PMID:24077611

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

2013-01-01

30

Atomic-number dependence of relativistic effects on chemical bonding  

NASA Astrophysics Data System (ADS)

The Atomic-number dependence of the relativistic effects on chemical bonding has been studied using the difference ([Delta]APB) in the bond overlap populations between the relativistic and nonrelativistic DV-X[alpha] calculations for various XH diatomic hydrides (X=Cu, Ag, and Au) and XF6 hexafluorides (X=S, Se, Mo, Ru, Rh, Te, W, Re, Os, Ir, Pt, U, Np, and Pu). The atomic-number dependence of [Delta]APB suggests that the absolute values of APB roughly increase with order ([alpha]Z)2 for Z up to about 80, and the higher order term ([alpha]Z)4 should be taken into account for Z larger than 80, where [alpha] is the fine structure constant (=1/c, c is the velocity of light).

Onoe, Jun

31

Local Optical Properties, Electron Densities, and London Dispersion Energies of Atomically Structured Grain Boundaries  

E-print Network

DuPont Company, Central Research, E356-384, Experimental Station, Wilmington, Delaware 19880, USA chemical compositions and atomic and electronic structures [6­10]. These variations strongly influence of atomically structured GBs can be significantly altered locally by structural and chemical changes

Rollins, Andrew M.

32

Semi-Experimental (r_s/r_e) Structures for the Heavy Atom Backbones of Two Moderately Large Molecules Obtained from Microwave Spectroscopy and Quantum Chemical Calculations  

NASA Astrophysics Data System (ADS)

From recent microwave investigations of 1-methyl-4-piperidone and tropinone ground state rotational constants are available for the equatorial conformers of the normal species and the isotopologues with single substitution of all the heavy atoms. Vibration-rotation constants (alphas) were computed with Gaussian 03 (G03) for the B3LYP/cc-pVTZ model and used to convert ground state rotational constants into equilibrium rotational constants. Using the Kraitchman equations (RS method), the equilibrium (RE) Cartesian coordinates were determined for all the heavy atoms in the principal axis framework. Equilibrium bond lengths and bond angles are compared with those computed with the B3LYP/cc-pVTZ model. We have compared the ground state rotational constants computed with G03, after scaling by factors based on the normal species, with observed values. The agreement is within 0.1% for the full set of constants (0.04% for methyl-piperidone and 0.1% for tropinone). This agreement between experiment and theory is so good that it seems possible to use calculated ground state rotational constants in place of experimental ones for determining RS/RE structures for organic molecules of this size. L. Evangelisti, A. Lesarri, M. Jahn, E. Cocinero, W. Caminati, J.-U. Grabow J. Phys. Chem. A, submitted. E. J. Concinero, A. Lesarri, P. Ecija, J.-U. Grabow, J. A. Fernandez, F. Castano PCCP 12, 6076-6083 (2010). } ground state rotational constants are available for the equatorial conformers of the normal species and the isotopologues with single substitution of all the heavy atoms. Vibration-rotation constants (alphas) were computed with Gaussian 03 (G03) for the B3LYP/cc-pVTZ model and used to convert ground state rotational constants into equilibrium rotational constants. Using the Kraitchman equations (RS method), the equilibrium (RE) Cartesian coordinates were determined for all the heavy atoms in the principal axis framework. Equilibrium bond lengths and bond angles are compared with those computed with the B3LYP/cc-pVTZ model. We have compared the ground state rotational constants computed with G03, after scaling by factors based on the normal species, with observed values. The agreement is within 0.1% for the full set of constants (0.04% for methyl-piperidone and 0.1% for tropinone). This agreement between experiment and theory is so good that it seems possible to use calculated ground state rotational constants in place of experimental ones for determining RS/RE structures for organic molecules of this size.

Craig, Norman C.; Lesarri, Alberto; Cocinero, Emilio J.; Grabow, Jens-Uwe

2011-06-01

33

The Structure of the Helium Atom  

Microsoft Academic Search

Models for the Helium Atom.-(1) Bohr's model is unsatisfactory because it gives too great a value for the ionizing potential and is not in accord with the optical and magnetic properties of helium. Now the chemical evidence suggests that each electron in an atom has its own separate orbit, and that these orbits are closely interrelated. Accordingly two new models

Irving Langmuir

1921-01-01

34

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

NASA Astrophysics Data System (ADS)

A new method for the chemical generation of atomic iodine intended for use in a chemical oxygen-iodine laser (COIL) was investigated experimentally. The method is based on the fast reaction of hydrogen iodide with chemically produced chlorine atoms. Effects of the initial ratio of reactants and their mixing in a flow of nitrogen were investigated experimentally and interpreted by means of a computational model for the reaction system. The yield of iodine atoms in the nitrogen flow reached 70-100% under optimum experimental conditions. Gain was observed in preliminary experiments on the chemical generation of atomic iodine in a flow of singlet oxygen.

Špalek, Otomar; Jirásek, Vít.; ?enský, Miroslav; Kodymová, Jarmila; Jakubec, Ivo; Hager, Gordon D.

2002-08-01

35

Chemical structure and dynamics: Annual report 1993  

SciTech Connect

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

Colson, S.D.

1994-07-01

36

Quantum Chemical Topology: Knowledgeable atoms in peptides  

NASA Astrophysics Data System (ADS)

The need to improve atomistic biomolecular force fields remains acute. Fortunately, the abundance of contemporary computing power enables an overhaul of the architecture of current force fields, which typically base their electrostatics on fixed atomic partial charges. We discuss the principles behind the electrostatics of a more realistic force field under construction, called QCTFF. At the heart of QCTFF lies the so-called topological atom, which is a malleable box, whose shape and electrostatics changes in response to a changing environment. This response is captured by a machine learning method called Kriging. Kriging directly predicts each multipole moment of a given atom (i.e. the output) from the coordinates of the nuclei surrounding this atom (i.e. the input). This procedure yields accurate interatomic electrostatic energies, which form the basis for future-proof progress in force field design.

Popelier, Paul L. A.

2012-06-01

37

Chemical generation of atomic iodine for a COIL via atomic fluorine  

NASA Astrophysics Data System (ADS)

Results of experimental investigation of the chemical generation of atomic iodine for a Chemical Oxygen-Iodine Laser (COIL) are presented. The work was focused on the reaction system with atomic fluorine as an intermediate species produced by the chemical way from gaseous reactants. At the first step, atomic fluorine is produced in reaction of molecular fluorine with nitrogen oxide. Then F atoms react with gaseous hydrogen iodide producing atomic iodine. The efficiency of this two-step process was studied thoroughly in dependence on mixing conditions, flow rate of reacting gases and pressure in the reactor. The results obtained on the small-scale device under experimental conditions simulating pressure and flow conditions in a COIL show that atomic iodine is generated by this alternative, advantageous method with rather high concentrations sufficient for operation of the supersonic COIL.

Censky, Miroslav; Spalek, Otomar; Jirasek, Vit; Kodymova, Jarmila; Jakubec, Ivo

2004-05-01

38

Evolution of atomic structure during nanoparticle formation  

PubMed Central

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

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

2014-01-01

39

Evolution of atomic structure during nanoparticle formation.  

PubMed

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

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

2014-05-01

40

The Atomic Structure of Oxide\\/Oxide Interface  

Microsoft Academic Search

The physical and chemical properties of thin or ultrathin oxide film deposited on another oxide bulk or thin film usually differ strongly from the bulk. The properties of the heterostructures ultimately rely on the structure and the chemistry of the oxide\\/oxide interface. Data in the literature indicated that atomically abrupt interfaces between oxides show abnormal electronic and magnetic properties. This

Qi-Hui Wu

2011-01-01

41

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

Microsoft Academic Search

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

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

2001-01-01

42

Unraveling the Atomic Structure of Ultrafine Iron Clusters  

PubMed Central

Unraveling the atomic structures of ultrafine iron clusters is critical to understanding their size-dependent catalytic effects and electronic properties. Here, we describe the stable close-packed structure of ultrafine Fe clusters for the first time, thanks to the superior properties of graphene, including the monolayer thickness, chemical inertness, mechanical strength, electrical and thermal conductivity. These clusters prefer to take regular planar shapes with morphology changes by local atomic shuffling, as suggested by the early hypothesis of solid-solid transformation. Our observations differ from observations from earlier experimental study and theoretical model, such as icosahedron, decahedron or cuboctahedron. No interaction was observed between Fe atoms or clusters and pristine graphene. However, preferential carving, as observed by other research groups, can be realized only when Fe clusters are embedded in graphene. The techniques introduced here will be of use in investigations of other clusters or even single atoms or molecules. PMID:23251781

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

2012-01-01

43

Unraveling the Atomic Structure of Ultrafine Iron Clusters  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

44

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

NASA Astrophysics Data System (ADS)

The mathematical modelling of reaction systems for chemical generation of atomic iodine is presented. This process is aimed to be applied in the chemical oxygen-iodine laser (COIL), where it can save a substantial part of energy of singlet oxygen and so increase the laser output power. In the suggested method, gaseous reactants for I atoms generation are admixed into the COIL primary gas flow containing singlet oxygen. Two reaction systems were proposed, based on the reaction of hydrogen iodide with chemically generated atomic fluorine or chlorine. It was found that the reaction path via Cl atoms better matches the experimental conditions of COIL with a yield of atomic iodine of up to 67%. As a result of modelling, a suitable reaction system and design of experimental arrangement for the effective production of atomic iodine in laser conditions were found.

Jirásek, Vít.; Špalek, Otomar; Kodymová, Jarmila; ?enský, Miroslav

2001-07-01

45

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.

Laura Moin

46

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

47

Introduction to Atomic Structure: Demonstrations and Labs.  

ERIC Educational Resources Information Center

Demonstrates a variety of electrical phenomena to help explain atomic structure. Topics include: establishing electrical properties, electrochemistry, and electrostatic charges. Recommends demonstration equipment needed and an explanation of each. (MVL)

Ciparick, Joseph D.

1988-01-01

48

Modeling of the chemical generation of atomic iodine in a chemical oxygen-iodine laser  

NASA Astrophysics Data System (ADS)

The mathematical modeling of reaction systems for chemical generation of atomic iodine is presented. This process can be applied in the chemical oxygen-iodine laser (COIL), where it can save a substantial part of energy of singlet oxygen and so increase the laser output power. The parametric study of the production of atomic fluorine and subsequently atomic iodine in dependence on the pressure and dilution with inert gas was made. The calculation of the interaction between produced atomic iodine and singlet oxygen was made with four different mixing/reacting schemes.

Jirasek, Vit; Spalek, Otomar; Kodymova, Jarmila; Censky, Miroslav

2002-05-01

49

COIL with supersonic injection of chemically produced atomic iodine  

NASA Astrophysics Data System (ADS)

An advanced Chemical Oxygen-Iodine Laser (COIL) using the chemical generation of atomic iodine was studied. Atomic iodine is produced by the reaction of atomic chlorine with hydrogen iodide (HI) in two separated reactors tightly attached to the supersonic laser cavity. The iodine-contained mixture is injected to the flow of singlet oxygen by means of the supersonic orifices located 5 mm downstream the nozzle throat. The atomic iodine number density in the laser cavity up to 1.2 x 10 15 cm -3 and a small-signal gain up to 0.35 %/cm were achieved. An rather high quenching of singlet oxygen by HI caused that the attained laser power was low. The results of small signal gain and the laser power are compared with the previous system including the mixing of reactants upstream the nozzle throat.

Jirásek, Vít; Špalek, Otomar; ?enský, Miroslav; Kodymová, Jarmila; Picková, Irena; Jakubec, Ivo

2007-05-01

50

Local atomic structures of palladium nanowire  

Microsoft Academic Search

In this paper, investigation of the structure of palladium nanowire has been performed by using genetic algorithm simulation based on the molecular dynamics. Our calculation employs a well-fitted, tight-binding many-body potential for Pd atoms. Some local atomic structures and defects in nanowires have been reported. The melting behavior of palladium nanowire has also been investigated. An interesting result is that

Li Hui; B. L. Wang; J. L. Wang; G. H. Wang

2004-01-01

51

Atom structures of relation algebras Ian Hodkinson \\Lambda  

E-print Network

Atom structures of relation algebras Ian Hodkinson \\Lambda October 24, 1995 Abstract We study atom structures of relation algebras. We prove that the class of atom structures that arise from representable is not determined by its atom structure, by exhibiting two (countable) relation algebras with the same atom

Hodkinson, Ian

52

Structure validation in chemical crystallography.  

PubMed

Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions. PMID:19171970

Spek, Anthony L

2009-02-01

53

Local atomic structure in thin films of silicon nitride and silicon diimide produced by remote plasma-enhanced chemical-vapor deposition  

Microsoft Academic Search

We have grown thin films of silicon nitride by remote plasma-enhanced chemical-vapor deposition and have studied the chemical bonding by infrared absorption, x-ray photoelectron spectroscopy, Rutherford backscattering, and Auger-electron spectroscopy. Films were grown using two different gases as the source of nitrogen, N2 and NH3. We have found that films grown from N2 and deposited at substrate temperatures in excess

D. V. Tsu; G. Lucovsky; M. J. Mantini

1986-01-01

54

Direct atomic structure determination by the inspection of structural phase  

PubMed Central

A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex ?-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities. PMID:23940343

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

2013-01-01

55

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

56

Local atomic structures of palladium nanowire.  

PubMed

In this paper, investigation of the structure of palladium nanowire has been performed by using genetic algorithm simulation based on the molecular dynamics. Our calculation employs a well-fitted, tight-binding many-body potential for Pd atoms. Some local atomic structures and defects in nanowires have been reported. The melting behavior of palladium nanowire has also been investigated. An interesting result is that the diffusion of the central atoms results in the beginning of the melting. The moving central atoms build up a monostrand atomic chain during the melting process. The single atomic chain is very stable which can exist in a wide temperature region (800-950 K). The formation of the single atomic chain causes some new defects in the nanowire. And the new defects result in the decrease of the thermal stability of the nanowire. Interestingly, the liquid from the nanowire melting has a supercooled feature because the splitting of the second peak of pair correlation function is observed. The curves of the internal energy and the local cluster are used to monitor the phase transition. The melting of the nanowire is not only due to the single atomic diffusion, but also the diffusion of the local clusters. PMID:15527365

Hui, Li; Wang, B L; Wang, J L; Wang, G H

2004-11-01

57

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

58

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

NASA Astrophysics Data System (ADS)

Two alternative chemical methods of atomic iodine generation for a chemical oxygen-iodine laser (COIL) were studied. These methods are based on fast reactions of gaseous hydrogen iodide with chemically produced chlorine and fluorine atoms. Both processes were studied first in small-scale reactors. A yield of atomic iodine in the Cl system and nitrogen (non-reactive) atmosphere exceeded 80%, while in the F system it was only up to 27% related to F2 or 50% related to HI. The process of atomic iodine generation via Cl atoms was employed in operation of the supersonic COIL. A laser power of 430 W at 40 mmol Cl2/s, and the small signal gain up to 0.4%/cm were attained. The proposed methods promise an increase in laser power, easier control of laser operation, and simpler iodine management in comparison with the conventional source of atomic iodine using I2. The experimental results obtained so far with this experimental arrangement did not proved yet increasing COIL chemical efficiency because some process quenching a part of singlet oxygen was indicated. Therefore a modified experimental set-up has been designed and prepared for further investigation.

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

2005-03-01

59

Atomic Structure Schrdinger equation has approximate solutions for multi-  

E-print Network

Atomic Structure Schrödinger equation has approximate solutions for multi- electron atoms, which indicate that all atoms are like hydrogen Atomic Structure Schrödinger equation has approximate solutions 3s 3p 3d Energy hydrogen multi-electron #12;Atomic Structure · orbitals are populated by electrons

Zakarian, Armen

60

Quantum Structures of the Hydrogen Atom  

E-print Network

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

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

2014-05-28

61

Atomic structure evolution in bulk metallic glass under compressive stress  

Microsoft Academic Search

The structural behavior of Cu64.5Zr35.5 bulk metallic glass under compressive stress was investigated by means of in situ high energy x-ray synchrotron diffraction. The topological and chemical short-range order of the glass changes reversible upon loading within the elastic range. The number density of Cu-(Zr,Cu) and Zr-Zr nearest neighbor atomic pairs becomes oriented along the loading direction. The macroscopic stress

G. Wang; N. Mattern; S. Pauly; J. Bednarcik; J. Eckert

2009-01-01

62

Making Matter: The Atomic Structure of Materials  

NSDL National Science Digital Library

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

63

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

SciTech Connect

Atomic-scale quantification of chemical composition across oxide interfaces is important for understanding physical properties of epitaxial oxide nanostructures. Energy-dispersive X-ray spectroscopy (EDS) in an aberration-corrected scanning transmission electron microscope was used to quantify chemical composition across the interface of ferromagnetic La{sub 0.7}Sr{sub 0.3}MnO{sub 3} and antiferromagnetic BiFeO{sub 3} quantum structure. This research demonstrates that chemical composition at atomic columns can be quantified by Gaussian peak-fitting of EDS compositional profiles across the interface. Cation diffusion was observed at both A- and B-sublattice sites; and asymmetric chemical profiles exist across the interface, consistent with the previous studies.

Lu, Ping; Van Benthem, Mark [Sandia National Laboratories, P.O. Box 5800, MS 1411, Albuquerque, New Mexico 87185-1411 (United States)] [Sandia National Laboratories, P.O. Box 5800, MS 1411, Albuquerque, New Mexico 87185-1411 (United States); Xiong, Jie; Jia, Quanxi [Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2013-04-29

64

Towards single atom analysis of biological structures.  

PubMed

Mapping single atoms in biological structures is now becoming within the reach of analytical electron microscopy. Electron energy-loss spectroscopy (EELS) in the field-emission scanning transmission electron microscope (STEM) provides a particularly high sensitivity for detecting the biologically important element, phosphorus. Imaging can be performed at low dose with dark-field STEM prior to analysis at high dose, so that structures of macromolecular assemblies can be correlated with the numbers of specific atoms that they contain. Measurements confirm theoretical predictions that single atom detection requires a nanometer-sized probe. Although phosphorus atoms may have moved several nanometers from their original positions by beam-induced structural degradation at the high required dose of approximately 10(9) e/nm2, damaged molecules are nevertheless stable enough to be analyzed at 1 or 2 nm resolution. Such analyses can only be achieved by means of spectrum-imaging with correction for specimen drift. Optimal strategies for mapping small numbers of phosphorus atoms have been investigated using well-characterized specimens of DNA plasmids and tobacco mosaic virus. PMID:10389278

Leapman, R D; Rizzo, N W

1999-06-01

65

Development of the Chemical Oxygen-Iodine Laser (COIL) with chemical generation of atomic iodine  

NASA Astrophysics Data System (ADS)

This article addresses the development of a Chemical Oxygen-Iodine Laser (COIL) with alternative chemical ways of generating atomic iodine. Injection of atomic iodine as opposed to molecular iodine has the potential to improve the COIL efficiency. This paper describes two chemical methods for generating iodine atoms based on the gas phase reactions of hydrogen/deuterium iodide with fluorine or chlorine atoms, which are also produced chemically. Simplified one-dimensional gas dynamic modeling that describes the stream-wise profiles of species concentrations within both reaction systems is used to gain a theoretical understanding of both reaction systems under COIL conditions. The modeling results are used for the design of an experimental device and the interpretation of experimental data. The first experimental investigation studies the production of iodine atoms produced from reactions of Cl with HI. Atomic iodine yields of 70-100% in nitrogen are obtained, and the gain on the I(2P1/2)-I(2P3/2) transition in a flow of singlet oxygen is measured.

Kodymová, J.; Špalek, O.; Jirásek, V.; ?enský, M.; Hager, G. D.

66

Atomic Structure Calculations from the Los Alamos Atomic Physics Codes  

DOE Data Explorer

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

Cowan, R. D.

67

Relativistic atomic structure: past, present and future  

Microsoft Academic Search

Developments in a relativistic atomic structure have been driven by a combination of advances in experimental methods, in the theory of quantum electrodynamics, in numerical algorithms, computer hardware and software. Today's programs are still in many respects ‘legacy codes’ containing many features going back nearly half a century. It is time for a rethink.

I P Grant

2010-01-01

68

Relativistic atomic structure: past, present and future  

Microsoft Academic Search

Developments in a relativistic atomic structure have been driven by a combination of advances in experimental methods, in the theory of quantum electrodynamics, in numerical algorithms, computer hardware and software. Today's programs are still in many respects 'legacy codes' containing many features going back nearly half a century. It is time for a rethink.

I. P. Grant

2010-01-01

69

Nuclear structure effects in light muonic atoms  

E-print Network

Nuclear structure corrections to energy levels of light muonic atoms are derived with particular attention to the correct nuclear mass dependence. The obtained result for the 2P-2S transition of 1.717(19) meV serves for determination of the nuclear charge radius from the spectroscopic measurement in muonic deuterium.

Pachucki, Krzysztof

2015-01-01

70

Structural materials: understanding atomic scale microstructures  

SciTech Connect

With the ability to locate and identify atoms in three dimensions, atom-probe tomography (APT) has revolutionized our understanding of structure-property relationships in materials used for structural applications. The atomic-scale details of clusters, second phases, and microstructural defects that control alloy properties have been investigated, providing an unprecedented level of detail on the origins of aging behavior, strength, creep, fracture toughness, corrosion, and irradiation resistance. Moreover, atomic-scale microscopy combined with atomistic simulation and theoretical modeling of material behavior can guide new alloy design. In this article, selected examples highlight how APT has led to a deeper understanding of materials structures and therefore properties, starting with the phase transformations controlling the aging and strengthening behavior of complex Al-, Fe-, and Ni-based alloys systems. The chemistry of interfaces and structural defects that play a crucial role in high-temperature strengthening, fracture, and corrosion resistance are also discussed, with particular reference to Zr- and Al-alloys and FeAl intermetallics.

