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Sample records for atomic structure ii

  1. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    PubMed

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin. PMID:25066915

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

    SciTech Connect

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

    1988-07-01

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

  3. Atomic resolution studies of carbonic anhydrase II

    SciTech Connect

    Behnke, Craig A.; Le Trong, Isolde; Godden, Jeff W.; Merritt, Ethan A.; Teller, David C.; Bajorath, Jürgen; Stenkamp, Ronald E.

    2010-05-01

    The structure of human carbonic anhydrase II has been solved with a sulfonamide inhibitor at 0.9 Å resolution. Structural variation and flexibility is seen on the surface of the protein and is consistent with the anisotropic ADPs obtained from refinement. Comparison with 13 other atomic resolution carbonic anhydrase structures shows that surface variation exists even in these highly ordered isomorphous crystals. Carbonic anhydrase has been well studied structurally and functionally owing to its importance in respiration. A large number of X-ray crystallographic structures of carbonic anhydrase and its inhibitor complexes have been determined, some at atomic resolution. Structure determination of a sulfonamide-containing inhibitor complex has been carried out and the structure was refined at 0.9 Å resolution with anisotropic atomic displacement parameters to an R value of 0.141. The structure is similar to those of other carbonic anhydrase complexes, with the inhibitor providing a fourth nonprotein ligand to the active-site zinc. Comparison of this structure with 13 other atomic resolution (higher than 1.25 Å) isomorphous carbonic anhydrase structures provides a view of the structural similarity and variability in a series of crystal structures. At the center of the protein the structures superpose very well. The metal complexes superpose (with only two exceptions) with standard deviations of 0.01 Å in some zinc–protein and zinc–ligand bond lengths. In contrast, regions of structural variability are found on the protein surface, possibly owing to flexibility and disorder in the individual structures, differences in the chemical and crystalline environments or the different approaches used by different investigators to model weak or complicated electron-density maps. These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available.

  4. Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational Study.

    PubMed

    Bowman, David N; Bondarev, Alexey; Mukherjee, Sriparna; Jakubikova, Elena

    2015-09-01

    Fe(II) polypyridines are an important class of pseudo-octahedral metal complexes known for their potential applications in molecular electronic switches, data storage and display devices, sensors, and dye-sensitized solar cells. Fe(II) polypyridines have a d(6) electronic configuration and pseudo-octahedral geometry and can therefore possess either a high-spin (quintet) or a low-spin (singlet) ground state. In this study, we investigate a series of complexes based on [Fe(tpy)2](2+) (tpy = 2,2';6',2″-terpyridine) and [Fe(dcpp)2](2+) (dcpp = 2,6-bis(2-carboxypyridyl)pyridine). The ligand field strength in these complexes is systematically tuned by replacing the central pyridine with five-membered (N-heterocyclic carbene, pyrrole, furan) or six-membered (aryl, thiazine-1,1-dioxide, 4-pyrone) moieties. To determine the impact of ligand substitutions on the relative energies of metal-centered states, the singlet, triplet, and quintet states of the Fe(II) complexes were optimized in water (PCM) using density functional theory at the B3LYP+D2 level with 6-311G* (nonmetals) and SDD (Fe) basis sets. It was found that the dcpp ligand scaffold allows for a more ideal octahedral coordination environment in comparison to the tpy ligand scaffold. The presence of six-membered central rings also allows for a more ideally octahedral coordination environment relative to five-membered central rings, regardless of the ligand scaffold. We find that the ligand field strength in the Fe(II) polypyridines can be tuned by altering the donor atom identity, with C donor atoms providing the strongest ligand field. PMID:26295275

  5. Relativistic atomic beam spectroscopy II

    SciTech Connect

    1989-12-31

    The negative ion of H is one of the simplest 3-body atomic systems. The techniques we have developed for experimental study of atoms moving near speed of light have been productive. This proposal request continuing support for experimental studies of the H{sup -} system, principally at the 800 MeV linear accelerator (LAMPF) at Los Alamos. Four experiments are currently planned: photodetachment of H{sup -} near threshold in electric field, interaction of relativistic H{sup -} ions with matter, high excitations and double charge escape in H{sup -}, and multiphoton detachment of electrons from H{sup -}.

  6. Atomic-Scale Characterization of II-VI Compound Semiconductors

    NASA Astrophysics Data System (ADS)

    Smith, David J.

    2013-11-01

    Alloys of II-VI compound semiconductors with suitable band gap selection potentially provide broad coverage of wavelengths for photodetector applications. Achievement of high-quality epitaxial growth is, however, essential for successful development of integrated photonic and optoelectronic devices. Atomic-scale characterization of structural defects in II-VI heterostructures using electron microscopy plays an invaluable role in accomplishing this goal. This paper reviews some recent high-resolution studies of II-VI compound semiconductors with zincblende crystal structure, as grown epitaxially on commonly used substrates. Exploratory studies using aberration-corrected electron microscopes are also briefly considered.

  7. Atomic far-IR fine-structure line mapping of L1630, M17, and W3: Comparison of (O I) and (C II) distributions

    NASA Technical Reports Server (NTRS)

    Howe, J. E.; Jaffe, Dan T.; Zhou, Shudong

    1995-01-01

    We mapped the distribution of atomic far-IR line emission from (O I) and (C II) over parsec scales in the Galactic star-forming regions L1630, M17, and W3 using the MPE Far-Infrared Fabry-Perot Imaging spectrometer (FIFI) on board the NASA Kuiper Airborne Observatory. The lines mapped include (O I) 63 microns, (O I) 146 microns, and (C II) 158 microns. Comparison of the intensities and ratios of these lines with models of photodissociation regions (e.g., Tielens & Hollenbach 1985, ApJ, 344, 770) allows us to derive temperatures and densities of the primarily neutral atomic gas layers lying on the surfaces of UV-illuminated molecular gas. In general, the (C II) line arises ubiquitously throughout the molecular clouds while the (O I) lines are mainly confined to warm, dense gas (T is greater than 100 K, n is greater than 10(exp 4)/cu cm) near the sites of O and B stars. The distribution of (C II) in the star-forming clouds implies that the (C II) emission arises on the surfaces of molecular clumps throughout the clouds, rather than only at the boundary layer between molecular gas and H II regions.

  8. BOOK REVIEW: Computational Atomic Structure

    NASA Astrophysics Data System (ADS)

    Post, Douglass E.

    1998-02-01

    The primary purpose of `Computational Atomic Structure' is to give a potential user of the Multi-Configuration Hartree-Fock (MCHF) Atomic Structure Package an outline of the physics and computational methods in the package, guidance on how to use the package, and information on how to interpret and use the computational results. The book is successful in all three aspects. In addition, the book provides a good overview and review of the physics of atomic structure that would be useful to the plasma physicist interested in refreshing his knowledge of atomic structure and quantum mechanics. While most of the subjects are covered in greater detail in other sources, the book is reasonably self-contained, and, in most cases, the reader can understand the basic material without recourse to other sources. The MCHF package is the standard package for computing atomic structure and wavefunctions for single or multielectron ions and atoms. It is available from a number of ftp sites. When the code was originally written in FORTRAN 77, it could only be run on large mainframes. With the advances in computer technology, the suite of codes can now be compiled and run on present day workstations and personal computers and is thus available for use by any physicist, even those with extremely modest computing resources. Sample calculations in interactive mode are included in the book to illustrate the input needed for the code, what types of results and information the code can produce, and whether the user has installed the code correctly. The user can also specify the calculational level, from simple Hartree-Fock to multiconfiguration Hartree-Fock. The MCHF method begins by finding approximate wavefunctions for the bound states of an atomic system. This involves minimizing the energy of the bound state using a variational technique. Once the wavefunctions have been determined, other atomic properties, such as the transition rates, can be determined. The book begins with an

  9. Structure of transcribing mammalian RNA polymerase II.

    PubMed

    Bernecky, Carrie; Herzog, Franz; Baumeister, Wolfgang; Plitzko, Jürgen M; Cramer, Patrick

    2016-01-28

    RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription. PMID:26789250

  10. Atomic structure of the sweet-tasting protein thaumatin I at pH 8.0 reveals the large disulfide-rich region in domain II to be sensitive to a pH change

    SciTech Connect

    Masuda, Tetsuya; Ohta, Keisuke; Mikami, Bunzo; Kitabatake, Naofumi; Tani, Fumito

    2012-03-02

    Highlights: Black-Right-Pointing-Pointer Structure of a recombinant thaumatin at pH 8.0 determined at a resolution of 1.0 A. Black-Right-Pointing-Pointer Substantial fluctuations of a loop in domain II was found in the structure at pH 8.0. Black-Right-Pointing-Pointer B-factors for Lys137, Lys163, and Lys187 were significantly affected by pH change. Black-Right-Pointing-Pointer An increase in mobility might play an important role in the heat-induced aggregation. -- Abstract: Thaumatin, an intensely sweet-tasting plant protein, elicits a sweet taste at 50 nM. Although the sweetness remains when thaumatin is heated at 80 Degree-Sign C for 4 h under acid conditions, it rapidly declines when heating at a pH above 6.5. To clarify the structural difference at high pH, the atomic structure of a recombinant thaumatin I at pH 8.0 was determined at a resolution of 1.0 A. Comparison to the crystal structure of thaumatin at pH 7.3 and 7.0 revealed the root-mean square deviation value of a C{alpha} atom to be substantially greater in the large disulfide-rich region of domain II, especially residues 154-164, suggesting that a loop region in domain II to be affected by solvent conditions. Furthermore, B-factors of Lys137, Lys163, and Lys187 were significantly affected by pH change, suggesting that a striking increase in the mobility of these lysine residues, which could facilitate a reaction with a free sulfhydryl residue produced via the {beta}-elimination of disulfide bonds by heating at a pH above 7.0. The increase in mobility of lysine residues as well as a loop region in domain II might play an important role in the heat-induced aggregation of thaumatin above pH 7.0.

  11. Agricultural Structures, Volume II.

    ERIC Educational Resources Information Center

    Linhardt, Richard E.; Burhoe, Steve

    This guide to a curriculum unit in agricultural structures is designed to expand the curriculum materials available in vocational agriculture in Missouri. It and Agricultural Structures I (see note) provide reference materials to systematize the curriculum. The six units cover working with concrete (19 lessons, 2 laboratory exercises), drawing and…

  12. Relativistic Configuration Interaction calculations of the atomic properties of selected transition metal positive ions; Ni II, V II and W II

    NASA Astrophysics Data System (ADS)

    Abdalmoneam, Marwa Hefny

    Relativistic Configuration Interaction (RCI) method has been used to investigate atomic properties of the singly ionized transition metals including Nickel (Ni II), Vanadium (V II), and Tungsten (W II). The methodology of RCI computations was also improved. Specifically, the method to shift the energy diagonal matrix of the reference configurations was modified which facilitated including the effects of many electronic configurations that used to be difficult to be included in the energy matrix and speeded-up the final calculations of the bound and continuum energy spectrum. RCI results were obtained for three different cases: i. Atomic moments and polarizabilities of Ni II; ii. Hyperfine structure constants of V II; iii. Lifetime, Lande g-values, and Oscillator strength of W II. Four atomic quantities of Ni II were calculated; scalar dipole polarizability, off-diagonal electric dipole polarizability, non-adiabatic scalar dipole polarizability, and quadrupole polarizability of Ni II. These quantities appear as effective parameters in an effective potential model. These quantities are computed for the first time. The two hyperfine structure (HFS) constants ; magnetic dipole interaction constant, A, and the electric quadrupole interaction constant, B, have been calculated for the V II 3d4, 3d3 4s, and 3d 2 4s2 J=1 to 5 even parity states . Analysis of the results shows the sum of HFS A of nearby energy levels to be conserved. The Lande g-value and the vector composition percentages for all the wavefunctions of those configurations have also been calculated. RCI results are in good agreement with most of the available experimental data. Lifetimes of 175 decay branches in W II have been calculated. Also, Lande g-values have been calculated for all measured W II odd parity levels J=1/2-11/2. The RCI oscillator strengths and branching fraction values of the lowest 10 energy levels for each odd parity J are presented. The calculated results are only in semi

  13. Infrared [Fe II] Emission Lines from Radiative Atomic Shocks

    NASA Astrophysics Data System (ADS)

    Koo, Bon-Chul; Raymond, John C.; Kim, Hyun-Jeong

    2016-06-01

    [Fe II] emission lines are prominent in the infrared (IR) and important as diagnostic tools for radiative atomic shocks. We investigate the emission characteristics of [Fe II] lines using a shock code developed by te{raymond1979} with updated atomic parameters. We first review general characteristics of the IR [Fe II] emission lines from shocked gas, and derive their fluxes as a function of shock speed and ambient density. We have compiled available IR [Fe II] line observations of interstellar shocks and compare them to the ratios predicted from our model. The sample includes both young and old supernova remnants in the Galaxy and the Large Magellanic Cloud and several Herbig-Haro objects. We find that the observed ratios of the IR [Fe II] lines generally fall on our grid of shock models, but the ratios of some mid-IR lines, e.g., fethreefive/fetwofive, fefive/fetwofive, and fefive/feoneseven, are significantly offset from our model grid. We discuss possible explanations and conclude that while uncertainties in the shock modeling and the observations certainly exist, the uncertainty in atomic rates appears to be the major source of discrepancy.

  14. Electrochemical Potential Derived from Atomic Cluster Structures.

    PubMed

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

    2016-02-01

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

  15. Some Experiments in Atomic Structure

    ERIC Educational Resources Information Center

    Logan, Kent R.

    1974-01-01

    The role of spectral color slides in laboratory situations is discussed, then experiments for secondary school students concerning color and wave length, evidence of quantization, and the ionization energy of the hydrogen atom are outlined. Teaching guidelines for creating a set of spectrograms and photographic specifications are provided. (DT)

  16. Structure and properties of a rapidly solidified Al-Li-Mn-Zr alloy for high-temperature applications: Part II. spray atomization and deposition processing

    NASA Astrophysics Data System (ADS)

    Baram, Joseph

    1991-10-01

    A new Al-Li alloy containing 2.3 wt pct Li, 6.5 wt pct Mn, and 0.65 wt pet Zr for high-temperature applications has been processed by a rapid solidification (RS) technique (as compacts by spray atomization and deposition) and then thermomechanically treated by hot extrusion. As-received and thermomechanically treated deposits were characterized by X-ray diffraction and scanning electron microscopy (SEM). Phase analyses in the as-processed materials revealed the presence of two Mn phases (Al4Mn and Al6Mn), one Zr phase (Al3Zr), two Li phases (the stable AlLi and the metastable Al3Li), and the aAl solid solution with high excess in Mn solubility (up to close the nominal composition in the as-atomized powders). As-deposited and extruded pieces were given heating treatments at 430 °C and 530 °C. A two-step aging treatment was practiced, to check for the optimal (for tensile properties) aging procedure, which was found to be the following: solutioning at 430 °C for 1 hour and water quenching + a first-step aging at 120 °C for 12 hours + a second-step aging at 175 °C for 15 hours. The mechanical properties, at room and elevated temperatures, of the hot extruded deposits are compared, following the optimal solutioning and aging treatments. The room-temperature (RT) strength of the proposed alloy is distinctly better for the as-deposited specimens (highest yield strength, 320 MPa) than for the as-atomized (highest yield strength, 215 MPa), though less than 65 pct of the RT strength is conserved at 250 °C. Ultimate strengths are quite comparable (in the 420 to 470 MPa range). Ductilities at RTs are in the low 1.5 to 2.5 pct range and show no improvement over other Al-Li alloys.

  17. Introduction to Atomic Structure: Demonstrations and Labs.

    ERIC Educational Resources Information Center

    Ciparick, Joseph D.

    1988-01-01

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

  18. About the atomic structures of icosahedral quasicrystals

    NASA Astrophysics Data System (ADS)

    Quiquandon, Marianne; Gratias, Denis

    2014-01-01

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

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

    SciTech Connect

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

    2007-01-01

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

  20. Structures and Properties of the Products of the Reaction of Lanthanide Atoms with H 2 O: Dominance of the +II Oxidation State

    DOE PAGESBeta

    Mikulas, Tanya C.; Chen, Mingyang; Fang, Zongtang; Peterson, Kirk A.; Andrews, Lester; Dixon, David A.

    2016-01-07

    We studied, lanthanides and H2O reactions using density functional theory with the B3LYP functional. H2O forms an initial Lewis acid-base complex with the lanthanides exothermically with interaction energies from -2 to -20 kcal/mol. For most of the Ln, formation of HLnOH is more exothermic than formation of H2LnO, HLnO + H, and LnOH + H. Moreover, the reactions to produce HLnOH are exothermic from -25 to -75 kcal/mol. The formation of LnO + H2 for La and Ce is slightly more exothermic than formation of HLnOH and is less or equally exothermic for the rest of the lanthanides. The Lnmore » in HLnOH and LnOH are in the formal +II and +I oxidation states, respectively. The Ln in H2LnO is mostly in the +III formal oxidation state with either Ln-O-/Ln-H- or Ln-(H2)-/Ln= O2- bonding interactions. A few of the H2LnO have the Ln in the +IV or mixed +III/+IV formal oxidation states with Ln=O2-/Ln-H- bonding interactions. The Ln in HLnO are generally in the +III oxidation state with the exception of Yb in the +II state. The orbital populations calculated within the natural bond orbital (NBO) analysis are consistent with the oxidation states and reaction energies. The more exothermic reactions to produce HLnOH are always associated with more backbonding from the O(H) and H characterized by more population in the 6s and 5d in Ln and the formation of a stronger Ln-O(H) bond. Overall, the calculations are consistent with the experiments in terms of reaction energies and vibrational frequencies.« less

  1. Structures and Properties of the Products of the Reaction of Lanthanide Atoms with H2O: Dominance of the +II Oxidation State.

    PubMed

    Mikulas, Tanya C; Chen, Mingyang; Fang, Zongtang; Peterson, Kirk A; Andrews, Lester; Dixon, David A

    2016-02-11

    The reactions of lanthanides with H2O have been studied using density functional theory with the B3LYP functional. H2O forms an initial Lewis acid-base complex with the lanthanides exothermically with interaction energies from -2 to -20 kcal/mol. For most of the Ln, formation of HLnOH is more exothermic than formation of H2LnO, HLnO + H, and LnOH + H. The reactions to produce HLnOH are exothermic from -25 to -75 kcal/mol. The formation of LnO + H2 for La and Ce is slightly more exothermic than formation of HLnOH and is less or equally exothermic for the rest of the lanthanides. The Ln in HLnOH and LnOH are in the formal +II and +I oxidation states, respectively. The Ln in H2LnO is mostly in the +III formal oxidation state with either Ln-O(-)/Ln-H(-) or Ln-(H2)(-)/Ln=O(2-) bonding interactions. A few of the H2LnO have the Ln in the +IV or mixed +III/+IV formal oxidation states with Ln=O(2-)/Ln-H(-) bonding interactions. The Ln in HLnO are generally in the +III oxidation state with the exception of Yb in the +II state. The orbital populations calculated within the natural bond orbital (NBO) analysis are consistent with the oxidation states and reaction energies. The more exothermic reactions to produce HLnOH are always associated with more backbonding from the O(H) and H characterized by more population in the 6s and 5d in Ln and the formation of a stronger Ln-O(H) bond. Overall, the calculations are consistent with the experiments in terms of reaction energies and vibrational frequencies. PMID:26741150

  2. Structural Variety of Cobalt(II), Nickel(II), Zinc(II), and Cadmium(II) Complexes with 4,4'-Azopyridine: Synthesis, Structure and Luminescence Properties.

    PubMed

    Pladzyk, Agnieszka; Ponikiewski, Łukasz; Dołęga, Anna; Słowy, Klaudia; Sokołowska, Agata; Dziubińska, Katarzyna; Hnatejko, Zbigniew

    2015-11-01

    Self-assembled bi- and polymetallic complexes of Co(II), Ni(II), Zn(II), and Cd(II) were obtained by the reaction of 4,4'-azopyridine (azpy) with metal tri-tert-butoxysilanethiolates (Co, 1; Cd, 2), acetylacetonates (Ni, 3; Zn, 4), and acetates (Cd, 5). All compounds were characterized by single-crystal X-ray structure analysis, elemental analysis, FTIR spectroscopy, and thermogravimetry. Complexes 1, 2 and 4, 5 exhibit diverse structural conformations: 1 is bimetallic, 2 and 4 are 1D coordination polymers, and 5 is a 2D coordination framework formed from bimetallic units. The obtained complexes contain metal atoms bridged by a molecule of azpy. The luminescent properties of 1-5 were investigated in the solid state. PMID:26178314

  3. Atomic vapor spectroscopy in integrated photonic structures

    SciTech Connect

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

    2015-07-27

    We investigate an integrated optical chip immersed in atomic vapor providing several waveguide geometries for spectroscopy applications. The narrow-band transmission through a silicon nitride waveguide and interferometer is altered when the guided light is coupled to a vapor of rubidium atoms via the evanescent tail of the waveguide mode. We use grating couplers to couple between the waveguide mode and the radiating wave, which allow for addressing arbitrary coupling positions on the chip surface. The evanescent atom-light interaction can be numerically simulated and shows excellent agreement with our experimental data. This work demonstrates a next step towards miniaturization and integration of alkali atom spectroscopy and provides a platform for further fundamental studies of complex waveguide structures.

  4. Atomic vapor spectroscopy in integrated photonic structures

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    We investigate an integrated optical chip immersed in atomic vapor providing several waveguide geometries for spectroscopy applications. The narrow-band transmission through a silicon nitride waveguide and interferometer is altered when the guided light is coupled to a vapor of rubidium atoms via the evanescent tail of the waveguide mode. We use grating couplers to couple between the waveguide mode and the radiating wave, which allow for addressing arbitrary coupling positions on the chip surface. The evanescent atom-light interaction can be numerically simulated and shows excellent agreement with our experimental data. This work demonstrates a next step towards miniaturization and integration of alkali atom spectroscopy and provides a platform for further fundamental studies of complex waveguide structures.

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

    DOE Data Explorer

    Cowan, R. D.

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

  6. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

    Robertson, Alex W; Lee, Gun-Do; He, Kuang; Gong, Chuncheng; Chen, Qu; Yoon, Euijoon; Kirkland, Angus I; Warner, Jamie H

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert. PMID:26524121

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

    PubMed

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

    2009-11-01

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

  8. Structural materials: understanding atomic scale microstructures

    SciTech Connect

    Marquis, E A; Miller, Michael K; Blavette, D; Ringer, S. P.; Sudbrack, C; Smith, G.D.W.

