Science.gov

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

    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.

  4. 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.

  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)

    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.

  12. 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

  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. 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

  5. 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

  6. 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

  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

    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).

  19. 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).

  20. 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.

  1. 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.

  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. 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.

  18. 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)

  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. 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.

  7. 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)

  8. 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.

  9. 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.

  10. 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.

  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. 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.

  16. 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.

  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. 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

  20. 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.

  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

    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.

  14. 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

  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. 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.

  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. 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)

  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. 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

  4. 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.

  5. 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.

  6. 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.

  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. 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.

  15. 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.

  16. 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).

  17. 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.

  18. 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

  19. 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

  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 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

  2. 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

  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(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.

  13. 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.

  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. 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.

  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. 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

  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. 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

  2. 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.

  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. 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.

  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. 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.

  8. 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

  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. 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

  12. 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.

  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. 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

  17. 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.

  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 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.

  20. 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

  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

    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.

  3. 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

  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. 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.

  12. 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.…

  13. 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

  14. 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.

  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.

  11. Local structures of high-entropy alloys (HEAs) on atomic scales: An overview

    DOE PAGESBeta

    Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; Egami, Takeshi; Liaw, Peter K.

    2015-01-01

    The high-entropy alloys, containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on the atomic level are essential to understand the mechanical behaviors and related mechanisms. This article covers the local structure and stress on the atomic level are reviewed by the pair-distribution function of neutron-diffraction data, ab-initio molecular dynamics simulations, and the atomic probe microscopy.

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

    SciTech Connect

    Paesler, M.; Sayers, D.

    1988-12-01

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

  13. A new Salen-type azo-azomethine ligand and its Ni(II), Cu(II) and Zn(II) complexes: Synthesis, spectral characterization, crystal structure and photoluminescence studies.

    PubMed

    Ozkan, Gozde; Kose, Muhammet; Zengin, Huseyin; McKee, Vickie; Kurtoglu, Mukerrem

    2015-11-01

    A novel Salen-type azo-azomethine ligand H2agen, 2,2'-{ethane-1,2-diylbis[nitrilomethylylidene]}bis{4-[ethylphenyldiazenyl]phenol}, formed by the 1:2M condensation of ethane-1,2-diamine with 5-[(4-ethylphenyl)diazenyl]-2-hydroxybenzaldehyde and its nickel(II), copper(II), and zinc(II) complexes were synthesized and characterized by the spectroscopic and analytical methods. The UV-vis spectra of the ligand were investigated in three organic solvents (DMSO, DMF and CHCl3). The ligand shows two absorption bands assigned to π-π(∗) and n-π(∗) transitions in the solvents used. Cu(II), and Ni(II) are tetra-coordinate binding to two phenolic oxygens and two imine nitrogens in approximate square planar geometry. Zn(II) also coordinates using the same sites like other metals but gave tetragonal configuration. Molecular structure of the Cu(II) complex [Cu(agen)] was determined by single crystal X-ray diffraction study. The X-ray data revealed that crystallographic imposed symmetry was absent for the complex molecule. In the structure, the Cu(II) ion is coordinated to two phenolate oxygen atoms and two imine nitrogen atoms of the azo-azomethine ligand with approximate square planar geometry. The ligand H2agen and its metal complexes exhibit strong blue emissions with irradiation. Fluorescence quantum yields and excited-state lifetimes for the ligand and its complexes were obtained. The H2agen ligand had a 35% quantum yield and a 3.27 ns excited-state lifetime. Complexation with metal ions caused reductions in intensities and quantum yields. PMID:26123514

  14. Testing the existence of non-Maxwellian electron distributions in H II regions after assessing atomic data accuracy

    SciTech Connect

    Mendoza, C.; Bautista, M. A. E-mail: manuel.bautista@wmich.edu

    2014-04-20

    The classic optical nebular diagnostics [N II], [O II], [O III], [S II], [S III], and [Ar III] are employed to search for evidence of non-Maxwellian electron distributions, namely κ distributions, in a sample of well-observed Galactic H II regions. By computing new effective collision strengths for all these systems and A-values when necessary (e.g., S II), and by comparing with previous collisional and radiative data sets, we have been able to obtain realistic estimates of the electron-temperature dispersion caused by the atomic data, which in most cases are not larger than ∼10%. If the uncertainties due to both observation and atomic data are then taken into account, it is plausible to determine for some nebulae a representative average temperature while in others there are at least two plasma excitation regions. For the latter, it is found that the diagnostic temperature differences in the high-excitation region, e.g., T{sub e} (O III), T{sub e} (S III), and T{sub e} (Ar III), cannot be conciliated by invoking κ distributions. For the low-excitation region, it is possible in some, but not all, cases to arrive at a common, lower temperature for [N II], [O II], and [S II] with κ ≈ 10, which would then lead to significant abundance enhancements for these ions. An analytic formula is proposed to generate accurate κ-averaged excitation rate coefficients (better than 10% for κ ≥ 5) from temperature tabulations of the Maxwell-Boltzmann effective collision strengths.

  15. Mononuclear copper (II) salicylate complexes with 1,2-dimethylimidazole and 2-methylimidazole: Synthesis, spectroscopic and crystal structure characterization and their superoxide scavenging activities

    NASA Astrophysics Data System (ADS)

    Abuhijleh, A. Latif

    2010-09-01

    The complexes cis-bis (1,2-dimethylimidazole) bis (salicylato) copper (II) ( 1) and tris (2-methylimidazole) (salicylato) copper (II) ( 2) have been prepared by the reaction of appropriate methylimidazole derivative with binuclear copper (II) aspirinate. Spectral and X-ray structural studies for complex 1 showed that the copper ion is coordinated in a cis arrangement to two imidazole nitrogen atoms and two carboxylate oxygen atoms from the salicylate mono-anion ligands. The second carboxylate oxygen atoms form weak axial interactions with the copper ion. Spectral, magnetic and analytical data for complex 2 showed that the copper ion is bonded to three 2-methylimidazole nitrogen atoms and one doubly deprotonated salicylate di-anion, which is chelated to Cu (II) ion through one of its carboxylate oxygen atoms and the deprotonated hydroxyl oxygen atom to form distorted square-pyramidal geometry having CuN 3O + O chromophore. The superoxide dismutase (SOD) mimetic activities (IC 50) of the complexes 1, 2 and the structurally known mixture complexes Cu (imidazole) n(salicylato) 2( 3) (where n = 2, 5 and 6) were determined using the xanthine-xanthine oxidase assay and compared with those reported for other copper (II) complexes with anti-inflammatory drugs. The results obtained indicated that complexes 1- 3 have high SOD-like activities, which may act as good mimics for native Cu, Zn-SOD enzyme.

  16. Surface enhanced Raman scattering, natural bond orbitals and Mulliken atomic charge distribution in the normal modes of diethyldithiocarbamate cadmium (II) complex, [Cd(DDTC)2

    NASA Astrophysics Data System (ADS)

    Téllez Soto, C. A.; Costa, A. C.; Versiane, O.; Lemma, T.; Machado, N. C. F.; Mondragón, M. A.; Martin, A. A.

    2015-07-01

    Theoretical and experimental bands have been assigned to the Fourier Transform Infrared (FT-IR) and FT-Raman spectra of the bis(diethyldithiocarbamate)Cd(II) complex, abbreviated as ([Cd(DDTC)2]). The calculations and spectral interpretation have been based on the DFT/B3LYP method, infrared and Raman second derivative spectra, and band deconvolution analysis to assist in the assignment of observed fundamentals. This study validated the unusual pseudo tetrahedral molecular structure formed around the Cd(II) cation. Surface-enhanced Raman scattering (SERS) was used to determine the interactions of the normal-modes of the diethyldithiocarbamate cadmium (II) complex on nano-structured silver surfaces. Natural bond orbital (NBO) analysis was also carried out to study the Cd(II) hybridization causing the pseudo tetrahedral geometry of the framework of the [Cd(DDTC)2] complex, and to confirm the charge transfer mechanisms through second order perturbation theory analysis of the Fox Matrix. In order to find out the electronic dispersion of the Mulliken atomic charges (MAC) in the normal modes, we calculated the MAC for each normal mode and correlated these values with the SERS effect. Experimental UV-Vis spectra were obtained and charge transfer bands were assigned. Good agreement between the calculated and experimental values for the vibrational and UV-Vis spectra was obtained.

  17. Surface enhanced Raman scattering, natural bond orbitals and Mulliken atomic charge distribution in the normal modes of diethyldithiocarbamate cadmium (II) complex, [Cd(DDTC)₂].