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

2009-01-01

71

Structural evolution during the reduction of chemically derived graphene oxide  

Microsoft Academic Search

The excellent electrical, optical and mechanical properties of graphene have driven the search to find methods for its large-scale production, but established procedures (such as mechanical exfoliation or chemical vapour deposition) are not ideal for the manufacture of processable graphene sheets. An alternative method is the reduction of graphene oxide, a material that shares the same atomically thin structural framework

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

2010-01-01

72

Atomic Structure and the Periodic Table  

NSDL National Science Digital Library

This is a section of an online textbook ("Chem 1 Virtual Textbook") on General Chemistry at the first-year college or advanced high-school level. It provides an introduction to the structure and properties of the elements and their relationship to the periodic table of the elements. The six lessons cover quantum theory, the properties of light, the Bohr model of the atom, the quantum model of the atom, electron configurations, and the periodic properties of the elements. Each lesson is accompanied by a concept map.

Dr. Steven Lower

2005-10-12

73

Chemical structure of multilayer oxidized epitaxial graphene  

NASA Astrophysics Data System (ADS)

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

Zhou, Si; Bongiorno, Angelo

2013-03-01

74

Transmission of Electronic Substituent Effects across the 1,12-Dicarba-closo-dodecaborane Cage: A Computational Study Based on Structural Variation, Atomic Charges, and (13)C NMR Chemical Shifts.  

PubMed

The ability of the 1,12-dicarba-closo-dodecaborane cage to transmit long-range substituent effects has been investigated by analyzing the structural variation of a phenyl probe bonded to C1, as caused by a remote substituent X at C12. The geometries of 41 Ph-CB10H10C-X molecules, including 11 charged species, have been determined by MO calculations at the B3LYP/6-311++G** level of theory. The structural variation of the phenyl probe is best represented by a linear combination of the internal ring angles, termed SF(CARB). Multiple regression analysis of SF(CARB), using appropriate explanatory variables, reveals the presence of resonance effects, superimposed onto the field effect of the remote substituent. The ability of the para-carborane cage to transmit resonance effects is, on average, about one-half of that of the para-phenylene frame in coplanar para-substituted biphenyls. Analysis of the ?-charge variation of the phenyl probe confirms that the para-carborane frame is less capable than the coplanar para-phenylene frame of transmitting ?-electrons from the remote substituent to the phenyl probe, or vice versa. The para-carborane cage is a better ?-acceptor than ?-donor; this makes ?-donor substituents less effective than ?-acceptors in exchanging ?-electrons with the phenyl probe across the cage. When the remote substituent is an uncharged group, the para-carborane cage acts as a very weak ?-acceptor toward the phenyl probe. The structural variation of the para-carborane cage has also been investigated. It consists primarily of a change of the C1···C12 nonbonded separation, coupled with a change of the five B-C-B angles at C12. This concerted geometrical change is controlled by the electronegativity of the substituent and the resonance interactions occurring between substituent and cage. These, however, appear to be important only when ?-donor substituents are involved. The (13)C NMR chemical shifts of the para-carbon of the phenyl probe correlate nicely with SF(CARB), pointing to the reliability of these quantities as measures of long-range substituent effects. On the contrary, the (11)B and (13)C chemical shifts of the cage atoms do not convey information on electronic substituent effects. PMID:25488467

Campanelli, Anna Rita; Domenicano, Aldo; Hnyk, Drahomír

2015-01-01

75

Beyond the Isotropic Atom Model in Crystal Structure Prediction of Rigid Molecules: Atomic Multipoles versus  

E-print Network

Beyond the Isotropic Atom Model in Crystal Structure Prediction of Rigid Molecules: Atomic ABSTRACT: The lattice energies of predicted and known crystal structures for 50 small organic molecules is described by atom-centered multipoles. In comparison to previous predictions using atomic point charge

de Gispert, Adrià

76

PROTEIN STRUCTURE REPORT Atomic resolution structure of the  

E-print Network

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

77

"atomicphysicsproof" --2003/10/7 --page 1 --#11 ATOMIC STRUCTURE  

E-print Network

"atomicphysicsproof" -- 2003/10/7 -- page 1 -- #11 1 ATOMIC STRUCTURE 1.1 Ground state. The study of atomic structure continues to be an exciting field, with increasingly precise measurements of phosphorus One of the most important topics in atomic physics is the description of atomic energy levels

Budker, Dmitry

78

Antiprotonic Radioactive Atom for Nuclear Structure Studies  

NASA Astrophysics Data System (ADS)

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 ?+ and ?- 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.; Yamazaki, Y.

2005-10-01

79

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

E-print Network

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

Heyrovska, Raji

2008-01-01

80

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

E-print Network

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

Raji Heyrovska

2008-06-21

81

Atomic scale structure of Si nanowire  

NASA Astrophysics Data System (ADS)

In this work, we have succeeded to observe the atomic structures of Au assisted Vapor-liquid-solid grown Si nanowire facetted sidewalls by scanning tunnelling microscopy (STM) at low temperature. By combining transmision microscopy observations with STM measurements, we were able to identify the differents facets along the growth direction of the nanowires. For nanowires with diameters larger than 150 nm, the facets orientation alternates between the [111] and [113] directions, whereas for smaller diameters, the 113 facets are replaced by facets with an orientations making a larger angle with the [111] direction. Imaging the facets at the atomic resolution clearly revealed that the facet reconstructions are induced by Au atoms. From the spectroscopic measurements, the facets are found to be metallic. In order to obtain the impurity distribution below the surface, 3D atom probe tomography analyses were performed. A uniform distribution of Boron impurities is observed in the core of the nanowire and the impurity concentration agrees well with the ratio of the flow rates between silane and diborane. Finally, such results are compared to the conductivities of single nanowires measured in field effect transistor devices.

Xu, Tao; Nys, Jean Philippe; Berthe, Maxime; Grandidier, Bruno; Stievenard, Didier; Chen, Wanghua; Larde, Rodrigue; Cadel, Emmanuel; Pareige, Philippe

2009-03-01

82

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

Microsoft Academic Search

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

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

2000-01-01

83

Galactic Chemical Evolution Redux: Atomic Numbers 6 ? Z ? 15  

NASA Astrophysics Data System (ADS)

Motivated by the inability of Galactic chemical evolution models to reproduce some of the observed solar neighbourhood distribution of elements (and isotopes) with atomic numbers 6 IMG Z IMG 15, we have revisited the relevant stellar and Galactic models as part of an ambitious new program aimed at resolving these long-standing discrepancies. Avoiding the use of (traditional) parametric models for low- and intermediate-mass stellar evolution, we have generated a new, physically self-consistent, suite of stellar models and integrated the nucleosynthetic outputs into GEtool, our semi-analytical galactic chemical evolution software package. The predicted temporal evolution of several light- and intermediate- mass elements (and their isotopes) in the solar neighbourhood - from carbon to phosphorus - demonstrate the efficacy of the new yields in reconciling theory and observation.

Gibson, B. K.; Fenner, Y.; Kiessling, A.

2005-07-01

84

An Atomic Environment Potential for use in Protein Structure Prediction  

E-print Network

An Atomic Environment Potential for use in Protein Structure Prediction Christopher M. Summa1 of a knowledge-based atomic environment potential for the modeling of protein structural energetics. An analysis of the probabilities of atomic interactions in a dataset of high- resolution protein structures shows

Summa, Christopher M.

85

Chemical Etiology of Nucleic Acid Structure  

NSDL National Science Digital Library

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

Albert Eschenmoser (The Scripps Research Institute ;)

1999-06-25

86

Atomic structure of ion tracks in Ceria  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

87

Determination of the kinetic parameters for the electrothermal atomization of gold with and without chemical modifiers  

Microsoft Academic Search

The effect of various experimental parameters and the presence of chemical modifiers on the atomization kinetics of gold have been investigated. The dissipation process of the atomic vapour is also studied and the diffusion parameters calculated in the absence and in the presence of chemical modifiers. The chemical modifiers studied are ascorbic acid, rhenium, palladium and rhodium. In the absence

Nikolaos S. Thomaidis; Efrosini A. Piperaki

1999-01-01

88

Unraveling the chemical dynamics of bimolecular reactions of ground state boron atoms, B(2  

E-print Network

Unraveling the chemical dynamics of bimolecular reactions of ground state boron atoms, B(2 PjArticle on the web 8th March 2004 The reaction dynamics of atomic boron, B(2 P), with acetylene, C2H2(X 1 Sg þ molecular beams technique. Only the atomic boron versus hydrogen atom exchange pathway was observed. Forward

Kaiser, Ralf I.

89

Classifying chemical elements and particles: from the atomic to the sub-atomic world  

E-print Network

This paper presents two facets. First, we show that the periodic table of chemical elements can be described, understood and modified (as far as its format is concerned) on the basis of group theory and more specifically by using the group SO(4,2)xSU(2). Second, we show that "periodic tables" also exist in the sub-atomic and sub-nuclear worlds and that group theory is of paramount importance for these tables. In that sense, this paper may be considered as an excursion, for non specialists, into nuclear and particle physics.

Maurice R. Kibler

2008-01-08

90

An Atomic Resolution Structure for Human Fibroblast Growth Factor 1  

E-print Network

An Atomic Resolution Structure for Human Fibroblast Growth Factor 1 Matthew J. Bernett. The backbone atoms of each structurally conserved region of the symmetry-related subdomains in FGF-1 overlay and Biochemistry, Florida State University, Tallahassee, Florida ABSTRACT A 1.10-Ã? atomic resolution X

Blaber, Michael

91

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

92

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

93

Atomic and electronic structure of gadolinium oxide  

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

94

Atomic resolution chemical bond analysis of oxygen in La2CuO4  

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

95

Electronic Structure of Superheavy Atoms. Revisited  

E-print Network

The electronic structure of an atom with Z 137 is inconsistent and physically meaningless because the formula for the lower energy level of the Dirac Hamiltonian formally gives imaginary eigenvalues. But a strict mathematical consideration shows that difficulties with the electronic spectrum for Z > 137 do not arise if the Dirac Hamiltonian is correctly defined as a self-adjoint operator, see [1]. In this article, we brie y summarize the main physical results of that consideration in a form suitable for physicists with some additional new details and numerical calculations of the electronic spectra. [1] B.L. Voronov, D.M. Gitman, and I.V. Tyutin, Theor. Math. Phys. 150(1) (2007) 34

D. M. Gitman; A. D. Levin; I. V. Tyutin; B. L. Voronov

2012-05-01

96

Valence-Bond Theory and Chemical Structure.  

ERIC Educational Resources Information Center

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

Klein, Douglas J.; Trinajstic, Nenad

1990-01-01

97

Arithmetic Aspects of Atomic Structures Charles L. Fefferman  

E-print Network

Arithmetic Aspects of Atomic Structures Charles L. Fefferman Department of Mathematics, Princeton success to explain the hydrogen atom, one of the early challenges of quantum mechanics was to study larger atoms. The problems encountered in this pro­ cess were numerous, and the quest for an understanding

Seco, Luis A.

98

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

99

Atomic Structure of Benzene Which Accounts for Resonance Energy  

E-print Network

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

Raji Heyrovska

2008-07-09

100

Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representations  

E-print Network

Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic the secondary structure level to the atomic level. Our technique represents -helices and -strands as vectors of vectors. The second step in our algorithm is based on the atomic coordinates of the protein structures

Brutlag, Doug

101

Chemical vapor generation—electrothermal atomic absorption spectrometry: new perspectives  

NASA Astrophysics Data System (ADS)

Volatile species of Ag, Cu, Cd, and Zn were generated at room temperature by the addition of sodium tetrahydroborate (III) to an acidified solution of the analytes. The vapor-phase species were rapidly transported to a pre-heated graphite tube, the surface of which was previously treated with Ir as a permanent chemical modifier. The volatile species were trapped at the Ir treated tube surface, and the further heating of the furnace permits their determination by atomic absorption spectrometry. A univariate approach was used to achieve optimized conditions and derive the figures of merit. The limits of detection based on a 3? b criterion were 10 (1); 0.006 (6×10 -4); 28 (2.8) and 1.1 (0.11) ng (?g ml -1) for Ag, Cd, Cu and Zn, respectively. Precision of replicate measurements was typically approximately 10% R.S.D. Using a transfer line as short as possible should minimize losses of analyte during the transport to the graphite furnace. The overall efficiency of the volatile species generation and trapping process estimated for silver was 13%.

Luna, Aderval S.; Borges Pereira, Hugo; Takase, Iracema; Araújo Gonçalves, Rodrigo; Sturgeon, Ralph Edward; Calixto de Campos, Reinaldo

2002-12-01

102

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

SciTech Connect

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

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

2009-05-12

103

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

SciTech Connect

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

Mantovan, R., E-mail: roberto.mantovan@mdm.imm.cnr.it; Vangelista, S.; Wiemer, C.; Lamperti, A.; Tallarida, G. [Laboratorio MDM IMM-CNR, I-20864 Agrate Brianza (MB) (Italy); Chikoidze, E.; Dumont, Y. [GEMaC, Université de Versailles St. Quentin en Yvelines-CNRS, Versailles (France); Fanciulli, M. [Laboratorio MDM IMM-CNR, I-20864 Agrate Brianza (MB) (Italy); Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Milano (Italy)

2014-05-07

104

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

105

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

PubMed

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

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

2014-08-26

106

Atomic and electronic structures of an extremely fragile liquid  

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

107

Atomic and electronic structures of an extremely fragile liquid  

PubMed Central

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

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

2014-01-01

108

Atomic and electronic structures of an extremely fragile liquid.  

PubMed

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

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

2014-01-01

109

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

2012-10-01

110

Surface structure, composition, and polarity of indium nitride grown by high-pressure chemical vapor deposition  

E-print Network

grown by high-pressure chemical vapor deposition have been studied. Atomic hydrogen cleaning produced and heterostructures--which can be accomplished by low- pressure metalorganic chemical vapor deposition MOCVD --the- rium vapor pressure of nitrogen during growth. This requires different approaches in growing structures

Dietz, Nikolaus

111

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

112

Teaching Atomic Structure Using Cooperative Learning  

NSDL National Science Digital Library

This lesson plan focuses on the concepts of atomic number, mass number, isotope, and nuclear atom. A student quiz is included as an assessment instrument. This resource is from PUMAS - Practical Uses of Math and Science - a collection of brief examples created by scientists and engineers showing how math and science topics taught in K-12 classes have real world applications.

2012-08-03

113

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.

The Concord Consortium

2011-01-01

114

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

115

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

116

Chemical structure and dynamics: Annual report 1996  

SciTech Connect

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

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

1997-03-01

117

Theory of quasicrystal surfaces: Probing the chemical reactivity by atomic and molecular adsorption  

NASA Astrophysics Data System (ADS)

The adsorption of oxygen and carbon atoms and of carbon monoxide molecules on a fivefold surface of icosahedral Al-Pd-Mn quasicrystals has been investigated using ab initio density-functional calculations. The quasicrystalline surface has been modeled by periodically repeated slabs cut from rational approximants to the quasicrystalline structure. Atomic and molecular adsorption have been studied for a large number of possible adsorption sites by performing three-dimensional static relaxations of the adsorbate/substrate complex. Four different scenarios for the dissociative adsorption of the CO molecule have been investigated via nudged-elastic band calculations of the transition states. Al and Mn-metal atoms present at the surface bind C and O atoms rather strongly, while Pd atoms are unstable adsorption sites: during relaxation, the adsorbate drifts to the nearest strong-binding site. The chemical reactivity with respect to a CO molecule varies very strongly across the surface. The adsorption close to Mn sites is promoted by rather strong covalent effects, but CO is only physisorbed at Al sites via weak polarization forces. On the basis of the observed local variations of the adsorption strength, we develop scenarios for dissociation and determine the potential energy barriers for this processes. We find that CO adsorbed close to a transition-metal atom can dissociate via an activated process, but the dissociation rate is expected to be rather low because of a high dissociation barrier and a "late" transition state. CO adsorbed close to Al atoms will desorb before dissociation. Surface vacancies present as a consequence of the irregular coordination of the Mackay cluster in the quasiperiodic structure will act as strongly attractive traps for diffusing molecules. Mn surface atoms are located in the center of truncated Mackay clusters. In scanning tunneling electron microscopy (STM) these truncated clusters are imaged as "white flowers". Surface vacancies are responsible for the "dark stars" in the STM images. Since both are molecular adsorption sites, our study predicts that these characteristic features should be affected by CO adsorption.

Kraj?í, M.; Hafner, J.

118

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

E-print Network

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

Heyrovska, Raji

2008-01-01

119

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

E-print Network

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

Raji Heyrovska; Saraswathi Narayan

2008-01-28

120

Cheminoes: A Didactic Game to Learn Chemical Relationships between Valence, Atomic Number, and Symbol  

ERIC Educational Resources Information Center

Cheminoes is a didactic game that enables the meaningful learning of some relations between concepts such as chemical element, valence, atomic number, and chemical symbol for the first 36 chemical elements of the periodic system. Among the students who have played the game, their opinions of the activity were positive, considering the game to be a…

Moreno, Luis F.; Hincapié, Gina; Alzate, María Victoria

2014-01-01

121

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

SciTech Connect

Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly-active and stable catalysts. However the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable a maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.

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

2014-05-05

122

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

PubMed

Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly active and stable catalysts. However, the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies. PMID:24794852

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

2014-05-14

123

The PubChem chemical structure sketcher  

PubMed Central

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

2009-01-01

124

The PubChem chemical structure sketcher.  

PubMed

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

Ihlenfeldt, Wolf D; Bolton, Evan E; Bryant, Stephen H

2009-01-01

125

The structure of 55-atom Cu Au bimetallic clusters: Monte Carlo study  

NASA Astrophysics Data System (ADS)

We have investigated segregation phenomena in Cu Au bimetallic clusters with decahedral structures at 100 K and 300 K, based on the second-moment approximation of the tight-binding (TB-SMA) potentials by using Monte Carlo method. The simulation results indicate that there are three regions (split, three-shell onion-like and core-shell region) at 100 K and two regions (split and core-shell) at 300 K with the structure of decahedral clusters, as the chemical potential difference ?? changes. It is found that the structure of decahedral clusters undergoes a division into smaller clusters in the split region. In the core-shell structure, Au atoms are enriched in surface and Cu atoms occupy the core of the clusters because of the different surface energy of Cu and Au. The Au atoms are enriched in the surface shell, and the Cu atoms are in the middle shell, while a single Au atom is located in the center to form the three-shell onion-like structure. The structure and binding energy of smaller clusters after splitting are also discussed. The Au atoms generally lie on the surface of the smaller clusters after splitting.

Cheng, D.; Huang, S.; Wang, W.

2006-07-01

126

Electronic structures and chemical bonding of actinyl nitrates dihydrates  

NASA Astrophysics Data System (ADS)

The electronic structures and chemical bonding of actinyl nitrates [AnO2 (NO3)2 · 2H2O, An=U, Np and Pu] was studied using the discrete-variational Dirac-Fock-Slater MO method. The strength of both the covalent and the ionic bonds decreases with atomic number of the actinide. This change arises from variations in both the occupancy and the energy of the HOMO. Changes in the energies of the HOMO and LUMO correspond to changes in the stability of the hexavalent state in the actinyl nitrates. The characteristics of each ligand bonds were also analyzed.

Hirata, Masaru; Tachimori, Shoichi; Sekine, Rika; Onoe, Jun; Nakamatsu, Hirohide

127

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

128

Fine structure changing collisions between ultra-cold lithium atoms  

SciTech Connect

The authors have designed and assembled an experiment to determine the rate of fine structure changing collisions between ultra-cold ({approximately} 1 mK) laser cooled Li atoms. The atoms are confined by a magneto-optical trap which consists of six polarized orthogonal laser beams tuned slightly below the 2S{sub 1/2}-2P{sub 3/2} resonance frequency of lithium. Measurements show that about 2 x 10{sup 7} atoms are confined to a roughly spherical region of about 1 mm in diameter. Fine structure changing collisions occur when an atom in the 2S{sub 1/2} state and an atom in the 2P{sub 3/2} state collide, and yield an atom in the 2S{sub 1/2} state and an atom in the 2P{sub 1/2} state, with an energy release corresponding to about 10 GHz. This energy adds kinetic energy to the atoms in the trap, and knocks atoms out of the trap. The authors have devised a method to measure the rate of this collisional loss mechanism. The method uses a laser diode and a dye laser to selectively photo-ionize the 2P{sub 1/2} atoms, and a channeltron particle multipiler measures the rate of ion formation. We will report the progress of this experiment.

Anderson, B.P.; Ritchie, N.W.M.; Xiao, Y.Y. [and others

1992-12-01

129

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

130

On the Structure and Application of BGP Policy Atoms  

E-print Network

The notion of Internet Policy Atoms has been recently introduced in [1], [2] as groups of prefixes sharing a common BGP AS path at any Internet backbone router. In this paper we further research these 'Atoms'. First we offer a new method for computing the Internet policy atoms, and use the RIPE RIS database [6] to derive their structure. Second, we show that atoms remain stable with only about 2-3% of prefixes changing their atom membership in eight hour periods. We support the 'Atomic' nature of the policy atoms by showing BGP update and withdraw notifications carry updates for complete atoms in over 70% of updates, while the complete set of prefixes in an AS is carried in only 21% of updates. We track the locations where atoms are created (first different AS in the AS path going back from the common origin AS 1 ) showing 86% are split between the origin AS and it's peers thus supporting the assumption that they are created by policies. Finally applying atoms to "real life" applications we achieve a modest savings in BGP updates due to the low average prefix count in the atoms.