    2009-01-01

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

  9. Atomic structure of titania nanosheet with vacancies

    PubMed Central

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

    2013-01-01

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

  10. Measurement of isotope shifts and hyperfine structure in Zr II

    NASA Astrophysics Data System (ADS)

    Rosner, S. D.; Holt, R. A.

    2016-06-01

    We have applied fast-ion-beam laser-fluorescence spectroscopy to measure the isotope shifts (IS) of 51 optical transitions in the wavelength range 420.6–461.4 nm and the hyperfine structures (hfs) of 11 even parity and 30 odd parity levels in Zr II. The IS and many of the hfs measurements are the first for these transitions and levels. These atomic data are very important for astrophysical studies of chemical abundances, allowing correction for saturation and the effects of blended lines. They also provide important constraints on stellar diffusion modeling and provide a benchmark for theoretical atomic structure calculations.

  11. Crystal structure of rat carnitine palmitoyltransferase II (CPT-II)

    PubMed Central

    Hsiao, Yu-Shan; Jogl, Gerwald; Esser, Victoria; Tong, Liang

    2010-01-01

    Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the β-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Å resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria. PMID:16781677

  12. Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)

    SciTech Connect

    Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.

    2006-01-01

    Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.

  13. Atomic Structure of Ultrathin Gold Nanowires.

    PubMed

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

    2016-05-11

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

  14. Atomic Structure and Valence: Level II, Unit 10, Lesson 1; Chemical Bonding: Lesson 2; The Table of Elements: Lesson 3; Electrolysis: Lesson 4. Advanced General Education Program. A High School Self-Study Program.

    ERIC Educational Resources Information Center

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

    This self-study program for high-school level contains lessons on: Atomic Structure and Valence, Chemical Bonding, The Table of Elements, and Electrolysis. Each of the lessons concludes with a Mastery Test to be completed by the student. (DB)

  15. Crystal structure and encapsulation dynamics of ice II-structured neon hydrate.

    PubMed

    Yu, Xiaohui; Zhu, Jinlong; Du, Shiyu; Xu, Hongwu; Vogel, Sven C; Han, Jiantao; Germann, Timothy C; Zhang, Jianzhong; Jin, Changqing; Francisco, Joseph S; Zhao, Yusheng

    2014-07-22

    Neon hydrate was synthesized and studied by in situ neutron diffraction at 480 MPa and temperatures ranging from 260 to 70 K. For the first time to our knowledge, we demonstrate that neon atoms can be enclathrated in water molecules to form ice II-structured hydrates. The guest Ne atoms occupy the centers of D2O channels and have substantial freedom of movement owing to the lack of direct bonding between guest molecules and host lattices. Molecular dynamics simulation confirms that the resolved structure where Ne dissolved in ice II is thermodynamically stable at 480 MPa and 260 K. The density distributions indicate that the vibration of Ne atoms is mainly in planes perpendicular to D2O channels, whereas their distributions along the channels are further constrained by interactions between adjacent Ne atoms. PMID:25002464

  16. Crystal structure and encapsulation dynamics of ice II-structured neon hydrate

    PubMed Central

    Yu, Xiaohui; Zhu, Jinlong; Du, Shiyu; Xu, Hongwu; Vogel, Sven C.; Han, Jiantao; Germann, Timothy C.; Zhang, Jianzhong; Jin, Changqing; Francisco, Joseph S.; Zhao, Yusheng

    2014-01-01

    Neon hydrate was synthesized and studied by in situ neutron diffraction at 480 MPa and temperatures ranging from 260 to 70 K. For the first time to our knowledge, we demonstrate that neon atoms can be enclathrated in water molecules to form ice II-structured hydrates. The guest Ne atoms occupy the centers of D2O channels and have substantial freedom of movement owing to the lack of direct bonding between guest molecules and host lattices. Molecular dynamics simulation confirms that the resolved structure where Ne dissolved in ice II is thermodynamically stable at 480 MPa and 260 K. The density distributions indicate that the vibration of Ne atoms is mainly in planes perpendicular to D2O channels, whereas their distributions along the channels are further constrained by interactions between adjacent Ne atoms. PMID:25002464

  17. Nitridation of Si(111) by nitrogen atoms. II

    NASA Technical Reports Server (NTRS)

    Schrott, A. G.; Fain, S. C., Jr.

    1982-01-01

    The reaction between Si(111) and nitrogen atoms has been investigated by LEED, Auger, and electron energy loss (ELS) techniques. The early stage of the reaction at 850-1050 C involves the formation of a chemically reacted monolayer which grows in islands. The sticking coefficient for the submonolayer is estimated to be of the order of unity. Two electronically different surface structures can be formed during these stages, yielding the '8 x 8' and the quadruplet LEED patterns; the quadruplet unit cell is the one with the highest nitrogen density. A pure quadruplet structure is obtained from samples with a carbon contamination of the Si monolayer of about 5 pct. During the multilayer stages, the influence of the substrate is not as important, and the reactions at 850 C and above produce quadruplet-like local structures.

  18. Atomic layer deposition of rutile and TiO2-II from TiCl4 and O3 on sapphire: Influence of substrate orientation on thin film structure

    NASA Astrophysics Data System (ADS)

    Möldre, Kristel; Aarik, Lauri; Mändar, Hugo; Niilisk, Ahti; Rammula, Raul; Tarre, Aivar; Aarik, Jaan

    2015-10-01

    Atomic layer deposition of TiO2 from TiCl4 and ozone on single crystal α-Al2O3 substrates was investigated and the possibility to control the phase composition by the substrate orientation was demonstrated. Epitaxial growth of rutile and high-pressure TiO2-II on α-Al2O3(0 0 0 1) and rutile on α-Al2O3(0 1 1¯ 2) were obtained at 400-600 °C. On α-Al2O3(0 0 0 1), the epitaxial relationships were determined to be [0 1 0]R // [2 1¯ 1¯ 0]S and [0 0 1]R // [0 1 1¯ 0]S for rutile and sapphire, and [0 0 1]II // [2 1¯ 1¯ 0]S and [0 1¯ 0]II // [0 1 1¯ 0]S for TiO2-II and sapphire. The TiO2-II concentration up to 50% was obtained in the films deposited at 425-500 °C. On α-Al2O3(0 1 1¯ 2), the epitaxial relationship of rutile was [0 1 0]R // [2 1¯ 1¯ 0]S and [0 0 1]R // [0 1 1¯ 0]S. The densities of epitaxial films reached 4.2-4.3 g/cm3 on substrates with both orientations but the epitaxial quality was markedly higher on α-Al2O3(0 0 0 1).

  19. Crystal structures of copper(II) nitrate, copper(II) chloride, and copper(II) perchlorate complexes with 2-formylpyridine semicarbazone

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Antosyak, B. Ya.; Bairac, N. N.; Simonov, Yu. A.; Bocelli, G.; Pahontu, E.; Gulea, A. P.

    2009-05-15

    Compounds dinitrato(2-formylpyridinesemicarbazone)copper (I), dichloro(2-formylpyridinesemicarbazone) copper hemihydrate (II), and bis(2-formylpyridinesemicarbazone)copper(2+) perchlorate hydrate (III) are synthesized and their crystal structures are determined. In compounds I-III, the neutral 2-formylpyridine semicarbazone molecule (L) is tridentately attached to the copper atom via the N,N,O set of donor atoms. In compounds I and II, the Cu: L ratio is equal to 1: 1, whereas, in III, it is 1: 2. In complex I, the coordination sphere of the copper atom includes two nitrate ions with different structural functions in addition to the L ligand. The structure is built as a one-dimensional polymer in which the NO{sub 3} bidentate group fulfills a bridging function. The coordination polyhedron of the copper(2+) atom can be considered a distorted tetragonal bipyramid (4 + 1 + 1). Compound II has an ionic structure in which the main element is the [CuLCl{sub 2} . Cu(H{sub 2}O)LCl]{sup +} dimer. In the dimer, the copper atoms are linked via one of the {mu}{sub 2}-bridging chlorine atoms. The coordination polyhedra of the central atoms of the Cu(H{sub 2})LCl and CuLCl{sub 2} complex fragments are tetragonal bipyramid and tetragonal pyramid, respectively. In compound III, the copper atom is octahedrally surrounded by two L ligands in the mer configuration.

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

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

  1. Synthesis, structural characterization, thermal and electrochemical studies of Mn(II), Co(II), Ni(II) and Cu(II) complexes containing thiazolylazo ligands

    NASA Astrophysics Data System (ADS)

    Chavan, S. S.; Sawant, V. A.

    2010-02-01

    Some thiazolylazo derivatives and their metal complexes of the type [M(L)(H 2O)Cl]; M = Mn(II), Co(II), Ni(II), Cu(II) and L = 6-(2'-thiazolylazo)-2-mercapto-quinazolin-4-one (HL 1), 6-(4'-phenyl-2'-thiazolylazo)-2-mercapto-quinazolin-4-one (HL 2), 6-(2'-thiazolylazo)-2-mercapto-3-( m-tolyl)-quinazolin-4-one (HL 3) and 6-(4'-phenyl-2'-thiazolylazo)-2-mercapto-3-( m-tolyl)-quinazolin-4-one (HL 4) have been prepared. All the complexes were characterized on the basis of elemental analysis, molar conductance, magnetic moment, IR, UV-vis, ESR, TG-DTA and powder X-ray diffraction studies. IR spectra of these complexes reveal that the complex formation occurred through thiazole nitrogen, azo nitrogen, imino nitrogen and sulfur atom of the ligands. On the basis of electronic spectral data and magnetic susceptibility measurement octahedral geometry has been proposed for the Mn(II), Co(II) and Ni(II) complexes and distorted octahedral geometry for the Cu(II) complexes. Electrochemical behavior of Ni(II) complexes exhibit quasireversible oxidation corresponding to Ni(III)/Ni(II) couple along with ligand reduction. X-ray diffraction study is used to elucidate the crystal structure of the complexes.

  2. Atomic effects in tritium beta-decay. II. Muon to electron conversion in atoms

    SciTech Connect

    Wampler, K.D.

    1989-01-01

    I. The final-state, atomic effects in the low energy end of the tritium beta decay spectrum are studied in detail. The author treats the instantaneous, two-electron repulsion in the final state, effectively to all orders in perturbation theory, by solving the eigenvalue problem with a discretized and truncated form of the Hamiltonian. He finds that these effects fail to explain the distortion in the spectrum observed by Simpson (Phys. Rev. Lett. 54, 649 (1985)). Simpson attributed this distortion to the admixture of a heavy mass antineutrino in the outgoing electron antineutrino state. In fact, the final-state Coulomb effects enhance the distortion. This calculation clears up some of the ambiguities of other theoretical analyses based on considerations of screening functions and perturbation theory. II. He presents a phenomenological study of separate lepton number violating muon to electron conversion in atoms. Previous work on this process has concentrated on elastic transitions where the nucleus characteristics have the gate on the substrate and the source-drain contacts on the top of the sample. The first use as an FET dielectric is reported of hydrogenated amorphous silicon-carbon (prepared from silane and propane mixture), photo-oxidised by UV lamp or laser. These FETs have similar characteristics to those with silicon nitride gate insulator but without the difficulties of preparing good insulator/semiconductor interfaces. Using the same materials attempts have been made to produce charge coupled devices.

  3. Atomic structures and compositions of internal interfaces

    SciTech Connect

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

    1992-03-01

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

  4. Structural studies on photosystem II of cyanobacteria.

    PubMed

    Gabdulkhakov, A G; Dontsova, M V

    2013-12-01

    Photosynthesis is one of the most important chemical processes in the biosphere responsible for the maintenance of life on Earth. Light energy is converted into energy of chemical bonds in photoreaction centers, which, in particular, include photosystem II (PS II). PS II is a multisubunit pigment-protein complex located in the thylakoid membrane of cyanobacteria, algae and plants. PS II realizes the first stage of solar energy conversion that results in decomposition of water to molecular oxygen, protons, and bound electrons via a series of consecutive reactions. During recent years, considerable progress has been achieved in determination of the spatial structures of PS II from various cyanobacteria. In the present review, we outline the current state of crystallographic studies on PS II. PMID:24490738

  5. Evolution of atomic structure during nanoparticle formation

    PubMed Central

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

    2014-01-01

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

  6. Evolution of atomic structure during nanoparticle formation.

    PubMed

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

    2014-05-01

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

  7. Crystal structure of ammonia dihydrate II.

    PubMed

    Griffiths, Gareth I G; Fortes, A Dominic; Pickard, Chris J; Needs, R J

    2012-05-01

    We have used density-functional-theory (DFT) methods together with a structure searching algorithm to make an experimentally constrained prediction of the structure of ammonia dihydrate II (ADH-II). The DFT structure is in good agreement with neutron diffraction data and verifies the prediction. The structure consists of the same basic structural elements as ADH-I, with a modest alteration to the packing, but a considerable reduction in volume. The phase diagram of the known ADH and ammonia monohydrate + water-ice structures is calculated with the Perdew-Burke-Ernzerhof density functional, and the effects of a semi-empirical dispersion corrected functional are investigated. The results of our DFT calculations of the finite-pressure elastic constants of ADH-II are compared with the available experimental data for the elastic strain coefficients. PMID:22583254

  8. Synthesis and crystal structure of thiosemicarbazide complexes of nickel(II) and copper(II)

    NASA Astrophysics Data System (ADS)

    Sadikov, G. G.; Antsyshkina, A. S.; Koksharova, T. V.; Sergienko, V. S.; Kurando, S. V.; Gritsenko, I. S.

    2012-07-01

    Thiosemicarbazide complexes of nickel(II) [Ni( TSC)2](H Sal)2 ( I) and copper(II) [Cu( TSC)2](H Sal)2 ( Ia) ( TSC is thiosemicarbazide and H Sal is a salycilate anion), as well as complexes [Ni( TSC)2](SO4) · 2H2O ( II) and [Ni( TSC)3]Cl2 · H2O ( III), are synthesized and characterized by IR spectroscopy and X-ray diffraction. Monoclinic crystals I and Ia are isostructural; space group P21/ n, Z = 2. Crystals II are monoclinic, space group P21/ m, Z = 2. Crystals III are orthorhombic, space group Pbca, Z = 8. In I and Ia, two planar salycilate anions sandwich a planar centrosymmetric [Ni( TSC)2]2+ cation to form a supermolecule. The cation and anions are additionally bound by hydrogen bonds. Other hydrogen bonds connect supermolecules into planar layers. In structure II, centrosymmetric [Ni( TSC)2]2+ cations are connected by π-stacking interactions into supramolecular ensembles of a specific type. The ensembles, water molecules, and (SO4)2- anions are bound in the crystal via hydrogen bonds. In the [Ni( TSC)3]2+ cation of structure III, ligands coordinate the Ni atom by the bidentate chelate pattern with the formation of five-membered metallocycles. These metallocycles have an envelope conformation unlike those in I and II, which are planar. In III (unlike in analogous complexes), a meridional isomer of the coordination octahedron of the Ni atom is formed. Together with Cl1- and Cl2- anions, cations form supermolecules, which are packed into planar layers with a square-cellular structure. The layers are linked by hydrogen bonds formed by crystallization water molecules that are located between the layers.

  9. Structurally uniform and atomically precise carbon nanostructures

    NASA Astrophysics Data System (ADS)

    Segawa, Yasutomo; Ito, Hideto; Itami, Kenichiro

    2016-01-01

    Nanometre-sized carbon materials consisting of benzene units oriented in unique geometric patterns, hereafter named nanocarbons, conduct electricity, absorb and emit light, and exhibit interesting magnetic properties. Spherical fullerene C60, cylindrical carbon nanotubes and sheet-like graphene are representative forms of nanocarbons, and theoretical simulations have predicted several exotic 3D nanocarbon structures. At present, synthetic routes to nanocarbons mainly lead to mixtures of molecules with a range of different structures and properties, which cannot be easily separated or refined into pure forms. Some researchers believe that it is impossible to synthesize these materials in a precise manner. Obtaining ‘pure’ nanocarbons is a great challenge in the field of nanocarbon science, and the construction of structurally uniform nanocarbons, ideally as single molecules, is crucial for the development of functional materials in nanotechnology, electronics, optics and biomedical applications. This Review highlights the organic chemistry approach — more specifically, bottom-up construction with atomic precision — that is currently the most promising strategy towards this end.

  10. MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES

    SciTech Connect

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

    2000-09-01

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

  11. Atomic vapor spectroscopy in integrated photonic structures

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    We investigate an integrated optical chip immersed in atomic vapor providing several waveguide geometries for spectroscopy applications. This includes integrated ring resonators, Mach Zehnder interferometers, slot waveguides and counterpropagating coupling schemes. The narrow-band transmission through a silicon nitride waveguide and interferometer is altered when the guided light is coupled to a vapor of rubidium atoms via the evanescent tail of the waveguide mode. We use grating couplers to couple between the waveguide mode and the radiating wave, which allow for addressing arbitrary coupling positions on the chip surface. The evanescent atom-light interaction can be numerically simulated and shows excellent agreement with our experimental data. This work demonstrates a next step towards miniaturization and integration of alkali atom spectroscopy and provides a platform for further fundamental studies of strong atom light coupling. Cooperativities on the order of 1 are within reach.

  12. Role Playing: The Atomic Bomb and the End of World War II

    ERIC Educational Resources Information Center

    Eggleston, Noel C.

    1978-01-01

    Describes how a role playing exercise can be used to teach students in a college level history course about the use of the atomic bomb in World War II. Information is presented on general use of role playing in history courses, objectives, questions to consider about use of the atomic bomb, and course evaluation. For journal availability, see so…

  13. The Last Act: The Atomic Bomb and the End of World War II.

    ERIC Educational Resources Information Center

    Smithsonian Institution, Washington, DC. National Air And Space Museum.

    This text was to have been the script for the National Air and Space Museum's exhibition of the Enola Gay, focusing on the end of World War II and the decision of the United States to use of the atomic bomb. The Enola Gay was a B-29 aircraft that carried the atomic bomb dropped on Hiroshima, Japan, on August 6, 1945. The atomic bomb brought a…

  14. Atomic data from the IRON Project. IX. Electron excitation of the ^2^P^0^_3/2_-^2^P^0^_1/2_ fine-structure transition in chlorine-like ions, from AR II to NI XII.

    NASA Astrophysics Data System (ADS)

    Pelan, J.; Berrington, K. A.

    1995-04-01

    Calculated effective collision strengths for the ground term fine-structure transitions of 11 chlorine-like ions (17 electrons) from Ar II to Ni XII are presented. There is currently very little published data for this sequence and so there is a strong motivation to satisfy the need for this information and to improve upon the accuracy of previous work where it does exist. The data are calculated using R-matrix techniques and are provided over a temperature range from 10^3^K up to 10^7^K over which the target models should be valid. Accuracy for the effective collision strengths is in the region of 10%. An independent calculation on Fex recently published by Mohan et al. (ApJ 434, 389) is shown to be wrong for this transition because of their omission of important low-energy contributions.

  15. A Variational Monte Carlo Approach to Atomic Structure

    ERIC Educational Resources Information Center

    Davis, Stephen L.

    2007-01-01

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

  16. Quantum Theory of Atomic and Molecular Structures and Interactions

    NASA Astrophysics Data System (ADS)

    Makrides, Constantinos

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

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

    PubMed

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

    2010-03-25

    Direct imaging and chemical identification of all the atoms in a material with unknown three-dimensional structure would constitute a very powerful general analysis tool. Transmission electron microscopy should in principle be able to fulfil this role, as many scientists including Feynman realized early on. It images matter with electrons that scatter strongly from individual atoms and whose wavelengths are about 50 times smaller than an atom. Recently the technique has advanced greatly owing to the introduction of aberration-corrected optics. However, neither electron microscopy nor any other experimental technique has yet been able to resolve and identify all the atoms in a non-periodic material consisting of several atomic species. Here we show that annular dark-field imaging in an aberration-corrected scanning transmission electron microscope optimized for low voltage operation can resolve and identify the chemical type of every atom in monolayer hexagonal boron nitride that contains substitutional defects. Three types of atomic substitutions were found and identified: carbon substituting for boron, carbon substituting for nitrogen, and oxygen substituting for nitrogen. The substitutions caused in-plane distortions in the boron nitride monolayer of about 0.1 A magnitude, which were directly resolved, and verified by density functional theory calculations. The results demonstrate that atom-by-atom structural and chemical analysis of all radiation-damage-resistant atoms present in, and on top of, ultra-thin sheets has now become possible. PMID:20336141

  18. Crystal structures of copper(II) chloride, copper(II) bromide, and copper(II) nitrate complexes with pyridine-2-carbaldehyde thiosemicarbazone

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Jeanneau, E.; Bairac, N. N.; Bocelli, G.; Poirier, D.; Roy, J.; Gulea, A. P.

    2008-09-15

    The crystal structures of chloro-(2-formylpyridinethiosemicarbazono)copper dimethyl sulfoxide solvate (I), bromo-(2-formylpyridinethiosemicarbazono)copper (II), and (2-formylpyridinethiosemicarbazono)copper(II) nitrate dimethyl sulfoxide solvate (III) are determined using X-ray diffraction. In the crystals, complexes I and II form centrosymmetric dimers in which the thiosemicarbazone sulfur atom serves as a bridge and occupies the fifth coordination site of the copper atom of the neighboring complex related to the initial complex through the center of symmetry. In both cases, the coordination polyhedron of the complexing ion is a distorted tetragonal bipyramid. Complex III in the crystal structure forms polymer chains in which the copper atom of one complex forms the coordination bond with the thicarbamide nitrogen atom of the neighboring complex. In this structure, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid. It is established that complexes I-III at a concentration of 10{sup -5} mol/l selectively inhibit the growth of 60 to 90 percent of the cancer tumor cells of the human myeloid leukemia (HL-60).

  19. Crystal structures of copper(II) chloride, copper(II) bromide, and copper(II) nitrate complexes with pyridine-2-carbaldehyde thiosemicarbazone

    NASA Astrophysics Data System (ADS)

    Chumakov, Yu. M.; Tsapkov, V. I.; Jeanneau, E.; Bairac, N. N.; Bocelli, G.; Poirier, D.; Roy, J.; Gulea, A. P.