    PubMed

    Soto, C A Téllez; Costa, A C; Versiane, O; Lemma, T; Machado, N C F; Mondragón, M A; Martin, A A

    2015-07-01

    Theoretical and experimental bands have been assigned to the Fourier Transform Infrared (FT-IR) and FT-Raman spectra of the bis(diethyldithiocarbamate)Cd(II) complex, abbreviated as ([Cd(DDTC)2]). The calculations and spectral interpretation have been based on the DFT/B3LYP method, infrared and Raman second derivative spectra, and band deconvolution analysis to assist in the assignment of observed fundamentals. This study validated the unusual pseudo tetrahedral molecular structure formed around the Cd(II) cation. Surface-enhanced Raman scattering (SERS) was used to determine the interactions of the normal-modes of the diethyldithiocarbamate cadmium (II) complex on nano-structured silver surfaces. Natural bond orbital (NBO) analysis was also carried out to study the Cd(II) hybridization causing the pseudo tetrahedral geometry of the framework of the [Cd(DDTC)2] complex, and to confirm the charge transfer mechanisms through second order perturbation theory analysis of the Fox Matrix. In order to find out the electronic dispersion of the Mulliken atomic charges (MAC) in the normal modes, we calculated the MAC for each normal mode and correlated these values with the SERS effect. Experimental UV-Vis spectra were obtained and charge transfer bands were assigned. Good agreement between the calculated and experimental values for the vibrational and UV-Vis spectra was obtained. PMID:25813176

  18. Syntheses, characterizations and crystal structures of two new lead(II) amino and carboxylate-sulfonates with a layered and a pillared layered structure

    NASA Astrophysics Data System (ADS)

    Yuan, Yan-Ping; Mao, Jiang-Gao; Song, Jun-Ling

    2004-03-01

    Reactions of lead(II) acetate with m-aminobenzenesulfonic acid (H L1) and 5-sulfoisophthalic acid (H 3L2) afforded two new lead(II) sulfonates, Pb( L1) 21 and Pb 2( L2)( μ3-OH)(H 2O) 2. In compound 1, the lead(II) ion is eight-coordinated by two sulfonate groups bidentately, two sulfonate groups unidentately and two amino groups from six ligands. Each L1 ligand is tetradentate and bridges with three Pb(II) ions. The interconnection of the Pb(II) ions via bridging sulfonate ligands resulted in <100> and <200> layers. In compound 2, one Pb(II) ion is six-coordinated by a carboxylate group bidentately, by two carboxylate groups unidentately, by a sulfonate oxygen atom and by an OH anion, whereas the other one is six-coordinated by a bidentate chelating carboxylate group, two μ3-OH anions, a sulfonate oxygen atom and an aqua ligand. The interconnection of irregular PbO 6 polyhedra via carboxylate-sulfonate ligands resulted in the formation of a pillared layered structure with the 2D layer being formed; the lead(II) ions, hydroxyl groups, carboxylate and sulfonate groups and the benzene ring as the pillar agent.

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

    SciTech Connect

    Dembczynski, J. . E-mail: Jerzy.Dembczynski@put.poznan.pl; Elantkowska, M.; Ruczkowski, J.; Stefanska, D.

    2007-01-15

    We report fine and hyperfine structure analysis of the system of even configurations of the Sc atom in a large multi-configuration basis. The complete energy scheme in the energy region up to about 50,000 cm{sup -1} has been established with the predicted values of the hyperfine cture constants A. The effects of the configuration interaction in the fine and hyperfine structure are discussed.

  20. Atomic data from the Iron project. XIII. Electron excitation rates and emissivity ratios for forbidden transitions in NI II and Fe II.

    NASA Astrophysics Data System (ADS)

    Bautista, M. A.; Pradhan, A. K.

    1996-02-01

    Electron impact excitation rates and emissivity line ratios are reported for Optical and IR transitions in Ni II and Fe II arising from low-lying even parity levels. A total of 7 LS terms were included for Ni II, which result in 17 fine structure levels and 136 transitions. Coupling effects and resonance structures considered in the present calculations result in significant differences with the earlier distorted wave calculations by Nussbaumer & Storey (1982), although a reasonable agreement is found for the line diagnostics of some strong transitions in Ni II. Whereas an extensive set of collisional data has been presented earlier by Zhang & Pradhan for Fe II in the Iron Project series, in this paper we report collision strengths for some transitions missing from their dataset using an improved eigenfunction expansion for Fe II which includes the lowest 18 LS terms giving 52 fine structure levels and 1326 transitions. The present dataset provides a useful check on several forbidden transitions in Fe II and essentially confirms the diagnostics derived from the earlier work. The present calculations were carried out on the massively parallel processor Cray T3D with a parallelized version of the Iron Project R-matrix codes; to our knowledge these are the first such calculations.

  1. Structural examination of lithium niobate ferroelectric crystals by combining scanning electron microscopy and atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Efremova, P. V.; Ped'ko, B. B.; Kuznecova, Yu. V.

    2016-02-01

    The structure of lithium niobate single crystals is studied by a complex technique that combines scanning electron microscopy and atomic force microscopy. By implementing the piezoresponse force method on an atomic force microscope, the domain structure of lithium niobate crystals, which was not revealed without electron beam irradiation, is visualized

  2. Laser-induced resonant structure in electron-atom scattering

    NASA Astrophysics Data System (ADS)

    Flegel, A. V.; Frolov, M. V.; Manakov, N. L.; Starace, Anthony F.

    2009-11-01

    Orders of magnitude increases are predicted in the cross sections for electron-atom scattering accompanied by absorption or emission of n laser photons for incident electron energies at which the electron, by emitting μ laser photons, can be captured by the atom to form a negative ion. Resonance enhancements are most significant in the plateau region (n gg μ) of the scattered electron spectrum, whose shape is predicted to replicate that of the ion's (n + μ)-photon detachment spectrum.

  3. Embedded-atom-method study of structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys

    NASA Astrophysics Data System (ADS)

    Asta, Mark; Morgan, Dane; Hoyt, J. J.; Sadigh, Babak; Althoff, J. D.; de Fontaine, D.; Foiles, S. M.

    1999-06-01

    Structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys have been studied by Monte Carlo and molecular-dynamics simulations based upon three different embedded-atom method (EAM) interatomic potentials, namely those due to Foiles and Daw (FD) [J. Mater. Res. 2, 5 (1987)], Voter and Chen (VC) [in Characterization of Defects in Materials, edited by R. W. Siegel et al. MRS Symposia Proceedings. No. 82 (Materials Research Society, Pittsburgh, 1987), p.175] and Ludwig and Gumbsch (LG) [Model. Simul. Mater. Sci. Eng. 3, 533 (1995)]. We present detailed comparisons between calculated results and experimental data for structure factors, atomic volumes, enthalpies of mixing, activities, and viscosities. Calculated partial structure factors are found to be in semiquantitative agreement with published neutron scattering measurements for Ni20Al80 alloys, indicating that short-range order in the liquid phase is qualitatively well described. Calculated thermodynamic properties of mixing are found to agree very well with experimental data for Ni compositions greater than 75 atomic %, while for alloys richer in Al the magnitudes of the enthalpies and entropies of mixing are significantly underestimated. The VC and LG potentials give atomic densities and viscosities in good agreement with experiment for Ni-rich compositions, while FD potentials consistently underestimate both properties at all concentrations. The results of this study demonstrate that VC and LG potentials provide a realistic description of the thermodynamic and atomic transport properties for NixAl1-x liquid alloys with x>=0.75, and point to the limitations of EAM potentials for alloys richer in Al.

  4. Smallest Nanoelectronic with Atomic Devices with Precise Structures

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige

    2000-01-01

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

  5. Supramolecular organization of the crystal structure of cis-bis(thiosemicarbazide)palladium(II) ortho-hydrophthalate

    NASA Astrophysics Data System (ADS)

    Simonov, Yu. A.; Revenco, M. D.; Bourosh, P. N.; Bulmaga, P. I.; Gdaniec, M.

    2009-09-01

    This paper reports on the synthesis of a new palladium(II) thiosemicarbazide complex of the composition [Pd(H L)2](H Pht)2 · 4H2O( I) (where H L is N(1)H2-N(2)H-C(3)(=S)-N(4)H2 and H Pht - is a monoanion of ortho-phthalic acid) and the results of an investigation of its structure. It has been demonstrated that two organic ligands are bidentately coordinated in the neutral form through a set of N and S donor atoms, which are located in the cis position with respect to the central metal atom. Three independent water molecules are joined by hydrogen bonds into the centrosymmetric associate {H2O}6. In the crystal, thiosemi-carbazide cationic complexes of palladium(II), monophthalate anions, and water molecules are self-organized into a supramolecular system with the formation of a three-dimensional structure based on ionic and hydrogen bonds.

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

    PubMed

    Helmich, Benjamin; Sierka, Marek

    2012-01-15

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

  7. Band-Structure Engineering of Gold Atomic Wires on Silicon by Controlled Doping

    NASA Astrophysics Data System (ADS)

    Choi, Won Hoon; Kang, Pil Gyu; Ryang, Kyung Deuk; Yeom, Han Woong

    2008-03-01

    We report on the systematic tuning of the electronic band structure of atomic wires by controlling the density of impurity atoms. The atomic wires are self-assembled on Si(111) by substitutional gold adsorbates and extra silicon atoms are deposited as the impurity dopants. The one-dimensional electronic band of gold atomic wires, measured by angle-resolved photoemission, changes from a fully metallic to semiconducting one with its band gap increasing above 0.3 eV along with an energy shift as a linear function of the Si dopant density. The gap opening mechanism is suggested to be related to the ordering of the impurities.