Yehuda Afek; Omer Ben-shalom; Anat Bremler-barr

2002-01-01

131

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

132

Atomic structure in Zr70Ni30 metallic glass  

NASA Astrophysics Data System (ADS)

Atomic structure of Zr70Ni30 metallic glass (MG) was investigated by reverse Monte Carlo simulation combining with x-ray diffraction and Ni and Zr K-edge extended x-ray absorption of fine structure measurements. Distributions of coordination number (CN) and Voronoi clusters were analyzed by Voronoi tessellation method. The average CN of atoms was obtained to be 11.4 together with the average CN of Zr and Ni atoms of about 11.8 and 10.6, respectively. It is found that Z11 Kasper polyhedron and distorted icosahedra are mainly favored structural units in Zr70Ni30 MG. The discrepancy in atomic structure between Zr70Ni30 MG and its corresponding crystalline (or quasicrystalline) phases can explain the fact that Zr70Ni30 MG does not transform to neither icosahedral nor fcc Zr2Ni phase during crystallization process.

Yang, L.; Yin, S.; Wang, X. D.; Cao, Q. P.; Jiang, J. Z.; Saksl, K.; Franz, H.

2007-10-01

133

Nanoscale structure and transport : from atoms to devices  

E-print Network

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

Evans, Matthew Hiram

2005-01-01

134

Extended Xray Absorption Fine Structure Spectroscopy (EXAFS) Provides details on how x rays are absorbed by an atom at energies near X18A,B,X19A Provides details on how xrays are absorbed by an atom at energies near  

E-print Network

to determine the chemical state and local atomic structure for a selected atomic species · Used in a varietyExtended Xray Absorption Fine Structure Spectroscopy (EXAFS) · Provides details on how x rays are absorbed by an atom at energies near X18A,B,X19A· Provides details on how xrays are absorbed by an atom

Ohta, Shigemi

135

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

136

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

137

Chemical profiling of silicon nitride structures  

NASA Technical Reports Server (NTRS)

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

Vasquez, R. P.

1989-01-01

138

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

139

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

140

Atomic Calligraphy: The Direct Writing of Nanoscale Structures using MEMS  

E-print Network

We present a micro-electromechanical system (MEMS) based method for the resist free patterning of nano-structures. Using a focused ion beam (FIB) to customize larger MEMS machines, we fabricate apertures as small as 50 nm on plates that can be moved with nanometer precision over an area greater than 20x20 {\\mu}m^2. Depositing thermally evaporated gold atoms though the apertures while moving the plate results in the deposition of nanoscale metal patterns. Adding a shutter only microns above the aperture, enables high speed control of not only where but also when atoms are deposited. Using a shutter, different sized apertures can be selectively opened and closed for nano-structure fabrication with features ranging from nano- to micrometers in scale. The ability to evaporate materials with high precision, and thereby fabricate circuits and structures in situ, enables new kinds of experiments based on the interactions of a small number of atoms and eventually even single atoms.

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

2013-04-04

141

Atomic structure of GTP cyclohydrolase I  

Microsoft Academic Search

Background: Tetrahydrobiopterin serves as the cofactor for enzymes involved in neurotransmitter biosynthesis and as a regulatory factor in immune cell proliferation and the biosynthesis of melanin. The biosynthetic pathway to tetrahydrobiopterin consists of three steps starting from GTP. The initial reaction is catalyzed by GTP cyclohydrolase I (GTP-CH-I) and involves the chemically complex transformation of the purine into the pterin

Herbert Nar; Robert Huber; Winfried Meining; Cornelia Schmid; Sevil Weinkauf; Adelbert Bacher

1995-01-01

142

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

143

Atomic structure calculations using MCHF and BSR  

NASA Astrophysics Data System (ADS)

Theoretical results of high accuracy can be obtained using B-spline R-matrix methods implemented in BSR codes. These require a description of targets and perturbers that include correlation. They can be computed efficiently using the multi-configuration Hartree-Fock (MCHF) program. This write-up describes the computational procedure for determining a variety of atomic properties by combining these two codes. Special attention is given to the calculation of transition probabilities for Rydberg series and to photoionization cross-sections.

Zatsarinny, Oleg; Froese Fischer, Charlotte

2009-11-01

144

Chemical and structural features influencing the biological activity of curcumin.  

PubMed

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

Priyadarsini, K Indira

2013-01-01

145

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

146

Atomic structures of tubulin and FtsZ  

Microsoft Academic Search

The recently published atomic structures of tubulin and FtsZ are a research milestone. The N-terminal GTP-binding domains of tubulin and FtsZ are virtually identical in structure, as expected from the substantial sequence identity. Sequence identity is absent from the C-terminal domains, but they also have virtually identical structures. A surprising finding is that the N-terminal GTP-binding domain is structurally homologous

Harold P Erickson

1998-01-01

147

Making Matter: The atomic structure of materials  

NSDL National Science Digital Library

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

Hewat, Alan

2003-10-10

148

Determination of the atomic structure of scanning probe microscopy tungsten tips by field ion microscopy  

E-print Network

Determination of the atomic structure of scanning probe microscopy tungsten tips by field ion of scanning probe microscopy SPM experiments usually need to make an assumption about the atomic tip structure ago that FIM could also be used to machine structures atom by atom.7 We have used such atomically

Grütter, Peter

149

Atomic-level structure and structure-property relationship in metallic glass  

NASA Astrophysics Data System (ADS)

One of the key tasks in material science is to understand the structure and structure-property relationship. The recently emerging bulk metallic glasses (BMGs) have demonstrated unique properties, especially intriguing mechanical properties such as their high strength and high propensity to localize deformation in shear bands. However, a comprehensive understanding of the structure of BMGs has been hindered by the complexity of these amorphous materials. Even more challenging is the structure-property correlation, which has been well established in crystals but has been seriously lacking for BMGs. This thesis presents a systematic study of the atomic-level structures of two representative BMGs, Cu-Zr and Cu-Zr-Al. The interpenetrating Cu-centered icosahedral clusters have been identified to be the primary structural feature. The fraction of icosahedra increases with increasing Cu or Al contents, and with decreasing cooling rate. The effect of Al in improving the icosahedral order is two-fold: the geometric effect due to the atomic-size mismatch and the chemical effect originated from the Cu-Al bond shortening. The resolved structure is used to study the structure-property relationship. The full icosahedra are found to be responsible for the dynamical slowdown of the supercooled liquid, which underlies the non-Arrhenius behavior, and explains the composition dependence of glass transition temperature, glass forming ability, and the room temperature strength. By simulated deformation, the initiation of plasticity and tendency for strain localization are also investigated. The full icosahedra are found to be the most rigid and resistant cluster with solid-like character, while the unstable clusters with liquid-like character serve as the fertile sites for initiating shear transformations. In addition, the elastic moduli are calculated and analyzed, and the origins of the different configurational dependence of shear modulus (G) and bulk modulus ( B) are explained. The Poisson's ratio, which scales with G/B, is then taken as a dimensionless indicator of the internal structural state. Combining the structure-plasticity and structure-elasticity relationships, the common structural origin of the elasticity-plasticity correlation is identified. More general implications are discussed by separating the effects of structural order and constituent elements (alloy composition), leading to a map that may guide the search for plastic BMGs.

Cheng, Yongqiang

150

Editorial . Quantum fluctuations and coherence in optical and atomic structures  

Microsoft Academic Search

From simple interference fringes, over molecular wave packets, to nonlinear optical patterns - the fundamental interaction between light and matter leads to the formation of structures in many areas of atomic and optical physics. Sophisticated technology in experimental quantum optics, as well as modern computational tools available to theorists, have led to spectacular achievements in the investigation of quantum structures.

Jürgen Eschner; Alessandra Gatti; Agnès Maître; Giovanna Morigi

2003-01-01

151

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

152

Atomic and Electronic Structure of Graphene-Oxide  

Microsoft Academic Search

ABSTRACT We elucidate the atomic and electronic structure of graphene oxide (GO) using annular dark field imaging of single and multilayer sheets and electron energy loss spectroscopy for measuring the fine structure of C and O K-edges in a scanning transmission electron microscope. Partial density of states and electronic plasma excitations are also measured for these GO sheets showing unusual

K. Andre Mkhoyan; Alexander W. Contryman; John Silcox; Derek A. Stewart; Goki Eda; Cecilia Mattevi; Steve Miller; Manish Chhowalla

2010-01-01

153

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

154

Electronic structure of atoms, molecules and solids  

SciTech Connect

There has been a great deal of development in some areas of electronic structure of matter with a high degree of specialization. As a consequence it is becoming more difficult to follow the developments in neighboring areas. This volume tries to fill the gap and collect in one single volume topics such as superlattice structure, polymers density functional theory, molecular photoionization, impurities in semiconductors, to mention a few.

Canuto, S. (Departamento de Fisica, Universidade Federal de Pernambuco, 50.739 Recife, Pernambuco (BR)); D'Albuquerque e Castro, J. (Instituto de Fisica, Universidade Federal Fluminense, 24.020 Rio de Janeiro (BR)); Paixao, F.J. (Instituto de Fisica, Universidade Estadual de Campinas, 13.081 Campinas, Sao Paulo (BR))

1990-01-01

155

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

156

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

PubMed

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

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

2013-09-01

157

Electronic structures of graphane sheets with foreign atom substitutions  

NASA Astrophysics Data System (ADS)

Using first-principles calculations, we investigate the electronic structures of the recently synthesized hydrogenated graphene, called graphane, with substitutional B, N, P, and Al atoms. We find that both the n-type and p-type substitutions can cause the semiconductor-to-metal transitions in graphane sheets. The substitutional B and Al atoms induce magnetic moments of nearby carbon atoms. Moreover, the B-substituted graphane sheets have the concentration-dependent magnetic properties, while the Al-substituted ones exhibit robust half-metallic behaviors. Our studies demonstrate that the substituted graphane sheets have potential applications in nanoelectronics and spintronics.

Wang, Yanli; Ding, Yi; Shi, Siqi; Tang, Weihua

2011-04-01

158

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

NASA Astrophysics Data System (ADS)

The results of theoretical and experimental investigation of gas phase chemical generation of atomic iodine, I(2P3/2), for stimulated emission in chemical oxygen-iodine laser (COIL) are presented. The method of I atoms generation employs a principal reaction X+HI implies I(2P3/2)+HX, where X equals F or Cl. A computational modeling was based on the 1D flow development exploring the chemical processes within the reaction systems, and was aimed at the theoretical understanding of the two complex reaction systems and finding out which is better applicable for conditions in COIL. The results of modeling were further used for a design of the device and conditions during the experimental investigation, and for an interpretation of the experimental results. The experimental work has been done, for the present, on the atomic iodine generation via Cl atoms. A high yield of atomic iodine of 70% to 100% (related to the initial HI flow rate) was attained in a flow of nitrogen. Gain was observed in preliminary experiments on the chemical generation of atomic iodine in a flow of singlet oxygen.

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

2002-09-01

159

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

PubMed Central

Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

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

2014-01-01

160

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

161

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

162

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. PMID:22245777

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

2012-01-01

163

Locally preferred structure in simple atomic liquids  

E-print Network

We propose a method to determine the locally preferred structure of model liquids. This latter is obtained numerically as the global minimum of the effective energy surface of clusters formed by small numbers of particles embedded in a liquid-like environment. The effective energy is the sum of the intra-cluster interaction potential and of an external field that describes the influence of the embedding bulk liquid at a mean-field level. Doing so we minimize the surface effects present in isolated clusters without introducing the full blown geometrical frustration present in bulk condensed phases. We find that the locally preferred structure of the Lennard-Jones liquid is an icosahedron, and that the liquid-like environment only slightly reduces the relative stability of the icosahedral cluster. The influence of the boundary conditions on the nature of the ground-state configuration of Lennard-Jones clusters is also discussed.

S. Mossa; G. Tarjus

2003-05-19

164

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

165

Relativistic calculations of pionic and kaonic atoms' hyperfine structure  

SciTech Connect

We present a relativistic calculation of the hyperfine structure in pionic and kaonic atoms. A perturbation method has been applied to the Klein-Gordon equation to take into account the relativistic corrections. The perturbation operator has been obtained via a multipole expansion of the nuclear electromagnetic potential. The hyperfine structure of pionic and kaonic atoms provides an additional term in the quantum electrodynamics calculation of the energy transition of these systems. Such a correction is required for a recent measurement of the pion mass.

Trassinelli, Martino [Gesellschaft fuer Schwerionenforschung, Planckstr. 1, 64291 Darmstadt (Germany); Laboratoire Kastler Brossel, Ecole Normale Superieure, CNRS, Universite Pierre et Marie Curie--Paris 6, Case 74, 4 Place Jussieu, 75005 Paris (France); Indelicato, Paul [Laboratoire Kastler Brossel, Ecole Normale Superieure, CNRS, Universite Pierre et Marie Curie--Paris 6, Case 74, 4 Place Jussieu, 75005 Paris (France)

2007-07-15

166

Insight into Amyloid Structure Using Chemical Probes  

PubMed Central

Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-? (A?) peptide. Over the past decade, it has become clear that these A? amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of A? peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

Reinke, Ashley A.; Gestwicki, Jason E.

2011-01-01

167

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

168

Hydrogen atom initiated chemistry. [chemical evolution in planetary atmospheres  

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

169

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

170

Solitonic fullerene structures in light atomic nuclei  

E-print Network

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

R. A. Battye; P. M. Sutcliffe

2001-02-16

171

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

PubMed

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

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

2010-12-01

172

Atomic Parity Nonconservation: Electroweak Parameters and Nuclear Structure  

E-print Network

There have been suggestions to measure atomic parity nonconservation (PNC) along an isotopic chain, by taking ratios of observables in order to cancel complicated atomic structure effects. Precise atomic PNC measurements could make a significant contribution to tests of the Standard Model at the level of one loop radiative corrections. However, the results also depend upon certain features of nuclear structure, such as the spatial distribution of neutrons in the nucleus. To examine the sensitivity to nuclear structure, we consider the case of Pb isotopes using various recent relativistic and non-relativistic nuclear model calculations. Contributions from nucleon internal weak structure are included, but found to be fairly negligible. The spread among present models in predicted sizes of nuclear structure effects may preclude using Pb isotope ratios to test the Standard Model at better than a one percent level, unless there are adequate independent tests of the nuclear models by various alternative strong and electroweak nuclear probes. On the other hand, sufficiently accurate atomic PNC experiments would provide a unique method to measure neutron distributions in heavy nuclei.

S. J. Pollock; E. N. Fortson; L. Wilets

1992-11-05

173

InChI - the worldwide chemical structure identifier standard  

PubMed Central

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

2013-01-01

174

Generation of atomic iodine via fluorine for chemical oxygen iodine laser  

NASA Astrophysics Data System (ADS)

A method of the chemical generation of atomic iodine for a chemical oxygen-iodine laser (COIL) using atomic fluorine as a reaction intermediate was studied experimentally. This method is based on the reaction between F 2 and NO providing F atoms, and the reaction of F with HI resulting in iodine atoms generation. Atomic iodine was produced with efficiency exceeding 40% relative to initial F 2 flow rate. This efficiency was nearly independent on pressure and total gas flow rate. The F atoms were stable in the reactor up to 2 ms. An optimum ratio of the reactants flow rates was F 2:NO:HI = 1:1:1. A rate constant of the reaction of F 2 with HI was determined. The numerical modelling showed that remaining HI and IF were probably consumed in their mutual reaction. The reaction system was found suitable for employing in a generator of atomic iodine with its subsequent injection into a supersonic nozzle of a COIL.

Jirásek, Vít; Špalek, Otomar; ?enský, Miroslav; Picková, Irena; Kodymová, Jarmila; Jakubec, Ivo

2007-04-01

175

Method for quantitative determination and separation of trace amounts of chemical elements in the presence of large quantities of other elements having the same atomic mass  

DOEpatents

Photoionization via autoionizing atomic levels combined with conventional mass spectroscopy provides a technique for quantitative analysis of trace quantities of chemical elements in the presence of much larger amounts of other elements with substantially the same atomic mass. Ytterbium samples smaller than 10 ng have been detected using an ArF* excimer laser which provides the atomic ions for a time-of-flight mass spectrometer. Elemental selectivity of greater than 5:1 with respect to lutetium impurity has been obtained. Autoionization via a single photon process permits greater photon utilization efficiency because of its greater absorption cross section than bound-free transitions, while maintaining sufficient spectroscopic structure to allow significant photoionization selectivity between different atomic species. Separation of atomic species from others of substantially the same atomic mass is also described.

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

1982-09-02

176

Editorial . Quantum fluctuations and coherence in optical and atomic structures  

NASA Astrophysics Data System (ADS)

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

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

2003-03-01

177

Atomic and electronic structure of Ni-Nb metallic glasses  

SciTech Connect

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

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

2013-12-07

178

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

179

Crystal structure and chemical bonding in tin(II) acetate  

Microsoft Academic Search

Tin(II) acetate was prepared and its crystal structure was solved from X-ray powder diffraction data. Tin(II) acetate adopts a polymeric structure consisting of infinite Sn(CH3COO)2 chains running along the c-axis which are packed into groups of four. The acetate groups bridge the Sn atoms along the chains. The Sn atoms are asymmetrically surrounded by four oxygen atoms with two short

Varvara S. Stafeeva; Alexander S. Mitiaev; Artem M. Abakumov; Alexander A. Tsirlin; Artem M. Makarevich; Evgeny V. Antipov

2007-01-01

180

Determining parameters of the local atomic structure of Cu-Ni and Cu-Mn alloys by the method of extended electron-loss fine structure spectroscopy  

NASA Astrophysics Data System (ADS)

In this work, we consider the possibility of analyzing local atomic structure based on strongly overlapping experimental extended electron-energy-loss fine structure (EELFS) spectra of two different chemical elements. M 2,3 EELFS spectra have been obtained from the surface of Cu x Ni1 - x and Cu x Mn1 - x ( x = 0.5) alloys. The method of determining the parameters of the local atomic structure (coordination numbers, lengths of the chemical bonds, and the parameters of their dispersion) of the nearest atomic surroundings in ultrathin (1-5 nm) surface layers of two-component alloys of 3 d metals has been suggested based on the overlapping extended fine structures of the electron-energy-loss spectra. The method was tested on experimental M 2,3 EELFS spectra of the surface of testing alloys Cu50Ni50 and Cu50Mn50.

Bakieva, O. R.; Nemtsova, O. M.; Gai, D. E.

2015-01-01

181

The relativistic hydrogen atom: a theoretical laboratory for structure functions  

E-print Network

Thanks to the Dirac equation, the hydrogen-like atom at high $Z$ offers a precise model of relativistic bound state, allowing to test properties of unpolarized and polarized structure functions analogous to the hadronic ones, in particular: Sivers effect, sum rules for the vector, axial, tensor charges and for the magnetic moment, positivity constraints, sea contributions and fracture functions

X. Artru; K. Benhizia

2006-01-17

182

Spectroscopic Imaging STM: Atomic-Scale Visualization of Electronic Structure  

E-print Network

Chapter 3 Spectroscopic Imaging STM: Atomic-Scale Visualization of Electronic Structure and Symmetry in Underdoped Cuprates Kazuhiro Fujita, Mohammad Hamidian, Inês Firmo, Sourin Mukhopadhyay, Chung) phases of underdoped cuprates, two distinct types of electronic states are observed K. Fujita (B) · M

Davis, James C.

183

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

184

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

185

Atomic structures at last: the ribosome in 2000  

Microsoft Academic Search

Last year, atomic structures of the 50S ribosomal subunit from Haloarcula marismortui and of the 30S ribosomal subunit from Thermus thermophilus were published. A year before that, a 7.8 Å resolution electron density map of the 70S ribosome from T. thermophilus appeared. This information is revolutionizing our understanding of protein synthesis.

V. Ramakrishnan; P. B. Moore

2001-01-01

186

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

187

On the structure of the interstellar atomic gas  

E-print Network

The interstellar atomic hydrogen is known to be a 2-phase medium in which turbul ence plays an important r\\^ole. Here we present high resolution numerical simulations describing the gas from tens of parsec down to hundreds of AU. This high resolut ion allows to probe numerically, the small scale structures which naturally arises from the turbulence and the 2-phase physics.

P. Hennebelle; E. Audit

2007-01-24

188

Atomic Structure of Intracellular Amorphous Calcium Phosphate Deposits  

Microsoft Academic Search

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

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

1975-01-01

189

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

PubMed

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

Berns, Veronica M; Fredrickson, Daniel C

2014-10-01

190

Ground State Hyperfine Structure of Muonic Helium Atom  

E-print Network

On the basis of the perturbation theory in the fine structure constant $\\alpha$ and the ratio of the electron to muon masses we calculate one-loop vacuum polarization and electron vertex corrections and the nuclear structure corrections to the hyperfine splitting of the ground state of muonic helium atom $(\\mu e ^4_2He)$. We obtain total result for the ground state hyperfine splitting $\\Delta \

A. A. Krutov; A. P. Martynenko

2008-07-21

191

Mobile Point Defects and Atomic Basis for Structural Transformations of a Crystal Surface  

E-print Network

Mobile Point Defects and Atomic Basis for Structural Transformations of a Crystal Surface [Articles diffusion and structural transformations proceed through mechanisms that operate on the atomic scale of impurity Pb atoms on a Ge surface catalyze atomic motions and structural changes without altering the basic

Golovchenko, Jene A.