    2008-09-01

    The crystal structures of chloro-(2-formylpyridinethiosemicarbazono)copper dimethyl sulfoxide solvate ( I), bromo-(2-formylpyridinethiosemicarbazono)copper ( II), and (2-formylpyridinethiosemicarbazono)copper(II) nitrate dimethyl sulfoxide solvate ( III) are determined using X-ray diffraction. In the crystals, complexes I and II form centrosymmetric dimers in which the thiosemicarbazone sulfur atom serves as a bridge and occupies the fifth coordination site of the copper atom of the neighboring complex related to the initial complex through the center of symmetry. In both cases, the coordination polyhedron of the complexing ion is a distorted tetragonal bipyramid. Complex III in the crystal structure forms polymer chains in which the copper atom of one complex forms the coordination bond with the thicarbamide nitrogen atom of the neighboring complex. In this structure, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid. It is established that complexes I III at a concentration of 10-5 mol/l selectively inhibit the growth of 60 to 90 percent of the cancer tumor cells of the human myeloid leukemia (HL-60).

  20. Structural characterization of some oxalato-bridged copper(II) and nickel(II) complexes

    NASA Astrophysics Data System (ADS)

    Mautner, Franz A.; Louka, Febee R.; Massoud, Salah S.

    2009-03-01

    A new series of dinuclear oxalato-bridged copper(II) and nickel(II) complexes derived from tridentate amines: [Cu 2(Medpt) 2(μ-C 2O 4)](ClO 4) 2 ( 1), [Cu 2(pmedien) 2(μ-C 2O 4)](ClO 4) 2 ( 2), [Cu 2(DPA) 2(μ-C 2O 4)(ClO 4) 2]·2H 2O (3), and [Ni 2(Et 2dien) 2(μ-C 2O 4)(H 2O) 2](ClO 4) 2·2H 2O ( 4) (C 2O 42- = oxalate dianion, Medpt = 3,3'-diamino- N-methyldipropylmine, pmedien = N, N, N', N'', N''-pentamethyldiethylenetriamine, DPA = di(2-pyridylmethyl)amine and Et 2dien = N, N-diethyldiethylenetriamine) were synthesized and structurally characterized by X-ray crystallography. The spectral and structural characterizations of these complexes are reported. In this series, structures consist of the C 2O 42- bridging the two M(II) centers in a bis-bidentate bonding mode. The Cu 2+ centers are coordinated to the tridentate amines Medpt or pmedien in distorted SP geometry in 1 and 2, respectively, with the ClO 4- groups as counter ions. In the other two complexes, distorted octahedral geometries were achieved by the three nitrogen donors of the DPA and by an oxygen atom from coordinated perchlorate ion in 3 and by the Et 2dien and one water molecule in 4.

  1. Probing Atomic Dynamics and Structures Using Optical Patterns

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2015-05-01

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

  2. Smart structures for rotorcraft control (SSRC) II

    NASA Astrophysics Data System (ADS)

    Jacot, A. Dean; Dadone, Leo

    1998-06-01

    The Smart Structures for Rotor Control (SSRC) is a consortium under the Defense Advanced Research Projects Agency (DARPA) Smart Structures program. Phase I of the program was administered by the Air Force Office of Scientific Research, with Boeing Seattle as the consortium administrator, and MIT, PSU and Boeing Helicopters as the other principal consortium members. Phase II, renamed Smart Materials and Structures Demonstration Consortium (SMSDC), is a combination of the proposed Phase II efforts of SSRC and the Boeing MESA Smart Materials Actuated Rotor Technology (SMART) program. This paper summarizes the SSRC efforts, introduces the SMSDC program, and provides a framework for the relationships between specific SSRC technical papers in this conference. The SSRC objectives were to research smart structure methods to achieve reduced rotorcraft vibration, reduce acoustic noise, and increased performance. The SSRC program includes dynamic piezoelectric actuation of flaps on the rotor blades, distributed dynamic piezo actuation of the rotor twist, and quasi-steady rotor twist control using shape memory alloys. The objective of Phase II is then to fly a rotorcraft to demonstrate such a system.

  3. Atomic scale interface structure in metallic superlattices

    NASA Astrophysics Data System (ADS)

    Uzdin, V. M.; Keune, W.

    2007-04-01

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

  4. Structure of an RNA polymerase II preinitiation complex

    PubMed Central

    Murakami, Kenji; Tsai, Kuang-Lei; Kalisman, Nir; Bushnell, David A.; Asturias, Francisco J.; Kornberg, Roger D.

    2015-01-01

    The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6–11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein–protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription. PMID:26483468

  5. Structure of an RNA polymerase II preinitiation complex.

    PubMed

    Murakami, Kenji; Tsai, Kuang-Lei; Kalisman, Nir; Bushnell, David A; Asturias, Francisco J; Kornberg, Roger D

    2015-11-01

    The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription. PMID:26483468

  6. Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures

    USGS Publications Warehouse

    Dowty, Eric; Clark, J.R.

    1972-01-01

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

  7. Crystal structures of salicylideneguanylhydrazinium chloride and its copper(II) and cobalt(III) chloride complexes

    SciTech Connect

    Chumakov, Yu. M. Tsapkov, V. I.; Bocelli, G.; Antosyak, B. Ya.; Shova, S. G.; Gulea, A. P.

    2006-01-15

    The crystal structures of salicylideneguanylhydrazinium chloride hydrate hemiethanol solvate (I), salicylideneguanylhydrazinium trichloroaquacuprate(II) (II), and bis(salicylideneguanylhydrazino)cobalt(III) chloride trihydrate (III) are determined using X-ray diffraction. The structures of compounds I, II, and III are solved by direct methods and refined using the least-squares procedure in the anisotropic approximation for the non-hydrogen atoms to the final factors R = 0.0597, 0.0212, and 0.0283, respectively. In the structure of compound I, the monoprotonated molecules and chlorine ions linked by hydrogen bonds form layers aligned parallel to the (010) plane. In the structure of compound II, the salicylaldehyde guanylhydrazone cations and polymer chains consisting of trichloroaquacuprate(II) anions are joined by an extended three-dimensional network of hydrogen bonds. In the structure of compound III, the [Co(LH){sub 2}]{sup +} cations, chloride ions, and molecules of crystallization water are linked together by a similar network.

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

    SciTech Connect

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

    1996-09-01

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

  9. Atomic Structure of Au 329 (SR) 84 Faradaurate Plasmonic Nanomolecules

    SciTech Connect

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

    2015-05-21

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

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

    DOE PAGESBeta

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

    2015-04-03

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

  11. Tetrabromidocuprates(II)-Synthesis, Structure and EPR.

    PubMed

    Zabel, André; Winter, Alette; Kelling, Alexandra; Schilde, Uwe; Strauch, Peter

    2016-01-01

    Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several "onium" cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g‖ and g⊥) of the tensors could be determined and information on the structural changes in the [CuBr₄](2-) anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids. PMID:27104522

  12. Presentation of Atomic Structure in Turkish General Chemistry Textbooks

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Costu, Bayram

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  14. Structures of 38-atom gold-platinum nanoalloy clusters

    SciTech Connect

    Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atoms are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.

  15. Graphene mechanics: II. Atomic stress distribution during indentation until rupture.

    PubMed

    Costescu, Bogdan I; Gräter, Frauke

    2014-06-28

    Previous Atomic Force Microscopy (AFM) experiments found single layers of defect-free graphene to rupture at unexpectedly high loads in the micronewton range. Using molecular dynamics simulations, we modeled an AFM spherical tip pressing on a circular graphene sheet and studied the stress distribution during the indentation process until rupture. We found the graphene rupture force to have no dependency on the sheet size and a very weak dependency on the indenter velocity, allowing a direct comparison to experiment. The deformation showed a non-linear elastic behavior, with a two-dimensional elastic modulus in good agreement with previous experimental and computational studies. In line with theoretical predictions for linearly elastic sheets, rupture forces of non-linearly elastic graphene are proportional to the tip radius. However, as a deviation from the theory, the atomic stress concentrates under the indenter tip more strongly than predicted and causes a high probability of bond breaking only in this area. In turn, stress levels decrease rapidly towards the edge of the sheet, most of which thus only serves the role of mechanical support for the region under the indenter. As a consequence, the high ratio between graphene sheets and sphere radii, hitherto supposed to be necessary for reliable deformation and rupture studies, could be reduced to a factor of only 5-10 without affecting the outcome. Our study suggests time-resolved analysis of forces at the atomic level as a valuable tool to predict and interpret the nano-scale response of stressed materials beyond graphene. PMID:24834440

  16. Wavelengths, energy levels and hyperfine structure of Mn II and Sc II.

    NASA Astrophysics Data System (ADS)

    Nave, Gillian; Pickering, Juliet C.; Townley-Smith, Keeley I. M.; Hala, .

    2015-08-01

    For many decades, the Atomic Spectroscopy Groups at the National Institute of Standards and Technology (NIST) and Imperial College London (ICL) have measured atomic data of astronomical interest. Our spectrometers include Fourier transform (FT) spectrometers at NIST and ICL covering the region 1350 Å to 5.5 μm and a 10.7-m grating spectrometer at NIST covering wavelengths from 300 - 5000 Å. Sources for these spectra include high-current continuous and pulsed hollow cathode (HCL) lamps, Penning discharges, and sliding spark discharges. Recent work has focused on the measurement and analysis of wavelengths, energy levels, and hyperfine structure (HFS) constants for iron-group elements. The analysis of FT spectra of Cr I, Mn I, and Mn II is being led by ICL and is described in a companion poster [1]. Current work being led by NIST includes the analysis of HFS in Mn II, analysis of Mn II in the vacuum ultraviolet, and a comprehensive analysis of Sc II.Comprehensive HFS constants for Mn II are needed for the interpretation of stellar spectra and incorrect abundances may be obtained when HFS is omitted. Holt et al. [2] have measured HFS constants for 59 levels of Mn II using laser spectroscopy. We used FT spectra of Mn/Ni and Mn/Cu HCLs covering wavelength ranges from 1350 Å to 5.4 μm to confirm 26 of the A constants of Holt et al. and obtain values for roughly 40 additional levels. We aim to obtain HFS constants for the majority of lines showing significant HFS that are observed in chemically-peculiar stars.Spectra of Sc HCLs have been recorded from 1800 - 6700 Å using a vacuum ultraviolet FT spectrometer at NIST. Additional measurements to cover wavelengths above 6700 Å and below 1800 Å are in progress. The spectra are being analyzed by NIST and Alighar Muslim University, India in order to derive improved wavelengths, energy levels, and hyperfine structure parameters.This work was partially supported by NASA, the STFC and PPARC (UK), the Royal Society of the UK

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

    ERIC Educational Resources Information Center

    Eilks, Ingo; Leerhoff, Gabriele

    2001-01-01

    Discusses an approach to teaching the structure of atoms using a teaching technique referred to as a jigsaw classroom. Reports that the jigsaw classroom involves arranging students in various types of groups for cooperative learning. (Author/MM)

  18. Quantum dynamics of hydrogen atoms on graphene. II. Sticking

    SciTech Connect

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene

    2015-09-28

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  19. Two experiments with cold atoms: I. Application of Bessel beams for atom optics, and II. Spectroscopic measurements of Rydberg blockade effect

    NASA Astrophysics Data System (ADS)

    Arakelyan, Ilya

    In this dissertation we report the results of two experimental projects with laser-cooled rubidium atoms: I. Application of Bessel beams for atom optics, and II. Spectroscopic measurements of Rydberg blockade effect. The first part of the thesis is devoted to the development of new elements of atom optics based on blue-detuned high-order Bessel beams. Properties of a 4thorder Bessel beam as an atomic guide were investigated for various parameters of the hollow beam, such as the detuning from an atomic resonance, size and the order of the Bessel beam. We extended its application to create more complicated interferometer-type structures by demonstrating a tunnel lock, a novel device that can split an atomic cloud, transport it, delay, and switch its propagation direction between two guides. We reported a first-time demonstration of an atomic beam switch based on the combination of two crossed Bessel beams. We achieved the 30% efficiency of the switch limited by the geometrical overlap between the cloud and the intersection volume of the two tunnels, and investigate the heating processes induced by the switch. We also showed other applications of crossed Bessel beams, such as a 3-D optical trap for atoms confined in the intersection volume of two hollow beams and a splitter of the atomic density. The second part of this dissertation is devoted to the spectroscopic measurements of the Rydberg blockade effect, a conditional suppression of Rydberg excitations depending on the state of a control atom. We assembled a narrow-linewidth, tunable, frequency stabilized laser system at 480 nm to excite laser-cooled rubidium atoms to Rydberg states with a high principal quantum number n ˜ 50 through a two-photon transition. We applied the laser system to observe the Autler-Townes splitting of the intermediate 5p3/2 state and used the broadening of the resonance features to investigate the enhancement of Rydberg-Rydberg interactions in the presence of an external electric field.

  20. Novel diffusions of interstitial atoms in II-VI compounds zinc selenide

    NASA Astrophysics Data System (ADS)

    Chen, Li An; Jiang, En Hai; Zhu, Xing Feng; Chen, Ling Fu

    2015-04-01

    The diffusion plays an important role in many applications when the impurities are employed to tune the semiconductor's electrical or optical properties, which make it essential to understand theoretically the microscopic mechanisms governing how dopant defects diffuse. Using first-principles calculations, we compare the diffusion behaviors and migration barriers of interstitial Cu, Ag, and Au atoms in II-VI compounds ZnSe. We consider interstitial diffusion mechanisms and calculate the corresponding activation energies. For noble atoms, we find that the interstitial mediated mechanism is the dominant one. We also find that the relative size of dopant atoms and constituent atoms of II-VI compounds is an important factor affecting the diffusion behaviors. The coupling in ZnSe between Cu d levels and unoccupied host s levels is not as strong as that in CdTe.

  1. Atomic structure of highly-charged ions. Final report

    SciTech Connect

    Livingston, A. Eugene

    2002-05-23

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

  2. Synthesis, structure and fluorescence properties of a novel 3D Sr(II) coordination polymer

    NASA Astrophysics Data System (ADS)

    Tan, Yu-Hui; Xu, Qing; Gu, Zhi-Feng; Gao, Ji-Xing; Wang, Bin; Liu, Yi; Yang, Chang-Shan; Tang, Yun-Zhi

    2016-09-01

    Solvothermal reaction of 2,2‧-bipyridine-5,5‧-dicarboxylic acid (H2bpdc) and SrCl2 affords a novel coordination polymer [Sr(Hbpdc)2]n1. X-ray structure determination shows that 1 exhibits a novel three-dimensional network. The unique Sr II cation sits on a two-fold axis and coordinated by four O-atom donors from four Hbptc- ligands and four N-atom donors from two Hbptc- ligands in distorted dodecahedral geometry. In 1 each Sr II cation connects to six different Hbptc- ligands and each Hbptc- ligand bridges three different Sr II cations which results in the formation of a three-dimensional polymeric structure. Corresponding to the free ligand, the fluorescent emission of complex 1 display remarkable "Einstain" shifts, which may be attributed to the coordination interaction of Sr atoms, thus reduce the rigidity of pyridyl rings.

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

    PubMed

    Hendrickson, Wayne A

    2016-06-01

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

  4. Synthesis and crystal structure of three mixed-ligand copper(II) complexes with nitrilotriacetic acid

    SciTech Connect

    Polyakova, I. N. Sergienko, V. S.; Poznyak, A. L.

    2006-05-15

    The synthesis and X-ray diffraction study of three Ca[CuX(Nta)] . 2H{sub 2}O complexes, where X = Cl (I) or Br (II and III are the monoclinic and orthorhombic modifications, respectively), are performed. Structures I-III are built of [CuX(Nta)]{sup 2-} anionic complexes and hydrated Ca{sup 2+} cations, which are linked by Ca-O bonds into a three-dimensional framework. In I-III, the coordination of the Cu atom includes the N atom and three O atoms of the tetradentate chelate Nta{sup 3-} ligand and the X{sup -} anion in the trans position with respect to N. The Cu-O bond lengths vary in the ranges 1.971-2.268 A in I, 1.958-2.289 A in II, and 2.040-2.110 A in III. The Cu-X bond lengths are 2.223, 2.364, and 2.354 A in I, II, and III, respectively. In I and II, the coordination polyhedron of the Cu atom is approximated by a distorted square pyramid with an O atom at the apical vertex, whereas in III, the polyhedron is described as a distorted trigonal bipyramid with the N and Br atoms at the axial sites. The structures are additionally stabilized by O(w)-H-O and O(w)-H-X hydrogen bonds.

  5. TIBER II configuration and structural design

    SciTech Connect

    Doggett, J.N.

    1986-08-29

    The TIBER-II machine is a minimum-size steady-state tokamak with sufficient fusion power, wall flux, and fluence to be used for undertaking a nuclear test mission. Although the machine is envisioned as an engineering device, it will demonstrate reactor-relevant physics. To achieve the small size and high performance goals of TIBER II, the engineered systems must be based on aggressive assumptions. In addition, the machine must be designed for ease of maintenance to ensure reaching the fluence goal of 5 MW yr/m/sup 2/ in a design lifetime of 13 years. This paper concentrates on the configuration and structural issues of designing a small, high-field, and high-flux device.

  6. Relating Dynamic Properties to Atomic Structure in Metallic Glasses

    SciTech Connect

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

    2012-07-18

    Atomic packing in metallic glasses is not completely random but displays various degrees of structural ordering. While it is believed that local structures profoundly affect the properties of glasses, a fundamental understanding of the structure–property relationship has been lacking. In this article, we provide a microscopic picture to uncover the intricate interplay between structural defects and dynamic properties of metallic glasses, from the perspective of computational modeling. Computational methodologies for such realistic modeling are introduced. Exploiting the concept of quasi-equivalent cluster packing, we quantify the structural ordering of a prototype metallic glass during its formation process, with a new focus on geometric measures of subatomic “voids.” Atomic sites connected with the voids are found to be crucial in terms of understanding the dynamic, including vibrational and atomic transport, properties. Normal mode analysis is performed to reveal the structural origin of the anomalous boson peak (BP) in the vibration spectrum of the glass, and its correlation with atomic packing cavities. Through transition-state search on the energy landscape of the system, such structural disorder is found to be a facilitating factor for atomic diffusion, with diffusion energy barriers and diffusion pathways significantly varying with the degree of structural relaxation/ordering. The implications of structural defects for the mechanical properties of metallic glasses are also discussed.

  7. Structural and Mechanistic Aspects of Copper Catalyzed Atom Transfer Radical Polymerization

    NASA Astrophysics Data System (ADS)

    Pintauer, Tomislav; Matyjaszewski, Krzysztof

    During the past decade, atom transfer radical polymerization (ATRP) has had a tremendous impact on the synthesis of macromolecules with well-defined compositions, architectures, and functionalities. Structural features of copper(I) and copper(II) complexes with bidentate, tridentate, tetradentate, and multidentate nitrogen-based ligands commonly utilized in ATRP are reviewed and discussed. Additionally, recent advances in mechanistic understanding of copper-mediated ATRP are outlined.

  8. Atomic emission line wavelength calculations below 2000 angstroms for Lithium II through Cobalt XXVI

    NASA Technical Reports Server (NTRS)

    Williams, M. D.

    1971-01-01

    Atomic-emission-line wavelengths are presented which were calculated from wavelengths of previously identified transition sequences using second-degree polynomials fitted to known wave numbers by the least squares method. Wavelengths less than 2000 angstroms are included for ions from Li II to Co XXVI. The computer program written in FORTRAN 4 is also included.

  9. Structural hierarchy in molecular films of two class II hydrophobins.

    PubMed

    Paananen, Arja; Vuorimaa, Elina; Torkkeli, Mika; Penttilä, Merja; Kauranen, Martti; Ikkala, Olli; Lemmetyinen, Helge; Serimaa, Ritva; Linder, Markus B

    2003-05-13

    Hydrophobins are highly surface-active proteins that are specific to filamentous fungi. They function as coatings on various fungal structures, enable aerial growth of hyphae, and facilitate attachment to surfaces. Little is known about their structures and structure-function relationships. In this work we show highly organized surface layers of hydrophobins, representing the most detailed structural study of hydrophobin films so far. Langmuir-Blodgett films of class II hydrophobins HFBI and HFBII from Trichoderma reesei were prepared and analyzed by atomic force microscopy. The films showed highly ordered two-dimensional crystalline structures. By combining our recent results on small-angle X-ray scattering of hydrophobin solutions, we found that the unit cells in the films have dimensions similar to those of tetrameric aggregates found in solutions. Further analysis leads to a model in which the building blocks of the two-dimensional crystals are shape-persistent supramolecules consisting of four hydrophobin molecules. The results also indicate functional and structural differences between HFBI and HFBII that help to explain differences in their properties. The possibility that the highly organized surface assemblies of hydrophobins could allow a route for manufacturing functional surfaces is suggested. PMID:12731866

  10. Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

    SciTech Connect

    Masuda, Tetsuya; Ohta, Keisuke; Tani, Fumito; Mikami, Bunzo; Kitabatake, Naofumi

    2011-07-08

    Highlights: {yields} X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. {yields} The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. {yields} The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. {yields} The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.

  11. Direct experimental determination of the atomic structure at internal interfaces

    SciTech Connect

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

    1995-07-01

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

  12. Glass formation and local topological instability of atomic structure

    SciTech Connect

    Egami, T.

    1997-12-31

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

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

    ERIC Educational Resources Information Center

    Rittenhouse, Robert C.

    2015-01-01

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

  14. Neutron powder diffraction studies as a function of temperature of structure II hydrate formed from propane

    USGS Publications Warehouse

    Rawn, C.J.; Rondinone, A.J.; Chakoumakos, B.C.; Circone, S.; Stern, L.A.; Kirby, S.H.; Ishii, Y.

    2003-01-01

    Neutron powder diffraction data confirm that hydrate samples synthesized with propane crystallize as structure type II hydrate. The structure has been modeled using rigid-body constraints to describe C3H8 molecules located in the eight larger polyhedral cavities of a deuterated host lattice. Data were collected at 12, 40, 100, 130, 160, 190, 220, and 250 K and used to calculate the thermal expansivity from the temperature dependence of the lattice parameters. The data collected allowed for full structural refinement of atomic coordinates and the atomic-displacement parameters.