  8. Gunshot residue testing in suicides: Part II: Analysis by inductive coupled plasma-atomic emission spectrometry.

    PubMed

    Molina, D Kimberley; Castorena, Joe L; Martinez, Michael; Garcia, James; DiMaio, Vincent J M

    2007-09-01

    Several different methods can be employed to test for gunshot residue (GSR) on a decedent's hands, including scanning electron microscopy with energy dispersive x-ray (SEM/EDX) and inductive coupled plasma-atomic emission spectrometry (ICP-AES). In part I of this 2-part series, GSR results performed by SEM/EDX in undisputed cases of suicidal handgun wounds were studied. In part II, the same population was studied, deceased persons with undisputed suicidal handgun wounds, but GSR testing was performed using ICP-AES. A total of 102 cases were studied and analyzed for caliber of weapon, proximity of wound, and the results of the GSR testing. This study found that 50% of cases where the deceased was known to have fired a handgun immediately prior to death had positive GSR results by ICP/AES, which did not differ from the results of GSR testing by SEM/EDX. Since only 50% of cases where the person is known to have fired a weapon were positive for GSR by either method, this test should not be relied upon to determine whether someone has discharged a firearm and is not useful as a determining factor of whether or not a wound is self-inflicted or non-self-inflicted. While a positive GSR result may be of use, a negative result is not helpful in the medical examiner setting as a negative result indicates that either a person fired a weapon prior to death or a person did not fire a weapon prior to death. PMID:17721164

  9. The room temperature structures of anhydrous zinc(II) hexanoate and pentadecanoate

    NASA Astrophysics Data System (ADS)

    Taylor, Richard A.; Ellis, Henry A.; Maragh, Paul T.; White, Nicole A. S.

    2006-04-01

    The room temperature structures of anhydrous zinc (II) hexanoate and pentadecanoate have been studied using infrared spectroscopy, X-ray diffraction and polarizing light microscopy. Lattice parameters from single crystal X-ray and powder diffraction data, for short chain length hexanoate, are compared to validate the powder method which is then used, in conjunction with density and other molecular calculations to determine the structure of the longer chain length pentadecanoate. The compounds are isostructural; in that, each zinc atom is tetrahedrally coordinated to oxygen atoms of four different carboxylate groups and each ligand forms a bidentate bridge with two tetrahedral zinc atoms in a syn-anti arrangement. Bonding is unsymmetrical around the zinc atom. For both compounds, hydrocarbon chains, in the fully extended all-trans configuration, are tilted at an average angle between 58 and 61° to the planes containing zinc ions, though, in the case of the hexanoate, a bilayer arrangement of hydrocarbon chains within a lamella is indicated. The arrangement of the chains within the bilayer is regular with a similar side chain interaction for all the hydrocarbon moieties. For the longer chain length compound, an interdigitated bilayer arrangement of chains within a lamella is proposed. For this, an alternating head-to-tail arrangement within the layers between zinc atoms is indicated from the X-ray data. Nevertheless, both compounds crystallize within a monoclinic unit cell with P1 c1 symmetry, at least for the hexanoate, with the chains arranged in a two dimensional network along the ac plane within the unit cell.

  10. Combined EXAFS and DFT Structure Calculations Provide Structural Insights into the 1:1 Multi-Histidine Complexes of CuII, CuI and ZnII with the Tandem Octarepeats of the Mammalian Prion Protein

    PubMed Central

    Pushie, M. Jake; Nienaber, Kurt H.; McDonald, Alex; Millhauser, Glenn L.; George, Graham N.

    2014-01-01

    The metal coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of copper interaction with PrP just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, and yet the structural details of the various metal coordination modes have not been fully elucidated in some cases. Herein we employ X-ray absorption near edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for CuII, CuI and ZnII with an N-terminal fragment of PrP. The PrP fragment constitutes four tandem repeats representative of the mammalian octarepeat domain, designated OR4, which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations provide additional structural and thermodynamic data, and candidate structures are used to inform EXAFS data analysis. The optimized geometries from DFT calculations are used to identify potential coordination complexes for multi-histidine coordination of CuII, CuI and ZnII in an aqueous medium, modeled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve fitting, using full multiple scattering on candidate structures from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of CuII, CuI and ZnII with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as a square planar [CuII(His)4]2+, digonal [CuI(His)2]+ and tetrahedral [ZnII(His)3(OH2)]2+, respectively. PMID:25042361

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

    PubMed Central

    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. Structural aspects in semicrystalline samples of the mannan II family.

    PubMed

    Heux, L; Hägglund, P; Putaux, J-L; Chanzy, H

    2005-01-01

    A series of samples having the mannan II character were prepared by either (i) desincrusting stems of Acetabularia crenulata, or (ii) acetylating these stems, followed by dissolution and recrystallization under deacetylation conditions, or (iii) recrystallizing at low temperature the alkali soluble fraction of ivory nut mannan. The samples were characterized by transmission electron microscopy, X-ray and electron diffraction analysis together with (13)C CP/MAS NMR spectroscopy. Whereas the A. crenulata stems consisted of a mixture of mannan I and mannan II, the recrystallized samples were all of the hydrated mannan II family and occurred in a ribbonlike morphology where the mannan chains were organized with their molecular axis perpendicular to the ribbon long axis. The recrystallized ivory nut mannan samples presented X-ray and electron diffraction diagrams, together with (13)C solid-state NMR spectra recorded at 95% RH, different from those of recrystallized A. crenulata recorded under the same RH conditions. They corresponded therefore to a new allomorph of the mannan II family. Despite this difference, when the recrystallized samples were in an aqueous environment, they revealed an additional well-defined perhydrated phase, which showed the same (13)C solid-state NMR spectrum for both samples. As this phase, which gave 6-band NMR spectra with narrow line-width and low T1, had no counterpart in X-ray diffraction, it was attributed to specific amorphous segments of mannan chains, gaining some mobility when swollen in water. When the samples were totally dried, their NMR spectra lost their resolution, thus indicating the role played by water for the structural organization of the crystalline and amorphous components of mannan II. PMID:15638536

  13. Observation of Metastable Structural Excitations and Concerted Atomic Motions on a Crystal Surface

    NASA Astrophysics Data System (ADS)

    Hwang, Ing-Shouh; Golovchenko, Jene

    1992-11-01

    The addition of a small number of lead atoms to a germanium(111) surface reduces the energy barrier for activated processes, and with a tunneling microscope it is possible to observe concerted atomic motions and metastable structures on this surface near room temperature. The formation and annihilation of these metastable structural surface excitations is associated with the shift in position of large numbers of germanium surface atoms along a specific row direction like beads on an abacus. The effect provides a mechanism for understanding the transport of atoms on a semiconductor surface.

  14. First-Principles Mobility Calculations and Atomic-Scale Interface Roughness in Nanoscale Structures

    SciTech Connect

    Evans, Matthew H; Zhang, Xiaoguang; Joannopoulos, J. D.; Pantelides, Sokrates T

    2005-01-01

    Calculations of mobilities have so far been carried out using approximate methods that suppress atomic-scale detail. Such approaches break down in nanoscale structures. Here we report the development of a method to calculate mobilities using atomic-scale models of the structures and density functional theory at various levels of sophistication and accuracy. The method is used to calculate the effect of atomic-scale roughness on electron mobilities in ultrathin double-gate silicon-on-insulator structures. The results elucidate the origin of the significant reduction in mobility observed in ultrathin structures at low electron densities.

  15. On the structure and electrochemical reactions with lithium of tin(II) phosphate chloride

    SciTech Connect

    Madrigal, F.J.F.; Vicente, C.P.; Tirado, J.L.

    2000-05-01

    A crystalline solid of Sn{sub 2}PO{sub 4}Cl stoichiometry and orthorhombic structure was characterized and used as electrode material vs. a lithium metal anode. The structure of the solid resembles that of SnO; tin atoms protrude from layers of PO{sub 4} tetrahedra, while chlorine atoms are located between Sn layers. Two-electrode electrochemical cells of the type Li/LiClO{sub 4}(PC:EC)/Sn{sub 2}PO{sub 4}Cl (PC, propylene carbonate; EC, ethylene carbonate) were mounted and discharged to a maximum capacity close to 6.4 faradays per Sn atom. This corresponds to the complete reduction of Sn(II) to Sn(0) followed by the formation of noncrystalline Li-Sn alloys up to a limiting composition of Li{sub 22}Sn{sub 5}. The second step of the discharge shows an interesting reversibility. After a decrease in capacity during the first ten cycles, ascribable to the increase in the size of tin domains, the charge and discharge capacities remain close to 300 Ah/kg (Sn) up to ca. 40 cycles.

  16. Structural studies on some dithiophosphonato complexes of Ni(II), Cd(II), Hg(II) and theoretical studies on a dithiophosphonato Ni(II) complex using density functional theory

    NASA Astrophysics Data System (ADS)

    Sağlam, Ertuğrul Gazi; Ebinç, Ahmet; Zeyrek, Celal Tuğrul; Ünver, Hüseyin; Hökelek, Tuncer

    2015-11-01

    In this study, three dithiophosphonic acid complexes, namely, trans-bis-[O-3-methylbutyl (4-methoxyphenyl)dithiophosphonato]nickel(II), Ni(L)2; bis-{bis-[O-3-phenylpropyl (4-methoxyphenyl)dithiophosphonato]cadmium(II)}, [Cd(L)2]2 and bis-{bis-[O-3-methylbutyl (4-methoxyphenyl)dithiophosphonato]mercury(II)}, [Hg(L)2]2 were prepared. The compounds were characterized by elemental analysis; MS; FTIR and Raman spectroscopies and were also investigated by 1H-, 13C- and 31P- NMR. The Ni(L)2 complex was elucidated by X-ray crystallography, molecular characterization and density functional modelling studies. The molecular structure obtained from X-ray single-crystal analysis of the Ni(L)2 complex in the ground state has been compared using density functional theory (DFT), B3LYP functional with 6-311G(d,p) basis set. In addition to the optimized geometrical structures, atomic charges and nonlinear optical (NLO) effects have been investigated by using DFT. The experimental (spectroscopic) and calculated vibrational frequencies (using DFT) of the Ni(L)2 have been compared. There exists a good correlation between experimental and theoretical data for the Ni(L)2 complex.