192

Pulsed chemical oxygen—iodine laser with bulk formation of iodine atoms by an electric discharge  

Microsoft Academic Search

A preliminary investigation was made of a chemical oxygen—iodine laser with bulk formation of iodine atoms in an electric discharge. The output energy was comparable with that obtained for a photolysis variant of the laser, but the technical efficiency of the investigated discharge variant was much higher (91%). The pulse power (~100 kW) was approximately three orders of magnitude higher

Nikolai P Vagin; V S Pazyuk; Nikolai N Yuryshev

1995-01-01

193

Constant centrifugal potential approximation for atom-diatom chemical reaction dynamics  

E-print Network

Constant centrifugal potential approximation for atom-diatom chemical reaction dynamics Kengo,Myodaiji, Okazaki 444. Japan (Received 28 September 1993; accepted 8 December 1993) The constant centrifugal of such practically useful approxima- tions the constant centrifugal potential approximation (CCPA) (or the energy

Takada, Shoji

194

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

E-print Network

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

Yukinori Nagatani

2005-01-04

195

Metal Oxide Nanoparticle Growth on Graphene via Chemical Activation with Atomic Oxygen  

PubMed Central

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

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

2013-01-01

196

Investigation of chemical modifiers for the determination of boron by electrothermal atomic absorption spectrometry  

NASA Astrophysics Data System (ADS)

A fast and efficient method for the determination of boron in aqueous solutions is described, using electrothermal atomic absorption spectrometry with a transversely heated graphite tube atomizer. The investigations were carried out with calcium chloride, zirconium chloride, and with mixtures of both reagents as chemical modifiers. Furthermore, the influence of zirconium treated graphite tubes on the sensitivity and stability of the analytical results was investigated. The developed method is suitable for the determination of boron over a concentration range from 0.1 to 2.0 mg/l without any additional dilution or enrichment steps. The atomization temperature could be lowered to 2550°C, and the best characteristic mass for boron of 0.19 ng was obtained for a zirconium-treated graphite tube and the addition of calcium chloride as a chemical modifier to the measurement solution. Sensitivity and precision of the measurement did not change significantly over an 8-h working day under these conditions.

Nowka, René; Eichardt, Klaus; Welz, Bernhard

2000-05-01

197

Anomalous decay of an atom in structured band gap reservoirs  

E-print Network

We analyze the spontaneous emission of a two-level atom interacting with a special class of structured reservoirs of field modes with band gap edge coinciding with the atomic transition frequency. The exact time evolution of the population of the excited level is evaluated analytically through series of Fox-$H$ functions. Over estimated long time scales, inverse power law relaxations emerge, with powers decreasing continuously to 2 according to the choice of the special reservoir. No trapping of the population of the excited level emerges. The same results are recovered in presence of $N-1$ atoms, each one in the ground state, described by the Dicke model. The power of the inverse power law decay results to be independent of $N$. A critical number $N_{\\alpha}^{(\\star)}$ is evaluated, such that, for $N \\gg N_{\\alpha}^{(\\star)}$, the inverse power law decay vanishes.

Filippo Giraldi; Francesco Petruccione

2011-04-09

198

Stable atomic structure of NiTi austenite  

SciTech Connect

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

Zarkevich, Nikolai A [Ames Laboratory; Johnson, Duane D [Ames Laboratory

2014-08-01

199

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

PubMed Central

For atoms and homonuclear diatomic molecules, it is argued that the electronic energies have the forms [Formula: see text] and [Formula: see text] [Formula: see text], respectively,where Z is the atomic number, N is the number of electrons, and R is the internuclear distance. By using the Lieb-Simon theorem that the Thomas-Fermi theory is exact in the limit of large atomic number and the Teller theorem that molecules are not bound in the Thomas-Fermi theory, it is then shown, among other results, that the electron-electron repulsion energy for neutral systems has no term in Z2 and that the nucleus-nucleus repulsion energy for neutral molecules is probably [unk](Z5/3). For neutral atoms, it is predicted and verified that the chemical potential (electronegativity) is [unk](Z-1/3) for large Z. Tetrahedral and octahedral molecules are briefly discussed. PMID:16592908

March, Norman H.; Parr, Robert G.

1980-01-01

200

Degradation of High-k/Interface Layer Structures by H Atoms and Interface Engineering with O Atom Manipulation  

NASA Astrophysics Data System (ADS)

With regard to the growing numbers of H atoms in high-k/SiO2/Si systems, it is revealed through first principles calculations that degradation of high-k/interface layer structures has been found to occur from the interface layers by H atoms, even if the interface defects are terminated with H atoms by forming gas annealing. O termination is proposed to prevent this degradation. The effects of H and O atoms are verified by experimental analyses.

Kato, K.; Hirano, I.; Matsushita, D.; Nakasaki, Y.; Mitani, Y.

2011-12-01

201

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase  

PubMed Central

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

2013-01-01

202

Dependence of the atomic structure and surface relief of platinum foils on the annealing and rolling conditions  

NASA Astrophysics Data System (ADS)

The effect of cold rolling, polishing, and thermal annealing conditions on the atomic structure and surface geometry of platinum foils has been studied. The surface morphology has been analyzed using low-energy electron diffraction, atomic force microscopy, and scanning tunneling microscopy. The chemical composition of the surface has been evaluated by Auger electron spectroscopy. It has been demonstrated that a variation in the conditions used for the preparation of the samples makes it possible to produce surfaces with different degrees of perfection from atomically smooth to rippled, fractal, and diffraction-disordered surfaces.

Korsukov, V. E.; Ankudinov, A. V.; Bu?nov, A. L.; Varkentin, M. S.; Knyazev, S. A.; Korsukova, M. M.; Obidov, B. A.; Pronin, I. I.

2010-07-01

203

Chemical quantification of atomic-scale EDS maps under thin specimen conditions.  

PubMed

We report our effort to quantify atomic-scale chemical maps obtained by collecting energy-dispersive X-ray spectra (EDS) using scanning transmission electron microscopy (STEM) (STEM-EDS). With thin specimen conditions and localized EDS scattering potential, the X-ray counts from atomic columns can be properly counted by fitting Gaussian peaks at the atomic columns, and can then be used for site-by-site chemical quantification. The effects of specimen thickness and X-ray energy on the Gaussian peak width are investigated using SrTiO3 (STO) as a model specimen. The relationship between the peak width and spatial resolution of an EDS map is also studied. Furthermore, the method developed by this work is applied to study cation occupancy in a Sm-doped STO thin film and antiphase boundaries (APBs) present within the STO film. We find that Sm atoms occupy both Sr and Ti sites but preferably the Sr sites, and Sm atoms are relatively depleted at the APBs likely owing to the effect of strain. PMID:25307942

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

2014-12-01

204

Atomic scale structure investigations of epitaxial Fe/Cr multilayers  

NASA Astrophysics Data System (ADS)

Fe/Cr multilayers were deposited by molecular beam epitaxy on the MgO(1 0 0) substrate. Structural properties of the samples were analyzed by low energy electron diffraction, high resolution transmission electron microscopy (HRTEM), as well as by X-ray reflectivity, conversion electron Mössbauer spectroscopy (CEMS) and Auger electron spectroscopy. Investigations revealed multilayered system built of well-ordered Fe and Cr thin films with (1 0 0) orientation. A high geometrical perfection of the system, i.e. planar form of interfaces and reproducible thickness of layers, was also proven. Fe/Cr interface roughness was determined to be 2-3 atomic layers. CEMS studies allowed to analyze at atomic scale the structure of buried Fe/Cr interfaces, as well as to distinguish origin of interface roughness. Roughnesses resulting from interface corrugations and from the Fe-Cr interdiffusion at interfaces were observed. Fe/Cr multilayers showed strong antiferromagnetic coupling of Fe layers.

K?c, M.; Morgiel, J.; Polit, A.; Zabila, Y.; Marsza?ek, M.

2014-06-01

205

Ab initio nanoplasmonics: The impact of atomic structure  

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

206

Atomically Controlled Processing for Group IV Semiconductors by Chemical Vapor Deposition  

NASA Astrophysics Data System (ADS)

One of the main requirements for Si-based ultrasmall devices is atomic-order control of process technology. Here we show the concept of atomically controlled processing for group IV semiconductors based on atomic-order surface reaction control. By ultraclean low-pressure chemical vapor deposition using SiH4 and GeH4 gases, high-quality low-temperature epitaxial growth of Si, Ge, and Si1-xGex with atomically flat surfaces and interfaces on Si(100) is achieved, and atomic-order surface reaction processes on group IV semiconductor surface are formulated based on a Langmuir-type surface adsorption and reaction scheme. In in-situ doped Si1-xGex epitaxial growth on the (100) surface in a SiH4-GeH4-dopant (PH3, or B2H6 or SiH3CH3)-H2 gas mixture, the deposition rate, the Ge fraction and the dopant concentration are explained quantitatively assuming that the reactant gas adsorption/reaction depends on the surface site material and that the dopant incorporation in the grown film is determined by Henry’s law. Self-limiting formation of 1-3 atomic layers of group IV or related atoms in the thermal adsorption and reaction of hydride gases on Si(100) and Ge(100) is generalized based on the Langmuir-type model. Si or SiGe epitaxial growth over N, P or B layer already-formed on Si(100) or SiGe(100) surface is achieved. Furthermore, the capability of atomically controlled processing for advanced devices is demonstrated. These results open the way to atomically controlled technology for ultralarge-scale integrations.

Murota, Junichi; Sakuraba, Masao; Tillack, Bernd

2006-09-01

207

Atom type preferences, structural diversity, and property profiles of known drugs, leads, and nondrugs: a comparative assessment.  

PubMed

A new characterization of known drug, lead, and representative nondrug databases was performed taking into account several properties at the atomic and molecular levels. This characterization included atom type preferences, intrinsic structural diversity (Atom Type Diversity, ATD), and other well-known physicochemical properties, as an approach for rapid assessment of druglikeness for small molecule libraries. To characterize ATD, an elaborate united atom classification, UALOGP (United Atom Log P), with 148 atom types, was developed along with associated atomic physicochemical parameters. This classification also enabled an analysis of atom type and physicochemical property distributions (for calculated log P, molar refractivity, molecular weight, total atom count, and ATD) of drug, lead, and nondrug databases, a reassessment of the Ro5 (Rule of Five) and GVW (Ghose?Viswanadhan?Wendoloski) criteria, and development of new criteria and ranges more accurately reflecting the chemical space occupied by small molecule drugs. A relative druglikeness parameter was defined for atom types in drugs, identifying the most preferred types. The present work demonstrates that drug molecules are constitutionally more diverse relative to nondrugs, while being less diverse than leads. PMID:21480669

Viswanadhan, Vellarkad N; Rajesh, Hariharan; Balaji, Vitukudi N

2011-05-01

208

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

PubMed

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

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

2014-07-15

209

Atomic displacements during structural relaxation in a metallic glass  

NASA Astrophysics Data System (ADS)

Structural relaxation in the metallic glass Pd40Ni40P20 has been studied by x-ray diffraction. For the first time the structural changes occurring in reversible relaxation have been directly observed. The data have been analyzed by a method that distinguishes effects due to processes where the density changes from those where it is conserved. The results show a clear contrast between reversible and irreversible relaxation and also that the nature of atomic displacements in reversible relaxation changes as the temperature is lowered.

Brüning, Ralf; Ström-Olsen, J. O.

1990-02-01

210

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

SciTech Connect

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

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

2013-06-15

211

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

212

Common Organizational Structures within Two Chemical Flip-Flops  

E-print Network

Common Organizational Structures within Two Chemical Flip-Flops Naoki Matsumaru1 , Thorsten Lenser1 explain their operation and reveal their common behavioral structure. Key words: Chemical organization and the operations are described in the form of reactions among those molecules. Given the inputs of the computation

Hinze, Thomas

213

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

ScienceCinema

The Institute for Atom-Efficient Chemical Transformations (IACT) is an Energy Frontier Research Center funded by the U.S. Department of Energy. IACT focuses on advancing the science of catalysis to improve the efficiency of producing fuels from biomass and coal. IACT is a collaborative effort that brings together a diverse team of scientists from Argonne National Laboratory, Brookhaven National Laboratory, Northwestern University, Purdue University and the University of Wisconsin. For more information, visit www.iact.anl.gov

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

2013-04-19

214

A directional representation for 3D tubular structures resulting from isotropic well-localized atoms  

E-print Network

, their interaction via convolution with the tubular structure is equivalent to a set of directional atoms at various, the directionality of our representation arises only in the presence of tubular structures. More precisely, the atoms structure is equivalent to a set of directional multiscale 3D atoms, oriented along any possible direction

Labate, Demetrio

215

The Meshless Dynamic Relaxation Techniques for Simulating Atomic Structures of Materials  

E-print Network

1 The Meshless Dynamic Relaxation Techniques for Simulating Atomic Structures of Materials By Li could result in a change of the local atomic structure. The present paper introduces new Dynamic, to find equilibrium positions of the block of atoms containing different structural defects. The internal

Niewczas, Marek

216

Fractional Band Filling in an Atomic Chain Structure J. N. Crain,1  

E-print Network

Fractional Band Filling in an Atomic Chain Structure J. N. Crain,1 A. Kirakosian,1 K. N. Altmann,1 [5­12]. X-ray dif- fraction from the Si(557)-Au structure shows that gold atoms are incorporated by increasing U. We have found a chain structure of gold atoms on silicon, which exhibits a 1=4-filled band. Two

Himpsel, Franz J.

217

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz  

E-print Network

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz Rhiju Das Abstract Consistently predicting biopolymer structure at atomic resolution from sequence alone remains: Das R (2013) Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz. PLo

Das, Rhiju

218

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

E-print Network

Atomically precise self-assembly of one-dimensional structures on silicon I. Barke, T.K. Ru-magnetic surface. An interesting by-product is a memory structure with self-assembled tracks that are five atom: Low-dimensional structures; Atomic wires; Silicon surfaces; One-dimensional physics; Scanning

Himpsel, Franz J.

219

A Distance-Dependent Atomic Knowledge-Based Potential for Improved Protein Structure Selection  

E-print Network

A Distance-Dependent Atomic Knowledge-Based Potential for Improved Protein Structure Selection Hui atomic potential to test sets obtained from the web, composed of native protein and decoy structures published atomic potentials in the task of selecting native and near-native structures. This newly developed

Lu, Hui

220

Imaging the Atomic Surface Structures of CeO2 Nanoparticles Yuyuan Lin,*,  

E-print Network

Imaging the Atomic Surface Structures of CeO2 Nanoparticles Yuyuan Lin,*, Zili Wu, Jianguo Wen ABSTRACT: Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear using aberration-corrected high-resolution elec- tron microscopy, we determined the atomic structures

Shull, Kenneth R.

221

Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images  

E-print Network

Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images A. J, TN 37831-6031, U.S.A. Key words. Atomic resolution, crystal structure retrieval, incoherent imaging be used to yield important information on unexpected atomic structures. Introduction The physical

Pennycook, Steve

222

Atomic Clocks and Variations of the FIne Structure Constant  

NASA Technical Reports Server (NTRS)

We describe a new test for possible variations of the fine structure constant alpha by comparisons of rates between clocks based on hyperfine transitions in alkali atoms with different atomic number Z. H-maser, Cs, and Hg(+) clocks have a different dependence on alpha via relativistic contributions of order (Z-alpha)(sup 2). Recent H-maser vs Hg(+) clock comparison data improve laboratory limits on a time variation by 100-fold to give dot-alpha less than or equal to 3.7 x 10(exp -14)/yr. Future laser cooled clocks (Be(+), Rb, Cs, Hg(+), etc.), when compared, will yield the most sensitive of all tests for dot-alpha/alpha.

Prestage, John D.; Tjoelker, Robert L.; Maleki, Lute

1995-01-01

223

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

224

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

225

Effects of xenon insertion into hydrogen bromide. Comparison of the electronic structure of the HBr···CO2 and HXeBr···CO2 complexes using quantum chemical topology methods: electron localization function, atoms in molecules and symmetry adapted perturbation theory.  

PubMed

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

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

2014-06-01

226

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

PubMed Central

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

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

2014-01-01

227

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

PubMed Central

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

2011-01-01

228

Atomic and electronic structure of graphene-oxide.  

PubMed

We elucidate the atomic and electronic structure of graphene oxide (GO) using annular dark field imaging of single and multilayer sheets and electron energy loss spectroscopy for measuring the fine structure of C and O K-edges in a scanning transmission electron microscope. Partial density of states and electronic plasma excitations are also measured for these GO sheets showing unusual pi* + sigma* excitation at 19 eV. The results of this detailed analysis reveal that the GO is rough with an average surface roughness of 0.6 nm and the structure is predominantly amorphous due to distortions from sp3 C-O bonds. Around 40% sp3 bonding was found to be present in these sheets with measured O/C ratio of 1:5. These sp2 to sp3 bond modifications due to oxidation are also supported by ab initio calculations PMID:19199476

Andre Mkhoyan, K; Contryman, Alexander W; Silcox, John; Stewart, Derek A; Eda, Goki; Mattevi, Cecilia; Miller, Steve; Chhowalla, Manish

2009-03-01

229

Atomic-resolution structures of prion AGAAAAGA amyloid fibrils  

E-print Network

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

Zhang, Jiapu

2011-01-01

230

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

E-print Network

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

Raji Heyrovska

2007-11-09

231

Chemical structure representations and applications in computational toxicity.  

PubMed

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

Karthikeyan, Muthukumarasamy; Vyas, Renu

2012-01-01

232

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

233

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

234

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

PubMed

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

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

2013-07-24

235

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

NASA Astrophysics Data System (ADS)

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

Xu, Ye

236

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

237

Modeling the atomic structure of amorphous steels using crystalline approximants  

NASA Astrophysics Data System (ADS)

Using the pair density function analysis of pulsed neutron diffraction data, the local topology of Fe-based metallic glasses with good glass forming ability was investigated upon alloying with transition metal ions of Y, Zr, or Mo. Distinct short and medium range atomic order with common characteristics in all the glasses is observed. The local order is well described by a geometrical model constructed from superposition of “crystalline approximant” phases which is different from Frank-Kasper polyhedra clustering or dense random packing models. The mechanism responsible for the structure in the glass phase might involve a frustration-induced structural disorder of the crystalline approximant phases as they are driven away from stable stoichiometric compositions.

Kazimirov, V. Yu.; Louca, Despina; Ponnambalam, V.; Poon, S. J.; Proffen, T.

2005-08-01

238

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

PubMed Central

The atomic structure of a SiGe/Si epitaxial interface grown via molecular beam epitaxy on a single crystal silicon substrate was investigated using an aberration-corrected scanning transmittance electron microscope equipped with a high-angle annular dark-field detector and an energy-dispersive spectrometer. The accuracy required for compensation of the various residual aberration coefficients to achieve sub-angstrom resolution with the electron optics system was also evaluated. It was found that the interfacial layer was composed of a silicon single crystal, connected coherently to epitaxial SiGe nanolaminates. In addition, the distance between the dumbbell structures of the Si and Ge atoms was approximately 0.136 nm at the SiGe/Si interface in the [110] orientation. The corresponding fast Fourier transform exhibited a sub-angstrom scale point resolution of 0.78 Å. Furthermore, the relative positions of the atoms in the chemical composition line scan signals could be directly interpreted from the corresponding incoherent high-angle annular dark-field image. PMID:25426003

2014-01-01

239

Local atomic structure of Fontainebleau sandstone: Evidence for an amorphous phase?  

E-print Network

Local atomic structure of Fontainebleau sandstone: Evidence for an amorphous phase? K. L. Page, Th be deduced from the properties of the component grains [Darling et al., 2004]. Enhanced atomic structure of Fontainebleau sandstone have shown clear evidence for the presence of an unexpected glass-like component. Atomic

240

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

E-print Network

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

241

Correlation between muonic levels and nuclear structure in muonic atoms  

E-print Network

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

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

2011-11-02

242

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

NASA Astrophysics Data System (ADS)

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.

2009-01-01

243

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. PMID:21141035

Hay, Mark E.

2012-01-01

244

The prediction of protein structural class using averaged chemical shifts  

Microsoft Academic Search

Knowledge of protein structural class can provide important information about its folding patterns. Many approaches have been developed for the prediction of protein structural classes. However, the information used by these approaches is primarily based on amino acid sequences. In this study, a novel method is presented to predict protein structural classes by use of chemical shift (CS) information derived

Hao Lin; Chen Ding; Qiang Song; Ping Yang; Hui Ding; Ke-Jun Deng; Wei Chen

2012-01-01

245

Local atomic structure inheritance in Ag{sub 50}Sn{sub 50} melt  

SciTech Connect

Local structure inheritance signatures were observed during the alloying process of the Ag{sub 50}Sn{sub 50} melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N{sub m} around Ag atom is similar in the alloy and in pure Ag melts (N{sub m}???10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Ag and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag{sub 50}Sn{sub 50} is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons.

Bai, Yanwen; Bian, Xiufang, E-mail: xfbian@sdu.edu.cn; Qin, Jingyu; Hu, Lina; Yang, Jianfei; Zhang, Kai; Zhao, Xiaolin; Yang, Chuncheng [Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Zhang, Shuo; Huang, Yuying [Shanghai Synchrotron Radiation Facilities, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204 (China)

2014-01-28

246

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

247

A Method for the Automatic Classification of Chemical Structures  

ERIC Educational Resources Information Center

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

Adamson, George W.; Bush, Judith A.