  15. Study of the interaction of DNA with cisplatin and other Pd(II) and Pt(II) complexes by atomic force microscopy.

    PubMed Central

    Onoa, G B; Cervantes, G; Moreno, V; Prieto, M J

    1998-01-01

    Modifications in the structure of a 260 bp DNA (hlyM) fragment from Escherichia coli caused by interaction with Pd(II) and Pt(II) complexes were studied. Cisplatin and transplatin [cis- and trans-PtCl2(NH3)2 respectively], Pt2Cl2(Spym)4 (Spym = 2-mercaptopyrimidine anion), Pd-famotidine and Pt-famotidine were incubated with DNA for 24 h at 37 degrees C and then observed with an atomic force microscope. Atomic force microscopy (AFM) provides the opportunity for nanometer resolution in research on the interaction between nucleic acids and metal complexes. The complexes induced noticeable changes in DNA topography according to their different characteristics and structure. In the case of cisplatin a shortening in DNA strands was observed. Transplatin and Pt2Cl2(Spym)4 caused shortening and compaction, whilst an aggregation of two strands was observed for the Pt-famotidine compound but not for the Pd-famotidine compound or the metal-free famotidine. PMID:9490794

  16. Compound semiconductor alloys: From atomic-scale structure to bandgap bowing

    SciTech Connect

    Schnohr, C. S.

    2015-09-15

    Compound semiconductor alloys such as In{sub x}Ga{sub 1−x}As, GaAs{sub x}P{sub 1−x}, or CuIn{sub x}Ga{sub 1−x}Se{sub 2} are increasingly employed in numerous electronic, optoelectronic, and photonic devices due to the possibility of tuning their properties over a wide parameter range simply by adjusting the alloy composition. Interestingly, the material properties are also determined by the atomic-scale structure of the alloys on the subnanometer scale. These local atomic arrangements exhibit a striking deviation from the average crystallographic structure featuring different element-specific bond lengths, pronounced bond angle relaxation and severe atomic displacements. The latter, in particular, have a strong influence on the bandgap energy and give rise to a significant contribution to the experimentally observed bandgap bowing. This article therefore reviews experimental and theoretical studies of the atomic-scale structure of III-V and II-VI zincblende alloys and I-III-VI{sub 2} chalcopyrite alloys and explains the characteristic findings in terms of bond length and bond angle relaxation. Different approaches to describe and predict the bandgap bowing are presented and the correlation with local structural parameters is discussed in detail. The article further highlights both similarities and differences between the cubic zincblende alloys and the more complex chalcopyrite alloys and demonstrates that similar effects can also be expected for other tetrahedrally coordinated semiconductors of the adamantine structural family.

  17. Vortex-ring-fractal Structure of Atom and Molecule

    SciTech Connect

    Osmera, Pavel

    2010-06-17

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

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

    NASA Astrophysics Data System (ADS)

    D'Avezac, Mayeul; Zunger, Alex

    2007-03-01

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

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

    SciTech Connect

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

    1988-12-01

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

  20. Hartree-Fock electronic structure calculations for free atoms and immersed atoms in an electron gas

    NASA Astrophysics Data System (ADS)

    Walsh, Kenneth Charles

    Electronic structure calculations for free and immersed atoms are performed in the context of unrestricted Hartree-Fock Theory. Spherical symmetry is broken, lifting degeneracies in electronic configurations involving the magnetic quantum number mℓ. Basis sets, produced from density functional theory, are then explored for completeness. Comparison to spectroscopic data is done by a configurational interaction of the appropriate L and S symmetry. Finally, a perturbation technique by Lowdin is used to couple the bound atomic states to a neutral, uniform background electronic gas (jellium).

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

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

  2. Atomic and electronic structure of Ni-Nb metallic glasses

    SciTech Connect

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

    2013-12-07

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

  3. Atomic and electronic structure of twin growth defects in magnetite

    PubMed Central

    Gilks, Daniel; Nedelkoski, Zlatko; Lari, Leonardo; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Kepaptsoglou, Demie; Ramasse, Quentin; Evans, Richard; McKenna, Keith; Lazarov, Vlado K.

    2016-01-01

    We report the existence of a stable twin defect in Fe3O4 thin films. By using aberration corrected scanning transmission electron microscopy and spectroscopy the atomic structure of the twin boundary has been determined. The boundary is confined to the (111) growth plane and it is non-stoichiometric due to a missing Fe octahedral plane. By first principles calculations we show that the local atomic structural configuration of the twin boundary does not change the nature of the superexchange interactions between the two Fe sublattices across the twin grain boundary. Besides decreasing the half-metallic band gap at the boundary the altered atomic stacking at the boundary does not change the overall ferromagnetic (FM) coupling between the grains. PMID:26876049

  4. Cu(ii)-catalyzed enantioselective oxygen atom transfer from oxaziridine to oxindole derivatives with chiral phenanthroline.

    PubMed

    Naganawa, Yuki; Aoyama, Tomotaka; Nishiyama, Hisao

    2015-12-21

    In the presence of a Cu(ii) complex of axially chiral, N,N,O-tridentate phenanthroline ligand (S)-2, asymmetric oxygen atom transfer of oxindole derivatives (3) using Davis' oxaziridine (4) occurred to give the corresponding 3-aryl-3-hydroxy-2-oxindole derivatives (1) with excellent enantioselectivity (up to 96% ee). The X-ray crystallographic analysis of the isolated Cu(ii) complex disclosed its N,N,O-tridentate coordination, which is critical to realize effective catalytic activity. PMID:26456035

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

    SciTech Connect

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

    2009-03-27

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

  6. The structures of the crystalline phase and columnar mesophase of rhodium (II) heptanoate and of its binary mixture with copper (II) heptanoate probed by EXAFS

    NASA Astrophysics Data System (ADS)

    Inb-Elhaj, M.; Guillon, D.; Skoulios, A.; Maldivi, P.; Giroud-Godquin, A. M.; Marchon, J.-C.

    1992-12-01

    EXAFS was used to investigate the local structure of the polar spines of rhodium (II) soaps in the columnar liquid crystalline state. It was also used to ascertain the degree of blending of the cores in binary mixtures of rhodium (II) and copper (II) soaps. For the pure rhodium soaps, the columns are shown to result from the stacking of binuclear metal-metal bonded dirhodium tetracarboxylate units bonded to one another by apical ligation of the metal atom of each complex with one of the oxygen atoms of the adjacent molecule. Mixtures of rhodium (II) and copper (II) soaps give a hexagonal columnar mesophase in which pure rhodium and pure copper columns are randomly distributed.

  7. Metal Atom Endohedrally Doped C20 CAGE Structure:

    NASA Astrophysics Data System (ADS)

    Erkoç, Şakir

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

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

    SciTech Connect

    1981-03-01

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

  9. A quantum interface between single atoms and nanophotonic structures

    NASA Astrophysics Data System (ADS)

    Thompson, Jeffrey Douglas

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

  10. Guiding of atoms in helical optical potential structures

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  11. Atomic diffusion processes in heteroepitaxial metallic systems using SLKMC-II

    NASA Astrophysics Data System (ADS)

    Shah, Syed Islamuddin; Karim, Altaf

    We have examined the diffusion of small islands of Cu on Ag(111) surface using a self-learning kinetic Monte Carlo (SLKMC-II) method with an improved pattern recognition scheme. Due to strain generated at the interface between metals with different bulk lattice constants, interesting single atom, multi-atom and concerted diffusion processes are automatically revealed in the simulations. Here we will report various processes for small islands in the case of Cu/Ag(111) system. Key processes responsible for island diffusion and their energetics together with trends in effective energy barriers as well as diffusion constants for small islands will also be provided. In addition to 2-D diffusion processes, as an application of SLKMC-II to the 3-dimensional heteroepitaxial systems, we will also report energy barriers of some of the 3-dimensional processes including down the A- and B-steps and exchange processes

  12. Detailed Atomic Structure of Neutral and Near-Neutral Systems

    SciTech Connect

    Oliver, Paul; Hibbert, Alan

    2011-05-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  14. Syntheses, crystal structures and spectroscopic properties of copper(II)-tetracyanometallate(II) complexes with nicotinamide and isonicotinamide ligands

    NASA Astrophysics Data System (ADS)

    Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

    2015-09-01

    Four new one dimensional (1D) cyanide complexes, namely {[Cu(NH3)4(μ-na)][M‧(CN)4]}n and {[Cu(NH3)2(ina)2M‧(μ-CN)2(CN)2]}n (M‧(II) = Pd (1 and 3) or Pt (2 and 4), na:nicotinamide and ina:isonicotinamide) have been synthesized and characterized by elemental, spectral (FT-IR and Raman), and thermal (TG, DTG and DTA) analyses. The crystal structures of complexes 1-3 have been determined by single crystal X-ray diffraction technique. In complexes 1 and 2, na ligand is coordinated to the adjacent Cu(II) ions as a bridging ligand, giving rise to 1D linear cationic chain and the [M‧(CN)4]2- anionic complex acts as a counter ion. Complexes 3 and 4 are also 1D linear chain in which two cyanide ligands bridged neighboring M‧(II) and Cu(II) ions, while ina ligand is coordinated Cu(II) ion through nitrogen atom of pyridine ring. In the complexes, the Cu(II) ions adopt distorted octahedral geometries, while M‧(II) ions are four coordinated with four carbon atoms from cyanide ligands in square-planar geometries. The adjacent chains are further stacked through intermolecular hydrogen bond, Nsbnd Hṡṡṡπ, Csbnd H⋯M‧ and M‧⋯π interactions to form 3D supramolecular networks. Vibration assignments are given for all the observed bands. In addition, thermal stabilities of the compounds are also discussed.

  15. Structure and production of deeply bound pionic atoms

    SciTech Connect

    Toki, H. )

    1991-04-10

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

  16. Atomic Structure and Properties of Extended Defects in Silicon

    SciTech Connect

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

    1998-10-15

    The Z-contrast technique represents a new approach to high-resolution electron microscopy allowing for the first time incoherent imaging of materials on the atomic scale. The key advantages of the technique, an intrinsically higher resolution limit and directly interpretable, compositionally sensitive imaging, allow a new level of insight into the atomic configurations of extended defects in silicon. This experimental technique has been combined with theoretical calculations (a combination of first principles, tight binding, and classical methods) to extend this level of insight by obtaining the energetic and electronic structure of the defects.

  17. Structure and dynamics in two-electron atoms

    NASA Astrophysics Data System (ADS)

    Shuman, Edward Somerville

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

  18. Synthesis and structural characterisation of iron(II) and copper(II) diphosphates containing flattened metal oxotetrahedra

    SciTech Connect

    Keates, Adam C.; Wang, Qianlong; Weller, Mark T.

    2014-02-15

    Single crystal and bulk polycrystalline forms of K{sub 2}MP{sub 2}O{sub 7} (M=Fe(II), Cu(II)) have been synthesised and their structures determined from single crystal X-ray diffraction data. Both compounds crystallize in the tetragonal system, space group P-42{sub 1}m. Their structures are formed from infinite sheets of linked oxopolyhedra of the stoichiometry [MP{sub 2}O{sub 7}]{sup 2−} with potassium cations situated between the layers. The MO{sub 4} tetrahedra share oxygen atoms with [P{sub 2}O{sub 7}]{sup 4−} diphosphate groups and the potassium ions have KO{sub 8} square prismatic geometry. In both compounds the M(II) centre has an unusual strongly flattened, tetrahedral coordination to oxygen, as a result of the Jahn–Teller (JT) effect for the high spin d{sup 6} Fe(II) and p-orbital mixing or a second order JT effect for d{sup 9} Cu(II) centres in four fold coordination. The uncommon transition metal ion environments found in these materials are reflected in their optical absorption spectra and magnetism data. - Graphical abstract: The structures of the tetragonal polymorphs of K{sub 2}MP{sub 2}O{sub 7}, M=Cu(II), Fe(II), consist of infinite sheets of stoichiometry [MP{sub 2}O{sub 7}]{sup 2−}, formed from linked pyrophosphate groups and MO{sub 4} tetrahedra, separated by potassium ions. In both compounds the unusual tetrahedral coordination of the M(II) centre is strongly flattened as a result of Jahn–Teller (JT) effects for high spin, d{sup 6} Fe(II) and p-orbital mixing and second-order JT effects for d{sup 9} Cu(II). Display Omitted - Highlights: • Tetrahedral copper and iron(II) coordinated by oxygen. • New layered phosphate structure. • Jahn–Teller and d{sup 10} distorted coordinations.

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

    SciTech Connect

    Merkle, K.L.; Thompson, L.J.

    1997-04-01

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

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

    PubMed

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

    2015-08-12

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

  1. Primary structure of Streptomyces griseus metalloendopeptidase II.

    PubMed

    Kojima, S; Kumazaki, T; Ishii, S; Miura, K

    1998-07-01

    Streptomyces griseus metalloendopeptidase II (SGMPII) is a unique protease, since it shows anomalous susceptibility to the proteinaceous "serine protease inhibitors" produced by Streptomyces, such as Streptomyces subtilisin inhibitor (SSI) and its homologous proteins. In this study, we analyzed the amino acid sequence of SGMPII by analyzing various peptide fragments produced enzymatically. The sequence of SGMPII, which is composed of 334 amino acids, showed no extensive similarity to SSI-insensitive metalloproteases produced by other species of Streptomyces, except for the amino acid residues essential for catalysis and zinc binding. However, SGMPII is 35-41% similar to thermolysin and its related metalloproteases, which are not inhibited by SSI, and the residues presumed to be critical for catalysis and zinc-binding are well conserved in SGMPII. Glu137 in a "His-Glu-Xaa-His" motif of SGMPII was identified as the residue modified by CICH2 CO-DL-(N-OH)Leu-Ala-Gly-NH2, an active-site-directed irreversible inhibitor of thermolysin-like metalloproteases. Based on the sequence comparison of SGMPII and other bacterial metalloproteases, we discuss the structural basis for the differences in substrate specificity and stability between SGMPII and other thermolysin-like proteases. A possible SSI-binding locus of SGMPII is also proposed. PMID:9720222

  2. Microtraps for neutral atoms using superconducting structures in the critical state

    SciTech Connect

    Emmert, A.; Brune, M.; Raimond, J.-M.; Nogues, G.; Lupascu, A.; Haroche, S.

    2009-12-15

    Recently demonstrated superconducting atom chips provide a platform for trapping atoms and coupling them to solid-state quantum systems. Controlling these devices requires a full understanding of the supercurrent distribution in the trapping structures. For type-II superconductors, this distribution is hysteretic in the critical state due to the partial penetration of the magnetic field in the thin superconducting film through pinned vortices. We report here an experimental observation of this memory effect. Our results are in good agreement with the predictions of the Bean model of the critical state without adjustable parameters. The memory effect allows to write and store permanent currents in micron-sized superconducting structures and paves the way toward engineered trapping potentials.

  3. Structural properties of lithium atom under weakly coupled plasma environment

    NASA Astrophysics Data System (ADS)

    Dutta, S.; Saha, J. K.; Chandra, R.; Mukherjee, T. K.

    2016-04-01

    The Rayleigh-Ritz variational technique with a Hylleraas basis set is being tested for the first time to estimate the structural modifications of a lithium atom embedded in a weakly coupled plasma environment. The Debye-Huckel potential is used to mimic the weakly coupled plasma environment. The wave functions for both the helium-like lithium ion and the lithium atom are expanded in the explicitly correlated Hylleraas type basis set which fully takes care of the electron-electron correlation effect. Due to the continuum lowering under plasma environment, the ionization potential of the system gradually decreases leading to the destabilization of the atom. The excited states destabilize at a lower value of the plasma density. The estimated ionization potential agrees fairly well with the few available theoretical estimates. The variation of one and two particle moments, dielectric susceptibility and magnetic shielding constant, with respect to plasma density is also been discussed in detail.

  4. New macrocyclic schiff base complexes incorporating a homopiperazine unit: Synthesis of some Co(II), Ni(II),Cu(II) and Zn(II) complexes and crystal structure and theoretical studies

    NASA Astrophysics Data System (ADS)

    Keypour, Hassan; Rezaeivala, Majid; Ramezani-Aktij, Ameneh; Bayat, Mehdi; Dilek, Nefise; Ünver, Hüseyin

    2016-07-01

    A new macrocyclic Schiff base ligand, L, was synthesized by condensation reaction of 1,4-bis(2-formylphenyl)homopiperazine and 1,4-diaminobutane in acetonitrile. The Schiff base ligand was characterized by using elemental analyses, FT-IR, 1H, 13C NMR and mass spectroscopic techniques. The metal (II) complexes [ML], were synthesized from the reaction of MCl2.nH2O (M: Co, Ni, Cu and Zn) with Schiff base ligand, L and characterized by elemental analyses and FT-IR. X-ray crystal structure of [CoLCl]+ distorted square pyramidal geometry with an N4Cl core, arising from coordination by the four donor nitrogen atoms from the macrocyclic framework and one Cl atom. It crystallizes triclinic space group, P-1 with a = 7.1777(1) Å, b = 11.0357 (2) Å, c = 15.1520(2) Å, V = 1183.14(3), Z = 2, Dc = 1.556 g cm-3, μ (MoKα) = 0.156 mm-1. Also, the bonding situation between the [MCl]+ and Ligand (L) fragments in [MLCl]ClO4 (M = Co(II), Ni(II), Cu(II), Zn(II)) complexes were carried out by energy-decomposition analysis (EDA). The results showed that there is an increasing trend in the case of ΔEelstat of the complexes by changing the M from Co(II) to Zn(II).

  5. Molecular structures, charge distributions, and vibrational analyses of the tetracoordinate Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine investigated by density functional theory in comparison with experiments

    NASA Astrophysics Data System (ADS)

    Bardakçı, Tayyibe; Kumru, Mustafa; Altun, Ahmet

    2016-07-01

    The Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine have been studied with B3LYP calculations by using def2-TZVP basis set at the metal atoms and using def2-TZVP and 6-311G+(d,p) basis sets at the remaining atoms. Both basis set combinations give analogous results, which validate the use of quickly converging 6-311G+(d,p) basis set in future studies. The molecular structures, atomic charge and spin distributions, and harmonic vibrational frequencies of the complexes have been calculated. The Zn, Cd and Hg complexes have been found to have distorted tetrahedral environments around the metal atoms whereas Cu complex has a square planar geometry. The NBO charge analysis have been found more accurate and less misleading compared with the Mulliken scheme. The present vibrational spectra calculations allow accurate assignment of the vibrational bands, which otherwise assigned tentatively in previous experimental-only studies.

  6. Stable atomic structure of NiTi austenite

    NASA Astrophysics Data System (ADS)

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2014-08-01

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

  7. Stable atomic structure of NiTi austenite

    SciTech Connect

    Zarkevich, Nikolai A; Johnson, Duane D

    2014-08-01

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

  8. Designing a heterotrinuclear Cu(II)-Ni(II)-Cu(II) complex from a mononuclear Cu(II) Schiff base precursor with dicyanamide as a coligand: synthesis, crystal structure, thermal and photoluminescence properties.

    PubMed

    Hopa, Cigdem; Cokay, Ismail

    2016-08-01

    Schiff bases are considered `versatile ligands' in coordination chemistry. The design of polynuclear complexes has become of interest due to their facile preparations and varied synthetic, structural and magnetic properties. The reaction of the `ligand complex' [CuL] {H2L is 2,2'-[propane-1,3-diylbis(nitrilomethanylylidene)]diphenol} with Ni(OAc)2·4H2O (OAc is acetate) in the presence of dicyanamide (dca) leads to the formation of bis(dicyanamido-1κN(1))bis(dimethyl sulfoxide)-2κO,3κO-bis{μ-2,2'-[propane-1,3-diylbis(nitrilomethanylylidene)]diphenolato}-1:2κ(6)O,O':O,N,N',O';1:3κ(6)O,O':O,N,N',O'-dicopper(II)nickel(II), [Cu2Ni(C17H16N2O2)2(C2N3)2(C2H6OS)2]. The complex shows strong absorption bands in the frequency region 2155-2269 cm(-1), which clearly proves the presence of terminal bonding dca groups. A single-crystal X-ray study revealed that two [CuL] units coordinate to an Ni(II) atom through the phenolate O atoms, with double phenolate bridges between Cu(II) and Ni(II) atoms. Two terminal dca groups complete the distorted octahedral geometry around the central Ni(II) atom. According to differential thermal analysis-thermogravimetric analysis (DTA-TGA), the title complex is stable up to 423 K and thermal decomposition starts with the release of two coordinated dimethyl sulfoxide molecules. Free H2L exhibits photoluminescence properties originating from intraligand (π-π*) transitions and fluorescence quenching is observed on complexation of H2L with Cu(II). PMID:27487333

  9. Interfacial Atomic Structure of Twisted Few-Layer Graphene

    PubMed Central

    Ishikawa, Ryo; Lugg, Nathan R.; Inoue, Kazutoshi; Sawada, Hidetaka; Taniguchi, Takashi; Shibata, Naoya; Ikuhara, Yuichi

    2016-01-01

    A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene. PMID:26888259

  10. Interfacial Atomic Structure of Twisted Few-Layer Graphene.

    PubMed

    Ishikawa, Ryo; Lugg, Nathan R; Inoue, Kazutoshi; Sawada, Hidetaka; Taniguchi, Takashi; Shibata, Naoya; Ikuhara, Yuichi

    2016-01-01

    A twist in bi- or few-layer graphene breaks the local symmetry, introducing a number of intriguing physical properties such as opening new bandgaps. Therefore, determining the twisted atomic structure is critical to understanding and controlling the functional properties of graphene. Combining low-angle annular dark-field electron microscopy with image simulations, we directly determine the atomic structure of twisted few-layer graphene in terms of a moiré superstructure which is parameterized by a single twist angle and lattice constant. This method is shown to be a powerful tool for accurately determining the atomic structure of two-dimensional materials such as graphene, even in the presence of experimental errors. Using coincidence-site-lattice and displacement-shift-complete theories, we show that the in-plane translation state between layers is not a significant structure parameter, explaining why the present method is adequate not only for bilayer graphene but also a few-layered twisted graphene. PMID:26888259

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

    PubMed Central

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

    2008-01-01

    The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS2 nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS2 nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism. PMID:18838681

  12. Zero-Temperature Structures of Atomic Metallic Hydrogen

    NASA Astrophysics Data System (ADS)

    McMahon, Jeffrey; Ceperley, David

    2011-03-01

    Since the first prediction of an atomic metallic phase of hydrogen by Wigner and Huntington over 75 years ago, there have been many theoretical efforts aimed at determining the crystal structures of the zero-temperature phases. We present results from ab initio random structure searching with density functional theory performed to determine the ground state structures from 500 GPa to 5 TPa. We estimate that molecular hydrogen dissociates into a monatomic body-centered tetragonal structure near 500 GPa (rs = 1.225), which then remains stable to 2.5 TPa (rs = 0.969). At higher pressures, hydrogen stabilizes in an . . . ABCABC . . . planar structure that is remarkably similar to the ground state of lithium, which compresses to the face-centered cubic lattice beyond 5 TPa (rs < 0.86). Our results provide a complete ab initio description of the atomic metallic crystal structures of hydrogen, resolving one of the most fundamental and long outstanding issues concerning the structures of the elements.