  17. Sequestration of chelated copper by structural Fe(II): Reductive decomplexation and transformation of Cu(II)-EDTA.

    PubMed

    He, Hongping; Wu, Deli; Zhao, Linghui; Luo, Cong; Dai, Chaomeng; Zhang, Yalei

    2016-05-15

    Chelated coppers, such as Cu(II)-EDTA, are characteristically refractory and difficult to break down because of their high stability and solubility. Cu(II)-EDTA sequestration by structural Fe(II) (Fe(II)) was investigated intensively in this study. Up to 101.21mgCu(II)/gFe(II) was obtained by Fe(II) in chelated copper sequestration under near neutral pH condition (pH 7.70). The mechanism of Cu(II)-EDTA sequestration by Fe(II) was concluded as follows: 3Cu(II)-EDTA+7Fe(II)+9H2O → Cu(0)↓+ Cu2O↓(the major product)+2Fe2O3·H2O↓+3Fe(II)-EDTA +14H(+) Novel results strongly indicate that Cu(II) reductive transformation induced by surface Fe(II) was mainly responsible for chelated copper sequestration. Cu(0) generation was initially facilitated, and subsequent reduction of Cu(II) into Cu(I) was closely combined with the gradual increase of ORP (Oxidation-Reduction Potential). Cu-containing products were inherently stable, but Cu2O would be reoxidized to Cu(II) with extra-aeration, resulting in the release of copper, which was beneficial to Cu reclamation. Concentration diminution of Cu(II)-EDTA within the electric double layer and competitive adsorption were responsible for the negative effects of Ca(2+), Mg(2+). By generating vivianite, PO4(3-) was found to decrease surface Fe(II) content. This study is among the first ones to identify the indispensible role of reductive decomplexation in chelated copper sequestration. Given the high feasibility and reactivity, Fe(II) may provide a potential alternative in chelated metals pollution controlling. PMID:26878707

  18. From electron microscopy maps to atomic structures using normal mode-based fitting.

    PubMed

    Hinsen, Konrad; Beaumont, Edward; Fournier, Bertrand; Lacapère, Jean-Jacques

    2010-01-01

    Electron microscopy (EM) has made possible to solve the structure of many proteins. However, the resolution of some of the EM maps is too low for interpretation at the atomic level, which is particularly important to describe function. We describe methods that combine low-resolution EM data with atomic structures for different conformations of the same protein in order to produce atomic models compatible with the EM map.We illustrate these methods with EM data from decavanadate-induced tubular crystals of a pseudo-phosphorylated intermediate of Ca-ATPase and the various atomic structures of other intermediates available in the Protein Data Bank (PDB). Determination of atomic structure permits not only to analyse protein-protein interactions in the crystals, but also to localize residues in the proximity of the crystallizing agent both within Ca-ATPase and between Ca-ATPase molecules. PMID:20665270

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

    NASA Astrophysics Data System (ADS)

    Heyrovska, Raji; Narayan, Sara

    2009-04-01

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

  20. Structural and spectroscopic characterization of two new blue luminescent pyridylbenzimidazole zinc(II) complexes.

    PubMed

    DeStefano, Matthew R; Geiger, David K

    2016-06-01

    Luminescent metal complexes are used in photooptical devices. Zinc(II) complexes are of interest because of the ability to tune their color, their high thermal stability and their favorable carrier transport character. In particular, some zinc(II) complexes with aryl diimine and/or heterocyclic ligands have been shown to emit brightly in the blue region of the spectrum. Zinc(II) complexes bearing derivatized imidazoles have been explored for possible optoelectronic applications. The structures of two zinc(II) complexes of 5,6-dimethyl-2-(pyridin-2-yl)-1-[(pyridin-2-yl)methyl]-1H-benzimidazole (L), namely dichlorido(dimethylformamide-κO){5,6-dimethyl-2-(pyridin-2-yl-κN)-1-[(pyridin-2-yl)methyl]-1H-benzimidazole-κN(3)}zinc(II) dimethylformamide monosolvate, [ZnCl2(C20H18N4)(C3H7NO)]·C3H7NO, (I), and bis(acetato-κ(2)O,O'){5,6-dimethyl-2-(pyridin-2-yl-κN)-1-[(pyridin-2-yl)methyl]-1H-benzimidazole-κN(3)}zinc(II) ethanol monosolvate, [Zn(C2H3O2)2(C20H18N4)]·C2H5OH, (II), are reported. Complex (I) crystallized as a dimethylformamide solvate and exhibits a distorted trigonal bipyramidal coordination geometry. The coordination sphere consists of a bidentate L ligand spanning axial to equatorial sites, two chloride ligands in equatorial sites, and an O-bound dimethylformamide ligand in the remaining axial site. The other complex, (II), crystallized as an ethanol solvate. The Zn(II) atom has a distorted trigonal prismatic coordination geometry, with two bidentate acetate ligands occupying two edges and a bidentate L ligand occupying the third edge of the prism. Complexes (I) and (II) emit in the blue region of the spectrum. The results of density functional theory (DFT) calculations suggest that the luminescence of L results from π*←π transitions and that the luminescence of the complexes results from interligand charge-transfer transitions. The orientation of the 2-(pyridin-2-yl) substituent with respect to the benzimidazole system was found to have an impact on

  1. An exploratory study of high school students' conceptions of atomic and cellular structure and the relationship between atoms and cells

    NASA Astrophysics Data System (ADS)

    Roland, Elizabeth Anne Edwards

    Constructivist learning theory is based upon the tenets that students come to learning experiences with prior knowledge and experiences that the learner will choose from to make sense of the present situation. This leads to a mixture of understandings among students. This study proposed to reveal students' understanding of atomic structure and cell structure as well as the relationships between atoms and cells. High school students from one private school participated in a paper-and-pencil test to uncover conceptual understanding and content knowledge of atoms and cells. The 120 participants were from grades: 9 (13m, 15f), 10 (9m, 20f), 11 (21m, 17f), and 12 (17m, 8f). All 120 students took the paper-and-pencil test and 16 students (4 per grade) participated in a follow-up interview. Drawings were analyzed by individual characteristics then using groups of characteristics models classes were formed. Open-ended questions were scored holistically by rubric scores and then deconstructed into individual content statements. A limited number of findings follow. Students were more likely to draw a Bohr model. Freshmen were less likely to indicate living materials contained atoms and more likely to indicate forms of energy contained atoms. As students progressed through high school, details included in cells decreased. Students failed to recognize that the sum of the products from cell division will be larger than the original cell due to the two growth periods included in the division cycle. Students were often able to provide the correct yes or no answer to are atoms and cells similar, different, or related but the follow-up answers often included non-scientific conceptions. Recommendations include implementing instructional strategies that promote long-term retention of conceptual understanding and the underlying content knowledge. Design evaluation methods to monitor student understanding throughout a unit of study that go beyond traditional closed-ended questions

  2. Structure Learning and Statistical Estimation in Distribution Networks - Part II

    SciTech Connect

    Deka, Deepjyoti; Backhaus, Scott N.; Chertkov, Michael

    2015-02-13

    Limited placement of real-time monitoring devices in the distribution grid, recent trends notwithstanding, has prevented the easy implementation of demand-response and other smart grid applications. Part I of this paper discusses the problem of learning the operational structure of the grid from nodal voltage measurements. In this work (Part II), the learning of the operational radial structure is coupled with the problem of estimating nodal consumption statistics and inferring the line parameters in the grid. Based on a Linear-Coupled(LC) approximation of AC power flows equations, polynomial time algorithms are designed to identify the structure and estimate nodal load characteristics and/or line parameters in the grid using the available nodal voltage measurements. Then the structure learning algorithm is extended to cases with missing data, where available observations are limited to a fraction of the grid nodes. The efficacy of the presented algorithms are demonstrated through simulations on several distribution test cases.

  3. Synthesis, Crystal Structure, and Spectra Properties of the Cadmium (II) Complex with Bis(N-allylbenzimidazol-2-ylmethyl)benzylamine

    PubMed Central

    Wu, Huilu; Yuan, Jingkun; Bai, Ying; Kou, Fan; Jia, Fei; Liu, Bin

    2011-01-01

    A novel complex of cadmium (II) picrate (pic) with V-shaped ligand bis(N-allylbenzimidazol-2-ylmethyl)benzylamine (babb), with composition [Cd(babb)2](pic)2, was synthesized and characterized by elemental analyses and electrical conductivity, IR, and UV/visible spectra. The crystal structure of the complex has been determined by the single-crystal X-ray diffraction. In the complex, the coordination sphere around Cd (II) is distorted octahedral, six nitrogen atoms involved in coordination afforded by two tridentate ligand babb. Moreover, The DNA-binding properties of the ligand babb and Cd (II) complex were investigated by spectrophotometric methods and viscosity measurements, and the results suggest that they bind to DNA via an intercalation binding mode, and the Cd (II) complex shows higher affinity than the ligand. PMID:22007154

  4. Synthesis, Crystal Structure, and Spectra Properties of the Cadmium (II) Complex with Bis(N-allylbenzimidazol-2-ylmethyl)benzylamine.