1973-01-01

248

PREDICTING MODES OF TOXIC ACTION FROM CHEMICAL STRUCTURE: AN OVERVIEW  

EPA Science Inventory

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

249

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

250

Physical and chemical evidence for metallofullerenes with metal atoms as part of the cage  

NASA Astrophysics Data System (ADS)

SINCE the discovery of fullerenes1, efforts have been made to trap metal atoms inside fullerene cages2, and both endohedral3,4 and exohedral5,6 metallofullerenes have been synthesized. There is, however, a third possibility: a 'networked' metallofullerene, where the metal atom is incorporated into the carbon cage. Here we report the results of experiments to study the structure and reactivity of gas-phase fullerenes doped with niobium (NbCn+ with n = 28-50). These experiments, which use injected-ion drift-tube tech-niques, indicate that for fullerenes containing an even number of carbon atoms the metal is endohedral, but for fullerenes with an odd number of carbon atoms, the niobium metal is bound as a part of the carbon cage. Thus, networked metallofullerenes appear to be a stable class of metallofullerene. We suggest that such metallo-fullerenes can form if the metal atom retains sufficient electron density to form several strong covalent metal-carbon bonds.

Clemmer, David E.; Hunter, Joanna M.; Shelimov, Konstantin B.; Jarrold, Martin F.

1994-11-01

251

Chromosome structure investigated with the atomic-force microscope  

NASA Astrophysics Data System (ADS)

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

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

1992-05-01

252

Sommerfeld Fine-Structure Formula for Two-Body Atoms  

E-print Network

For relativistic atomic two-body systems such as the hydrogen atom, positronium, and muon-proton bound states, a two-body generalisation of the single-particle Sommerfeld fine-structure formula for the relativistic bound-state energies is found. The two-body Sommerfeld bound-state energy formula is obtained from a two-body wave equation which is physically correct to order $(Z\\alpha)^4$. The two-body Sommerfeld formula makes two predictions in order $(Z\\alpha)^6$ for every bound state and every mass ratio. With $N$ the Bohr quantum number: (a) The coefficient of the $(Z\\alpha)^6/N^6$ energy term has a specified value which depends only on the masses of the bound particles, not on angular quantum numbers; (b) The coefficient of the $(Z\\alpha)^6/N^4$ energy term is a specified multiple of the {\\em square} of the coefficient of the $(Z\\alpha)^4/N^3$ energy term. Both these predictions are verified in positronium by previous calculations to order $(Z\\alpha)^6$ which used second-order perturbation theory. They are also correct in the Coulomb-Dirac limit. The effect of the two-body Sommerfeld formula on calculations of muon-proton bound-state energies is examined.

John H. Connell

2013-03-20

253

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

254

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

E-print Network

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

Huirong Yan; A. Lazarian

2006-12-13

255

We present a unique approach to the design and synthesis of "giant molecules" based on "nano-atoms" for engineering structures across multiple length scales and controlling their macroscopic properties.  

E-print Network

on "nano-atoms" for engineering structures across multiple length scales and controlling their macroscopic properties. Herein, "nano-atoms" refer to shape-persistent molecular nanoparticles (MNPs) with precisely-defined chemical structures and surface functionalities that can serve as elemental building blocks

Pennycook, Steve

256

The Nuclear Physics of Hyperfine Structure in Hydrogenic Atoms  

E-print Network

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

J. L. Friar; G. L. Payne

2005-02-01

257

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

258

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

NASA Astrophysics Data System (ADS)

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

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

2003-04-01

259

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils  

E-print Network

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

Zhang, Jiapu

2010-01-01

260

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

261

Structural changes at grain boundaries in bcc iron induced by atomic collisions  

E-print Network

Structural changes at grain boundaries in bcc iron induced by atomic collisions F. Javier P boundaries, is to model the static microstructure for a better understanding of the atomic structure 22, 1999 Abstract Symmetrical tilt and twist grain boundary structures have been simu- lated in bcc

262

Structural study of biotic and abiotic poorly-crystalline manganese oxides using atomic  

E-print Network

Structural study of biotic and abiotic poorly-crystalline manganese oxides using atomic pair structures. In this study, the crystal structures of their synthetic analogs includ- ing acid birnessite using atomic pair distribution function (PDF) analysis. Results unambiguously verify that these Mn

Sparks, Donald L.

263

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

264

Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures  

E-print Network

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

Chang, D. E.

265

Epitaxial and stoichiometric effects on structural and chemical ordering in Heusler alloys  

NASA Astrophysics Data System (ADS)

The Heusler alloys of Co2MnGe and Co2MnSi have been predicted to be half-metallic, where the minority spin density of states shows a gap at the Fermi Level. However, half-metallicity has not yet been realized owing to its expected sensitivity to atomic disorders associated with off-stoichiometry and epitaxial constraints. Combinatorial epitaxial films of CoxMnyGez and CoxMnySiz have been grown on Ge (111) substrates in and around the Heusler stoichiometry using molecular beam epitaxy. The structural and chemical ordering of the films has been examined using synchrotron x-ray microbeam techniques, including x-ray diffraction and energy dependent anomalous diffraction. A comprehensive model has been developed for anomalous diffraction, allowing for detection and quantification of various disorders even at small amounts, including site-dependent vacancies and elemental site swapping. The x-ray experiments reveal that the ordering is very sensitive to the Co:Mn atomic ratio and that epitaxial strain can cause a shift in the composition of highest structural ordering away from the Heusler stoichiometry, accompanied by increased chemical disorders. These findings have made it possible to explore spin dependent states as a function of structural and chemical ordering.

Collins, Brian A.; He, Liang; Tsui, Frank; Zhong, Yuncheng; Chu, Yong S.

2008-10-01

266

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

PubMed

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

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

2014-07-01

267

Structure, Thermodynamics and Kinetics of Chemically Heterogeneous Interfaces  

NASA Astrophysics Data System (ADS)

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

Palafox Hernandez, Jesus Pablo

2011-12-01

268

RNA structure experimental analysis--chemical modification.  

PubMed

The purpose of this protocol is to identify 'footprints' of protein on RNA. However, it can also be used to analyze the secondary structure of RNA. This protocol is optimized for large RNA molecules; however, it can be adapted for the study of small RNAs. PMID:24034333

Xu, Zhili; Culver, Gloria

2013-01-01

269

Chemical composition in relation with biomass ash structure  

NASA Astrophysics Data System (ADS)

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

Holubcik, Michal; Jandacka, Jozef

2014-08-01

270

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

NASA Astrophysics Data System (ADS)

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

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

2008-07-01

271

Earth's interdependent thermal, structural, and chemical evolution  

NASA Astrophysics Data System (ADS)

The popular view that 30-55% of Earth's global power is primordial, with deep layers emanating significant power, rests on misunderstandings and models that omit magmatism and outgassing. These processes link Earth's chemical and thermal evolution, while creating layers, mainly because magmas transport latent heat and radioactive isotopes rapidly upwards. We link chemistry to heat flow, measured and theoretical, to understand the interior layering and workings. Quasi-steady state conditions describe most of Earth's history: (1) Accretion was cold and was not a source of deep heat. (2) Friction during core formation cannot have greatly heated the interior (thermodynamics plus buoyancy). (3) Conduction is the governing microscopic mechanism in the deep Earth. (4) Using well-constrained values of thermal conductivity (k), we find that homogeneously distributed radionuclides provide extremely high internal temperature (T) under radial symmetry. Moreover, for any given global power, sequestering heat producing elements into the upper mantle reduces Earth's central temperature by a factor of 10 from a homogeneous distribution. Hence, (5) core formation was a major cooling event. From modern determinations of k(T) we provide a reference conductive geotherm. Present-day global power of 30 TW from heat flux measurements and sequestering of heat producing elements in the upper mantle and transition zone, produces nearly isothermal T = 5300 K below 670 km, which equals experimentally determined freezing of pure Fe0 at the inner core boundary. Core freezing buffers the interior temperatures, while the Sun constrains the surface temperature, providing steady state conditions: Earth's deep interior is isothermal due to these constraints, low flux and high k. Our geotherms point to a stagnant lower mantle and convection above 670 km. Rotational flattening cracks the brittle lithosphere, providing paths for buoyant magmas to ascend. Release of latent heat augments the conductive gradient, making these oriented cracks equivalent to vertical hot plates, thereby imparting a large lateral component and preferred direction to upper mantle circulation. The latent heat release limits lower mantle flux to 1 TW and its temperature change to 500 K High lower mantle temperatures require a bulk composition more like the Moon than chondrites, which is consistent with proposals that calcuim-aluminum inclusions constitute a presolar reservoir near the nebula center. From oxygen isotopes and chemical composition of meteorites, we provide a new class of meteoritic model, based on mixing and not volatile element depletion, for the types and amounts of Earth's heat producing elements. Our model permits crust preservation at ~ 4 Ga, whereas hypothetical primordial heat would delay this significantly. The lower mantle is chemically distinct from the peridotite (chondritic) upper mantle, being comprised of refractory phases with much higher Ca, Al and Ti contents than previously considered. Huge changes in chemistry and temperature are required across the transition zone and profoundly affect the workings of the Earth. The lower mantle formed during gravitational sorting very early on, as did the core, in the drive towards energy minimization.

Hofmeister, A.; Criss, R. E.

2012-12-01

272

Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures D. E. Chang,1  

E-print Network

Trapping and Manipulation of Isolated Atoms Using Nanoscale Plasmonic Structures D. E. Chang,1 J. D of Physics, MIT-Harvard Center for Ultracold Atoms, and Research Laboratory of Electronics, Massachusetts September 2009) We propose and analyze a scheme to interface individual neutral atoms with nanoscale solid

Heller, Eric

273

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

274

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

PubMed Central

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

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

2014-01-01

275

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

PubMed

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

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

2014-01-01

276

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database  

PubMed Central

Background Structural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization of the intermolecular interactions that underlie these assemblies and mediate molecular recognition, these are not well described by standard representations. Results Here we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Distance and angle terms are used to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified by an analysis of residue propensity and interface contact preferences derived from a much larger data set than previously reported. However, PICCOLO also supports detailed inspection of particular systems of interest. Conclusions The current PICCOLO database comprises more than 260 million interacting atom pairs from 38,202 protein complexes. A web interface for the database is available at http://www-cryst.bioc.cam.ac.uk/piccolo. PMID:21801404

2011-01-01

277

Materials by Design—A Perspective From Atoms to Structures  

PubMed Central

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

Buehler, Markus J.

2013-01-01

278

Materials by Design-A Perspective From Atoms to Structures.  

PubMed

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

Buehler, Markus J

2013-02-01

279

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

PubMed

Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684

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

2014-05-30

280

Electronic structure and chemical bonding of LiYSi  

NASA Astrophysics Data System (ADS)

The electronic structure of the ternary silicide LiYSi (ZrNiAl type, P6¯2m N°189, a = 702.3, c = 421.2 pm) is examined from ab initio with an assessment of the properties of chemical bonding. The compound is found semi-conducting with a very small gap and the chemical bonding is found mainly between Y and Si as well as Li-Si with differentiated Li-Si1/Li-Si2. The structure with totally de-intercalated Li keeps the characteristics of LiYSi with a reduction of the c/a ratio and of the volume albeit with less stability than binary YSi with orthorhombic CrB type structure. The electronic structure calculations indicate the possibility of an at least partial delithiation Li1-xYSi while keeping the hexagonal structure.

Matar, Samir F.; Pöttgen, Rainer; Ouaini, Naïm

2012-03-01

281

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

PubMed

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

Fink, Tobias; Reymond, Jean-Louis

2007-01-01

282

PREDICTING EXPLOSIBILITY PROPERTIES OF CHEMICALS FROM QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIPS  

E-print Network

PREDICTING EXPLOSIBILITY PROPERTIES OF CHEMICALS FROM QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIPS to predict physico- chemical properties is a growing interest. In this context, an original approach associating QSPR methods and quantum chemical calculations for the prediction of chemicals explosibility

Paris-Sud XI, Université de

283

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

NASA Astrophysics Data System (ADS)

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

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

2013-05-01

284

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

285

Comparison of chemical modifiers for the determination of selenium by electrothermal atomic-absorption spectrometry*1  

NASA Astrophysics Data System (ADS)

Nickel, copper and palladium were investigated as chemical modifiers in several modes of electrothermal atomic-absorption spectrometry for the determination of selenium present in the samples in different valence states. Among the investigated metals, palladium alone, either thermally reduced in the graphite furnace or electrodeposited on the graphite surface, gave the best analytical performance for the determination of selenium in the sample with organic matrix. In both cases the sensitivity was nearly independent of the valence state of selenium and a characteristic mass ( mo) of 50-55 pg (0.0044 s) -1 was obtained. The amount and the reduction conditions of the modifiers and the pyrolysis temperature for Se were optimized to find best conditions for permanent modification. It is shown that thermally deposited palladium can serve for about ten firings. Tubes pretreated with electrodeposited palladium exhibit had analytical lifetime, up to 500 firings without loss of sensitivity.

Bulska, Ewa; Pyrzy?ska, Krystyna

1997-07-01

286

Determination of selenium by tungsten coil atomic absorption spectrometry using iridium as a permanent chemical modifier  

NASA Astrophysics Data System (ADS)

Permanent chemical modifiers have been shown to prolong graphite tube lifetime while reducing the furnace cycle time, thus improving cost-effectiveness. In this work, iridium is used as a permanent chemical modifier for the first time in the determination of selenium by tungsten-coil atomic absorption spectrometry (W-Coil AAS). The iridium modifier is thermally coated onto the tungsten coil. After coating, the coil can be used for 300-400 firings without further application of the modifier. Thermal treatment with iridium permits operating with higher pyrolysis temperature and coil lifetime is extended up to 1600 firings. The sensitivity and linearity of the method is improved, and the analytical procedure allows the use of analyte solutions containing up to 8% nitric acid. The short-term stability of the absorbance measurements is demonstrated by the reproducibility in the measurements of a Se amount (6 ng) 30 times higher than the limit of detection (0.2 ng). A 7% relative standard deviation (R.S.D.) was observed for 10 consecutive measurements of 6 ng Se. The long-term stability is almost as good: less than 9% R.S.D. over a 3-week period and 1500 firings. The surface of the tungsten-coil treated with iridium is examined before and after intensive use by scanning electron microscopy. Finally, the thermal treatment of the tungsten-coil with iridium appears to delay the appearance of selenium atoms by approximately 0.2 s although the integrated absorbance measurements are unaffected. The magnitude of delay decreases with coil age.

Hou, Xiandeng; Yang, Zheng; Jones, Bradley T.

2001-02-01

287

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

SciTech Connect

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

Paesler, M.; Sayers, D.

1988-12-01

288

Correlating atomic structure and transport in suspended graphene nanoribbons.  

PubMed

Graphene nanoribbons (GNRs) are promising candidates for next generation integrated circuit (IC) components; this fact motivates exploration of the relationship between crystallographic structure and transport of graphene patterned at IC-relevant length scales (<10 nm). We report on the controlled fabrication of pristine, freestanding GNRs with widths as small as 0.7 nm, paired with simultaneous lattice-resolution imaging and electrical transport characterization, all conducted within an aberration-corrected transmission electron microscope. Few-layer GNRs very frequently formed bonded-bilayers and were remarkably robust, sustaining currents in excess of 1.5 ?A per carbon bond across a 5 atom-wide ribbon. We found that the intrinsic conductance of a sub-10 nm bonded bilayer GNR scaled with width as GBL(w) ? 3/4(e(2)/h)w, where w is the width in nanometers, while a monolayer GNR was roughly five times less conductive. Nanosculpted, crystalline monolayer GNRs exhibited armchair-terminated edges after current annealing, presenting a pathway for the controlled fabrication of semiconducting GNRs with known edge geometry. Finally, we report on simulations of quantum transport in GNRs that are in qualitative agreement with the observations. PMID:24954396

Qi, Zhengqing John; Rodríguez-Manzo, Julio A; Botello-Méndez, Andrés R; Hong, Sung Ju; Stach, Eric A; Park, Yung Woo; Charlier, Jean-Christophe; Drndi?, Marija; Johnson, A T Charlie

2014-08-13

289

Revealing electronic structure in atomically-engineered manganite thin films  

NASA Astrophysics Data System (ADS)

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

Monkman, Eric Justin

290

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

USGS Publications Warehouse

Five manganese nodules, including the USGS reference nodules A-1 and P-1, were analyzed for Co, Cu, Fe, K, Mg, Mn, Na, Ni and Zn without prior chemical separation by using a simultaneous multi-element atomic absorption spectrometer with an air-cetylene flame. The nodules were prepared in three digestion matrices. One of these solutions was measured using sixteen different combinations of burner height and air/acetylene ratios. Results for A-1 and P-1 are compared to recommended values and results for all nodules are compared to those obtained with an inductively coupled plasma. The elements Co, Cu, Fe, K, Mg, Mn, Na, Ni, and Zn are simultaneously determined with a composite recovery for all elements of 100 ?? 7%, independent of the digestion matrices, heights in the flame, or flame stoichiometries examined. Individual recoveries for Co, K, and Ni are considerably poorer in two digests than this composite figure, however. The optimum individual recoveries of 100 ?? 5% and imprecisions of 1-4%, except for zinc, are obtained when Co, K, Mn, Na and Ni are determined simultaneously in a concentrated digest, and in another analytical sequence, when Cu, Fe, Mg, Mn and Zn are measured simultaneously after dilution. Determination of manganese is equally accurate in the two sequences; its measurement in both assures internal consistency between the two measurement sequences. This approach improves analytical efficiency over that for conventional atomic absorption methods, while minimizing loss of accuracy or precision for individual elements. ?? 1982.

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

1982-01-01

291

Influence of structure on chemical and thermal stability of aliphatic diesters.  

PubMed

Ester group interactions with each other and with the atoms between them were investigated in order to determine dependence of chemical and thermal stabilities of aliphatic diesters on structure. Novel glycol-derived diesters with chemical formula (C17H33COO)2C(n)H(2n) were used as model systems. Chemical stability was determined using (1)H NMR and FTIR, and thermal stability and weight-loss kinetics were examined using nonisothermal TGA. Chemical stability increased with the number of methylene units (n, carbon) between the ester groups until n = 6, and no significant improvement was observed past n > 6. It is argued that other ester-dense materials, including polyesters, would behave similarly. Evidence of a strong dependence of thermal stability on chemical stability is also provided. This work shows that the chemical and thermal stabilities of ester-dense functional materials such as diesters, oligo-esters, and polyesters can be manipulated by varying the distance between the ester groups, and hence the interactions of the electron-withdrawing ester groups with its neighbors. PMID:24171430

Raghunanan, Latchmi; Narine, Suresh S

2013-11-27

292

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

E-print Network

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

Zhu, Xiangdong

293

ALMOST: An All Atom Molecular Simulation Toolkit for Protein Structure Determination  

E-print Network

ALMOST: An All Atom Molecular Simulation Toolkit for Protein Structure Determination Biao Fu,[d] Michele Vendruscolo,[a] and Andrea Cavalli*[a,e] Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems

Caflisch, Amedeo

294

Structural Transition in Atomic Chains Driven by Transient Doping P. C. Snijders,2  

E-print Network

Structural Transition in Atomic Chains Driven by Transient Doping S. Polei,1 P. C. Snijders,2 S. C, Wisconsin 53706, USA (Received 30 April 2013; published 8 October 2013) A reversible structural transition into the surface. The periodicity of atomic chains near the step edges changes from the 1 Ã? 3 ground state to a 1 Ã?

Himpsel, Franz J.

295

Electronic structure of heavily doped graphene: The role of foreign atom states  

Microsoft Academic Search

Using density functional theory calculations we investigate the electronic structure of graphene doped by deposition of foreign atoms. We demonstrate that, as the charge transfer to the graphene layer increases, the band structure of the pristine graphene sheet is substantially affected. This is particularly relevant when Ca atoms are deposed on graphene at CaC6 stoichiometry. Similarly to what happens in

Matteo Calandra; Francesco Mauri

2007-01-01

296

Entangling strings of neutral atoms in 1D atomic pipeline structures.  