  13. Synthesis, characterization, crystal structure and cytotoxic properties of thiosemicarbazide Ni(II) and Zn(II) complexes.

    PubMed

    Mathan Kumar, S; Rajesh, J; Anitha, K; Dhahagani, K; Marappan, M; Indra Gandhi, N; Rajagopal, G

    2015-05-01

    Synthesis of new complexes of Ni(II) (1) and Zn(II) (2) with [1-(2-hydroxy-3,5-diiodobenzylidene)-4-phenylthiosemicarbazide] have been reported. The composition of these two complexes 1 and 2 is discussed on the basis of IR, (1)H NMR and UV spectral data along with their X-ray crystallographic data. The crystal structure of these two complexes has revealed that the free ligand (L) is deprotonated twice at the oxygen and sulfur atoms and they are coordinated with the complexes through phenoxide-O, azomethine-N and thiolate-S atoms. The single-crystal X-ray structures of complex (1) exhibits a square planar structure, while complex (2) reveals trigonal bipyramidal distorted square based pyramidal structure. Anticancer activity of ligand and the complexes 1-2 are evaluated in human adenocarcinoma (MCF-7) cells. The preliminary bioassay indicates that the free ligand and the complexes 1-2 exhibit inhibitory activity against the human adenocarcinoma cancer cell lines. PMID:25706599

  14. Synthesis, characterization, crystal structure and cytotoxic properties of thiosemicarbazide Ni(II) and Zn(II) complexes

    NASA Astrophysics Data System (ADS)

    Mathan Kumar, S.; Rajesh, J.; Anitha, K.; Dhahagani, K.; Marappan, M.; Indra Gandhi, N.; Rajagopal, G.

    2015-05-01

    Synthesis of new complexes of Ni(II) (1) and Zn(II) (2) with [1-(2-hydroxy-3,5-diiodobenzylidene)-4-phenylthiosemicarbazide] have been reported. The composition of these two complexes 1 and 2 is discussed on the basis of IR, 1H NMR and UV spectral data along with their X-ray crystallographic data. The crystal structure of these two complexes has revealed that the free ligand (L) is deprotonated twice at the oxygen and sulfur atoms and they are coordinated with the complexes through phenoxide-O, azomethine-N and thiolate-S atoms. The single-crystal X-ray structures of complex (1) exhibits a square planar structure, while complex (2) reveals trigonal bipyramidal distorted square based pyramidal structure. Anticancer activity of ligand and the complexes 1-2 are evaluated in human adenocarcinoma (MCF-7) cells. The preliminary bioassay indicates that the free ligand and the complexes 1-2 exhibit inhibitory activity against the human adenocarcinoma cancer cell lines.

  15. First-principles study of the atomic and electronic structures of crystalline and amorphous B4C

    NASA Astrophysics Data System (ADS)

    Ivashchenko, V. I.; Shevchenko, V. I.; Turchi, P. E. A.

    2009-12-01

    The atomic and electronic structures of crystalline and amorphous B4C were determined within density function theory using the local density approximation and a plane-wave pseudopotential method. For the crystalline phases, chain, and polar structures were considered. The structural parameters were obtained by minimizing the total energy with respect to the size, shape, and internal degrees of freedom of 15 and 45-atom unit cells. The amorphous 120 and 135-atom samples of a-B4C were generated using molecular dynamic simulations in the NVT ensemble using different initial structures. The 120-atom sample was generated from a rhombohedral c-B4C cell, whereas the a-135 sample was obtained from a fcc B4C initial structure that differs essentially from the real crystalline B4C structure. Analysis of the computed results shows that: (i) a random icosahedral network connected with the amorphous B-C matrix is identified in the case of a-B4C ; (ii) carbon clusters are observed in the case of the 120-atom sample of an amorphous matrix; (iii) no chain atoms are found in both amorphous samples that can be explained by their bulk moduli that are lower compared to those of their crystalline counterparts; (iv) the chain and polar B4C phases transform into a-B4C under high pressure; and (v) all crystalline structures studied so far are semiconducting, whereas a-B4C is a semimetal.

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

    NASA Astrophysics Data System (ADS)

    Crépin, C.; Tramer, A.

    1997-08-01

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

  17. Magnetism and surface structure of atomically controlled ultrathin metal films.

    SciTech Connect

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

    2007-01-01

    We review the correlation of magnetism and surface structure in ultrathin metal films, including the tailoring of novel magnetic properties using atomic scale control of the nanostructure. We provide an overview of modern fabrication and characterization techniques used to create and explore these fascinating materials, and highlight important phenomena of interest. We also discuss techniques that control and characterize both the magnetic and structural properties on an atomic scale. Recent advances in the development and applications of these techniques allow nanomagnetism to be investigated in an unprecedented manner. A system cannot necessarily retain a two-dimensional structure as it enters the ultrathin region, but it can transform into a three-dimensional, discontinuous structure due to the Volmer-Weber growth mechanism. This structural transformation can give rise to superparamagnetism. During this evolution, competing factors such as interparticle interactions and the effective magnetic anisotropy govern the magnetic state. These magnetic parameters are influenced by the nanostructure of the film. In particular, controlling the magnetic anisotropy is critical for determining the magnetic properties. Surface effects play especially important roles in influencing both the magnitude and direction of the magnetic anisotropy in ultrathin films. By properly altering the surface structure, the strength and direction of the magnetic anisotropy are controlled via spin-orbit and/or dipole interactions.

  18. Ground-State Structures of Atomic Metallic Hydrogen

    NASA Astrophysics Data System (ADS)

    McMahon, Jeffrey M.; Ceperley, David M.

    2011-04-01

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

  19. Psychological Action and Structure in "Richard II."

    ERIC Educational Resources Information Center

    Toole, William B., III

    1978-01-01

    Explores the theme that the suffering arising from Richard II's loss of power, a power that consisted more of appearance than of intrinsic worth, led him to spiritual growth and the development of real value as a person. (MB)

  20. Cavities and Atomic Packing in Protein Structures and Interfaces

    PubMed Central

    Sonavane, Shrihari; Chakrabarti, Pinak

    2008-01-01

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

  1. Atomic and electronic structure of exfoliated black phosphorus

    SciTech Connect

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

    2015-11-15

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

  2. Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite

    SciTech Connect

    Shelobolina, Evgenya S.; Xu, Huifang; Konishi, Hiromi; Kukkadapu, Ravi K.; Wu, Tao; Blothe, Marco; Roden, Eric E.

    2012-06-08

    Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through production of organic ligands and acids, and through uptake of products of weathering. Here we show that a lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture (Straub, 6 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Moessbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 107 cells were produced per {micro}mol Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including decrease in unit cell b-dimension toward dioctahedral levels and iron and potassium release. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms may be directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere.

  3. Structural basis for exon recognition by a group II intron

    SciTech Connect

    Toor, Navtej; Rajashankar, Kanagalaghatta; Keating, Kevin S.; Pyle, Anna Marie

    2008-11-18

    Free group II introns are infectious retroelements that can bind and insert themselves into RNA and DNA molecules via reverse splicing. Here we report the 3.4-A crystal structure of a complex between an oligonucleotide target substrate and a group IIC intron, as well as the refined free intron structure. The structure of the complex reveals the conformation of motifs involved in exon recognition by group II introns.

  4. Tin(II) ketoacidoximates: synthesis, X-ray structures and processing to tin(II) oxide.

    PubMed

    Khanderi, Jayaprakash; Davaasuren, Bambar; Alshankiti, Buthainah Ameen; Rothenberger, Alexander

    2015-12-14

    Tin(II) ketoacidoximates of the type [HON=CRCOO]2Sn (R = Me 1, CH2Ph 2) and (MeON=CMeCOO)3Sn](-) NH4(+)·2H2O 3 were synthesized by reacting pyruvate- and hydroxyl- or methoxylamine RONH2 (R = H, Me) with tin(II) chloride dihydrate SnCl2·2H2O. The single crystal X-ray structure reveals that the geometry at the Sn atom is trigonal bipyramidal in 1, 2 and trigonal pyramidal in 3. Inter- or intramolecular hydrogen bonding is observed in 1-3. Thermogravimetric (TG) analysis shows that the decomposition of 1-3 to SnO occurs at ca. 160 °C. The evolved gas analysis during TG indicates complete loss of the oximato ligand in one step for 1 whereas a small organic residue is additionally removed at temperatures >400 °C for 2. Above 140 °C, [HON=C(Me)COO]2Sn (1) decomposes in air to spherical SnO particles of size 10-500 nm. Spin coating of 1 on Si or a glass substrate followed by heating at 200 °C results in a uniform film of SnO. The band gap of the produced SnO film and nanomaterial was determined by diffuse reflectance spectroscopy to be in the range of 3.0-3.3 eV. X-ray photoelectron spectroscopy indicates surface oxidation of the SnO film to SnO2 in ambient atmosphere. PMID:26528675

  5. The role of atomic lines in radiation heating of the experimental space vehicle Fire-II

    NASA Astrophysics Data System (ADS)

    Surzhikov, S. T.

    2015-10-01

    The results of calculating the convective and radiation heating of the Fire-II experimental space vehicle allowing for atomic lines of atoms and ions using the NERAT-ASTEROID computer platform are presented. This computer platform is intended to solve the complete set of equations of radiation gas dynamics of viscous, heat-conductive, and physically and chemically nonequilibrium gas, as well as radiation transfer. The spectral optical properties of high temperature gases are calculated using ab initio quasi-classical and quantum-mechanical methods. The calculation of the transfer of selective thermal radiation is performed using a line-by-line method using specially generated computational grids over the radiation wavelengths, which make it possible to attain a noticeable economy of computational resources.

  6. Theoretical studies of nickel atoms and nickel(II) ions coordinated with CO and BF ligands

    NASA Astrophysics Data System (ADS)

    McDowell, Sean A. C.; David Buckingham, A.

    2011-11-01

    A computational study of a neutral Ni atom and Ni(II) atoms coordinated with CO and BF ligands was undertaken using density functional theory. Neutral compounds with general formula Ni(CO)x(BF)4-x (x = 0-4) were predicted to have tetrahedral geometries, and cationic Ni(CO)x(BF)4-x2+ square-planar geometries. Sequential replacement of the CO molecules in the well known tetrahedral Ni(CO)4 molecule yields a substantially more stable tetrahedral Ni(BF)4 molecule, and substitution of the CO ligands in the square-planar [Ni(CO)4]2+ cation yields a more stable [Ni(BF)4]2+ analogue. Stable complexes were also obtained by substitution of the OC ligands by FB in the [Ni(OC)4]2+ cation.

  7. Structure of a Quantized Vortex in Fermi Atom Gas

    SciTech Connect

    Machida, Masahiko; Koyama, Tomio

    2006-09-07

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

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

    NASA Astrophysics Data System (ADS)

    Usman, Muhammad

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

  9. TlII excitation cross-sections in collisions of slow electrons with thallium atoms

    NASA Astrophysics Data System (ADS)

    Smirnov, Yu M.

    2016-09-01

    Excitation of a singly-charged thallium ion in electron collisions with thallium atoms has been studied experimentally. Seventy excitation cross sections have been measured at an exciting electron energy of 30 eV. Ten optical excitation functions (OEFs) have been recorded in the incident electron energy range of 0–200 eV. For seven TlII spectral series, the dependence of excitation cross-sections on the principal quantum numbers of upper levels has been studied. A comparison of findings with data from preceding publications is presented.

  10. Synthesis and structural characterization of two half-sandwich nickel(II) complexes with the scorpionate ligands

    SciTech Connect

    Wang, G.-F. E-mail: s-shuwen@163.com; Zhang, X.; Sun, S.-W.; Sun, H.; Ma, H.-X.

    2015-12-15

    The synthesis and characterization of two new halfsandwich mononuclear nickel(II) complexes with the scorpionate ligands, [k{sup 3}-N, N',N''-Tp{sup t-Bu}, {sup Me}NiI] (1) and [k{sup 3}-N,N',N''-Tp{sup t-Bu}, {sup Me}NiNO{sub 3}] (2), are reported. These complexes have been fully characterized by elemental analyses and infrared spectra. Their molecular structures were determined by single crystal X-ray diffraction. The nickel(II) ion of complex 1 is in a four-coordinate environment, in which the donor atoms are provided by three nitrogen atoms of a hydrotris(pyrazolyl) borate ligand and one iodide atom, while that of complex 2 is in a five-coordinate environment with three nitrogen atoms from a hydrotris(pyrazolyl)borate ligand and two oxygen atoms from a nitrate ion.

  11. Synthesis and structural characterization of two half-sandwich nickel(II) complexes with the scorpionate ligands

    NASA Astrophysics Data System (ADS)

    Wang, G.-F.; Zhang, X.; Sun, S.-W.; Sun, H.; Ma, H.-X.

    2015-12-01

    The synthesis and characterization of two new halfsandwich mononuclear nickel(II) complexes with the scorpionate ligands, [ k 3- N, N', N''- Tp t-Bu, Me NiI] ( 1) and [ k 3- N, N', N''- Tp t-Bu, Me NiNO3] ( 2), are reported. These complexes have been fully characterized by elemental analyses and infrared spectra. Their molecular structures were determined by single crystal X-ray diffraction. The nickel(II) ion of complex 1 is in a four-coordinate environment, in which the donor atoms are provided by three nitrogen atoms of a hydrotris(pyrazolyl) borate ligand and one iodide atom, while that of complex 2 is in a five-coordinate environment with three nitrogen atoms from a hydrotris(pyrazolyl)borate ligand and two oxygen atoms from a nitrate ion.

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

    PubMed

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

    2013-03-29

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

  13. Syntheses, characterizations and structures of NO donor Schiff base ligands and nickel(II) and copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Şenol, Cemal; Hayvali, Zeliha; Dal, Hakan; Hökelek, Tuncer

    2011-06-01

    New Schiff base derivatives ( L 1 and L 2) were prepared by the condensation of 2-hydroxy-3-methoxybenzaldehyde ( o-vanillin) and 3-hydroxy-4-methoxybenzaldehyde ( iso-vanillin) with 5-methylfurfurylamine. Two new complexes [Ni(L 1) 2] and [Cu(L 1) 2] have been synthesized with bidentate NO donor Schiff base ligand ( L 1). The Ni(II) and Cu(II) atoms in each complex are four coordinated in a square planar geometry. Schiff bases ( L 1 and L 2) and complexes [Ni(L 1) 2] and [Cu(L 1) 2] were characterized by elemental analyses, FT-IR, UV-vis, mass and 1H, 13C NMR spectroscopies. The crystal structures of the ligand ( L 2) and complexes [Ni(L 1) 2] and [Cu(L 1) 2] have also been determined by using X-ray crystallographic technique.

  14. A revised structure and hydrogen bonding system in cellulose II from a neutron fiber diffraction analysis

    SciTech Connect

    Langan, P.; Nishiyama, Y.; Chanzy, H.

    1999-11-03

    The crystal and molecular structure and hydrogen bonding system in cellulose II have been revised using new neutron diffraction data extending to 1.2 {angstrom} resolution collected from two highly crystalline fiber samples of mercerized flax. Mercerization was achieved in NaOH/H{sub 2}O for one sample and in NaOD/D{sub 2}O for the other, corresponding to the labile hydroxymethyl moieties being hydrogenated and deuterated, respectively. Fourier difference maps were calculated in which neutron difference amplitudes were combined with phases calculated from two revised X-ray models of cellulose II. The revised phasing models were determined by refinement against the X-ray data set of Kolpak and Blackwell, using the LALS methodology. Both models have two antiparallel chains organized in a P2{sub 1} space group and unit cell parameters: a = 8.01 {angstrom}, b = 9.04 {angstrom}, c = 10.36 {angstrom}, and {gamma} = 117.1{degree}. One has equivalent backbone conformations for both chains but different conformations for the hydroxymethyl moieties: gt for the origin chain and tg for the center chain. The second model based on the recent crystal structures of cellotetraose, has different conformations for the two chains but nearly equivalent conformations for the hydroxymethyl moieties. On the basis of the X-ray data alone, the models could not be differentiated. From the neutron Fourier difference maps, possible labile hydrogen atom positions were identified for each model and refined using LALS. The second model is significantly different from previous proposals based on the crystal structures of cellotetraose, MD simulations of cellulose II, and any potential hydrogen-bonding network in the structure of cellulose II determined in earlier X-ray fiber diffraction studies. The exact localization of the labile hydrogen atoms involved in this bonding, together with their donor and acceptor characteristics, is presented and discussed. This study provides, for the first time

  15. Atomic Clocks and Variations of the FIne Structure Constant

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  16. Spatial multimode structure of atom-generated squeezed light

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  17. Absence of a stable atomic structure in fluorinated graphene.

    PubMed

    Boukhvalov, Danil W

    2016-05-21

    Based on the results of first-principles calculations we demonstrate that significant distortion of graphene sheets caused by adsorption of fluorine atoms leads to the formation of metastable patterns for which the next step of fluorination is considerably less energetically favorable. Existence of these stable patterns oriented along the armchair direction makes possible the synthesis of various CFx structures. The combination of strong distortion of the nonfluorinated graphene sheet with the doping caused by the polar nature of C-F bonds reduces the energy cost of migration and the energy of migration barriers, making possible the migration of fluorine atoms on the graphene surface as well as transformation of the shapes of fluorinated areas. The decreasing energy cost of migration with increasing fluorine content also leads to increasing numbers of single fluorine adatoms, which could be the source of magnetic moments. PMID:27116897

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

    SciTech Connect

    Goeken, M.; Vehoff, H.

    1996-10-15

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

  19. Deciphering Adsorption Structure on Insulators at the Atomic Scale

    SciTech Connect

    Thurmer, Konrad; Feibelman, Peter J.

    2014-09-01

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

  20. Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite

    PubMed Central

    Xu, Huifang; Konishi, Hiromi; Kukkadapu, Ravi; Wu, Tao; Blöthe, Marco; Roden, Eric

    2012-01-01

    Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. Here we show that the lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458–1460, 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay-sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Mössbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 1.5 × 107 cells were produced per μmol of Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including a decrease in the unit cell b dimension toward dioctahedral levels and Fe and K release. Structural Fe(II) oxidation may involve either direct enzymatic oxidation, followed by solid-state mineral transformation, or indirect oxidation as a result of the formation of aqueous Fe, followed by electron transfer from Fe(II) in the mineral to Fe(III) in solution. Although it is not possible to distinguish between these two mechanisms with available data, the complete absence of aqueous Fe in oxidation experiments favors the former alternative. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms are directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere. PMID:22685132

  1. Atomic structure of anthrax protective antigen pore elucidates toxin translocation.

    PubMed

    Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  2. Atomic structure of anthrax PA pore elucidates toxin translocation

    PubMed Central

    Jiang, Jiansen; Pentelute, Bradley L.; Collier, R. John; Zhou, Z. Hong

    2015-01-01

    Summary Anthrax toxin, comprising protective antigen (PA), lethal factor (LF) and edema factor (EF), is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in human and animals. PA forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes LF and EF into the cytosol of target cells1. PA is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. Based on biochemical and electrophysiological results, researchers have proposed that a Φ-clamp composed of Phe427 residues of PA catalyzes protein translocation via a charge-state dependent Brownian ratchet2–9. Although atomic structures of PA prepores are available10–14, how PA senses low pH, converts to active pore and translocates LF and EF are not well defined without an atomic model of the PA pore. Here, by cryo electron microscopy (cryoEM) with direct electron counting, we have determined the PA pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low-pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  3. Synthesis, structure and magnetic properties of cobalt(II) and copper(II) coordination polymers assembled by phthalate and 4-methylimidazole

    NASA Astrophysics Data System (ADS)

    Baca, Svetlana G.; Malinovskii, Stanislav T.; Franz, Patrick; Ambrus, Christina; Stoeckli-Evans, Helen; Gerbeleu, Nicolae; Decurtins, Silvio

    2004-08-01

    New coordination polymers [ M(Pht)(4-MeIm) 2(H 2O)] n ( M=Co ( 1), Cu ( 2); Pht 2-=dianion of o-phthalic acid; 4-MeIm=4-methylimidazole) have been synthesized and characterized by IR spectroscopy, X-ray crystallography, thermogravimetric analysis and magnetic measurements. The crystal structures of 1 and 2 are isostructural and consist of [ M(4-MeIm) 2(H 2O)] building units linked in infinite 1D helical chains by 1,6-bridging phthalate ions which also act as chelating ligands through two O atoms from one carboxylate group in the case of 1. In complex 1, each Co(II) atom adopts a distorted octahedral N 2O 4 geometry being coordinated by two N atoms from two 4-MeIm, three O atoms of two phthalate residues and one O atom of a water molecule, whereas the square-pyramidal N 2O 3 coordination of the Cu(II) atom in 2 includes two N atoms of N-containing ligands, two O atoms of two carboxylate groups from different Pht, and a water molecule. An additional strong O-H⋯O hydrogen bond between a carboxylate group of the phthalate ligand and a coordinated water molecule join the 1D helical chains to form a 2D network in both compounds. The thermal dependences of the magnetic susceptibilities of the polymeric helical Co(II) chain compound 1 were simulated within the temperature range 20-300 K as a single ion case, whereas for the Cu(II) compound 2, the simulations between 25 and 300 K, were made for a linear chain using the Bonner-Fisher approximation. Modelling the experimental data of compound 1 with MAGPACK resulted in: g=2.6, | D|=62 cm -1. Calculations using the Bonner-Fisher approximation gave the following result for compound 2: g=2.18, J=-0.4 cm -1.