    PubMed

    Wu, Huilu; Yuan, Jingkun; Bai, Ying; Kou, Fan; Jia, Fei; Liu, Bin

    2011-01-01

    A novel complex of cadmium (II) picrate (pic) with V-shaped ligand bis(N-allylbenzimidazol-2-ylmethyl)benzylamine (babb), with composition [Cd(babb)(2)](pic)(2), was synthesized and characterized by elemental analyses and electrical conductivity, IR, and UV/visible spectra. The crystal structure of the complex has been determined by the single-crystal X-ray diffraction. In the complex, the coordination sphere around Cd (II) is distorted octahedral, six nitrogen atoms involved in coordination afforded by two tridentate ligand babb. Moreover, The DNA-binding properties of the ligand babb and Cd (II) complex were investigated by spectrophotometric methods and viscosity measurements, and the results suggest that they bind to DNA via an intercalation binding mode, and the Cd (II) complex shows higher affinity than the ligand. PMID:22007154

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

    PubMed Central

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

    2013-01-01

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

  6. Copper(II) complexes with pyrazole derivatives - Synthesis, crystal structure, DFT calculations and cytotoxic activity

    NASA Astrophysics Data System (ADS)

    Kupcewicz, Bogumiła; Ciolkowski, Michal; Karwowski, Boleslaw T.; Rozalski, Marek; Krajewska, Urszula; Lorenz, Ingo-Peter; Mayer, Peter; Budzisz, Elzbieta

    2013-11-01

    The series of pyrazole derivatives (1a-4a) were used as bidentate N,N' ligands to obtain neutral Cu(II) complexes of ML2Cl2 type (1b-4b). The molecular structures of ligand 1a and Cu(II) complex 4b were determined by X-ray crystallography and theoretical DFT calculations. In this study, three functionals B3LYP, BP86 and mPW1PW91 with different basis sets and two effective core potentials Los Alamos and Stuttgart/Dresden were performed. The DFT study disclosed the usefulness of BP86 functional with SDD-ECP for Cu(II) ion and dedicated D95 basis set for other non-transition metal atoms, with the exclusion of Cl for which 6-31++G(2df,2pd) were used. The structural analysis shows that the presence of phenyl substituent in a pyrazole ring contributed to Cu-N bond elongation, which can result in different reactivity of complexes 1b and 3b. The cytotoxicity of the obtained compounds was evaluated on three cancer cells lines: HL-60, NALM-6 and WM-115. The complexes have exhibited similar moderate antiproliferative activity. All the complexes, except for 1b, were found to be more active against three cancer cell lines than uncomplexed pyrazoles. The lipophilicity and electrochemical properties of ligands and complexes was also studied. For complexes with ligand 1a and 3a only one reduction process at the metal centre occurs (Cu(II) → Cu(I)) with oxidization of Cu(I)-Cu(II) in the backward step.

  7. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    SciTech Connect

    Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; Mullins, David R.; Carroll, Kyler J.; Meisner, Roberta; Crumlin, Ethan; Liu, Xiason; Yang, Wanli; Veith, Gabriel M.

    2014-09-25

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na14.78Sn4 (Pnma), better described as Na16-xSn4, is Na-richer than cubic Na15Sn4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na7Sn3 and Na15Sn4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.

  8. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    DOE PAGESBeta

    Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; Mullins, David R.; Carroll, Kyler J.; Meisner, Roberta; Crumlin, Ethan; Liu, Xiason; Yang, Wanli; Veith, Gabriel M.

    2014-09-25

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) hasmore » relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na14.78Sn4 (Pnma), better described as Na16-xSn4, is Na-richer than cubic Na15Sn4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na7Sn3 and Na15Sn4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.« less

  9. Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics.

    PubMed

    Widdifield, Cory M; Robson, Harry; Hodgkinson, Paul

    2016-05-10

    The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples. While the structures differ in the placement of one H atom, using this approach, we verify one of the structures in the Cambridge Structural Database using quantitative tools, while establishing that the other structure does not meet the verification criteria. PMID:27115483

  10. TEMPERATURE STRUCTURE AND METALLICITY IN H II REGIONS

    SciTech Connect

    Rodriguez, Monica; GarcIa-Rojas, Jorge E-mail: jogarcia@iac.e

    2010-01-10

    The metallicities implied by collisionally excited lines (CELs) of heavy elements in H II regions are systematically lower than those implied by recombination lines (RLs) by factors of approx2, introducing uncertainties of the same order in the metallicities inferred for the interstellar medium of any star-forming galaxy. Most explanations of this discrepancy are based on the different sensitivities of CELs and RLs to electron temperature, and invoke either some extra heating mechanism producing temperature fluctuations in the ionized region or the addition of cold gas in metal-rich inclusions or ionized by cosmic rays or X-rays. These explanations will change the temperature structure of the ionized gas from the one predicted by simple photoionization models, and depending on which one is correct, will imply different metallicities for the emitting gas. We select nine H II regions with observed spectra of high quality and show that simple models with metallicities close to the ones implied by oxygen CELs reproduce easily their temperature structure, measured with T{sub e}([N II])/T{sub e}([O III]), and their oxygen CELs emission. We discuss the strong constraints that this agreement places on the possible explanations of the discrepancy and suggest that the simplest explanation, namely errors in the line recombination coefficients by factors approx2, might be the correct one. In such case, CELs will provide the best estimates of metallicity.

  11. Atomic and Electronic Structure of Polar Oxide Interfaces

    SciTech Connect

    Gajdardziska-Josifovska, Marija

    2014-01-17

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

  12. Structure and oxidation state of hematite surfaces reacted with aqueous Fe(II) at acidic and neutral pH

    NASA Astrophysics Data System (ADS)

    Catalano, Jeffrey G.; Fenter, Paul; Park, Changyong; Zhang, Zhan; Rosso, Kevin M.

    2010-03-01

    Structural changes and surface oxidation state were examined following the reaction of hematite (0 0 1), (0 1 2), and (1 1 0) with aqueous Fe(II). X-ray reflectivity measurements indicated that Fe(II) induces changes in the structure of all three surfaces under both acidic (pH 3) and neutral (pH 7) conditions. The structural changes were generally independent of pH although the extent of surface transformation varied slightly between acidic and neutral conditions; no systematic trends with pH were observed. Induced changes on the (1 1 0) and (0 1 2) surfaces include the addition or removal of partial surface layers consistent with either growth or dissolution. In contrast, a <1 nm thick, discontinuous film formed on the (0 0 1) surface that appears to be epitaxial yet is not a perfect extension of the underlying hematite lattice, being either structurally defective, compositionally distinct, or nanoscale in size and highly relaxed. Resonant anomalous X-ray reflectivity measurements determined that the surface concentration of Fe(II) present after reaction at pH 7 was below the detection limit of approximately 0.5-1 μmol/m 2 on all surfaces. These observations are consistent with Fe(II) oxidative adsorption, whereby adsorbed Fe(II) is oxidized by structural Fe(III) in the hematite lattice, with the extent of this reaction controlled by surface structure at the atomic scale. The observed surface transformations at pH 3 show that Fe(II) oxidatively adsorbs on hematite surfaces at pH values where little net adsorption occurs, based on historical macroscopic Fe(II) adsorption behavior on fine-grained hematite powders. This suggests that Fe(II) plays a catalytic role, in which an electron from an adsorbed Fe(II) migrates to and reduces a lattice Fe(III) cation elsewhere, which subsequently desorbs in a scenario with zero net reduction and zero net adsorption. Given the general pH-independence and substantial mass transfer involved, this electron and atom exchange

  13. One-dimensional Co(II)/Ni(II) complexes of 2-hydroxyisophthalate: Structures and magnetic properties

    SciTech Connect

    Wang, Kai; Zou, Hua-Hong; Chen, Zi-Lu; Zhang, Zhong; Sun, Wei-Yin; Liang, Fu-Pei

    2015-03-15

    The solvothermal reactions of 2-hydroxyisophthalic acid (H{sub 3}ipO) with M(NO{sub 3}){sub 2}∙6H{sub 2}O (M=Co, Ni) afforded two complexes [Co{sub 2}(HipO){sub 2}(Py){sub 2}(H{sub 2}O){sub 2}] (1) and [Ni(HipO)(Py)H{sub 2}O] (2) (Py=pyridine). They exhibit similar zig-zag chain structures with the adjacent two metal centers connected by a anti-syn bridging carboxylate group from the HipO{sup 2−} ligand. The magnetic measurements reveal the dominant antiferromagnetic interactions and spin-canting in 1 while ferromagnetic interactions in 2. Both of them exhibit magnetocaloric effect (MCE) with the resulting entropy changes (−ΔS{sub m}) of 12.51 J kg{sup −1} K{sup −1} when ΔH=50 kOe at 3 K for 1 and 11.01 J kg{sup −1} K{sup −1} when ΔH=50 kOe at 3 K for 2, representing the rare examples of one-dimensional complexes with MCE. - Graphical abstract: Synopsis: Two Co(II)/Ni(II) complexes with zig-zag chain structures have been reported. 1-Co shows cant-antiferromagnetism while 2-Ni shows ferromagnetism. Magnetocaloric effect is also found in both of them. - Highlights: • Two one-dimensional Co(II)/Ni(II) complexes were solvothermally synthesized. • The Co-complex exhibits canted antiferromagnetism. • The Ni-complex exhibits ferromagnetism. • Both of the complexes display magnetocaloric effect.

  14. Atomic structure of cascades of atomic displacements in metals and alloys after different types of radiation

    NASA Astrophysics Data System (ADS)

    Ivchenko, V. A.