PubMed

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. PMID:12935017

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

2003-08-15

297

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

298

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

PubMed

Atomic length-scale order characteristics of binary and ternary amorphous oxides are presented within the framework of ab initio theory. A combined numerically efficient density functional based tight-binding molecular dynamics and density functional theory approach is applied to model the amorphous (a) phases of SiO2 and TiO2 as well as the amorphous phase of atomically mixed TixSi1-xO2 hybrid-oxide alloys over the entire composition range. Short and mid-range order in the disordered material phases are characterized by bond length and bond-angle statistics, pair distribution function analysis, coordination number and coordination polyhedra statistics, as well as ring statistics. The present study provides fundamental insights into the order characteristics of the amorphous hybrid-oxide frameworks formed by versatile types of TiOn and SiOm coordination polyhedra. In a-SiO2 the fourfold crystal coordination of Si ions is almost completely preserved and the atomic structure is widely dominated by ring-like mid-range order characteristics. In contrast, the structural disorder of a-TiO2 arises from short-range disorder in the local coordination environment of the Ti ion. The coordination number analysis indicates a large amount of over and under-coordinated Ti ions (coordination defects) in a-TiO2. Aside from the ubiquitous distortions of the crystal-like coordinated polyhedra, even the basic coordination-polyhedra geometry type changes for a significant fraction of TiO6 units (geometry defects). The combined effects of topological and chemical disorder in a-TixSi1-xO2 alloys lead to a continuos increase in both the Si as well as the Ti coordination number with the chemical composition x. The important roles of intermediate fivefold coordination states of Ti and Si cations are highlighted for ternary a-TixSi1-xO2 as well as for binary a-TiO2. The continuous decrease in ring size with increasing Ti content reflects the progressive loss of mid-range order structure characteristics and the competing roles of network forming and network modifying SiOm and TiOn units in the mixed hybrid oxides. PMID:24848713

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

2014-06-25

299

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

300

Role of chemical potential in relaxation of faceted crystal structure  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

301

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

302

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

303

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

SciTech Connect

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

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

2007-02-15

304

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

E-print Network

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

Savely G. Karshenboim

2005-09-01

305

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

SciTech Connect

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

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

2013-06-10

306

Chemical and structural instabilities of lithium ion battery cathodes  

Microsoft Academic Search

The chemical and structural stabilities of various layered Li1?xNi1?y?zMnyCozO2 cathodes are compared by characterizing the samples obtained by chemically extracting lithium from the parent Li1?xNi1?y?zMnyCozO2 with NO2BF4 in an acetonitrile medium. The nickel- and manganese-rich compositions such as Li1?xNi1\\/3Mn1\\/3Co1\\/3O2 and Li1?xNi0.5Mn0.5O2 exhibit better chemical stability than the LiCoO2 cathode. While the chemically delithiated Li1?xCoO2 tends to form a P3 type

A. Manthiram; J. Choi

2006-01-01

307

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

308

LASERS: Pulsed chemical oxygen—iodine laser with bulk formation of iodine atoms by an electric discharge  

NASA Astrophysics Data System (ADS)

A preliminary investigation was made of a chemical oxygen—iodine laser with bulk formation of iodine atoms in an electric discharge. The output energy was comparable with that obtained for a photolysis variant of the laser, but the technical efficiency of the investigated discharge variant was much higher (91%). The pulse power (~100 kW) was approximately three orders of magnitude higher than the power of a cw chemical oxygen—iodine laser with the same chlorine flow rate.

Vagin, Nikolai P.; Pazyuk, V. S.; Yuryshev, Nikolai N.

1995-08-01

309

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

Microsoft Academic Search

A pulsed electric discharge is the most effective means to turn chemical oxygen-iodine laser (COIL) operation into the pulse mode by fast production of iodine atoms. Experimental studies and numerical simulations are performed on a pulsed COIL initiated by an electric discharge in a mixture CF3I : N2 : O2(3X) : O2(a 1Deltag) flowing out of a chemical singlet oxygen

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

2011-01-01

310

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. PMID:11102292

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

2000-01-01

311

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

PubMed

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

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

2014-11-10

312

[18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful,  

E-print Network

[18] improving structures using all-atom contacts 385 The methodology of macromolecular of protein and nucleic acid crystal structures. [18] New Tools and Data for Improving Structures, Using All-atom criteria for protein structure validation: (1) development of the all-atom contact method, which can

Richardson, David

313

Atomic structure and thermally induced transformation of the crystalline BaO/Si(100) junction  

NASA Astrophysics Data System (ADS)

Atomic structure of interfaces between oxide layers and semiconductors is usually challenging to probe because of its buried nature. Here, we present a synchrotron photoemission approach to unveil the interface structure of BaO/Si(100), a prototype model of crystalline-oxide/semiconductor junctions, and demonstrate that such interface outspreads over four Si atomic planes and contains five different crystal sites for Si atoms, including three Si-O bonding sites. An atomic model is suggested for this system. Heating enhances Si diffusion and oxidation, but the junction still remains crystalline at 500 °C, promising potential for integration of III-V films and Si(100).

Kuzmin, M.; Laukkanen, P.; Punkkinen, M. P. J.; Yasir, M.; Tuominen, M.; Dahl, J.; Lâng, J. J. K.; Mäkelä, J.; Kokko, K.

2014-12-01

314

Semiflexible polymer rings on topographically and chemically structured surfaces  

E-print Network

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

Petra Gutjahr; Reinhard Lipowsky; Jan Kierfeld

2014-05-25

315

Control of membrane structure and organization through chemical recognition.  

PubMed

Cell membranes consist of a fluidic medium of lipids and proteins that organize into specific submicron scale structures for signaling and molecular trafficking processes. These organized molecular assemblies form as a result of the structure and chemistry of the membrane components as well as the interactions of those components with analytes from solution. Although considerable research has focused on the structure and chemistry of membrane components and their ability to form organized assemblies, less attention has been paid toward the influence that chemical recognition has upon membrane reorganization. This review focuses on the recognition and binding of metal ions, small molecules, polyelectrolytes, and proteins on model membrane systems to assess the effects of long- and short-range interactions upon the molecular organization of the membrane. Chemical recognition can induce dramatic changes on the membrane's phase transition temperature and the clustering or dispersion of membrane components. PMID:14515020

Sasaki, Darryl Y

2003-01-01

316

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

Microsoft Academic Search

The pulsed chemical oxygen–iodine laser (COIL) development is aimed at many new applications. Pulsed electric discharge is most effective in turning COIL operation into the pulse mode by instant production of iodine atoms. A numerical model is developed for simulations of the pulsed COIL initiated by an electric discharge. The model comprises a system of kinetic equations for neutral and

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

2009-01-01

317

LASERS: Pulsed chemical oxygen---iodine laser with bulk formation of iodine atoms by an electric discharge  

Microsoft Academic Search

A preliminary investigation was made of a chemical oxygen---iodine laser with bulk formation of iodine atoms in an electric discharge. The output energy was comparable with that obtained for a photolysis variant of the laser, but the technical efficiency of the investigated discharge variant was much higher (91%). The pulse power (~100 kW) was approximately three orders of magnitude higher

Nikolai P. Vagin; V. S. Pazyuk; Nikolai N. Yuryshev

1995-01-01

318

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

Microsoft Academic Search

The pulsed chemical oxygen-iodine laser (COIL) development is aimed at many new applications. Pulsed electric discharge is most effective in turning COIL operation into the pulse mode by instant production of iodine atoms. A numerical model is developed for simulations of the pulsed COIL initiated by an electric discharge. The model comprises a system of kinetic equations for neutral and

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

2009-01-01

319

Atomic shell structure from the Single-Exponential Decay Detector  

SciTech Connect

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

Silva, Piotr de, E-mail: piotr.desilva@unige.ch [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland); Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland); Korchowiec, Jacek [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland)] [K. Gumi?ski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland); Wesolowski, Tomasz A. [Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland)] [Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland)

2014-04-28

320

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. Program SummaryProgram title: GRASP2K, version 1_1 Catalogue identifier: ADZL_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine structure parameters, Landé gJ-factors, and specific mass shift parameters — using a multiconfiguration Dirac-Hartree-Fock approach. Solution method: The computational method is the same as in the previous GRASP2K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A comprehensive user manual in pdf format for the program package has been added. Restrictions: The packing

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

2013-09-01

321

Smallest Nanoelectronic with Atomic Devices with Precise Structures  

NASA Technical Reports Server (NTRS)

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

Yamada, Toshishige

2000-01-01

322

Electronic structure and chemical bonding of a highly stable and aromatic auro-aluminum oxide cluster.  

PubMed

We have produced an auro-aluminum oxide cluster, Au2(AlO)2(-), as a possible model for an Au-alumina interface and investigated its electronic and structural properties using photoelectron spectroscopy and density functional theory. An extremely large energy gap (3.44 eV) is observed between the lowest unoccupied and the highest occupied molecular orbitals of Au2(AlO)2, suggesting its high electronic stability. The global minima of both Au2(AlO)2(-) and Au2(AlO)2 are found to have D2h symmetry with the two Au atoms bonded to the Al atoms of a nearly square-planar (AlO)2 unit. Chemical bonding analyses reveal a strong ? bond between Au and Al, as well as a completely delocalized ? bond over the (AlO)2 unit, rendering aromatic character to the Au2(AlO)2 cluster. The high electronic stability and novel chemical bonding uncovered for Au2(AlO)2 suggest that it may be susceptible to chemical syntheses as a stable compound if appropriate ligands can be found. PMID:24964367

Lopez, Gary V; Jian, Tian; Li, Wei-Li; Wang, Lai-Sheng

2014-07-17

323

Chemical structure of phenothiazines and their biological activity.  

PubMed

Phenothiazines belong to the oldest, synthetic antipsychotic drugs, which do not have their precursor in the world of natural compounds. Apart from their fundamental neuroleptic action connected with the dopaminergic receptors blockade, phenothiazine derivatives also exert diverse biological activities, which account for their cancer chemopreventive-effect, as: calmodulin- and protein kinase C inhibitory-actions, anti-proliferative effect, inhibition of P-glycoprotein transport function and reversion of multidrug resistance. According to literature data on relations between chemical structure of phenothiazines and their biological effects, the main directions for further chemical modifications have been established. They are provided and discussed in this review paper. PMID:22580516

Jaszczyszyn, Agata; G?siorowski, Kazimierz; ?wi?tek, Piotr; Malinka, Wies?aw; Cie?lik-Boczula, Katarzyna; Petrus, Joanna; Czarnik-Matusewicz, Bogus?awa

2012-01-01

324

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

325

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

326

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

PubMed Central

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

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

2013-01-01

327

Applications of the Cambridge Structural Database in chemical education.  

PubMed

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

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

2010-10-01

328

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

PubMed

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

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

2014-02-17

329

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

330

Ultrahigh resolution protein structures using NMR chemical shift tensors  

PubMed Central

NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13C? and 15N (peptide backbone) groups in a protein, the ?1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13C? and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13C?. The orientations of the 13C? CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in ?-helical versus ?-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13C? CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 ? (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 ? agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-? crystal structures, based upon empirical metrics such as Ramachandran geometries and ?1/?2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

2011-01-01

331

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

SciTech Connect

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

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

2008-06-30

332

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

PubMed

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

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

2002-07-15

333

Investigation of plasma-doped fin structure and characterization of dopants by atom probe tomography  

SciTech Connect

As and P dopants in a plasma-doped Si-based fin structure were analyzed using atom probe tomography. The distributions and concentrations of As and P atoms in various regions of the fin structure and the oxidation levels for different dopants were determined. Most dopants were segregated at the fin boundary, and the As and P concentrations exceeded 9 Multiplication-Sign 10{sup 20} atoms/cm{sup 3} and 2 Multiplication-Sign 10{sup 20} atoms/cm{sup 3}, respectively. The atomic oxygen and SiO{sub 2} concentrations depended on the dopant type. The larger and heavier As dopant severely damaged the surface of the fin structure and could cause more severe oxidation.

Kim, B. H.; Park, S. M. [Department of Materials Science and Engineering, POSTECH, Pohang (Korea, Republic of); Park, S. W.; Park, Y. B.; Kim, H. J. [Research and Development Division, SK Hynix, 2091, Gyeongchung-daero, Bubal-eub, Ichon-si, Gyeonggi-do (Korea, Republic of); Park, C. G. [Department of Materials Science and Engineering, POSTECH, Pohang (Korea, Republic of); National Center for Nanomaterials Technology (NCNT), Pohang 790-784 (Korea, Republic of)

2012-11-19

334

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

PubMed Central

A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs. PMID:24469299

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

2014-01-01

335

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

E-print Network

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

Yunqi Li; Ambrish Roy; Yang Zhang

2009-01-01

336

Bifunctional Sensing Characteristics of Chemical Vapor Deposition Synthesized Atomic-Layered MoS2.  

PubMed

Two-dimensional (2D) molybdenum disulfide (MoS2) atomic layers have a strong potential to be adopted for 2D electronic components due to extraordinary and novel properties not available in their bulk foams. Unique properties of the MoS2, including quasi-2D crystallinity, ultrahigh surface-to-volume, and a high absorption coefficient, have enabled high-performance sensor applications. However, implementation of only a single-functional sensor presents a limitation for various advanced multifunctional sensor applications within a single device. Here, we demonstrate the charge-transfer-based sensitive (detection of 120 ppb of NO2) and selective gas-sensing capability of the chemical vapor deposition synthesized MoS2 and good photosensing characteristics, including moderate photoresponsivity (?71 mA/W), reliable photoresponse, and rapid photoswitching (<500 ms). A bifunctional sensor within a single MoS2 device to detect photons and gas molecules in sequence is finally demonstrated, paving a way toward a versatile sensing platform for a futuristic multifunctional sensor. PMID:25575096

Cho, Byungjin; Kim, Ah Ra; Park, Youngjin; Yoon, Jongwon; Lee, Young-Joo; Lee, Sangchul; Yoo, Tae Jin; Kang, Chang Goo; Lee, Byoung Hun; Ko, Heung Cho; Kim, Dong-Ho; Hahm, Myung Gwan

2015-02-01

337

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

E-print Network

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

Raji Heyrovska

2008-06-21

338

Identifying Atomic Structure as a Threshold Concept: Student mental models and troublesomeness  

Microsoft Academic Search

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 troublesome nature of this fundamental scientific concept. In

Eun Jung Park; Gregory Light

2009-01-01

339

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

340

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

341

HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations  

Microsoft Academic Search

The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of bead models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used

J Garc??a de la Torre; M. L. Huertas; B. Carrasco

2000-01-01

342

Interferometer-Type Structures for Guided Atoms R. Dumke, T. Muther, M. Volk, W. Ertmer, and G. Birkl*  

E-print Network

Interferometer-Type Structures for Guided Atoms R. Dumke, T. Mu¨ther, M. Volk, W. Ertmer, and G structures for neutral atoms based on dipole potentials created by microfabricated optical systems atom optical setups based on microfabricated guiding structures. Using mi- crofabricated current

Birkl, Gerhard

343

Time-resolved diffraction profiles and atomic dynamics in short-pulse laser-induced structural transformations: Molecular dynamics study  

E-print Network

Time-resolved diffraction profiles and atomic dynamics in short-pulse laser-induced structural on the atomic-level structural rearrangements available from the simulations to the diffraction spectra measured of the irradiated surface and provides limited direct information on atomic structural rearrangements. Recent

Zhigilei, Leonid V.

344

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

E-print Network

superior long term structural stability. Such atomically ordered quantum dots should, therefore-12]. In these systems it appears that it is atomically ordered or phase separated QDs that are structurally stable, i]. The general observation is that only parts of epitaxial layers transform into atomically ordered structures

Moeck, Peter

345

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization  

E-print Network

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-step, atomic-level energy minimization. The main-chain structures are first constructed from initial Ca traces physics- and knowledge-based force field. We tested the method by performing an atomic structure

Zhang, Yang

346

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

347

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

348

Synthesis and structure of chemically vapour-deposited boron nitride  

Microsoft Academic Search

Chemically vapour-deposited boron nitride (CVD-BN) plates have been synthesized on a graphite substrate by the reaction of the BCl3-NH3-H2 gas system in a deposition temperature (Tdep) range from 1200 to 2000° C, with a total gas pressure (Ptot) which was varied from 5 to 60 torr. The effects ofPtot andTdep on the crystal structure and the microstructure of the CVD-BN

Toshitsugu Matsuda; Naoki Uno; Hiroyuki Nakae; Toshio Hirai

1986-01-01

349

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

350

Photovoltaic structures using chemically deposited tin sulfide thin films  

Microsoft Academic Search

Chemically deposited thin films of tin sulfide forms in two crystalline structures depending on the bath compositions used: orthorhombic, SnS(OR), and zinc-blende, SnS(ZB). These films posses p-type electrical conductivity and have band gaps of 1.2 and 1.7 eV, respectively. The photovoltaic structure: SnO2:F\\/CdS\\/SnS(ZB)\\/SnS(OR) with evaporated Ag-electrode reported here shows an open circuit voltage (VOC) of 370 mV, a short circuit current density

David Avellaneda; M. T. S. Nair; P. K. Nair

2009-01-01

351

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

PubMed Central

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

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

2013-01-01

352

Atomic and Electronic Structure of Polar Oxide Interfaces  

SciTech Connect

In this project we developed fundamental understanding of atomic and electronic mechanisms for stabilization of polar oxide interfaces. An integrated experimental and theoretical methodology was used to develop knowledge on this important new class of ionic materials with limited dimensionality, with implications for multiple branches of the basic and applied energy sciences.

Gajdardziska-Josifovska, Marija [University of Wisconsin Milwaukee] [University of Wisconsin Milwaukee

2014-01-17

353

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

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

354

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.

Jirasek, Vit; Spalek, Otomar; Kodymova, Jarmila; Censky, Miroslav

2003-11-01

355

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

SciTech Connect

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

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

2007-09-19

356

MOLView: A program for analyzing and displaying atomic structures on the Macintosh personal computer  

Microsoft Academic Search

A program is described that allows the user to analyze and display atomic structures on any Macintosh personal computer. The program reads ASCII format structure files including PDB, plot files from the graphics programs O and FRODO, and Cartesian coordinates from ChemDraw 3D. The program has a graphical interface that features floating button palettes for objects and tools. The structures

Thomas James Smith

1995-01-01

357

The Dependence of All-Atom Statistical Potentials on Structural Training Database  

E-print Network

The Dependence of All-Atom Statistical Potentials on Structural Training Database Chi Zhang, Song An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high

Zhou, Yaoqi

358

Atomic local structure around Cu in CuâCd{sub 1-x}Te thin films  

Microsoft Academic Search

X-ray absorption spectroscopy (XAS) was used to investigate the local atomic structure around Cu atoms in CuâCd{sub 1-x}Te thin films, for x = 10 and 15 at.% nominal Cu concentrations. X-ray absorption near edge spectra (XANES) reveal a Cu local electronic structure different from that encountered in Cu metal. X-ray diffraction measurements have shown the presence of a single zincblende

J. Mustre de Leon; V. A. Perez; F. J. Espinosa; S. Jimenez-Sandoval; S. Lopez-Lopez; P. A. Montano; Cinvestav-Merida; Cinvestav-Queretaro; Cinvestav-Mexico

2000-01-01

359

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

SciTech Connect

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

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

1997-04-01

360

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

SciTech Connect

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

Curtis, L. J.

2004-05-01

361

Atomic Substitutions in Yba2cu3o7 - Modification of the Electronic-Structure  

E-print Network

, College Station, Texas 77843 (Received 1 February 1988) %e have performed semiempirical tight-binding calculations of the electronic structure of YBapCu307, wreath d and s orbitals included for all the metal atoms and p and s orbitals for the oxygen... effect on T?3 s indicating a remarkable insensitivity of the relevant electronic and structural properties to the species on this site. In particu- lar, the magnetic moment of the substituted atom does not appear to affect the superconducting...

RICHERT, BA; Allen, Roland E.

1988-01-01

362

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

SciTech Connect

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

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

2013-05-01

363

Nanoscale chemical and structural study of Co- based FEBID structures by STEM-EELS and HRTEM  

E-print Network

NANO EXPRESS Open Access Nanoscale chemical and structural study of Co- based FEBID structures by STEM-EELS and HRTEM Rosa Córdoba1,2, Rodrigo Fernández-Pacheco1,3, Amalio Fernández-Pacheco1,2, Alexandre Gloter3, César Magén1,2,4, Odile Stéphan3... electron microscopy at the nanometric scale. The obtained results allow us to correlate the chemical and structural properties with the functionality of these magnetic nanostructures. Keywords: Co deposits, FEBID, EELS, HRTEM Background Despite its great...

Cordoba, Rosa; Fernandez-Pacheco, Rodrigo; Fernandez-Pacheco, Amalio; Gloter, Alexandre; Magen, Cesar; Stephan, Odile; Ricardo Ibarra, Manuel; De Teresa, Jose Maria

2011-11-15

364

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

SciTech Connect

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

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

2003-03-01

365

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

366

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

367

A distance-dependent atomic knowledge-based potential for improved protein structure selection.  

PubMed

A heavy atom distance-dependent knowledge-based pairwise potential has been developed. This statistical potential is first evaluated and optimized with the native structure z-scores from gapless threading. The potential is then used to recognize the native and near-native structures from both published decoy test sets, as well as decoys obtained from our group's protein structure prediction program. In the gapless threading test, there is an average z-score improvement of 4 units in the optimized atomic potential over the residue-based quasichemical potential. Examination of the z-scores for individual pairwise distance shells indicates that the specificity for the native protein structure is greatest at pairwise distances of 3.5-6.5 A, i.e., in the first solvation shell. On applying the current atomic potential to test sets obtained from the web, composed of native protein and decoy structures, the current generation of the potential performs better than residue-based potentials as well as the other published atomic potentials in the task of selecting native and near-native structures. This newly developed potential is also applied to structures of varying quality generated by our group's protein structure prediction program. The current atomic potential tends to pick lower RMSD structures than do residue-based contact potentials. In particular, this atomic pairwise interaction potential has better selectivity especially for near-native structures. As such, it can be used to select near-native folds generated by structure prediction algorithms as well as for protein structure refinement. PMID:11455595

Lu, H; Skolnick, J

2001-08-15

368

Atomic volumes and local structure of metallic glasses  

Microsoft Academic Search

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

I. Bakonyi

2005-01-01

369

Atomic structures of amyloid cross-? spines reveal varied steric zippers  

Microsoft Academic Search

Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-? spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of ?-sheets, with the facing side chains of the two sheets interdigitated in a dry ‘steric

Michael R. Sawaya; Shilpa Sambashivan; Rebecca Nelson; Magdalena I. Ivanova; Stuart A. Sievers; Marcin I. Apostol; Michael J. Thompson; Melinda Balbirnie; Jed J. W. Wiltzius; Heather T. McFarlane; Anders Ø. Madsen; Christian Riekel; David Eisenberg

2007-01-01

370

PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)  

EPA Science Inventory

Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

371

STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY  

EPA Science Inventory

Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

372

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

NASA Astrophysics Data System (ADS)

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

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

2009-03-01

373

Thermal stability and structural characteristics of HfO2 films on Si (100) grown by atomic-layer deposition  

NASA Astrophysics Data System (ADS)

The thermal stability and structural characteristics for gate stack structure of HfO2 dielectrics deposited by atomic-layer deposition (ALD) were investigated. The structural characteristics and chemical state of the HfO2 films in relation to the film thickness and postannealing temperature were examined by x-ray diffraction and x-ray photoelectron spectroscopy. An interfacial layer of hafnium silicate with an amorphous structure was grown on the oxidized Si substrate at an initial growth stage. The structural characteristics of the HfO2 films are closely affected by the interfacial layer and are depended on the thickness of the films. The 45 A thick HfO2 film with an amorphous structure was changed into a polycrystalline structure after rapid temperature annealing of 750 degC for 5 min, while thicker films were grown into a polycrystalline structure of monoclinic or tetragonal crystal structure. The silicate layer grown at the interfacial region is not stable even at 700 degC under ultrahigh vacuum condition and changes into the silicide layers.