  4. INTENSITY MAPPING OF THE [C II] FINE STRUCTURE LINE DURING THE EPOCH OF REIONIZATION

    SciTech Connect

    Gong Yan; Cooray, Asantha; Silva, Marta; Santos, Mario G.; Bock, James; Bradford, C. Matt; Zemcov, Michael

    2012-01-20

    The atomic C II fine-structure line is one of the brightest lines in a typical star-forming galaxy spectrum with a luminosity {approx}0.1%-1% of the bolometric luminosity. It is potentially a reliable tracer of the dense gas distribution at high redshifts and could provide an additional probe to the era of reionization. By taking into account the spontaneous, stimulated, and collisional emission of the C II line, we calculate the spin temperature and the mean intensity as a function of the redshift. When averaged over a cosmologically large volume, we find that the C II emission from ionized carbon in individual galaxies is larger than the signal generated by carbon in the intergalactic medium. Assuming that the C II luminosity is proportional to the carbon mass in dark matter halos, we also compute the power spectrum of the C II line intensity at various redshifts. In order to avoid the contamination from CO rotational lines at low redshift when targeting a C II survey at high redshifts, we propose the cross-correlation of C II and 21 cm line emission from high redshifts. To explore the detectability of the C II signal from reionization, we also evaluate the expected errors on the C II power spectrum and C II-21 cm cross power spectrum based on the design of the future millimeter surveys. We note that the C II-21 cm cross power spectrum contains interesting features that capture physics during reionization, including the ionized bubble sizes and the mean ionization fraction, which are challenging to measure from 21 cm data alone. We propose an instrumental concept for the reionization C II experiment targeting the frequency range of {approx}200-300 GHz with 1, 3, and 10 m apertures and a bolometric spectrometer array with 64 independent spectral pixels with about 20,000 bolometers.

  5. Crystal structures of copper(II) and nickel(II) nitrate and chloride complexes with 4-bromo-2-[(2-hydroxyethylimino)-methyl]phenol

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Filippova, I. G.; Bocelli, G.; Gulea, A. P.

    2008-07-15

    The crystal structures of {l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}aquacopper(II) nitrate hemihydrate (I), chloro-{l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}copper hemihydrate (II), and chloro-{l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}aquanickel (III) are determined using X-ray diffraction. Crystals of compound I are formed by cationic complexes, nitrate ions, and solvate water molecules. In the cation, the copper atom coordinates the singly deprotonated molecule of tridentate azomethine and the water molecule. The copper complexes are joined into centrosymmetric dimers by the O{sub w}-H...O hydrogen bonds. The crystal structure of compound II is composed of binuclear copper complexes and solvate water molecules. The copper atom coordinates the O,N,O ligand molecule and the chlorine ion, which fulfills a bridging function. The coordination polyhedron of the metal atom is a distorted tetragonal bipyramid in which the vertex is occupied by the chlorine atom of the neighboring complex in the dimer. Compound III is a centrosymmetric dimer complex. The coordination polyhedra of two nickel atoms related via the inversion center are distorted octahedra shared by the edge.

  6. Three-dimensional structure of photosystem II from Thermosynechococcus elongates in complex with terbutryn

    SciTech Connect

    Gabdulkhakov, A. G. Dontsova, M. V.; Saenger, W.

    2011-11-15

    Photosystem II is a key component of the photosynthetic pathway producing oxygen at the thylakoid membrane of cyanobacteria, green algae, and plants. The three-dimensional structure of photosystem II from the cyanobacterium Thermosynechococcus elongates in a complex with herbicide terbutryn (a photosynthesis inhibitor) was determined for the first time by X-ray diffraction and refined at 3.2 Angstrom-Sign resolution (R{sub factor} = 26.9%, R{sub free} = 29.9%, rmsd for bond lengths is 0.013 Angstrom-Sign , and rmsd for bond angles is 2.2 Degree-Sign ). The terbutryn molecule was located in the binding pocket of the mobile plastoquinone. The atomic coordinates of the refined structure of photosystem II in a complex with terbutryn were deposited in the Protein Data Bank.

  7. First Structural Steel Erected at NSLS-II

    SciTech Connect

    2009-09-14

    Ten steel columns were incorporated into the ever-growing framework for the National Synchrotron Light Source II last week, the first structural steel erected for the future 400,000-square-foot facility.

  8. First Structural Steel Erected at NSLS-II

    ScienceCinema

    None

    2010-01-08

    Ten steel columns were incorporated into the ever-growing framework for the National Synchrotron Light Source II last week, the first structural steel erected for the future 400,000-square-foot facility.

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

    PubMed

    Murshudov, G N

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

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

  11. Using graphs to interrogate the atomic structure of polymer blends

    NASA Astrophysics Data System (ADS)

    Wodo, Olga; Ganapathysubramanian, Baskar

    2015-03-01

    The nanomorphology of polymer blend thin films critically affects performance especially in electronic devices. However, many aspects of the underlying physics linking morphology to performance are still poorly understood. Furthermore, there is increasing evidence that atomic organization can hold the key to efficient charge transport within organic electronic devices. In this work, we take advantage of recent advances in molecular dynamic simulations and quantify atomic-scale morphological aspects of the thin films. Specifically, we present a graph-based technique that allows quantifying the point-cloud data. In our approach, we first convert the point cloud data from atomistic simulation into a labelled, weighted, undirected graph and then use standard graph-based algorithms to calculate and quantify morphology features. The conversion of the CGMD-data into a graph preserves all the topological and geometric information about the internal structure, and local connectivity between individual atoms/beads (along and across the polymer chains). Our method provides hierarchical information about the charge paths that a hole/electron needs to take to reach the electrode (path length, fraction of intra-molecular hops, path balance). We showcase capabilities of our approach by analyzing coarse grained molecular simulations, and quantifying effect of various thermal treatment as well as electrode materials on the P3HT:PCBM blend.

  12. Synthesis and crystal structure of catena-bis(nicotinamide)aqua({mu}-phthalato)copper(II) hemihydrate

    SciTech Connect

    Sadikov, G. G.; Koksharova, T. V.; Antsyshkina, A. S.; Gritsenko, I. S.; Sergienko, V. S.

    2008-07-15

    The copper(II) phthalate complex with nicotinamide [CuL{sub 2}({mu}-Pht)(H{sub 2}O)] . 0.5H{sub 2}O(I) (where L is nicotinamide and Pht{sup 2-} is an anion of phthalic acid) is synthesized and investigated using IR spectroscopy and X-ray diffraction. The crystals of compound I are monoclinic, a = 13.368(2) A, b = 7.891(3) A, c = 20.480(2) A, {beta} = 108.69(2){sup o}, Z = 4, and space group P2{sub 1}/c. The structural units of crystal I are linear chains formed by bridging phthalate anions and crystallization water molecules. The copper atom is coordinated by two pyridine nitrogen atoms of two nicotinamide ligands (Cu-N, 2.001 and 2.045 A), two oxygen atoms of different phthalate anions (Cu-O, 1.964 and 2.235 A), and the oxygen atom of the H{sub 2} O molecule (Cu-O, 2.014 A). The coordination polyhedron of the copper atom is completed to an elongated (4 + 1 + 1) tetragonal bipyramid by the second (chelating) oxygen atom of the carboxyl group (Cu-O, 2.587 A), which is one of the anions of phthalic acid. The linear polymer molecules are joined into complex macromolecular dimers with the closest internal contacts of the specific type. The macromolecular dimers are the main supramolecular ensembles of the crystal structure.

  13. Synthesis and crystal structure of catena-bis(nicotinamide)aqua(μ-phthalato)copper(II) hemihydrate

    NASA Astrophysics Data System (ADS)

    Sadikov, G. G.; Koksharova, T. V.; Antsyshkina, A. S.; Gritsenko, I. S.; Sergienko, V. S.

    2008-07-01

    The copper(II) phthalate complex with nicotinamide [Cu L 2(μ- Pht)(H2O)] · 0.5H2O( I) (where L is nicotinamide and Pht 2- is an anion of phthalic acid) is synthesized and investigated using IR spectroscopy and X-ray diffraction. The crystals of compound I are monoclinic, a = 13.368(2) Å, b = 7.891(3) Å, c = 20.480(2) Å, β = 108.69(2)°, Z = 4, and space group P21/ c. The structural units of crystal I are linear chains formed by bridging phthalate anions and crystallization water molecules. The copper atom is coordinated by two pyridine nitrogen atoms of two nicotinamide ligands (Cu-N, 2.001 and 2.045 Å), two oxygen atoms of different phthalate anions (Cu-O, 1.964 and 2.235 Å), and the oxygen atom of the H2 O molecule (Cu-O, 2.014 Å). The coordination polyhedron of the copper atom is completed to an elongated (4 + 1 + 1) tetragonal bipyramid by the second (chelating) oxygen atom of the carboxyl group (Cu-O, 2.587 Å), which is one of the anions of phthalic acid. The linear polymer molecules are joined into complex macromolecular dimers with the closest internal contacts of the specific type. The macromolecular dimers are the main supramolecular ensembles of the crystal structure.

  14. Formal Nuclear and Atomic Structure of the Elements

    NASA Astrophysics Data System (ADS)

    Nduka, Amagh

    2004-05-01

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

  15. The ionization structure of helium in H II region complexes

    NASA Astrophysics Data System (ADS)

    Pena, Miriam

    1986-10-01

    Ionization structure models of H II regions are constructed to analyze the behavior of the helium ionization correction factor, icf, for combinations of different stellar radiation fields as well as for mixtures of individual H II regions of different degrees of ionization. It is found that the amount of neutral He is less than 3 percent and that icf is between 0.98 and 1.00, for H II region coomplexes ionized by OB associations where the hottest stars are earlier than O6, if the ionizing stars are distributed according to a normal IMF. This result applies for a single H II region or for a mixture of unconnected H II regions. This result implies that the He(+)/H(+) ratio observed in extragalactic H II regions of high degree of ionization corresponds to the true He/H abundance ratios.

  16. Polarized Atomic Hydrogen Beam Tests in the Mark-II Ultra-Cold Jet Target.

    NASA Astrophysics Data System (ADS)

    Luppov, V. G.; Blinov, B. B.; Gladycheva, S. E.; Kageya, T.; Kantsyrev, D. Yu.; Krisch, A. D.; Murray, J. R.; Neumann, J. J.; Raymond, R. S.; Borisov, N. S.; Kleppner, D.; Davidenko, A. M.; Grishin, V. N.

    2000-04-01

    To study spin effects in high energy collisions, we are developing an ultra-cold high-density jet target of proton-spin-polarized hydrogen atoms (Mark-II). The target uses a 12 Tesla magnetic field and a 0.3 K separation cell coated with superfluid helium-4 to produce a slow monochromatic electron-spin-polarized atomic hydrogen beam; an rf transition unit then converts this into a proton-spin-polarized beam, which is focused by a superconducting sextupole into the interaction region. Recently, the Jet produced a measured electron-spin-polarized atomic hydrogen beam of about 10^15 H s-1 into a 0.3 cm^2 area at the detector. This intensity corresponds to the free jet density of about 10^11 H cm-3 with a proton polarization of about 50%. So far, the intensity is limited by the high insulation vacuum pressure due to the evaporation of the separation cell's helium film. The beam's angular and radial distributions were measured. A test of a new superfluid-^4He-coated parabolic mirror, attached to the separation cell, appeared to increase the beam intensity by a factor of about 3, as expected.

  17. Structure of the Glycyl-L-histidyl-L-lysine--copper(II) complex in solution.

    PubMed

    Freedman, J H; Pickart, L; Weinstein, B; Mims, W B; Peisach, J

    1982-09-14

    Optical, electron paramagnetic resonance, and electron spin-echo envelope spectroscopies were used to examine the structure of the Cu(II) complex of glycyl-L-histidyl-L-lysine (GHL) in solution. At neutral pH, GHL forms a mononuclear 1:1 Cu(II) compound having an EPR spectrum resembling that of Cu(II) equatorially coordinated by two or three nitrogen atoms. Electron spin-echo studies demonstrate that one of these is located in the histidyl imidazole ring. A pH titration of Cu(II)-GHL shows three optical transitions with apparent pKs of 3.6, 9.2 and 11.4 and molecularities, with respect to protons, of 2, 2, and 1, respectively. At the lowest pK, GHL binds Cu(II), forming the species present at physiological pH. At elevated pH, spectroscopic experiments suggest that an alteration of the Cu(II) structure occurs, yet the bound imidazole is retained. These solution studies are consistent with nitrogen coordination of Cu(II) in Cu(II)-GHL, but the solid-state polymeric structure, with oxygen-bridged Cu(II) pairs as previously determined by X-ray crystallographic analysis [Pickart, L., Freedman, J. H., Loker, W. J., Peisach, J., Perkins, C. M., Steinkamp, R. E., & Weinstein, B. (1980) Nature (London) 288, 715-717; C. M. Perkins, N. J. Rose, R. E. Steinkamp, L. H. Jensen, B. Weinstein, and L. Pickart, unpublished results], does not exist in solution. PMID:6291585

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

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

  19. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    PubMed

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

    2016-08-01

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

  20. In Situ D-periodic Molecular Structure of Type II Collagen

    SciTech Connect

    Antipova, Olga; Orgel, Joseph P.R.O.

    2010-05-06

    Collagens are essential components of extracellular matrices in multicellular animals. Fibrillar type II collagen is the most prominent component of articular cartilage and other cartilage-like tissues such as notochord. Its in situ macromolecular and packing structures have not been fully characterized, but an understanding of these attributes may help reveal mechanisms of tissue assembly and degradation (as in osteo- and rheumatoid arthritis). In some tissues such as lamprey notochord, the collagen fibrillar organization is naturally crystalline and may be studied by x-ray diffraction. We used diffraction data from native and derivative notochord tissue samples to solve the axial, D-periodic structure of type II collagen via multiple isomorphous replacement. The electron density maps and heavy atom data revealed the conformation of the nonhelical telopeptides and the overall D-periodic structure of collagen type II in native tissues, data that were further supported by structure prediction and transmission electron microscopy. These results help to explain the observed differences in collagen type I and type II fibrillar architecture and indicate the collagen type II cross-link organization, which is crucial for fibrillogenesis. Transmission electron microscopy data show the close relationship between lamprey and mammalian collagen fibrils, even though the respective larger scale tissue architecture differs.

  1. Synthesis, crystal structure and fluorescence spectrum of a cadmium(II) sulfaquinoxaline complex.

    PubMed

    Zhao, Xiu-Hua; Zhao, Ya-Yun; Zhang, Jie; Pan, Jian-Guo; Li, Xing

    2013-11-01

    catena-Poly[[[4-amino-N-(quinoxalin-2-yl)benzenesulfonamidato]aquacadmium(II)]-μ-4-amino-N-(quinoxalin-2-yl)benzenesulfonamidato], [Cd(C14H11N4O2S)2(H2O)], has been synthesized hydrothermally and characterized by single-crystal X-ray diffraction, elemental analysis, fluorescence, IR and thermal analysis. Single-crystal X-ray analysis reveals that the complex is a one-dimensional zigzag chain structure, and the Cd(II) cation has a distorted octahedral coordination geometry formed by five N atoms from three different sulfaquinoxaline ligands and one O atom from a water molecule. The fluorescence spectrum reveals that the complex emits strong blue fluorescence and thermal analysis shows that the complex has high thermal stability. PMID:24192183

  2. 158 micron forbidden C II mapping of NGC 6946 - Probing the atomic medium

    NASA Technical Reports Server (NTRS)

    Madden, S. C.; Geis, N.; Genzel, R.; Herrmann, F.; Jackson, J.; Poglitsch, A.; Stacey, G. J.; Townes, C. H.

    1993-01-01

    A well-sampled map (23 x 17 kpc) of the strong 158 micron forbidden C II cooling line in the Scd galaxy NGC 6946 at 55 arcsec resolution is presented which was taken with the MPE/UCB Far-infrared Imaging Fabry-Perot Interferometer (FIFI) in the Kuiper Airborne Observatory. It is concluded that the line emission in NGC 6946 is present in three spatially distinct components including nucleus, spiral arms, and extended region. An extended emission region is a source of most of the forbidden C II luminosity in NGC 6946. The 1 arcmin nuclear component has a line luminosity of 1.5 x 10 exp 7 solar luminosity and contributes 0.15 percent of the galaxy's total FIR luminosity. An extended component of forbidden C II emission is found to exist past the molecular extent of the galaxy and to be present to at least the full dimensions of the map. This component is attributed to a mixture of neutral and atomic clouds.

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

    PubMed Central

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

    2015-01-01

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

  4. Polynuclear complexes incorporating Cu(II) and Mn(II) centers bridged by acetylenedicarboxylate: Structure, thermal stability and magnetism

    NASA Astrophysics Data System (ADS)

    Shao, Min; Li, Ming-Xing; Dai, Hui; Lu, Wen-Cong; An, Bao-Li

    2007-03-01

    Two acetylenedicarboxylate complexes, [Mn 2(C 4O 4)(phen) 4(H 2O) 2](ClO 4) 2·H 2O ( 1) and [Cu(C 4O 4)(2,2'-bpy)] n ( 2), have been synthesized and characterized by elemental analyses and IR spectra. Mn II ions have distorted octahedral coordination geometry and bridged by C 4O 42- to form a binuclear structure. Thermal analysis shows C 4O 42- released in the range of 180-280 °C. Cu II is five-coordinated by 2,2'-bipyridine and three oxygen atoms from three different C 4O 42- ligands, leading to a square-pyramidal coordination geometry. Each C 4O 42- links three Cu II centers through bifunctional carboxylate to form a polymeric structure of (4, 4) layers with nodes being dimer of Cu 2O 2 and bridges of C 4O 42-. Its variable-temperature magnetism was also investigated.

  5. Structure and mode of action of cyclic lipopeptide pseudofactin II with divalent metal ions.

    PubMed

    Janek, Tomasz; Rodrigues, Lígia R; Gudiña, Eduardo J; Czyżnikowska, Żaneta

    2016-10-01

    The interaction of natural lipopeptide pseudofactin II with a series of doubly charged metal cations was examined by matrix-assisted laser-desorption ionization-time of flight (MALDI-TOF) mass spectrometry and molecular modelling. The molecular modelling for metal-pseudofactin II provides information on the metal-peptide binding sites. Overall, Mg(2+), Ca(2+) and Zn(2+) favor the association with oxygen atoms spanning the peptide backbone, whereas Cu(2+) is coordinated by three nitrogens. Circular dichroism (CD) results confirmed that Zn(2+) and Cu(2+) can disrupt the secondary structure of pseudofactin II at high concentrations, while Ca(2+) and Mg(2+) did not essentially affect the structure of the lipopeptide. Interestingly, our results showed that the addition of Zn(2+) and Cu(2+) helped smaller micelles to form larger micellar aggregates. Since pseudofactin II binds metals, we tested whether this phenomena was somehow related to its antimicrobial activity against Staphylococcus epidermidis and Proteus mirabilis. We found that the antimicrobial effect of pseudofactin II was increased by supplementation of culture media with all tested divalent metal ions. Finally, by using Gram-positive and Gram-negative bacteria we showed that the higher antimicrobial activity of metal complexes of pseudofactin II is attributed to the disruption of the cytoplasmic membrane. PMID:27416562

  6. Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

    SciTech Connect

    Linko, R. V.; Sokol, V. I.; Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V.; Sergienko, V. S.

    2013-05-15

    The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

  7. Palladium(II) and platinum(II) complexes containing benzimidazole ligands: Molecular structures, vibrational frequencies and cytotoxicity

    NASA Astrophysics Data System (ADS)

    Abdel Ghani, Nour T.; Mansour, Ahmed M.

    2011-04-01

    (1H-benzimidazol-2-ylmethyl)-(4-methoxyl-phenyl)-amine (L 1), (1H-benzimidazol-2-ylmethyl)-(4-methyl-phenyl)-amine (L 2) and their Pd(II) and Pt(II) complexes have been synthesized as potential anticancer compounds and their structures were elucidated using a variety of physico-chemical techniques. Theoretical calculations invoking geometry optimization, vibrational assignments, 1H NMR, charge distribution and molecular orbital description HOMO and LUMO were done using density functional theory. Natural bond orbital analysis (NBO) method was performed to provide details about the type of hybridization and the nature of bonding in the studied complexes. Strong coordination bonds (LP(1)N11 → σ *(M sbnd Cl22)) and (LP(1)N21 → σ *(M sbnd Cl23)) (M = Pd or Pt) result from donation of electron density from a lone pair orbital on the nitrogen atoms to the acceptor metal molecular orbitals. The experimental results and the calculated molecular parameters revealed square-planar geometries around the metallic centre through the pyridine-type nitrogen of the benzimidazole ring and secondary amino group and two chlorine atoms. The activation thermodynamic parameters were calculated using non-isothermal methods. The synthesized ligands, in comparison to their metal complexes were screened for their antibacterial activity. In addition, the studied complexes showed activity against three cell lines of different origin, breast cancer (MCF-7), Colon Carcinoma (HCT) and human heptacellular carcinoma (Hep-G2) comparable to cis-platin.

  8. Interaction of F atoms with SiOCH ultra low-k films. Part II: etching

    NASA Astrophysics Data System (ADS)

    Rakhimova, T. V.; Lopaev, D. V.; Mankelevich, Yu A.; Kurchikov, K. A.; Zyryanov, S. M.; Palov, A. P.; Proshina, O. V.; Maslakov, K. I.; Baklanov, M. R.

    2015-05-01

    The etch mechanism of porous SiOCH-based low-k films by F atoms is studied. Five types of ultra-low-k (ULK) SiOCH films with k-values from 1.8 to 2.5 are exposed to F atoms in the far downstream of an SF6 inductively coupled plasma discharge. The evolution of etching with an F dose was studied using various techniques of surface and material analysis such as FTIR, XPS, EDS and SE. It is revealed that the etch mechanism is connected with surface fluorination and formation of -CHxFy species on the surface due to H abstraction by F atoms from -CH3 groups. It is shown that the etching includes two phases. The first one is observed at the low F doses and is connected with chemical modification and etching of walls in the topmost pores, which finishes when the walls are fully etched. At the same time, the additional etching in the underlying pores due to F penetration forms the etch depth profile, after that the second etching phase starts. This phase is characterized by the higher etch rate due to the propagation of the etch depth profile further into the film. The preliminary treatment of pore walls inside porous channels effectively accelerates etching many times compared to non-porous material. The acceleration depends on the modification depth, which in turn is a function of pore structure and interconnectivity as well as the F atom reaction mechanism. The combined random walk (Monte-Carlo) & kinetics model developed to describe F penetration inside SiOCH films together with reactions of F atoms leading to -CHxFy depletion and opening SiOx bonds for F access allowed relating the increased etch rates with increasing the total number of F atom collisions inside interconnected pores. The etch mechanism of SiOCH films is found in many respects to be similar to the SiO2 etch mechanism on the elementary level, but as whole it is ruled by the SiOCH structure: porosity degree, pore size, pore interconnectivity as well as structural features of SiOx bonds.