    2016-02-01

    Using the methods of field ion microscopy, we studied radiation induced defects on an atomically clean surface and within a subsurface volume of platinum initiated by the interaction of neutron (E > 0.1MeV) and Ar+ beams (E = 30 keV). It is shown that the interaction of fast neutrons (E > 0.1 MeV) F = 6.7-1021 m-2, F = 3.5-1022 m-2 with matter leads to the formation in the amount of platinum such as radiation damage which occur after ion irradiation by beams of charged Ar+ ions with E = 30 keV, F = 1020 ion/m2. They are observed at a depth of about 1.5-2 nm irradiated under the surface of Pt by ions Ar+. Thus, we have carried out modeling of neutron impact with matter when replacing the neutron beam by an ion beam that causes the same radiation damage in the bulk of the material. Experimental results on atomic-spatial investigation of radiative defect formation in surface layers of materials, initiated by neutron bombardment (of Pt, E > 0.1 MeV) and ion implantation (in Cu3Au: E = 40 keV, F = 1020 ion/m2, j = 10-3 A/cm2), are considered. Quantitative estimates obtained for the size, shape, and volume fraction of cascades of atomic displacements formed under various types of irradiation in the surface layers of the materials. It is showing that the average size of radiation clusters after irradiation of platinum to a fast neutron fluence of 6.7-1022 m-2 (E > 0.1 MeV) is about 3.2 nm. The experimentally established average size of a radiation cluster (disordered zone) in the alloy after ion bombardment is 4×4×1.5 nm.

  15. The atom in a molecule: Implications for molecular structure and properties

    NASA Astrophysics Data System (ADS)

    Langhoff, Peter; Mills, Jeffrey; Boatz, Jerry

    2016-05-01

    The apparent impossibility of meaningful assignments of indistinguishable electrons to particular atomic nuclei in a molecule seemingly precludes quantum-mechanical definition of fragment atomic Hamiltonian operators. Structural symmetry, conformations, and isomers, as well as the electronic energies and properties of constituent atoms are accordingly perceived as ill defined. Here we provide assignments of electrons to atoms in molecules and define their energies and properties. A separable Hilbert space in the form of orthonormal (Eisenschitz-London) outer-products of atomic eigenstates facilitates assignments of electrons to particular atomic nuclei and also provides support for totally antisymmetric solutions of the Schrödinger equation. Self-adjoint atomic operators within a molecule are shown to have Hermitian matrix representatives and physically significant expectation values in molecular eigenstates. Nuanced descriptions of molecular structures and properties emerge naturally from this representation in the absence of additional subjective conditions, including the interplay between atomic promotion and interaction energies, atomic hybridization and charge apportionment, and atomic-state entanglements upon dissociation, attributes revealed by illustrative calculations. Work support in part by Grants from AFRL, NRC, ASEE, NSF.

  16. Structural characterization of a metal-based perfusion tracer: copper(II) pyruvaldehyde bis(N4-methylthiosemicarbazone).

    PubMed

    John, E; Fanwick, P E; McKenzie, A T; Stowell, J G; Green, M A

    1989-01-01

    Copper(II) pyruvaldehyde bis(N4-methylthiosemicarbazone), Cu(PTSM), has been obtained as a dark red crystalline solid from EtOH-DMSO solvent mixture and structurally characterized by x-ray crystallography. The molecule possesses the expected pseudo-square planar N2S2 metal coordination sphere; however, the copper center also interacts through its axial coordination site with the sulfur atom of an adjacent Cu(PTSM) molecule in the crystal lattice. The structure of this compound is compared with the structures of other metal complexes that have been proposed in the nuclear medicine literature as perfusion tracers. PMID:2621114

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  19. Atomic structure and magnetic properties of Fe1-xCox alloys

    SciTech Connect

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

    2012-03-09

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

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

    DOEpatents

    Lim, Chong Wee; Ohmori, Kenji; Petrov, Ivan Georgiev; Greene, Joseph E.

    2004-07-13

    A method for forming atomic-scale structures on a surface of a substrate on a large-scale includes creating a predetermined amount of surface vacancies on the surface of the substrate by removing an amount of atoms on the surface of the material corresponding to the predetermined amount of the surface vacancies. Once the surface vacancies have been created, atoms of a desired structure material are deposited on the surface of the substrate to enable the surface vacancies and the atoms of the structure material to interact. The interaction causes the atoms of the structure material to form the atomic-scale structures.

  1. Characteristics of Spontaneous Emission of Polarized Atoms in Metal Dielectric Multiple Layer Structures

    NASA Astrophysics Data System (ADS)

    Zhao, Li-Ming; Gu, Ben-Yuan; Zhou, Yun-Song

    2007-11-01

    The spontaneous emission (SE) progress of polarized atoms in a stratified structure of air-dielectric(D0)-metal(M)-dielectric(D1)-air can be controlled effectively by changing the thickness of the D1 layer and rotating the polarized direction of atoms. It is found that the normalized SE rate of atoms located inside the D0 layer crucially depends on the atomic position and the thickness of the D1 layer. When the atom is located near the D0-M interface, the normalized atomic SE rate as a function of the atomic position is abruptly onset for the thin D1 layer. However, with the increasing thickness of the D1 layer, the corresponding curve profile exhibits plateau and stays nearly unchanged. The substantial change of the SE rate stems from the excitation of the surface plasmon polaritons in metal-dielectric interface, and the feature crucially depends on the thickness of D1 layer. If atoms are positioned near the D0-air interface, the substantial variation of the normalized SE rate appears when rotating the polarized direction of atoms. These findings manifest that the atomic SE processes can be flexibly controlled by altering the thickness of the dielectric layer D1 or rotating the orientation of the polarization of atoms.

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

    NASA Astrophysics Data System (ADS)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

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

    PubMed Central

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

    2013-01-01

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

  4. An intramolecular antiferromagnetically coupled pentanuclear Mn(II) cluster containing acetate and tetracarboxylate linkers: Synthesis, structure and magnetism

    NASA Astrophysics Data System (ADS)

    Wu, Jian; Liu, Wei-Cong; Wu, Xi-Ren; Liu, Jian-Qiang; Sakiyama, Hiroshi; Yadav, Reena; Kumar, Abhinav

    2016-06-01

    A new Mn(II) complex {[Mn5(CH3COO)2(L)2(DMF)8](DMF)}n (1), (H4L = 3,5-bis(3‧,5‧-dicarboxylphenyl)-1H-1,2,3-triazole), has been synthesized and structurally characterized. The complex 1 have pentanuclear Mn(II) core, where the two sides of metal centers (Mn2 and Mn3) have trigonal bipyramidal arrangement and the middle metal center (Mn1) have octahedral environment utilizing two O atoms from adjacent bridging bidentate carboxylate groups and four O atoms from four coordinated DMF molecules. The planar arrangement of pentanuclear Mn(II) atoms are linked by L linkage to generate two dimensional sheet. The magnetic property of the compound indicates χMT value for the five Mn(II) unit to be 21.3 cm3 K mol-1 at 300 K, which is close to the spin-only value (21.9 cm3 K mol-1) for the pentamer having S = 5/2. Also, the Hirshfeld surface analyses have been performed which indicated the absence of weak Mn···Mn interaction thereby corroborating the results of observed magnetic properties.

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

    ERIC Educational Resources Information Center

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

    2002-01-01

    Reports on a study aimed at facilitating freshman general chemistry students' understanding of atomic structure based on the work of Thomson, Rutherford, and Bohr. Hypothesizes that classroom discussions based on arguments/counterarguments of the heuristic principles on which these scientists based their atomic models can facilitate students'…

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

    ERIC Educational Resources Information Center

    Park, Eun Jung; Light, Gregory

    2009-01-01

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

  7. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga.

    PubMed

    Ago, Hideo; Adachi, Hideyuki; Umena, Yasufumi; Tashiro, Takayoshi; Kawakami, Keisuke; Kamiya, Nobuo; Tian, Lirong; Han, Guangye; Kuang, Tingyun; Liu, Zheyi; Wang, Fangjun; Zou, Hanfa; Enami, Isao; Miyano, Masashi; Shen, Jian-Ren

    2016-03-11

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII. PMID:26757821

  8. Atomic structure calculations for F-like tungsten

    NASA Astrophysics Data System (ADS)

    Sunny, Aggarwal

    2014-09-01

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

  9. Structural basis of initial RNA polymerase II transcription

    PubMed Central

    Cheung, Alan C M; Sainsbury, Sarah; Cramer, Patrick

    2011-01-01

    During transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II–DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3′-proximal phosphate of short RNAs. Short DNA–RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2′-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis. PMID:22056778

  10. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)

    SciTech Connect

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C.

    2009-01-12

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6{angstrom} resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12{angstrom} deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.

  11. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)*

    PubMed Central

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C.

    2008-01-01

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6Å resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12Å deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates. PMID:18667417

  12. Molecular-dynamics study of structure II hydrogen clathrates.

    PubMed

    Alavi, Saman; Ripmeester, J A; Klug, D D

    2005-07-01

    Molecular-dynamics simulations are used to study the stability of structure II hydrogen clathrates with different H2 guest occupancies. Simulations are done at pressures of 2.5 kbars and 1.013 bars and for temperatures ranging from 100 to 250 K. For a structure II unit cell with 136 water molecules, H2 guest molecule occupancies of 0-64 are studied with uniform occupancies among each type of cage. The simulations show that at 100 K and 2.5 kbars, the most stable configurations have single occupancy in the small cages and quadruple occupancy in the large cages. The optimum occupancy for the large cages decreases as the temperature is raised. Double occupancy in the small cages increases the energy of the structures and causes tetragonal distortion in the unit cell. The spatial distribution of the hydrogen guest molecules in the cages is determined by studying the guest-water and guest-guest radial distribution functions at various temperatures. PMID:16050759

  13. Synthesis, Characterization and Thermal Studies of Zn(II), Cd(II) and Hg(II) Complexes of N-Methyl-N-Phenyldithiocarbamate: The Single Crystal Structure of [(C6H5)(CH3)NCS2]4Hg2

    PubMed Central

    Onwudiwe, Damian C.; Ajibade, Peter A.