Cho, M.-H.; Roh, Y. S.; Whang, C. N.; Jeong, K.; Nahm, S. W.; Ko, D.-H.; Lee, J. H.; Lee, N. I.; Fujihara, K.

2002-07-01

374

Studying the local chemical environment of sulfur atoms at buried interfaces in CdS\\/ZnSe superlattices  

Microsoft Academic Search

Soft x-ray emission spectroscopy has been employed to study the local chemical environment of sulfur atoms in sulfide II-VI semiconductors (ZnS, CdS, HgS) and CdS\\/ZnSe superlattices. By using fluorescence transitions involving metal d-state-derived valence bands and S 2p core holes, a distinction between S-Zn and S-Cd bonds in the superlattices can be made. We find that, in addition to the

C. Heske; U. Groh; O. Fuchs; L. Weinhardt; E. Umbach; M. Grün; S. Petillon; A. Dinger; C. Klingshirn; W. Szuszkiewicz; A. Fleszar

2003-01-01

375

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

PubMed

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

Wong, Keith T; Lewis, Nathan S

2014-10-21

376

Structural Features of Toxic Chemicals for Specific Toxicity Jiansuo Wang, Luhua Lai,* and Youqi Tang  

E-print Network

Structural Features of Toxic Chemicals for Specific Toxicity Jiansuo Wang, Luhua Lai,* and Youqi Received April 22, 1999 We have studied the structural features of toxic chemicals from the RTECS database are gained by computational chemistry approaches. These structural features of toxic chemicals

Luhua, Lai

377

Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces.  

PubMed

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

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

2014-10-22

378

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

PubMed

The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory. PMID:22999222

Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

2012-10-24

379

A structure refinement strategy for NMR crystallography: an improved crystal structure of silica-ZSM-12 zeolite from 29Si chemical shift tensors.  

PubMed

A strategy for performing crystal structure refinements with NMR chemical shift tensors is described in detail and implemented for the zeolite silica-ZSM-12 (framework type code MTW). The 29Si chemical shift tensors were determined from a slow magic-angle spinning spectrum obtained at an ultrahigh magnetic field of 21.1T. The Si and O atomic coordinate parameters were optimized to give the best agreement between experimentally measured and ab initio calculated principal components of the 29Si chemical shift tensors, with the closest Si-O, O-O, and Si-Si distances restrained to correspond with the distributions of the distances found in a set of single-crystal X-ray diffraction (XRD) structures of high-silica zeolites. An improved structure for the silica-ZSM-12 zeolite, compared to a prior structure derived from powder XRD data, is obtained in which the agreement between the experimental and calculated 29Si chemical shift tensors is dramatically improved, the Si-O, O-O, and Si-Si distances correspond to the expected distributions, while the calculated powder XRD pattern remains in good agreement with the experimental powder XRD data. It is anticipated that this "NMR crystallography" structure refinement strategy will be an important tool for the accurate structure determination of materials that are difficult to fully characterize by traditional diffraction methods. PMID:18656402

Brouwer, Darren H

2008-09-01

380

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

E-print Network

J. Phys. Chem. 1995, 99, 15557-15564 15557 Confined Clusters of Rare Gas Atoms: Structures and the rare gas atoms. The main interests are the differencesin structures and dynamics of rare gas clusters Classical-mechanicalisoenergetic molecular dynamics simulations model Xe atoms and XeN clusters trapped

Berry, R. Stephen

381

Mapping chemical disorder and ferroelectric distortions in the double perovskite compound Sr 2-x Gd x MnTiO6 by atomic resolution electron microscopy and spectroscopy.  

PubMed

In this work we report a study of the chemical and structural order of the double perovskite compound Sr 2-x Gd x MnTiO6 for compositions x=0, 0.25, 0.5, 0.75, and 1. A noticeable disorder at the B-site in the Mn and Ti sublattice is detected at the atomic scale by electron energy-loss spectroscopy for all x values, resulting in Mn-rich and Ti-rich regions. For x ? 0.75, the cubic unit cell doubles and lowers its symmetry because of structural rearrangements associated with a giant ferroelectric displacement of the perovskite B-site cation. We discuss this finding in the light of the large electroresistance observed in Sr 2-x Gd x MnTiO6, x ? 0.75. PMID:24690379

Biškup, Neven; Álvarez-Serrano, Inmaculada; Veiga, Maria; Rivera-Calzada, Alberto; Garcia-Hernandez, Mar; Pennycook, Stephen J; Varela, Maria

2014-06-01

382

High-precision atomic structure measurements in thallium  

NASA Astrophysics Data System (ADS)

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

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

2004-05-01

383

Nuclear Corrections to Hyperfine Structure in Light Hydrogenic Atoms  

E-print Network

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

J. L. Friar; G. L. Payne

2005-04-04

384

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

PubMed

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

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

2014-07-01

385

Virtual reality based approach to protein heavy-atom structure reconstruction  

E-print Network

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C-alpha coordinates. Each heavy atom can be visualised on the surfaces of the different two-spheres, that are centered at the other heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters which display strong dependence on the underlying backbone secondary structure. Our method easily detects those atoms in a crystallographic protein structure which have been been likely misplaced. Our approach forms a basis for the development of a new generation, visualisation based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy over existing methods.

Xubiao Peng; Alireza Chenani; Shuangwei Hu; Yifan Zhou; Antti J. Niemi

2014-12-26

386

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

NASA Astrophysics Data System (ADS)

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

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

2011-11-01

387

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

SciTech Connect

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

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

2013-12-12

388

Atomic structure of PdNiP bulk metallic glass from ab initio simulations  

NASA Astrophysics Data System (ADS)

The atomic structure of Pd40Ni40P20 bulk metallic glass (BMG) has been simulated using ab initio molecular dynamics plane wave method and PAW pseudopotentials. We use generalized gradient approximation to calculate the exchange-correlation energy and a cubic simulation box whose size and shape have been optimized after the BMG has been formed in simulations. The resulting radial distribution function and density agree remarkably well with the experimental data. The structure is analysed in terms of local clusters centered around Pd, Ni and P atoms and their electronic structures have been used to understand the bonding, stability, and the formation of the PdNiP BMG.

Kumar, Vijay; Fujita, T.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

2009-03-01

389

THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS  

EPA Science Inventory

Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

390

Simultaneous determination of highly precise Debye-Waller factors and structure factors for chemically ordered NiAl.  

PubMed

Accurate Debye-Waller (DW) factors and several low-index structure factors of chemically ordered ?-NiAl at different temperatures have been measured using an off-zone-axis multi-beam convergent-beam electron diffraction method. The temperature dependences of DW factors of Ni and Al atoms are compared with previous experimental measurements and theoretical calculations. The temperature below which the DW factor of Ni becomes smaller than that of Al was found to be lower than previously reported. Structure factors are determined with an accuracy of 0.05% and compared with prior reports. PMID:20962379

Sang, X H; Kulovits, A; Wiezorek, J M K

2010-11-01

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

What do we really know about the atomic scale structures of nanophase materials?  

SciTech Connect

Robert W. Balluffi has spent a rich research lifetime critically investigating and elucidating the atomic scale defect structures of materials. Now, a new class of ultrafine-grained materials has been created in which such defects exercise a dominant role. The structures of these new nanophase materials, both metals and ceramics, have been investigated over the past several years by a wide range of experimental methods. These studies have included observations by x-ray and neutron scattering, transmission and scanning electron microscopy, Moessbauer, Raman, and positron annihilation spectroscopy, and most recently scanning tunneling and atomic force microscopy and nuclear magnetic resonance. While the experiments have yielded considerable useful information about the structures of nanophase materials on a variety of length scales, much about the local atomic arrangements in the grains and interfaces of these materials remains to be elucidated. The present status of the author`s knowledge of these structures is reviewed and some future research needs and opportunities are considered.

Siegel, R.W. [Argonne National Lab., IL (United States). Materials Science Div.

1994-06-01

393

Theoretical Chemical Kinetic Study of the H-Atom Abstraction Reactions from Aldehydes and Acids by ? Atoms and ?H, H?2, and ?H3 Radicals.  

PubMed

We have performed a systematic, theoretical chemical kinetic investigation of H atom abstraction by ? atoms and ?H, H?2, and ?H3 radicals from aldehydes (methanal, ethanal, propanal, and isobutanal) and acids (methanoic acid, ethanoic acid, propanoic acid, and isobutanoic acid). The geometry optimizations and frequencies of all of the species in the reaction mechanisms of the title reactions were calculated using the MP2 method and the 6-311G(d,p) basis set. The one-dimensional hindered rotor treatment for reactants and transition states and the intrinsic reaction coordinate calculations were also determined at the MP2/6-311G(d,p) level of theory. For the reactions of methanal and methanoic acid with ? atoms and ?H, H?2, and ?H3 radicals, the calculated relative electronic energies were obtained with the CCSD(T)/cc-pVXZ (where X = D, T, and Q) method and were extrapolated to the complete basis set limit. The electronic energies obtained with the CCSD(T)/cc-pVTZ method were benchmarked against the CCSD(T)/CBS energies and were found to be within 1 kcal mol(-1) of one another. Thus, the energies calculated using the less expensive CCSD(T)/cc-pVTZ method were used in all of the reaction mechanisms and in calculating our high-pressure limit rate constants for the title reactions. Rate constants were calculated using conventional transition state theory with an asymmetric Eckart tunneling correction, as implemented in Variflex. Herein, we report the individual and average rate constants, on a per H atom basis, and total rate constants in the temperature range 500-2000 K. We have compared some of our rate constant results to available experimental and theoretical data, and our results are generally in good agreement. PMID:25387985

Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

2014-12-26

394

Chemical Structural Novelty: On-Targets and Off-Targets  

PubMed Central

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

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

2011-01-01

395

Determination of structural transitions of atomic clusters from local and global bond orientational order parameters  

Microsoft Academic Search

Designing an effective order parameter for the identification of geometries in atomic clusters is an important step toward understanding the structural transitions occurring in these systems. We propose a method that simultaneously utilizes the local and global bond orientational order parameters for structural transitions. When applied to Lennard-Jones clusters at finite temperature over the size range 30<=N<=146, this method identified

Lixin Zhan; Jeff Z. Y. Chen; Wing-Ki Liu

2007-01-01

396

What do we really know about the atomic-scale structures of nanophase materials?  

Microsoft Academic Search

Robert W. Balluffi has spent a rich research lifetime critically investigating and elucidating the atomic scale defect structures of materials. Now, a new class of ultrafine-grained materials has been created in which such defects exercise a dominant role. The structures of these new nanophase materials, both metals and ceramics, have been investigated over the past several years by a wide

R. Siegel

1994-01-01

397

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

E-print Network

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

Crofts, Antony R.

398

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

E-print Network

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

Xing, Eric P.

399

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

E-print Network

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

Langmead, Christopher James

400

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

E-print Network

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

Langmead, Christopher James

401

Atomic structure and chemistry of human serum albumin  

NASA Technical Reports Server (NTRS)

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

He, Xiao M.; Carter, Daniel C.

1992-01-01

402

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

403

Atomic Models of Strong Solids Interfaces Viewed as Composite Structures  

NASA Astrophysics Data System (ADS)

This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture energy of a composite interface is needed. Using an interface model based on atomic interaction forces, it is shown that a single layer of contaminant atoms between the matrix and the reinforcement can reduce the interface fracture energy by an order of magnitude, giving a large delamination effect. The paper also looks to a future in which cars will be made largely from composite materials. Radical improvements in automobile design are necessary because the number of cars worldwide is predicted to double. This paper predicts gains in fuel economy by suggesting a new theory of automobile fuel consumption using an adaptation of Coulomb's friction law. It is demonstrated both by experiment and by theoretical argument that the energy dissipated in standard vehicle tests depends only on weight. Consequently, moving from metal to fibre construction can give a factor 2 improved fuel economy performance, roughly the same as moving from a petrol combustion drive to hydrogen fuel cell propulsion. Using both options together can give a factor 4 improvement, as demonstrated by testing a composite car using the ECE15 protocol.

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

2014-02-01

404

Electronic structure boundary value problems without all of the atoms  

SciTech Connect

A mixed atomistic/continuum technique, in the spirit of the quasicontinuum method, is formulated and used to solve boundary value problems in strained semiconductor structures in which the mechanical fields and the local electronic structure are fully coupled. The technique is implemented by means of a standard structural mechanics finite element package. Within each element in the mesh, tight binding calculations are made for mechanical properties based on the local electronic structure. The finite element program calculates equilibrium mechanical fields based on this atomistic constitutive information; the underlying electronic properties can then be extracted at the element level. The technique is demonstrated by examining several simple plane strain boundary value problems for coherently strained silicon.

Johnson, H.T.; Phillips, R.; Freund, L.B.

1999-07-01

405

Atomic structure of a Na+- and K+-conducting channel  

Microsoft Academic Search

Ion selectivity is one of the basic properties that define an ion channel. Most tetrameric cation channels, which include the K+, Ca2+, Na+ and cyclic nucleotide-gated channels, probably share a similar overall architecture in their ion-conduction pore, but the structural details that determine ion selection are different. Although K+ channel selectivity has been well studied from a structural perspective, little

Ning Shi; Sheng Ye; Amer Alam; Liping Chen; Youxing Jiang

2006-01-01

406

Influences of deuterium atoms on local bonding structures of SiO 2 studied by HREELS  

Microsoft Academic Search

We have investigated the initial oxidation processes on D-terminated Si(100)-2 × 1 and -1 × 1 surfaces and influences of Si-D bonding on SiO2 local bonding structures by high-resolution electron energy loss spectroscopy. It was found from experimental and simulated results that O atoms preferentially adsorb on one of two Si-Si back bonds of a surface Si atom. However, the

Hiroya Ikeda; Yasuyuki Nakagawa; Kenji Sato; Makoto Higashi; Shigeaki Zaima; Yukio Yasuda

1999-01-01

407

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

408

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

NASA Technical Reports Server (NTRS)

Fine-structure splittings of atomic oxygen (O-16) in the ground state have been accurately measured using a tunable far-infrared spectrometer. The 3P0-3pl splitting is 2,060,069.09 (10) MHz, and the 3Pl-3P2 splitting is 4,744,777.49 (16) MHz. These frequencies are important for measuring atomic oxygen concentration in earth's atmosphere and the interstellar medium.

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

1991-01-01

409

GRASP92: A package for large-scale relativistic atomic structure calculations  

Microsoft Academic Search

We describe a suite of programs for multiconfiguration or configuration-interaction relativistic atomic structure calculations with large configuration state function lists. Atomic orbitals are taken to be four-component spinors. Multiconfiguration self-consistent-field calculations are based on the Dirac-Coulomb Hamiltonian; at this level nuclei are assumed stationary and may be modelled either as point sources or as spherically-symmetric extended sources; in the latter

F. A. Parpia; C. Froese Fischer; I. P. Grant

1996-01-01

410

Atomic-Scale Structure and Catalytic Reactivity of the RuO2(110) Surface  

Microsoft Academic Search

The structure of RuO2(110) and the mechanism for catalytic carbon monoxide oxidation on this surface were studied by low-energy electron diffraction, scanning tunneling microscopy, and density-functional calculations. The RuO2(110) surface exposes bridging oxygen atoms and ruthenium atoms not capped by oxygen. The latter act as coordinatively unsaturated sites-a hypothesis introduced long ago to account for the catalytic activity of oxide

H. Over; Y. D. Kim; A. P. Seitsonen; S. Wendt; E. Lundgren; M. Schmid; P. Varga; A. Morgante; G. Ertl

2000-01-01

411

Electronic structures of graphene layers on a metal foil: The effect of atomic-scale defects  

NASA Astrophysics Data System (ADS)

Here, we report a facile method to generate a high density of atomic-scale defects in graphene on metal foil and show how these defects affect the electronic structures of graphene layers. Our scanning tunneling microscope measurements, complemented by first-principles calculations, reveal that the atomic-scale defects result in both the intervalley and intravalley scattering of graphene. The Fermi velocity is reduced in the vicinity area of the defect due to the enhanced scattering.

Yan, Hui; Liu, Cheng-Cheng; Bai, Ke-Ke; Wang, Xuejiao; Liu, Mengxi; Yan, Wei; Meng, Lan; Zhang, Yanfeng; Liu, Zhongfan; Dou, Rui-fen; Nie, Jia-Cai; Yao, Yugui; He, Lin

2013-09-01

412

Atomic structure of misfit dislocations in nonpolar ZnO/Al2O3 heterostructures  

E-print Network

Atomic structure of misfit dislocations in nonpolar ZnO/Al2O3 heterostructures H. Zhou,1,2,a M. F at non-polar 112¯0 ZnO/ 11¯02 Al2O3 a-ZnO/r-Al2O3 interface. The atomic configuration of the core the incorporation of Zn in the Al2O3 side of the dislocation. © 2010 American Institute of Physics. doi:10

Pennycook, Steve

413

Relativistic effects on the electronic structure and chemical bonding of UF6  

NASA Astrophysics Data System (ADS)

We have studied the relativistic effects in the electronic structure and chemical bonding for the ground state of UF6, using the relativistic and nonrelativistic discrete-variational X? molecular orbital calculations. It is found that two relativistic effects appear in the valence levels; the energy level splitting and upward shift of energies of the molecular orbitals. From the Mulliken population analysis of the valence levels, it is shown that the level splitting is due to mixing of the uranium atomic orbitals with a strong spin-orbit interaction, such as U6p, and the upward shift due to the increase in the screening of the nuclear charge and charge redistribution. The strength of U-F bonding remarkably increases for the relativistic case, because the changes in the radial distributions due to the relativistic effects induce both the decrease in the antibonding interactions and the increase in the bonding ones.

Onoe, Jun; Takeuchi, Kazuo; Nakamatsu, Hirohide; Mukoyama, Takeshi; Sekine, Rika; Kim, Bong-Il; Adachi, Hirohiko

1993-11-01

414

Atomic Physics  

NSDL National Science Digital Library

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

Christopher Griffith

415

Non-RRKM decomposition of chemically activated radicals: Reaction of fluorine atoms with tetraallyl germanium  

NASA Astrophysics Data System (ADS)

Thermal F atoms react with gaseous (CH 2?CHCH 2) 4Ge to produce CH 2?CHF through dissociation of the (CH 2?CHCH 2) 3-GeCH 2CHFCH 2* radical. The rapid decomposition is attributed to non-RRKM behavior with excitation energy largely confined to the CH 2CHFCH 2 side group. The central atoms mass effect found in linear seven-atom trajectory calculations has not yet appeared in (CH 2?CHCH 2) 4M with the replacement of Sn by Ge.

Rogers, Patricia J.; Selco, Jodye I.; Rowland, F. S.

1983-05-01

416

Virtual reality based approach to protein heavy-atom structure reconstruction  

E-print Network

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C-alpha coordinates. Each heavy atom can be visualised on the surfaces of the different two-spheres, that are centered at the other heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters which display strong dependence on the underlying backbone secondary structure. Our method easily detects those atoms in a crystallographic protein structure which have been been likely misplaced. Our approach forms a basis for the development of a new generation, visualisation based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondar...

Peng, Xubiao; Hu, Shuangwei; Zhou, Yifan; Niemi, Antti J

2014-01-01

417

Quantitative Structure-Toxicity Relationships for Chlorophenols to Bioluminescent Lux-Marked Bacteria Using Atom-Based SemiEmpirical Molecular-Orbital Descriptors  

Microsoft Academic Search

Literature data on the toxicity of chlorophenols for three luminescent bacteria (Vibrio fischeri, and the lux-marked Pseudomonas fluorescens 10586spUCD607 and Burkholderia spp. RASC c2 (Tn4431)) have been analysed in relation to a set of computed molecular physico-chemical properties. The quantitative structure-toxicity relationships of the compounds in each species showed marked differences when based upon semi-empirical molecular-orbital molecular and atom based

M. A. Warne; E. M. Boyd; A. A. Meharg; D. Osborn; K. Killham; J. C. Lindon; J. K. Nicholson

1999-01-01

418

Structure, chemical ordering and thermal stability of Pt-Ni alloy nanoclusters.  