  9. Atomic and electronic structures of an extremely fragile liquid

    PubMed Central

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

    2014-01-01

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

  10. Fast atom bombardment mass spectrometry of multiply charged polynuclear rhenium(I)-ruthenium(II) complexes

    SciTech Connect

    Argazzi, R., Bignozzi, C.A.; Bortolini, O. ); Traldi, P. )

    1993-03-31

    The fast atom bombardment (FAB) mass spectrometric behavior of some involatile polynuclear rhenium(I)-ruthenium(II) complexes of general formula [Re(CO)[sub 3](phen)(CN)-[Ru(bpy)[sub 2](CN)]n-Ru(bpy)[sub 2](CN)][sup (n+1)+] (n = 0-2, bpy = 2,2[prime]-bipyridine, phen = 1,10-phenanthroline) is presented. Singly, double, and, for n = 2, also triply charged ions were detected, and the fragmentation patterns of these ionic species were determined by studying unimolecular dissociation reactions. The decomposition pathways involve losses of CO and bpy neutral ligands, oxidative addition of coordinated bpy with expulsion of HX (X = CN[sup [minus

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  13. Topological Properties of Atomic Lead Film with Honeycomb Structure

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2016-08-01

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

  15. Topological Properties of Atomic Lead Film with Honeycomb Structure

    PubMed Central

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

    2016-01-01

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

  16. Electronic Structure of Helium Atom in a Quantum Dot

    NASA Astrophysics Data System (ADS)

    Jayanta, K. Saha; Bhattacharyya, S.; T. K., Mukherjee

    2016-03-01

    Bound and resonance states of helium atom have been investigated inside a quantum dot by using explicitly correlated Hylleraas type basis set within the framework of stabilization method. To be specific, precise energy eigenvalues of bound 1sns (1Se) (n = 1-6) states and the resonance parameters i.e. positions and widths of 1Se states due to 2sns (n = 2-5) and 2pnp (n = 2-5) configurations of confined helium below N = 2 ionization threshold of He+ have been estimated. The two-parameter (Depth and Width) finite oscillator potential is used to represent the confining potential due to the quantum dot. It has been explicitly demonstrated that the electronic structural properties become sensitive functions of the dot size. It is observed from the calculations of ionization potential that the stability of an impurity ion within a quantum dot may be manipulated by varying the confinement parameters. A possibility of controlling the autoionization lifetime of doubly excited states of two-electron ions by tuning the width of the quantum cavity is also discussed here. TKM Gratefully Acknowledges Financial Support under Grant No. 37(3)/14/27/2014-BRNS from the Department of Atomic Energy, BRNS, Government of India. SB Acknowledges Financial Support under Grant No. PSW-160/14-15(ERO) from University Grants Commission, Government of India

  17. Structural relaxation in atomic clusters: Master equation dynamics

    NASA Astrophysics Data System (ADS)

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

    1999-10-01

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

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

    SciTech Connect

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

    2015-06-24

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

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

    SciTech Connect

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

    2011-08-15

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

  20. THE FORMATION OF IRIS DIAGNOSTICS. I. A QUINTESSENTIAL MODEL ATOM OF Mg II AND GENERAL FORMATION PROPERTIES OF THE Mg II h and k LINES

    SciTech Connect

    Leenaarts, J.; Pereira, T. M. D.; Carlsson, M.; De Pontieu, B.; Uitenbroek, H. E-mail: tiago.pereira@astro.uio.no E-mail: bdp@lmsal.com

    2013-08-01

    NASA's Interface Region Imaging Spectrograph (IRIS) space mission will study how the solar atmosphere is energized. IRIS contains an imaging spectrograph that covers the Mg II h and k lines as well as a slit-jaw imager centered at Mg II k. Understanding the observations will require forward modeling of Mg II h and k line formation from three-dimensional (3D) radiation-MHD models. This paper is the first in a series where we undertake this forward modeling. We discuss the atomic physics pertinent to h and k line formation, present a quintessential model atom that can be used in radiative transfer computations, and discuss the effect of partial redistribution (PRD) and 3D radiative transfer on the emergent line profiles. We conclude that Mg II h and k can be modeled accurately with a four-level plus continuum Mg II model atom. Ideally radiative transfer computations should be done in 3D including PRD effects. In practice this is currently not possible. A reasonable compromise is to use one-dimensional PRD computations to model the line profile up to and including the central emission peaks, and use 3D transfer assuming complete redistribution to model the central depression.

  1. Atomic structure of the actin: DNase I complex

    NASA Astrophysics Data System (ADS)

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

    1990-09-01

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

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

    PubMed

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

    2015-10-15

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

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  5. X-ray and solution structures of Cu(II) GHK and Cu(II) DAHK complexes: influence on their redox properties.

    PubMed

    Hureau, Christelle; Eury, Hélène; Guillot, Régis; Bijani, Christian; Sayen, Stéphanie; Solari, Pier-Lorenzo; Guillon, Emmanuel; Faller, Peter; Dorlet, Pierre

    2011-08-29

    The Gly-His-Lys (GHK) peptide and the Asp-Ala-His-Lys (DAHK) sequences are naturally occurring high-affinity copper(II) chelators found in the blood plasma and are hence of biological interest. A structural study of the copper complexes of these peptides was conducted in the solid state and in solution by determining their X-ray structures, and by using a large range of spectroscopies, including EPR and HYSCORE (hyperfine sub-level correlation), X-ray absorption and (1)H and (13)C NMR spectroscopy. The results indicate that the structures of [Cu(II)(DAHK)] in the solid state and in solution are similar and confirm the equatorial coordination sphere of NH(2), two amidyl N and one imidazole N. Additionally, a water molecule is bound apically to Cu(II) as revealed by the X-ray structure. As reported previously in the literature, [Cu(II)(GHK)], which exhibits a dimeric structure in the solid state, forms a monomeric complex in solution with three nitrogen ligands: NH(2), amidyl and imidazole. The fourth equatorial site is occupied by a labile oxygen atom from a carboxylate ligand in the solid state. We probe that fourth position and study ternary complexes of [Cu(II)(GHK)] with glycine or histidine. The Cu(II) exchange reaction between different DAHK peptides is very slow, in contrast to [Cu(II)(GHK)], in which the fast exchange was attributed to the presence of a [Cu(II)(GHK)(2)] complex. The redox properties of [Cu(II)(GHK)] and [Cu(II)(DAHK)] were investigated by cyclic voltammetry and by measuring the ascorbate oxidation in the presence of molecular oxygen. The measurements indicate that both Cu(II) complexes are inert under moderate redox potentials. In contrast to [Cu(II)(DAHK)], [Cu(II)(GHK)] could be reduced to Cu(I) around -0.62 V (versus AgCl/Ag) with subsequent release of the Cu ion. These complete analyses of structure and redox activity of those complexes gave new insights with biological impact and can serve as models for other more complicated Cu(II

  6. Structure of Self-Assembled Mn Atom Chains on Si(001).

    PubMed

    Villarreal, R; Longobardi, M; Köster, S A; Kirkham, Ch J; Bowler, D; Renner, Ch

    2015-12-18

    Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy, and density functional theory we find that a simple necklacelike chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modeling the electronic and magnetic properties of Mn atom chains on Si(001). PMID:26722930

  7. On the atomic structure of cocaine in solution.

    PubMed

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

    2016-01-14

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

  8. First Optical Hyperfine Structure Measurement in an Atomic Anion

    SciTech Connect

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

    2010-02-19

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

  9. Coordination structure of adsorbed Zn(II) at Water-TiO2 interfaces

    SciTech Connect

    He, G.; Pan, G.; Zhang, M.; Waychunas, G.A.

    2011-01-15

    The local structure of aqueous metal ions on solid surfaces is central to understanding many chemical and biological processes in soil and aquatic environments. Here, the local coordination structure of hydrated Zn(II) at water-TiO{sub 2} interfaces was identified by extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectroscopy combined with density functional theory (DFT) calculations. A nonintegral coordination number of average {approx}4.5 O atoms around a central Zn atom was obtained by EXAFS analysis. DFT calculations indicated that this coordination structure was consistent with the mixture of 4-coordinated bidentate binuclear (BB) and 5-coordinated bidentate mononuclear (BM) metastable equilibrium adsorption (MEA) states. The BB complex has 4-coordinated Zn, while the monodentate mononuclear (MM) complex has 6-coordinated Zn, and a 5-coordinated adsorbed Zn was found in the BM adsorption mode. DFT calculated energies showed that the lower-coordinated BB and BM modes were thermodynamically more favorable than the higher-coordinated MM MEA state. The experimentally observed XANES fingerprinting provided additional direct spectral evidence of 4- and 5-coordinated Zn-O modes. The overall spectral and computational evidence indicated that Zn(II) can occur in 4-, 5-, and 6-oxygen coordinated sites in different MEA states due to steric hindrance effects, and the coexistence of different MEA states formed the multiple coordination environments.

  10. Crystal structures of copper(II) nitrate complexes containing 4,4'-bipyridyl and halogen-substituted 2-[(2-hydroxyethylimino)methyl]phenols

    NASA Astrophysics Data System (ADS)

    Chumakov, Yu. M.; Tsapkov, V. I.; Petrenko, P. A.; Popovski, L. G.; Simonov, Yu. A.; Bocelli, G.; Gulea, A. P.

    2009-03-01

    The crystal structures of (μ-4,4’-bipyridyl)-di{nitrato-2,4-dibromo-6-[(2-hydroxyethylimino)methyl]phenolo (1-)copper} ( I), (μ-4,4’-bipyridyl)-di{nitrato-2,4-dichloro-6-[(2-hydroxyethylimino)methyl]phenolo(1-)copper} ( II), and (μ-4,4’-bipyridyl)-{4-chloro-2-[(2-hydroxyethylimino)methyl]phenolo(2-)copper-nitrato-4-chloro-2-[(2-hydroxyethylimino)methyl]phenolo(1-)copper} tetrahydrate ( III) are determined. The crystal structures of compounds I and II contain binuclear complexes, in which each copper atom is coordinated by the singly deprotonated tridentate molecule of the corresponding azomethine, the monodentate nitrate ion, and bipyridyl that plays the role of a bridge between the central atoms. In the structures of compounds I and II, the coordination polyhedra of the copper atoms are slightly distorted tetragonal pyramids. The pyramid base is formed by the imine and bipyridyl nitrogen atoms and the phenol and alcohol oxygen atoms. The axial vertices of the pyramids are occupied by the oxygen atoms of the monodentate nitrato groups. The crystal structure of compound III involves tetranuclear complexes in which the coordination polyhedra of the central copper atoms are (4 + 1 + 1) bipyramids. The base of these bipyramids is formed by the imine and bipyridyl nitrogen atoms and the phenol and alcohol oxygen atoms. One apical vertex is occupied by the bridging phenol oxygen atom of the nearest complex. The sixth coordination site of the first copper atom is occupied by the chlorine atom of the salicylidene fragment of the neighboring complex related to the initial complex through the center of symmetry. In turn, the sixth coordination site of the second copper atom is occupied by the oxygen atom of the monodentate nitrato group.

  11. COLLISIONAL EXCITATION OF THE [C II] FINE STRUCTURE TRANSITION IN INTERSTELLAR CLOUDS

    SciTech Connect

    Goldsmith, Paul F.; Langer, William D.; Pineda, Jorge L.; Velusamy, T.

    2012-11-15

    We analyze the collisional excitation of the 158 {mu}m (1900.5 GHz) fine structure transition of ionized carbon in terms of line intensities produced by simple cloud models. The single C{sup +} fine structure transition is a very important coolant of the atomic interstellar medium (ISM) and of photon-dominated regions in which carbon is partially or completely in ionized form. The [C II] line is widely used as a tracer of star formation in the Milky Way and other galaxies. Excitation of the [C II] fine structure transition can be via collisions with hydrogen molecules, atoms, and electrons. Analysis of [C II] observations is complicated by the fact that it is difficult to determine the optical depth of the line. We discuss the excitation of the [C II] line, deriving analytic results for several limiting cases and carry out numerical solutions using a large velocity gradient model for a more inclusive analysis. For antenna temperatures up to 1/3 of the brightness temperature of the gas kinetic temperature, the antenna temperature is linearly proportional to the column density of C{sup +} irrespective of the optical depth of the transition. This is appropriately referred to as the effectively optically thin approximation. We review the critical densities for excitation of the [C II] line by various collision partners, briefly analyze C{sup +} absorption, and conclude with a discussion of C{sup +} cooling and how the considerations for line intensities affect the behavior of this important coolant of the ISM.

  12. Cation-Poor Complex Metallic Alloys in Ba(Eu)-Au-Al(Ga) Systems: Identifying the Keys that Control Structural Arrangements and Atom Distributions at the Atomic Level.

    PubMed

    Smetana, Volodymyr; Steinberg, Simon; Mudryk, Yaroslav; Pecharsky, Vitalij; Miller, Gordon J; Mudring, Anja-Verena

    2015-11-01

    Four complex intermetallic compounds BaAu(6±x)Ga(6±y) (x = 1, y = 0.9) (I), BaAu(6±x)Al(6±y) (x = 0.9, y = 0.6) (II), EuAu6.2Ga5.8 (III), and EuAu6.1Al5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn13-type structure (cF104-112, Fm3̅c), III (tP52, P4/nbm) is derived from the tetragonal Ce2Ni17Si9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupation by Au and triel (Tr = Al, Ga) atoms, while a successive decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution ("coloring scheme"). Chemical bonding analyses for two different "EuAu6Tr6" models reveal maximization of the number of heteroatomic Au-Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the "EuAu6Tr6" models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu6.2Ga5.8 (III) and EuAu6.1Al5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at TC = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. The effective moments of 8.3 μB/f.u., determined from Curie-Weiss fits, point to divalent oxidation states for europium in both III and IV. PMID:26479308

  13. Crystal Structure of a Self-Spliced Group II Intron

    SciTech Connect

    Toor, Navtej; Keating, Kevin S.; Taylor, Sean D.; Pyle, Anna Marie

    2008-04-10

    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.

  14. The grasp2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

    This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel

  15. OD(X/sup 2/II) and SD(X/sup 2/II) from reactions of D atoms with OCS under bulk and precursor geometry limited conditions

    SciTech Connect

    Haeusler, D.; Rice, J.; Wittig, C.

    1987-10-08

    Reactions of D atoms with OCS were studied by 193-nm pulsed laser photolysis of DBr as a nearly monoenergetic D-atom source. Nascent OD(X/sup 2/II) and SD(X/sup 2/II) rotational, vibrational, spin-orbit, and ..lambda..-doublet populations were obtained under single-collision bulk conditions at 300 K. The SD channel is favored energetically (..delta.. H = -43 +/- 13 and 230 +/- 13 kJ mol/sup -1/ for the SD and OD channels, respectively) and is the dominant pathway ((SD)/(OD) = 5 +/- 2). Nascent OD(X/sup 2/II) products were also obtained from a precursor geometry limited (PGL) reaction by using the weakly bound van der Waals complex SCO-DBr. The OD(X/sup 2/II) rotational distributions are the same for both bulk and PGL conditions and can be reproduced by using a statistical model. Due to experimental difficulties, SD(X/sup 2/II) distributions could not be obtained under PGL conditions. The SD(X/sup 2/II) distribution obtained under bulk conditions is very nonstatistical, suggesting that this species is not formed via a long-lived DSCO intermediate complex in which vibrational energy is randomized.

  16. Solubility of Structurally Complicated Materials: II. Bone

    NASA Astrophysics Data System (ADS)

    Horvath, Ari L.

    2006-12-01

    Bone is a structurally complex material, formed of both organic and inorganic chemicals. The organic compounds constitute mostly collagen and other proteins. The inorganic or bone mineral components constitute predominantly calcium, phosphate, carbonate, and a host of minor ingredients. The mineralized bone is composed of crystals which are closely associated with a protein of which collagen is an acidic polysaccharide material. This association is very close and the protein integrates into the crystalline structure. The mineralization involves the deposition of relatively insoluble crystals on an organic framework. The solubility process takes place when the outermost ions in the crystal lattice breakaway from the surface and become separated from the crystal. This is characteristic for ions dissolving in water or aqueous solutions at the specified temperature. The magnitude of solubility is temperature and pH dependent. Bone is sparingly soluble in most solvents. Enamel is less soluble than bone and fluoroapatite is the least soluble of all apatites in acid buffers. Collagen is less soluble in neutral salt solution than in dilute acid solutions at ambient temperatures. The solubility of collagens in solvents gradually decreases with increasing age of the bone samples.

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

    PubMed

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

    2009-11-01

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

  18. Synthesis, Crystal Structure, and Thermal Decomposition of the Cobalt(II) Complex with 2-Picolinic Acid

    PubMed Central

    Li, Di

    2014-01-01

    The cobalt(II) complex of 2-picolinic acid (Hpic), namely, [Co(pic)2(H2O)2] · 2H2O, was synthesized with the reaction of cobalt acetate and 2-picolinic acid as the reactants by solid-solid reaction at room temperature. The composition and structure of the complex were characterized by elemental analysis, infrared spectroscopy, single crystal X-ray diffraction, and thermogravimetry-differential scanning calorimetry (TG-DSC). The crystal structure of the complex belongs to monoclinic system and space group P2(1)/n, with cell parameters of a = 9.8468(7) Å, b = 5.2013(4) Å, c = 14.6041(15) Å, β = 111.745(6)°, V = 747.96(11) Å3, Z = 2, Dc = 1.666 g cm−3, R1 = 0.0297, and wR2 = 0.0831. In the title complex, the Co(II) ion is six-coordinated by two pyridine N atoms and two carboxyl O atoms from two 2-picolinic acid anions, and two O atoms from two H2O molecules, and forming a slightly distorted octahedral geometry. The thermal decomposition processes of the complex under nitrogen include dehydration and pyrolysis of the ligand, and the final residue is cobalt oxalate at about 450°C. PMID:24578654

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  20. Atomic layer epitaxy of II-VI quantum wells and superlattices

    NASA Astrophysics Data System (ADS)

    Faschinger, W.

    1993-01-01

    Atomic Layer Epitaxy (ALE) under ultra high vacuum conditions is a variation of MBE which makes use of a self-regulating growth process, leading to digital growth in steps of monolayers or even fractions of monolayers. We report on fundamental aspects of the ALE growth of tellurides and selenides, and give three examples on the physics of ALE-grown structures: (a) Phonon confinement in CdTe/ZnTe superlattices (b) "Spin Sheet" superlattices of cubic MnTe with CdTe and (c) Luminescence tuning in ultra-thin CdSe quantum wells embedded in ZnSe.

  1. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    SciTech Connect

    Chen, Liqing Wang, Yujun; Wells, David; Toh, Diana; Harold, Hunt; Zhou, Jing; DiGiammarino, Enrico; Meehan, Edward J.

    2006-09-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

  2. An atomic structure of human γ-secretase

    PubMed Central

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

    2015-01-01

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

  3. An atomic structure of human γ-secretase

    NASA Astrophysics Data System (ADS)

    Bai, Xiao-Chen; Yan, Chuangye; Yang, Guanghui; Lu, Peilong; Ma, Dan; Sun, Linfeng; Zhou, Rui; Scheres, Sjors H. W.; Shi, Yigong

    2015-09-01

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

  4. Elongation factor TFIIS contains three structural domains: solution structure of domain II.

    PubMed Central

    Morin, P E; Awrey, D E; Edwards, A M; Arrowsmith, C H

    1996-01-01

    Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. Limited proteolytic digestion showed that yeast TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III) are required for transcription activity. The structure of domain III has been solved previously by using NMR spectroscopy. Here, we report the NMR-derived structure of domain II: a three-helix bundle built around a hydrophobic core composed largely of three tyrosines protruding from one face of the C-terminal helix. The arrangement of known inactivating mutations of TFIIS suggests that two surfaces of domain II are critical for transcription activity. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855225

  5. Which One Is Better? Jigsaw II versus Jigsaw IV on the Subject of the Building Blocks of Matter and Atom

    ERIC Educational Resources Information Center

    Turkmen, Hakan; Buyukaltay, Didem

    2015-01-01

    In this study, the effect of using Jigsaw II and Jigsaw IV techniques on the subject of "Atoms-The Basic Unit of Matter" in science course of 6th grade on academic achievement was examined. Pre-test post-test control group research was used in the study. Study population is all secondary schools in Turgutlu district of Manisa province…

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

    PubMed

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

    2009-05-01

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

  7. Synthesis, X-Ray Structure, and Characterization of Catena-bis(benzoate)bis{N,N-bis(2-hydroxyethyl)glycinate}cadmium(II)

    PubMed Central

    Katsoulakou, Eugenia; Konidaris, Konstantis F.; Raptopoulou, Catherine P.; Psyharis, Vassilis; Manessi-Zoupa, Evy; Perlepes, Spyros P.

    2010-01-01

    The reaction of N, N-bis(2-hydroxyethyl)glycine (bicine; bicH3) with Cd(O2CPh)2 · 2H2O in MeOH yielded the polymeric compound [Cd2(O2CPh)2(bicH2)2]n(1). The complex crystallizes in the tetragonal space group P41212. The lattice constants are a = b = 12.737(5) and c = 18.288(7) Å. The compound contains chains of repeating {Cd2(O2CPh)2(bicH2)2} units. One CdII atom is coordinated by two carboxylate oxygen, four hydroxyl oxygen, and two nitrogen atoms from two symmetry-related 2.21111 (Harris notation) bicH2− ligands. The other CdII atom is coordinated by six carboxylate oxygen atoms, four from two bicH2− ligands and two from the monodentate benzoate groups. Each bicinate(-1) ligand chelates the 8-coordinate, square antiprismatic CdII atom through one carboxylate oxygen, the nitrogen, and both hydroxyl oxygen atoms and bridges the second, six-coordinate trigonal prismatic CdII center through its carboxylate oxygen atoms. Compound 1 is the first structurally characterized cadmium(II) complex containing any anionic form of bicine as ligand. IR data of 1 are discussed in terms of the coordination modes of the ligands and the known structure. PMID:20976297

  8. Synthesis, X-Ray Structure, and Characterization of Catena-bis(benzoate)bis{N,N-bis(2-hydroxyethyl)glycinate}cadmium(II).