    2011-01-01

    Zn(II), Cd(II) and Hg(II) complexes of N-methyl-N-phenyl dithiocarbamate have been synthesized and characterized by elemental analysis and spectral studies (IR, 1H and 13C-NMR). The single crystal X-ray structure of the mercury complex revealed that the complex contains a Hg centre with a distorted tetrahedral coordination sphere in which the dinuclear Hg complex resides on a crystallographic inversion centre and each Hg atom is coordinated to four S atoms from the dithiocarbamate moiety. One dithiocarbamate ligand acts as chelating ligand while the other acts as chelating bridging ligand between two Hg atoms, resulting in a dinuclear eight-member ring. The course of the thermal degradation of the complexes has been investigated using thermogravimetric and differential thermal analyses techniques. Thermogravimetric analysis of the complexes show a single weight loss to give MS (M = Zn, Cd, Hg) indicating that they might be useful as single source precursors for the synthesis of MS nanoparticles and thin films. PMID:21673933

  14. Local structure of the metal-organic perovskite dimethylammonium manganese(ii) formate.

    PubMed

    Duncan, Helen D; Dove, Martin T; Keen, David A; Phillips, Anthony E

    2016-03-14

    We report total neutron scattering measurements on the metal-organic perovskite analogue dimethylammonium manganese(ii) formate, (CD3)2ND2[Mn(DCO2)3]. Reverse Monte Carlo modelling shows that, in both the disordered high-temperature and ordered low-temperature phases, the ammonium moiety forms substantially shorter hydrogen bonds (N...O = 2.4 Å and 2.6 Å) than are visible in the average crystal structures. These bonds result from a pincer-like motion of two adjacent formate ions about the dimethylammonium ion in such a way that the framework can adjust independently to the positions of nearest-neighbour dimethylammonium ions. At low temperatures the shortest hydrogen bond is less favourable, apparently because it involves a greater distortion of the framework. Furthermore, in the high-temperature phase, in addition to the three disordered nitrogen positions expected from the average crystal structure, there appear to be also smaller probability maxima between these positions, corresponding to orientations in which the dimethylammonium is hydrogen-bonded to the two oxygen atoms of a single formate ion. The spontaneous strain across the phase transition reveals a contraction of the framework about the dimethylammonium cation, continuing as the material is cooled below the transition temperature. These results provide direct evidence of the local atomic structure of the guest-framework hydrogen bonding, and in particular the distortions of the framework responsible for the phase transition in this system. PMID:26763144

  15. Ultrathin atomic vapor film transmission spectroscopy: analysis of Dicke narrowing structure

    NASA Astrophysics Data System (ADS)

    Li, Yuanyuan; Zhang, Yanpeng; Gan, Chenli

    2005-11-01

    Transmission sub-Doppler spectroscopy with confined atomic vapor film between two dielectric walls is theoretically studied. Because of atoms flying from wall to wall, where they get de-excited, the atom-field interaction time is anisotropic so that the contribution of slow atoms is enhanced, a sub-Doppler transmission spectroscopy (Dicke narrowing effect) can be obtained when the thickness of the film is much small or comparable with the wavelength even at small angle oblique incidence. It is feasible to get a sub-Doppler structure in a new region (L < ?/4) in experiments.

  16. Theoretical investigation of hydrogen bonding between water and platinum(II): an atom in molecule (AIM) study

    NASA Astrophysics Data System (ADS)

    Li, Yan; Zhang, Guiqiu; Chen, Dezhan

    2012-02-01

    Recently, Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] [1] reported a hydrogen-bonding-like interaction between a water molecule and a d8 metal ion (PtII) based on neutron diffraction, and provided the first crystallographic evidence for this interaction. We studied the hydrogen bonding of the O-H ... Pt interaction theoretically using atoms in molecule (AIM) and natural bond orbital analysis (NBO) in the crystallographic geometries. The method used density functional theory (DFT) with the hybrid B3LYP function. For platinum atoms, we used the Los Alamos National Laboratory 2-Double-Zeta (LANL2DZ) basis set, and for the other atoms we used 6-311++G(d,p) basis sets. Criteria based on a topological analysis of the electron density were used in order to characterize the nature of interactions in the complexes. The main purpose of the present work is to provide an answer to the following questions: Why can a filled d orbital of square-planar d8 metal ions such as platinum(II) also act as hydrogen-bond acceptors? Can a study based on the electron charge density answer this question? A good correlation between the density at the intermolecular bond critical point and the energy interaction was found. The interaction is mainly closed-shell and there is some charge transfer in this system.

  17. Research as a guide for curriculum development: An example from introductory spectroscopy. II. Addressing student difficulties with atomic emission spectra

    NASA Astrophysics Data System (ADS)

    Ivanjek, L.; Shaffer, P. S.; McDermott, L. C.; Planinic, M.; Veza, D.

    2015-02-01

    This is the second of two closely related articles (Paper I and Paper II) that together illustrate how research in physics education has helped guide the design of instruction that has proved effective in improving student understanding of atomic spectroscopy. Most of the more than 1000 students who participated in this four-year investigation were science majors enrolled in the introductory calculus-based physics course at the University of Washington (UW) in Seattle, WA, USA. The others included graduate and undergraduate teaching assistants at UW and physics majors in introductory and advanced physics courses at the University of Zagreb, Zagreb, Croatia. About half of the latter group were preservice high school physics teachers. Paper I describes how several conceptual and reasoning difficulties were identified among university students as they tried to relate a discrete line spectrum to the energy levels of atoms in a light source. This second article (Paper II) illustrates how findings from this research informed the development of a tutorial that led to improvement in student understanding of atomic emission spectra.

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

    PubMed

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

    2013-01-01

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

  19. Structural Fluctuations and Thermophysical Properties of Molten II-VI Compounds

    NASA Technical Reports Server (NTRS)

    Su, Ching-Hua; Zhu, Shen; Li, Chao; Scripa, R.; Lehoczky, Sandra L.; Kim, Y. W.; Baird, J. K.; Lin, B.; Ban, Heng; Benmore, Chris

    2003-01-01

    The objectives of the project are to conduct ground-based experimental and theoretical research on the structural fluctuations and thermophysical properties of molten II-VI compounds to enhance the basic understanding of the existing flight experiments in microgravity materials science programs as well as to study the fundamental heterophase fluctuation phenomena in these melts by: 1) conducting neutron scattering analysis and measuring quantitatively the relevant thermophysical properties of the II-VI melts (such as viscosity, electrical conductivity, thermal diffusivity and density) as well as the relaxation characteristics of these properties to advance the understanding of the structural properties and the relaxation phenomena in these melts and 2) performing theoretical analyses on the melt systems to interpret the experimental results. All the facilities required for the experimental measurements have been procured, installed and tested. It has long been recognized that liquid Te presents a unique case having properties between those of metals and semiconductors. The electrical conductivity for Te melt increases rapidly at melting point, indicating a semiconductor-metal transition. Te melts comprise two features, which are usually considered to be incompatible with each other: covalently bound atoms and metallic-like behavior. Why do Te liquids show metallic behavior? is one of the long-standing issues in liquid metal physics. Since thermophysical properties are very sensitive to the structural variations of a melt, we have conducted extensive thermophysical measurements on Te melt.

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

    SciTech Connect

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

    2013-08-01

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

  1. Atom and Amine Adsorption on Flat and Stepped Gold Surfaces & Structure, Stability and Spin Ordering in Manganese Sulfide Clusters

    NASA Astrophysics Data System (ADS)

    Lewoczko, April D.

    In part I, we investigate gold catalysis in the chemistry of organonitrogen compounds. We examine the adsorption of oxygen, nitrogen and sulfur atoms on the gold (111), (100) and (211) surfaces using density functional theory (DFT). Sulfur atoms bind most strongly, followed by oxygen and nitrogen atoms with stronger adsorption for greater coordination to the surface. We see a trend of stronger adsorption to undercoordinated gold, but find it is non-universal with the adsorption strength trend: (111) > (211) > (100). We consider the diffusion of oxygen, nitrogen and sulfur adatoms and find facile long-range diffusion of oxygen atoms on the (100) surface. Lastly, we compare the adsorption of methylamine on gold to that of a selection of alkylamines, methanol and methanethiol. In each case, the ontop site is preferred with stronger adsorption at low coordinated gold. At oxygen atom coverages of 0.125 -- 0.25 ML on Au (111), we find cooperative adsorption of methylamine and oxygen atoms. Energetic costs for adsorbate tilt from the surface normal and rotation about the gold-nitrogen bond are calculated. While methylamine rotation is barrierless on the (111) and (211) surfaces, it has a low energetic barrier for the 0.125 ML and 0.25 ML O atom pre-covered Au (111) surfaces. In part II, we interpret the experimental mass spectrum of small gas phase manganese sulfide clusters using DFT and elucidate the role of ionicity and spin ordering in sizes with special stability, i.e. magic clusters. We first consider nine low lying minima (MnS)6 structures and reveal antiferromagnetic (AFM) spin ordering with a ˜0.1 eV/pair AFM energy benefit and a ˜0.1 A shrinkage of average Mn-Mn distances over clusters with ferromagnetic (FM) spin ordering. We calculate energetic barriers for interconversion between the two lowest lying (MnS)6 isomers and predict an elevated cluster melting temperature due to increased configurational entropy in a pre-melted state. Second, we demonstrate the

  2. The Three-Dimensional Structural Basis of Type II Hyperprolinemia

    SciTech Connect

    Srivastava, Dhiraj; Singh, Ranjan K.; Moxley, Michael A.; Henzl, Michael T.; Becker, Donald F.; Tanner, John J.