PubMed

Equilibrium structures, chemical ordering and thermal properties of Pt-Ni nanoalloys are investigated by using basin hopping-based global optimization, Monte Carlo (MC) and molecular dynamics (MD) methods, based on the second-moment approximation of the tight-binding potentials (TB-SMA). The TB-SMA potential parameters for Pt-Ni nanoalloys are fitted to reproduce the results of density functional theory calculations for small clusters. The chemical ordering in cuboctahedral (CO) Pt-Ni nanoalloys with 561 and 923 atoms is obtained from the so called semi-grand-canonical ensemble MC simulation at 100 K. Two ordered phases of L12 (PtNi3) and L10 (PtNi) are found for the CO561 and CO923 Pt-Ni nanoalloys, which is in good agreement with the experimental phase diagram of the Pt-Ni bulk alloy. In addition, the order-disorder transition and thermal properties of these nanoalloys are studied by using MC and MD methods, respectively. It is shown that the typical perfect L10 PtNi structure is relatively stable, showing high order-disorder transition temperature and melting point among these CO561 and CO923 Pt-Ni nanoalloys. PMID:23913101

Cheng, Daojian; Yuan, Shuai; Ferrando, Riccardo

2013-09-01

419

Structure, chemical ordering and thermal stability of Pt-Ni alloy nanoclusters  

NASA Astrophysics Data System (ADS)

Equilibrium structures, chemical ordering and thermal properties of Pt-Ni nanoalloys are investigated by using basin hopping-based global optimization, Monte Carlo (MC) and molecular dynamics (MD) methods, based on the second-moment approximation of the tight-binding potentials (TB-SMA). The TB-SMA potential parameters for Pt-Ni nanoalloys are fitted to reproduce the results of density functional theory calculations for small clusters. The chemical ordering in cuboctahedral (CO) Pt-Ni nanoalloys with 561 and 923 atoms is obtained from the so called semi-grand-canonical ensemble MC simulation at 100 K. Two ordered phases of L12 (PtNi3) and L10 (PtNi) are found for the CO561 and CO923 Pt-Ni nanoalloys, which is in good agreement with the experimental phase diagram of the Pt-Ni bulk alloy. In addition, the order-disorder transition and thermal properties of these nanoalloys are studied by using MC and MD methods, respectively. It is shown that the typical perfect L10 PtNi structure is relatively stable, showing high order-disorder transition temperature and melting point among these CO561 and CO923 Pt-Ni nanoalloys.

Cheng, Daojian; Yuan, Shuai; Ferrando, Riccardo

2013-09-01

420

STRUCTURAL BIOLOGY: The Atomic Architecture of a Gas Channel  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Both prokaryotic and eukaryotic cells need to be able to transport ammonia gas. In their Perspective, Knepper and Agre discuss an exciting study (Khademi et al.) that reports resolution of the crystallographic structure of a bacterial ammonia transport channel, AmtB, to an astonishing 1.35 angstroms, an amazing feat for an integral membrane protein. The structure reveals how ammonia is transported in bacteria and sheds light on how related ammonia transport proteins work in eukaryotic cells.

Mark A. Knepper (National Institutes of Health;Laboratory of Kidney and Electrolyte Metabolism); Peter Agre (National Institutes of Health;Laboratory of Kidney and Electrolyte Metabolism)

2004-09-10

421

Atomic structure of interface states in silicon heterojunction solar cells.  

PubMed

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

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

2013-03-29

422

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

PubMed

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

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

2007-05-22

423

BioSM: A metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space  

PubMed Central

The structural identification of unknown biochemical compounds in complex biofluids continues to be a major challenge in metabolomics research. Using LC/MS there are currently two major options for solving this problem: searching small biochemical databases, which often do not contain the unknown of interest, or searching large chemical databases which include large numbers of non-biochemical compounds. Searching larger chemical databases (larger chemical space) increases the odds of identifying an unknown biochemical compound, but only if non-biochemical structures can be eliminated from consideration. In this paper we present BioSM; a cheminformatics tool that uses known endogenous mammalian biochemical compounds (as scaffolds) and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space. The results of a comprehensive set of empirical experiments suggest that BioSM identifies endogenous mammalian biochemical structures with high accuracy. In a leave-one-out cross validation experiment, BioSM correctly predicted 95% of 1,388 Kyoto Encyclopedia of Genes and Genomes (KEGG) compounds as endogenous mammalian biochemicals using 1,565 scaffolds. Analysis of two additional biological datasets containing 2,330 human metabolites (HMDB) and 2,416 plant secondary metabolites (KEGG) resulted in biochemical annotations of 89% and 72% of the compounds respectively. When a dataset of 3,895 drugs (DrugBank and USAN) was tested, 48% of these structures were predicted to be biochemical. However, when a set of synthetic chemical compounds (Chembridge and Chemsynthesis databases) were examined, only 29% of the 458,207 structures were predicted to be biochemical. Moreover, BioSM predicted that 34% of 883,199 randomly selected compounds from PubChem were biochemical. We then expanded the scaffold list to 3,927 biochemical compounds and reevaluated the above datasets to determine whether scaffold number influenced model performance. Although there were significant improvements in model sensitivity and specificity using the larger scaffold list, the dataset comparison results were very similar. These results suggest that additional biochemical scaffolds will not further improve our representation of biochemical structure space and that the model is reasonably robust. BioSM provides a qualitative (yes/no) and quantitative (ranking) method for endogenous mammalian biochemical annotation of chemical space, and thus will be useful in the identification of unknown biochemical structures in metabolomics. BioSM is freely available at http://metabolomics.pharm.uconn.edu. PMID:23330685

Hamdalla, Mai A.; Mandoiu, Ion I.; Hill, Dennis W.; Rajasekaran, Sanguthevar; Grant, David F.

2013-01-01

424

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

Microsoft Academic Search

A non-destructive x-ray scatter (XRS) approach has been developed, along with a rapid atomic scatter algorithm for the detection and analysis of low atomic-numbered elements in solids, powders, and liquids. The present method of energy dispersive x-ray fluorescence spectroscopy (EDXRF) makes the analysis of light elements (i.e., less than sodium; less than 11) extremely difficult. Detection and measurement become progressively

H. Richard Ross

1993-01-01

425

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

NASA Technical Reports Server (NTRS)

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

Cohen, W.

1973-01-01

426

Regularities and symmetries in atomic structure and spectra  

NASA Astrophysics Data System (ADS)

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

Pain, Jean-Christophe

2013-09-01

427

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

PubMed

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

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

2014-05-14

428

TOPICAL REVIEW: Extended x-ray absorption fine structure studies of the atomic structure of nanoparticles in different metallic matrices  

NASA Astrophysics Data System (ADS)

It has been appreciated for some time that the novel properties of particles in the size range 1-10 nm are potentially exploitable in a range of applications. In order to ultimately produce commercial devices containing nanosized particles, it is necessary to develop controllable means of incorporating them into macroscopic samples. One way of doing this is to embed the nanoparticles in a matrix of a different material, by co-deposition for example, to form a nanocomposite film. The atomic structure of the embedded particles can be strongly influenced by the matrix. Since some of the key properties of materials, including magnetism, strongly depend on atomic structure, the ability to determine atomic structure in embedded nanoparticles is very important. This review focuses on nanoparticles, in particular magnetic nanoparticles, embedded in different metal matrices. Extended x-ray absorption fine structure (EXAFS) provides an excellent means of probing atomic structure in nanocomposite materials, and an overview of this technique is given. Its application in probing catalytic metal clusters is described briefly, before giving an account of the use of EXAFS in determining atomic structure in magnetic nanocomposite films. In particular, we focus on cluster-assembled films comprised of Fe and Co nanosized particles embedded in various metal matrices, and show how the crystal structure of the particles can be changed by appropriate choice of the matrix material. The work discussed here demonstrates that combining the results of structural and magnetic measurements, as well as theoretical calculations, can play a significant part in tailoring the properties of new magnetic cluster-assembled materials.

Baker, S. H.; Roy, M.; Gurman, S. J.; Binns, C.

2009-05-01

429

Small clusters of tin: Atomic structures, energetics, and fragmentation behavior  

Microsoft Academic Search

Ab initio electronic structure calculations on Snn (n=10 to be only about 11% less than the calculated bulk value. This is likely to be responsible for the recently reported [Phys. Rev. Lett. 85, 2530 (2000)] higher melting temperatures of these clusters than the bulk value. The growth behavior is found to differ from the one known for Si and Ge

C. Majumder; V. Kumar; H. Mizuseki; Y. Kawazoe

2001-01-01

430

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

431

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

E-print Network

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

Carl Heiles

2007-01-22

432

Atomic layer structure of manganese atoms on wurtzite gallium nitride Abhijit Chinchore, Kangkang Wang, Wenzhi Lin, Jeongihm Pak, and Arthur R. Smitha  

E-print Network

Atomic layer structure of manganese atoms on wurtzite gallium nitride ,,0001¯... Abhijit Chinchore of Physics. DOI: 10.1063/1.3006434 Mn-doped gallium nitride GaN was proposed as a pos- sible dilute magnetic evident in Figs. 1 a and 1 b are 3 and higher- order streaks indicating gallium adatom reconstructions

433

Ceramic Materials and Nano-structures for Chemical Sensing Abdul-Majeed Azad  

E-print Network

Ceramic Materials and Nano-structures for Chemical Sensing Abdul-Majeed Azad Department of Chemical in the solid-state ceramic-based chemical sensors. Since the sensing mechanism and catalytic activity: Semiconducting ceramic oxides, Redox reactions, Microstructure, Chemical sensors Proceedings of Optics East SPIE

Azad, Abdul-Majeed

434

Growth and Characterization of Electrodeposited Zinc Sulphide and Chemical Vapour Atomic Layer Deposited Zinc Oxide, Sulphide, and Oxysulphide Thin Films  

NASA Astrophysics Data System (ADS)

Thin films of ZnS and ZnO_{ rm 1-x}S_{rm x} were prepared by electrodeposition and chemical vapour atomic layer deposition (CVALD), respectively. This represents the first effort to apply the technique of electrodeposition to ZnS for the purposes of electroluminescence. This is also the first time thin films of ZnO_{ rm 1-x}S_{rm x} were grown by CVALD and represents the first analysis of how the films properties vary with a known stoichiometry. Characterization methods performed on the thin films include: Auger spectroscopy, Rutherford backscattering spectroscopy, scanning electron microscopy, x-ray powder diffraction, Hall measurements and uv/visible transmittance. The as electrodeposited films were nearly stoichiometric but conductive and oriented in a <200 > direction. After annealing the films became discontinuous and lost their crystallinity, but their absorption characteristics more closely resembled that of evaporated films. Ion implantation with Mn was successful and the films exhibited yellow-orange cathodoluminescence. The value of x in the formula ZnO_ {rm 1-x}S_{ rm x} could be varied from 0 to 0.95 by changing the amount of hydrogen sulphide admitted to the reaction chamber. Films with values of x near 0 grow in the <200> direction (of ZnO) and have a fine grained structure. As the value of x increases the films become more and more amorphous but split into a two phase structure close to x = 0.55. At this point the films exhibit a minimum bandgap. As x increases further the films become one phase again and become oriented into the <111 > direction of ZnS. The cathodoluminescent characteristics of these films also change with x. When x is zero the films appear to luminescence green or yellow depending on the deposition temperature. Even 5% S removes this luminescence however and the spectrum is dominated by a peak in the red. This peak steadily decreases then increases again as x increases.

Sanders, Brian Wayne

435

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

NASA Astrophysics Data System (ADS)

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

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

2011-09-01

436

Observations of Small Scale ISM Structure in Dense Atomic Gas  

E-print Network

We present high resolution (R~170,000) Kitt Peak National Observatory Co'ude Feed telescope observations of the interstellar KI 7698 angstrom line towards 5 multiple star systems with saturated NaI components. We compare the KI absorption line profiles in each of the two (or three) lines of sight in these systems, and find significant differences between the sight-lines in 3 out of the 5 cases. We infer that the small scale structure traced by previous NaI observations is also present in at least some of the components with saturated NaI absorption lines, and thus the small scale structures traced by the neutral species are occurring at some level in clouds of all column densities. We discuss the implications of that conclusion and a potential explanation by density inhomogeneities.

J. T. Lauroesch; David M. Meyer

1999-05-14

437

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

PubMed

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

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

2014-01-27

438

Constructing Atomic-Resolution RNA Structural Ensembles Using MD and Motionally Decoupled NMR RDCs  

PubMed Central

A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-resolution and with timescales extending up to milliseconds. The protocol combines molecular dynamics (MD) simulations with experimental residual dipolar couplings (RDCs) measured in partially aligned 13C/15N isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions. PMID:19699798

Stelzer, Andrew C.; Frank, Aaron T.; Bailor, Maximillian H.; Andricioaei, Ioan; Al-Hashimi, Hashim M.

2012-01-01

439

PII S0016-7037(00)00455-5 Atomic-scale structure of the orthoclase (001)water interface measured with  

E-print Network

PII S0016-7037(00)00455-5 Atomic-scale structure of the orthoclase (001)­water interface measured-ray specular reflectivity and atomic force microscopy were used to determine the structure of the orthoclase measurements of the orthoclase­water interface structure performed to �ngstro¨m-scale resolution

Illinois at Chicago, University of

440

Characterization of Atomic Structure, Relaxation and Phase Transformation Mechanisms in Bulk and Thin Film Amorphous Chalcogenides and Gallium Antimonide  

NASA Astrophysics Data System (ADS)

This dissertation details the characterization of the atomic structure, relaxation processes and phase transformation mechanisms in a variety of chalcogenide (selenides and tellurides) and other non-oxide (Ga-Sb alloys) glasses which are highly relevant to optoelectronic and phase change memory applications. One of the principal goals of these studies is to develop a fundamental, atomistic understanding of the structure-property relationships in these materials. Variable temperature Raman spectroscopy is used to the study the structure and its temperature dependent relaxation in GexSe100-x glasses and supercooled liquids with x ? 33.33 %. It is shown that the compositional dependence of the relative fractions of the edge- and corner-shared GeSe4 tetrahedra is fully consistent with a structural model based on random connectivity between the tetrahedral and chain elements. Temperature-dependent structural changes involve a progressive conversion of edge-shared to corner shared GeSe4 tetrahedra with decreasing equilibration temperature. The time scale of this structural conversion agrees with both enthalpy and shear relaxation near the glass transition. The temperature dependent change in the edge- vs. corner- sharing tetrahedral speciation is shown to be related to the production of configurational entropy, indicating a connection between structural relaxation, configurational entropy, and viscous flow. A combination of Raman and 77Se nuclear magnetic resonance (NMR) spectroscopy is applied to study the structure of a series of Se-deficient GexSe100-x glasses, with 42 ? x ? 33.33. Considerable violation of chemical order in the nearest-neighbor coordination environments of the constituent atoms is observed in the stoichiometric GeSe2 glass. On the other hand, the presence of a random distribution of Ge-Ge bonds can be inferred in the Se-deficient glasses. Furthermore, the results of this study conclusively indicate that the structure of these glasses is intermediate between a randomly connected and a fully clustered network of GeSe4 tetrahedra and Se chains. Additionally, a new two-dimensional NMR spectroscopic technique is developed and applied to Ge-Se glasses that allowed the separation of isotropic and anisotropic chemical shifts. Through the analysis of the anisotropic sideband pattern in the second dimension it is possible to detect up to four distinct types of Se environments in the glass structure on the basis of their characteristic chemical shift anisotropies. 125Te NMR chemical shift systematics is established for coordination environments of Te atoms in a wide range of crystalline and glassy tellurides in the Ga-As-Sb-Te system. 125Te NMR spectroscopy is then used to investigate the short-range structure of amorphous and crystalline Ge1Sb2 Te4 and Ge2Sb2Te5 phase change alloys. Both alloys are found to consist of only heteropolar Ge/Sb-Te bonds in the amorphous and crystalline state and strong vacancy clustering in the nanocrystalline state that may facilitate a rapid displacive transformation between the amorphous and crystalline states without the need of significant atomic rearrangement or diffusion. Based on these 125Te NMR results a Te-centric model of the phase change mechanism in GST alloys is proposed. Structure and phase changes in amorphous Ga-Sb alloys are studied using synchrotron x-ray diffraction and 71Ga and 121Sb NMR spectroscopy. Pressure induced phase transformations in amorphous GaSb is shown to be consistent with the existence of an underlying polyamorphic phase transition between a low and a high-density amorphous phase. NMR results for amorphous Ga46Sb54 indicate that both Ga and Sb atoms are fourfold coordinated with 40% of these atoms participating in homopolar bonding in the as-deposited film. Subsequent crystallization into the zinc blend structure therefore requires extensive bond switching and elimination of homopolar bonds. For amorphous Ga14Sb86 both Ga and Sb atoms are found to be threefold coordinated allowing for a fast phase change kinetics although crystallization of thi

Edwards, Trenton Gerard

441

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

PubMed

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

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

2014-01-01

442

The local atomic quasicrystal structure of the icosahedral Mg25Y11Zn64 alloy  

NASA Astrophysics Data System (ADS)

A local and medium range atomic structure model for the face centred icosahedral (fci) Mg25Y11Zn64 alloy has been established in a sphere of r = 27 Å. The model was refined by least squares techniques using the atomic pair distribution (PDF) function obtained from synchrotron powder diffraction. Three hierarchies of the atomic arrangement can be found: (i) five types of local coordination polyhedra for the single atoms, four of which are of Frank-Kasper type. In turn, they (ii) form a three-shell (Bergman) cluster containing 104 atoms, which is condensed sharing its outer shell with its neighbouring clusters, and (iii) a cluster connecting scheme corresponding to a three-dimensional tiling leaving space for a few glue atoms. Inside adjacent clusters, Y8 cubes are tilted with respect to each other and thus allow for overall icosahedral symmetry. It is shown that the title compound is essentially isomorphic to its holmium analogue. Therefore, fci-Mg-Y-Zn can be seen as the representative structure type for the other rare earth analogues fci-Mg-Zn-RE (RE = Dy, Er, Ho, Tb) reported in the literature.

Brühne, S.; Uhrig, E.; Gross, C.; Assmus, W.; Masadeh, A. S.; Billinge, S. J. L.

2005-03-01

443

Hybrid carrageenans: isolation, chemical structure, and gel properties.  

PubMed

Hybrid carrageenan is a special class of carrageenan with niche application in food industry. This polysaccharide is extracted from specific species of seaweeds belonging to the Gigartinales order. This chapter focuses on hybrid carrageenan showing the ability to form gels in water, which is known in the food industry as weak kappa or kappa-2 carrageenan. After introducing the general chemical structure defining hybrid carrageenan, the isolation of the polysaccharide will be discussed focusing on the interplay between seaweed species, extraction parameters, and the hybrid carrageenan chemistry. Then, the rheological experiments used to determine the small and large deformation behavior of gels will be detailed before reviewing the relationships between gel properties and hybrid carrageenan chemistry. PMID:25081075

Hilliou, Loic

2014-01-01

444

3rd annual symposium of chemical and pharmaceutical structure analysis.  

PubMed

The 3rd Annual Symposium on Chemical and Pharmaceutical Structure Analysis was once again held in Shanghai, where a rich history of 'East meets West' continued. This meeting is dedicated to bringing together scientists from pharmaceutical companies, academic institutes, CROs and instrument vendors to discuss current challenges and opportunities on the forefront of pharmaceutical research and development. The diversified symposia and roundtables are highly interactive events where scientists share their experiences and visions in a collegial setting. The symposium highlighted speakers and sessions that provided first-hand experiences as well as the latest guidance and industrial/regulatory thinking, which was reflected by the theme of this year's meeting 'From Bench to Decision Making - from Basics to Application.' In addition to the highly successful Young Scientist Excellence Award, new events were featured at this year's meeting, such as the Executive Roundtable and the inaugural Innovator Award. PMID:22943615

Weng, Naidong; Zheng, Jenny; Lee, Mike

2012-08-01

445

Chemical structure of two phytotoxic exopolysaccharides produced by Phomopsis foeniculi.  

PubMed

The two main exocellular polysaccharides produced in vitro by Phomopsis foeniculi, a fungal pathogen of fennel, were isolated and characterized by chemical and spectroscopic methods as a galactan with the known structure [-->6)-beta-D-Galf-(1-->5)-beta-D- Galf-(1-->5)-beta-D-Galf-(1-->]n and a mannan. The latter consists of a backbone of alpha-(1-->6)-linked mannopyranose units. Almost all of these are branched at the 2 position with arms containing 2- and 3-linked mannopyranose units. The crude polysaccharide fraction and its components, galactan and mannan, showed phytotoxic effects, i.e. chlorosis, necrosis and/or wilting, on fennel and on two non-host plants, tobacco and tomato. PMID:9711828

Corsaro, M M; De Castro, C; Evidente, A; Lanzetta, R; Molinaro, A; Mugnai, L; Parrilli, M; Surico, G

1998-06-01

446

Atomic structures and electronic properties of 2H-NbSe{sub 2}: The impact of Ti doping  

SciTech Connect

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

Li, Hongping, E-mail: hpli@mail.ujs.edu.cn, E-mail: zcwang@wpi-aimr.tohoku.ac.jp; Chen, Lin; Zhang, Kun; Liang, Jiaqing; Tang, Hua; Li, Changsheng [Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013 (China); Liu, Xiaojuan; Meng, Jian [State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022 (China); Wang, Zhongchang, E-mail: hpli@mail.ujs.edu.cn, E-mail: zcwang@wpi-aimr.tohoku.ac.jp [Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan)

2014-09-14

447

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

448

Atomic structure of the ectodomain from HIV1 gp41  

Microsoft Academic Search

Fusion of viral and cellular membranes by the envelope glyco-protein gp120\\/gp41 effects entry of HIV-1 into the cell. The precursor, gp160, is cleaved post-translationally into gp120 and gp41 (refs 1,2), which remain non-covalently associated. Binding to both CD4 and a co-receptor leads to the conformational changes in gp120\\/gp41 needed for membrane fusion3. We used X-ray crystallography to determine the structure

W. Weissenhorn; A. Dessen; S. C. Harrison; J. J. Skehel; D. C. Wiley

1997-01-01

449