    PubMed

    Katsoulakou, Eugenia; Konidaris, Konstantis F; Raptopoulou, Catherine P; Psyharis, Vassilis; Manessi-Zoupa, Evy; Perlepes, Spyros P

    2010-01-01

    The reaction of N, N-bis(2-hydroxyethyl)glycine (bicine; bicH(3)) with Cd(O(2)CPh)(2) · 2H(2)O in MeOH yielded the polymeric compound [Cd(2)(O(2)CPh)(2)(bicH(2))(2)](n)(1). The complex crystallizes in the tetragonal space group P4(1)2(1)2. The lattice constants are a = b = 12.737(5) and c = 18.288(7) Å. The compound contains chains of repeating {Cd(2)(O(2)CPh)(2)(bicH(2))(2)} units. One Cd(II) atom is coordinated by two carboxylate oxygen, four hydroxyl oxygen, and two nitrogen atoms from two symmetry-related 2.21111 (Harris notation) bicH(2) (-) ligands. The other Cd(II) atom is coordinated by six carboxylate oxygen atoms, four from two bicH(2) (-) ligands and two from the monodentate benzoate groups. Each bicinate(-1) ligand chelates the 8-coordinate, square antiprismatic Cd(II) atom through one carboxylate oxygen, the nitrogen, and both hydroxyl oxygen atoms and bridges the second, six-coordinate trigonal prismatic Cd(II) center through its carboxylate oxygen atoms. Compound 1 is the first structurally characterized cadmium(II) complex containing any anionic form of bicine as ligand. IR data of 1 are discussed in terms of the coordination modes of the ligands and the known structure. PMID:20976297

  9. New version: GRASP2K relativistic atomic structure package

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  10. Does atomic polarizability play a role in hydrogen radio recombination spectra from Galactic H II regions?

    NASA Astrophysics Data System (ADS)

    Hey, J. D.

    2013-09-01

    Since highly excited atoms, which contribute to the radio recombination spectra from Galactic H II regions, possess large polarizabilities, their lifetimes are influenced by ion (proton)-induced dipole collisions. It is shown that, while these ion-radiator collisional processes, if acting alone, would effectively limit the upper principal quantum number attainable for given plasma parameters, their influence is small relative to that of electron impacts within the framework of line broadening theory. The present work suggests that ion-permanent dipole interactions (Hey et al 2004 J. Phys. B: At. Mol. Opt. Phys. 37 2543) would also be of minor importance in limiting the occupation of highly excited states. On the other hand, the ion-induced dipole collisions are essential for ensuring equipartition of energy between atomic and electron kinetic distributions (Hey et al 1999 J. Phys. B: At. Mol. Opt. Phys. 32 3555; 2005 J. Phys. B: At. Mol. Opt. Phys. 38 3517), without which Voigt profile analysis to extract impact broadening widths would not be possible. Electron densities deduced from electron impact broadening of individual lines (Griem 1967 Astrophys. J. 148 547; Watson 2006 J. Phys. B: At. Mol. Opt. Phys. 39 1889) may be used to check the significance of the constraints arising from the present analysis. The spectra of Bell et al (2000 Publ. Astron. Soc. Pac. 112 1236; 2011 Astrophys. Space Sci. 333 377; 2011 Astrophys. Space Sci. 335 451) for Orion A and W51 in the vicinity of 6.0 and 17.6 GHz are examined in this context, and also in terms of a possible role of the background ion microfield in reducing the near-elastic contributions to the electron impact broadening below the predictions of theory (Hey 2012 J. Phys. B: At. Mol. Opt. Phys. 45 065701). These spectra are analysed, subject to the constraint that calculated relative intensities of lines, arising from upper states in collisional-radiative equilibrium, should be consistent with those obtained from

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

    ERIC Educational Resources Information Center

    Inner London Education Authority (England).

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

  12. General contraction of Gaussian basis sets. II - Atomic natural orbitals and the calculation of atomic and molecular properties

    NASA Technical Reports Server (NTRS)

    Almlof, Jan; Taylor, Peter R.

    1990-01-01

    A recently proposed scheme for using natural orbitals from atomic configuration interaction wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outermost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital sets.

  13. Structured Forms Reference Set of Binary Images II (SFRS2)

    National Institute of Standards and Technology Data Gateway

    NIST Structured Forms Reference Set of Binary Images II (SFRS2) (PC database for purchase)   The second NIST database of structured forms (Special Database 6) consists of 5,595 pages of binary, black-and-white images of synthesized documents containing hand-print. The documents in this database are 12 different tax forms with the IRS 1040 Package X for the year 1988.

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

    PubMed

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

    2004-12-01

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

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

    PubMed

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

    2016-04-21

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

  16. Atomic structures and electronic properties of phosphorene grain boundaries

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    SciTech Connect

    Sobolev, Andrey; Mirzoev, Alexander

    2015-08-17

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

  18. A new tetranuclear copper(II) Schiff base complex containing Cu 4O 4 cubane core: Structural and spectral characterizations

    NASA Astrophysics Data System (ADS)

    Shit, Shyamapada; Rosair, Georgina; Mitra, Samiran

    2011-04-01

    A new tetra-nuclear coordination complex [Cu 4(HL) 4] ( 1) containing Cu 4O 4 cubane core has been synthesized by using Schiff base ligand [(OH)C 6H 4CH dbnd N sbnd C(CH 3)(CH 2OH) 2] (H 3L), obtained by the 1:1 condensation of 2-amino-2-methyl-1,3-propanediol with salicylaldehyde and thoroughly characterized by micro-analytical, FT-IR, UV-Vis, thermal and room temperature magnetic susceptibility measurements. Structural characterization of the complex has been done by single crystal X-ray diffraction analysis. Structural elucidation reveals versatile coordination modes for two identical alkoxo oxygen atoms of the Schiff base ligand; one in its deprotonated form exhibits μ 3-bridging to bind three similar copper(II) centers whilst the protonated one remains as monodentate or non-coordinating. Structural analysis also shows that the Cu 4O 4 cubane core in 1 consists of four μ 3-alkoxo oxygen bridged copper(II) atoms giving an approximately cubic array of alternating oxygen atoms and copper(II) atoms where the metal centers display both distorted square pyramidal and distorted octahedral geometries.

  19. Cis-Diammine(Pyridine)Chloroplatinum(II), a Monofunctional Platinum(II) Antitumor Agent: Uptake, Structure, Function, And Prospects

    SciTech Connect

    Lovejoy, K.S.; Todd, R.C.; Zhang, S.; McCormick, M.S.; D'Aquino, J.A.; Reardon, J.T.; Sancar, A.; Giacomini, K.M.; Lippard, S.J.

    2009-05-19

    We have identified unique chemical and biological properties of a cationic monofunctional platinum(II) complex, cis-diammine(pyridine)chloroplatinum(II), cis-[Pt(NH{sub 3}){sub 2}(py)Cl]{sup +} or cDPCP, a coordination compound previously identified to have significant anticancer activity in a mouse tumor model. This compound is an excellent substrate for organic cation transporters 1 and 2, also designated SLC22A1 and SLC22A2, respectively. These transporters are abundantly expressed in human colorectal cancers, where they mediate uptake of oxaliplatin, cis-[Pt(DACH)(oxalate)] (DACH = trans-R,R-1,2-diaminocyclohexane), an FDA-approved first-line therapy for colorectal cancer. Unlike oxaliplatin, however, cDPCP binds DNA monofunctionally, as revealed by an x-ray crystal structure of cis-{l_brace}Pt(NH{sub 3}){sub 2}(py){r_brace}{sup 2+} bound to the N7 atom of a single guanosine residue in a DNA dodecamer duplex. Although the quaternary structure resembles that of B-form DNA, there is a base-pair step to the 5{prime} side of the Pt adduct with abnormally large shift and slide values, features characteristic of cisplatin intrastrand cross-links. cDPCP effectively blocks transcription from DNA templates carrying adducts of the complex, unlike DNA lesions of other monofunctional platinum(II) compounds like {l_brace}Pt(dien){r_brace}{sup 2+}. cDPCP-DNA adducts are removed by the nucleotide excision repair apparatus, albeit much less efficiently than bifunctional platinum-DNA intrastrand cross-links. These exceptional characteristics indicate that cDPCP and related complexes merit consideration as therapeutic options for treating colorectal and other cancers bearing appropriate cation transporters.

  20. Atomic layer deposited titanium dioxide coatings on KD-II silicon carbide fibers and their characterization

    NASA Astrophysics Data System (ADS)

    Cao, Shiyi; Wang, Jun; Wang, Hao

    2016-03-01

    To provide oxidation protection and/or to act as an interfacial coating, titanium oxide (TiO2) coatings were deposited on KD-II SiC fibers by employing atomic layer deposition (ALD) technique with tetrakis(dimethylamido)titanium (TDMAT) and water (H2O) as precursors. The average deposition rate was about 0.08 nm per cycle, and the prepared coatings were smooth, uniform and conformal, shielding the fibers entirely. The as-deposited coatings were amorphous regardless of the coating thickness, and changed to anatase and rutile crystal phase after annealing at 600 °C and 1000 °C, respectively. The oxidation measurement suggests that the TiO2 coating enhanced the oxidation resistance of SiC fibers obviously. SiC fibers coated with a 70-nm-thick TiO2 layer retained a relatively high tensile strength of 1.66 GPa even after exposition to air at 1400 °C for 1 h, and thick silica layer was not observed. In contrast, uncoated SiC fibers were oxidized dramatically through the same oxidation treatment, covered with a macro-cracked thick silica film, and the tensile strength was not measurable due to interfilament adhesion. The above results indicate that TiO2 films deposited by ALD are a promising oxidation resistance coating for SiC fibers.

  1. Nickel(II) and zinc(II) dibenzoylmethanates: molecular and crystal structure, polymorphism, and guest- or temperature-induced oligomerization.

    PubMed

    Soldatov, D V; Henegouwen, A T; Enright, G D; Ratcliffe, C I; Ripmeester, J A

    2001-03-26

    Four forms of nickel(II) and two of zinc(II) dibenzoylmethanates have been isolated and characterized with powder and single-crystal X-ray diffraction analyses, differential scanning calorimetry, magnetic susceptibility measurements, and solid-state 13C cross-polarization/magic angle spinning NMR. Nickel dibenzoylmethanate, Ni(DBM)2 (DBM = PhCOCHCOPh-), forms three polymorphic forms (light-green, brown, and green) and a fourth clathrate form with guest benzene included. The light-green polymorph is metastable. Substituted benzenes induce recrystallization of the polymorph into a stable brown form (C30H22NiO4; a = 26.502(3) A, b = 5.774(1) A, c = 16.456(2) A, beta = 116.03(1) degrees; monoclinic, C2/c; Z = 4). Unlike the other forms, the brown form is diamagnetic and is comprised of monomers of the low-spin [Ni(DBM)2] complex. The Ni(II) is chelated by two DBM ligands in a square planar environment by four donor oxygen atoms. When heated, the brown form transforms to a green form which is stable above 202 degrees C (C90H66Ni3O12; a = 13.819(2) A, b = 16.252(2) A, c = 17.358(2) A, beta = 108.28(1) degrees; monoclinic, P2(1)/n; Z = 2). This polymorph is formed by van der Waals packing of trimers [Ni3(DBM)6] containing linear Ni3 clusters with an Ni-Ni distance of 2.81 A. The cluster is surrounded by six DBM ligands, providing a distorted octahedral environment about each Ni by six oxygen atoms. Benzene stabilizes the trimeric structure at room temperature, forming a [Ni3(DBM)6].2(benzene) inclusion compound (Ni-Ni distance of 2.83 A) with guest benzene molecules located in channels (C90H66Ni3O12 + 2(C6H6); a = 17.670(2) A, b = 20.945(3) A, c=11.209(2) A, beta = 102.57(1) degrees; monoclinic, P2(1)/c; Z = 2). Zinc dibenzoylmethanate has been prepared in two polymorphic forms. The monomeric form contains [Zn(DBM)2] molecules with the zinc center in a distorted tetrahedral environment of four oxygens from the two chelated DBMs (C30H22O4Zn; a = 10.288(2) A, b = 10

  2. Conserved structures of mediator and RNA polymerase II holoenzyme.

    PubMed

    Asturias, F J; Jiang, Y W; Myers, L C; Gustafsson, C M; Kornberg, R D

    1999-02-12

    Single particles of the mediator of transcriptional regulation (Mediator) and of RNA polymerase II holoenzyme were revealed by electron microscopy and image processing. Mediator alone appeared compact, but at high pH or in the presence of RNA polymerase II it displayed an extended conformation. Holoenzyme contained Mediator in a fully extended state, partially enveloping the globular polymerase, with points of apparent contact in the vicinity of the polymerase carboxyl-terminal domain and the DNA-binding channel. A similarity in appearance and conformational behavior of yeast and murine complexes indicates a conservation of Mediator structure among eukaryotes. PMID:9974391

  3. Crystal structure of di-chlorido-bis-(dimethyl N-cyano-dithio-imino-carbonate)cobalt(II).

    PubMed

    Diop, Mouhamadou Birame; Diop, Libasse; Oliver, Allen G

    2016-01-01

    The structure of the mononuclear title complex, [{(H3CS)2C=NC  N}2CoCl2], consists of a Co(II) atom coordinated in a distorted tetra-hedral manner by two Cl(-) ligands and the terminal N atoms of two dimethyl N-cyano-dithio-imino-carbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6)° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C-H⋯Cl and C-H⋯S inter-actions and π-π stacking [centroid-to-centroid distance = 3.515 (su?) Å]. Additional C-H⋯Cl and C-H⋯S inter-actions, as well as Cl⋯S contacts < 3.6 Å, consolidate the crystal packing. PMID:26870588

  4. Theoretical Study of the Properties of the Type II Clathrate A^xSn^136, (A = alkali atom; 0 <= x <= 24)

    NASA Astrophysics Data System (ADS)

    Xue, Dong; Higgins, Craig; Myles, Charley

    2012-10-01

    Motivated by recent experimental and theoretical interest in the x dependence of the properties of the Si and Ge-based Type II clathrate materials A^xSi^136 and A^xGe^136 (A = alkali atom) [1,2] we are carrying out a systematic theoretical study of the properties of the Sn-based Type II clathrate system A^xSn^136. Type II clathrates have cage-like lattices in which Si, Ge, or Sn atoms are tetrahedrally-coordinated and sp3 covalently bonded. The cages can contain ``guests''; usually alkali or alkaline earth atoms. These materials are particularly interesting because of their potential use as thermoelectrics. Recent powder X-ray diffraction experiments have found the very interesting result that, for increasing x in the range 0 <= x <= 8 a lattice contraction occurs, and that x is increased further (8 <= x <= 24), a contrasting lattice expansion results. These observations have motivated us to study the behavior of the lattice constant and other properties as a function of guest concentration in other Type II clathrates. In the present paper, we report preliminary results of a density functional based theoretical study of the properties of K^xSn^136 as a function of x. We present results for the x dependence of the lattice constant as well as for other structural and electronic properties of this material. [4pt] [1] S. Stefanoski and G. Nolas, Cryst. Growth Des. 2011, dx.doi.org/10.1021/cg200756r[0pt] [2] M. Beekman, E. Nenghabi, K. Biswas, C. Myles, M. Baitinger, Y. Grin, G.S. Nolas, Inorg. Chem. 49 2010, DOI: 10.1021/ic1005049

  5. Atomic Force Microscopy of Photosystem II and Its Unit Cell Clustering Quantitatively Delineate the Mesoscale Variability in Arabidopsis Thylakoids

    PubMed Central

    Onoa, Bibiana; Schneider, Anna R.; Brooks, Matthew D.; Grob, Patricia; Nogales, Eva; Geissler, Phillip L.; Niyogi, Krishna K.; Bustamante, Carlos

    2014-01-01

    Photoautotrophic organisms efficiently regulate absorption of light energy to sustain photochemistry while promoting photoprotection. Photoprotection is achieved in part by triggering a series of dissipative processes termed non-photochemical quenching (NPQ), which depend on the re-organization of photosystem (PS) II supercomplexes in thylakoid membranes. Using atomic force microscopy, we characterized the structural attributes of grana thylakoids from Arabidopsis thaliana to correlate differences in PSII organization with the role of SOQ1, a recently discovered thylakoid protein that prevents formation of a slowly reversible NPQ state. We developed a statistical image analysis suite to discriminate disordered from crystalline particles and classify crystalline arrays according to their unit cell properties. Through detailed analysis of the local organization of PSII supercomplexes in ordered and disordered phases, we found evidence that interactions among light-harvesting antenna complexes are weakened in the absence of SOQ1, inducing protein rearrangements that favor larger separations between PSII complexes in the majority (disordered) phase and reshaping the PSII crystallization landscape. The features we observe are distinct from known protein rearrangements associated with NPQ, providing further support for a role of SOQ1 in a novel NPQ pathway. The particle clustering and unit cell methodology developed here is generalizable to multiple types of microscopy and will enable unbiased analysis and comparison of large data sets. PMID:25007326

  6. X-ray crystal structure of anhydrous chitosan at atomic resolution.

    PubMed

    Naito, Philip-Kunio; Ogawa, Yu; Sawada, Daisuke; Nishiyama, Yoshiharu; Iwata, Tadahisa; Wada, Masahisa

    2016-07-01

    We determined the crystal structure of anhydrous chitosan at atomic resolution, using X-ray fiber diffraction data extending to 1.17 Å resolution. The unit cell [a = 8.129(7) Å, b = 8.347(6) Å, c = 10.311(7) Å, space group P21 21 21 ] of anhydrous chitosan contains two chains having one glucosamine residue in the asymmetric unit with the primary hydroxyl group in the gt conformation, that could be directly located in the Fourier omit map. The molecular arrangement of chitosan is very similar to the corner chains of cellulose II implying similar intermolecular hydrogen bonding between O6 and the amine nitrogen atom, and an intramolecular bifurcated hydrogen bond from O3 to O5 and O6. In addition to the classical hydrogen bonds, all the aliphatic hydrogens were involved in one or two weak hydrogen bonds, mostly helping to stabilize cohesion between antiparallel chains. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 361-368, 2016. PMID:26930586

  7. Tetranuclear manganese(II) complexes of sulfonylcalix[4]arene macrocycles: synthesis, structure, spectroscopic and magnetic properties.

    PubMed

    Lamouchi, Meriem; Jeanneau, Erwann; Pillonnet, Anne; Brioude, Arnaud; Martini, Matteo; Stéphan, Olivier; Meganem, Faouzi; Novitchi, Ghenadie; Luneau, Dominique; Desroches, Cédric

    2012-03-01

    Two tetranuclear manganese(II) complexes {K(+)[Mn(4)(ThiaSO(2))(2)(OH)](-)} (1) and {K(+)[Mn(4)(ThiaSO(2))(2)(F)](-)} (2) have been synthesized under solvothermal conditions in methanol with p-tert-butylsulfonylcalix[4]arene (ThiaSO(2)). For both complexes, the structure has been established from single-crystal X-ray diffraction. The two complexes are best described as manganese squares sandwiched between two thiacalixarene macrocycles. In both complexes, in the center of the square formed by the four manganese(II) atoms, the unexpected presence of μ(4)-OH(-) or μ(4)-F(-) gives a negative charge to the cluster. The two tetranuclear complexes exhibit strong orange luminescence behavior resulting from the symbiosis between the ThiaSO(2) and the Mn(2+). Despite similar chemical formulation, (1) and (2) present difference in emission intensity and lifetime τ. PMID:22266843

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

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

  9. Structural insights into transcription initiation by RNA polymerase II

    PubMed Central

    Grünberg, Sebastian; Hahn, Steven

    2013-01-01

    Transcriptional regulation is one of the most important steps in control of cell identity, growth, differentiation and development. Many signaling pathways controlling these processes ultimately target the core transcription machinery that, for protein coding genes, consists of RNA polymerase II (Pol II) and the general transcription factors (GTFs). New studies on the structure and mechanism of the core assembly and how it interfaces with promoter DNA and coactivator complexes have given tremendous insight into early steps in the initiation process, genome-wide binding, and mechanisms conserved for all nuclear and archaeal Pols. Here we review recent developments in dissecting the architecture of the Pol II core machinery with a focus on early and regulated steps in transcription initiation. PMID:24120742

  10. The structure of the local interstellar medium. VI. New Mg II, Fe II, and Mn II observations toward stars within 100 pc

    SciTech Connect

    Malamut, Craig; Redfield, Seth; Linsky, Jeffrey L.; Wood, Brian E.; Ayres, Thomas R. E-mail: sredfield@wesleyan.edu

    2014-05-20

    We analyze high-resolution spectra obtained with the Space Telescope Imaging Spectrograph onboard the Hubble Space Telescope toward 34 nearby stars (≤100 pc) to record Mg II, Fe II, and Mn II absorption due to the local interstellar medium (LISM). Observations span the entire sky, probing previously unobserved regions of the LISM. The heavy ions studied in this survey produce narrow absorption features that facilitate the identification of multiple interstellar components. We detected one to six individual absorption components along any given sight line, and the number of absorbers roughly correlates with the pathlength. This high-resolution near-ultraviolet (NUV) spectroscopic survey was specifically designed for sight lines with existing far-UV (FUV) observations. The FUV spectra include many intrinsically broad absorption lines (i.e., of low atomic mass ions) and are often observed at medium resolution. The LISM NUV narrow-line absorption component structure presented here can be used to more accurately interpret the archival FUV observations. As an example of this synergy, we present a new analysis of the temperature and turbulence along the line of sight toward ε Ind. The new observations of LISM velocity structure are also critical in the interpretation of astrospheric absorption derived from fitting the saturated H I Lyα profile. As an example, we reanalyze the spectrum of λ And and find that this star likely does have an astrosphere. Two stars in the sample that have circumstellar disks (49 Cet and HD141569) show evidence for absorption due to disk gas. Finally, the substantially increased number of sight lines is used to test and refine the three-dimensional kinematic model of the LISM and search for previously unidentified clouds within the Local Bubble. We find that every prediction made by the Redfield and Linsky kinematic model of the LISM is confirmed by an observed component in the new lines of sight.