    2012-08-31

    Type II hyperprolinemia is an autosomal recessive disorder caused by a deficiency in {Delta}{sup 1}-pyrroline-5-carboxylate dehydrogenase (P5CDH; also known as ALDH4A1), the aldehyde dehydrogenase that catalyzes the oxidation of glutamate semialdehyde to glutamate. Here, we report the first structure of human P5CDH (HsP5CDH) and investigate the impact of the hyperprolinemia-associated mutation of Ser352 to Leu on the structure and catalytic properties of the enzyme. The 2. 5-{angstrom}-resolution crystal structure of HsP5CDH was determined using experimental phasing. Structures of the mutant enzymes S352A (2.4 {angstrom}) and S352L (2.85 {angstrom}) were determined to elucidate the structural consequences of altering Ser352. Structures of the 93% identical mouse P5CDH complexed with sulfate ion (1.3 {angstrom} resolution), glutamate (1.5 {angstrom}), and NAD{sup +} (1.5 {angstrom}) were determined to obtain high-resolution views of the active site. Together, the structures show that Ser352 occupies a hydrophilic pocket and is connected via water-mediated hydrogen bonds to catalytic Cys348. Mutation of Ser352 to Leu is shown to abolish catalytic activity and eliminate NAD{sup +} binding. Analysis of the S352A mutant shows that these functional defects are caused by the introduction of the nonpolar Leu352 side chain rather than the removal of the Ser352 hydroxyl. The S352L structure shows that the mutation induces a dramatic 8-{angstrom} rearrangement of the catalytic loop. Because of this conformational change, Ser349 is not positioned to interact with the aldehyde substrate, conserved Glu447 is no longer poised to bind NAD{sup +}, and Cys348 faces the wrong direction for nucleophilic attack. These structural alterations render the enzyme inactive.

  3. Structural studies of six and four coordinate zinc(II), nickel(II) and dioxovanadium(V) complexes with thiosemicarbazones

    NASA Astrophysics Data System (ADS)

    Sreekanth, A.; Sivakumar, S.; Prathapachandra Kurup, M. R.

    2003-07-01

    Three Zn(II) complexes of di-2-pyridyl ketone thiosemicarbazone, an octahedral Ni(II) complex of 2-acetylpyridine hexamethyleneiminyl-3-thiosemicarbazone, and a V(V) complex of 2-acetylpyridine morpholyl-3-thiosemicarbazone were prepared and characterized. Crystal structure of Ni(II) and V(V) complexes are reported. The ligand in the nickel complex is found to coordinate in the thione form with a pseudo octahedral geometry and the vanadium(V) complex has trigonal bipyramidal geometry.

  4. FASTRAN II - FATIGUE CRACK GROWTH STRUCTURAL ANALYSIS (UNIX VERSION)

    NASA Technical Reports Server (NTRS)

    Newman, J. C.

    1994-01-01

    Predictions of fatigue crack growth behavior can be made with the Fatigue Crack Growth Structural Analysis (FASTRAN II) computer program. As cyclic loads are applied to a selected crack configuration with an initial crack size, FASTRAN II predicts crack growth as a function of cyclic load history until either a desired crack size is reached or failure occurs. FASTRAN II is based on plasticity-induced crack-closure behavior of cracks in metallic materials and accounts for load-interaction effects, such as retardation and acceleration, under variable-amplitude loading. The closure model is based on the Dugdale model with modifications to allow plastically deformed material to be left along the crack surfaces as the crack grows. Plane stress and plane strain conditions, as well as conditions between these two, can be simulated in FASTRAN II by using a constraint factor on tensile yielding at the crack front to approximately account for three-dimensional stress states. FASTRAN II contains seventeen predefined crack configurations (standard laboratory fatigue crack growth rate specimens and many common crack configurations found in structures); and the user can define one additional crack configuration. The baseline crack growth rate properties (effective stress-intensity factor against crack growth rate) may be given in either equation or tabular form. For three-dimensional crack configurations, such as surface cracks or corner cracks at holes or notches, the fatigue crack growth rate properties may be different in the crack depth and crack length directions. Final failure of the cracked structure can be modelled with fracture toughness properties using either linear-elastic fracture mechanics (brittle materials), a two-parameter fracture criterion (brittle to ductile materials), or plastic collapse (extremely ductile materials). The crack configurations in FASTRAN II can be subjected to either constant-amplitude, variable-amplitude or spectrum loading. The applied

  5. FASTRAN II - FATIGUE CRACK GROWTH STRUCTURAL ANALYSIS (IBM PC VERSION)

    NASA Technical Reports Server (NTRS)

    Newman, J. C.

    1994-01-01

    Predictions of fatigue crack growth behavior can be made with the Fatigue Crack Growth Structural Analysis (FASTRAN II) computer program. As cyclic loads are applied to a selected crack configuration with an initial crack size, FASTRAN II predicts crack growth as a function of cyclic load history until either a desired crack size is reached or failure occurs. FASTRAN II is based on plasticity-induced crack-closure behavior of cracks in metallic materials and accounts for load-interaction effects, such as retardation and acceleration, under variable-amplitude loading. The closure model is based on the Dugdale model with modifications to allow plastically deformed material to be left along the crack surfaces as the crack grows. Plane stress and plane strain conditions, as well as conditions between these two, can be simulated in FASTRAN II by using a constraint factor on tensile yielding at the crack front to approximately account for three-dimensional stress states. FASTRAN II contains seventeen predefined crack configurations (standard laboratory fatigue crack growth rate specimens and many common crack configurations found in structures); and the user can define one additional crack configuration. The baseline crack growth rate properties (effective stress-intensity factor against crack growth rate) may be given in either equation or tabular form. For three-dimensional crack configurations, such as surface cracks or corner cracks at holes or notches, the fatigue crack growth rate properties may be different in the crack depth and crack length directions. Final failure of the cracked structure can be modelled with fracture toughness properties using either linear-elastic fracture mechanics (brittle materials), a two-parameter fracture criterion (brittle to ductile materials), or plastic collapse (extremely ductile materials). The crack configurations in FASTRAN II can be subjected to either constant-amplitude, variable-amplitude or spectrum loading. The applied

  6. Local atomic structure around Ni, Nb, and Zr atoms in Ni-Nb-Zr-H glassy alloys

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

    In order to elucidate the hydrogen effect on the atomic configuration in the Ni-Nb-Zr glassy alloys, we measured Ni, Nb, and Zr K-edge XAFS spectra of the Ni-Nb-Zr glassy alloy films with two different chemical compositions, i.e., Ni42Nb28Zr30 and Ni36Nb24Zr40, and their hydrogen-charged ones, i.e., (Ni42Nb28Zr30)0.91H0.09 and (Ni36Nb24Zr40)0.89H0.11. The Fourier transforms of the XAFS oscillations of these samples clearly shows that there is a significant difference in the structural response between the Zr30at.% and the Zr40at.% alloys when hydrogen atoms are charged. The curve-fitting analysis indicates that the hydrogenation does not alter the local alignment around the three metal atoms for the Zr30at.% alloy, but for the Zr40at.% alloy; it elongates the inter-atomic distances of Zr-Zr, Zr-Nb and Nb-Ni. On the basis of the curve fitting analysis, we propose the distorted icosahedral Zr5Ni5Nb3 cluster models. The XANES spectra at each (Ni, Zr and Nb) edge of (Ni36Nb24Zr40)0.89H0.11 also present the distinct shape from the other samples. The pre-edge peak (shoulder) vanishes or weakens, suggesting the conversion of the electronic state of the metal ions owing to the hydrogenation. The post-edge energy region shows clear multi-scattering effects from hydrogen atoms by charging these.

  7. Microstructural Characterization of Hierarchical Structured Surfaces by Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    In this work, we evaluate the hierarchical surface topography of reactively sputtered nanocrystalline Pb(Zr,Ti)O3 and TiO2 thin films as well as plasma-treated antireflective PET films by means of determining the fractal dimension and power spectral density (PSD) of surface topography recorded by atomic force microscopy (AFM). Local fractal dimension was obtained using the triangulation method. The PSDs of all samples were fitted to the k-correlation model (also called ABC model) valid for a self-affine surface topography. Fractal analysis of AFM images was shown to be an appropriate and easy to use tool for the characterization of hierarchical nanostructures.

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

    SciTech Connect

    Curtis, L. J.

    2004-05-01

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

  9. Geometric structure, electronic structure, and spin transition of several Fe{sup II} spin-crossover molecules

    SciTech Connect

    Tuan, Nguyen Anh

    2012-04-01

    We present a density functional study on the geometric structure, electronic structure, and spin transition of a series of Fe{sup II} spin-crossover (SCO) molecules, i.e., [Fe(abpt){sub 2}(NCS){sub 2}] (1), [Fe(abpt){sub 2}(NCSe){sub 2}] (2), and [Fe(dpbo)(HIm){sub 2}] (3) with dpbo diethyl(E,E)-2,2'-[1,2-phenylbis(iminomethylidyne)]bis[3-oxobutanoate](2-), N',O{sup 3},O{sup 3}', and abpt = 4-amino-3,5-bis(pyridin-2-yl)-1,2,4-triazole in order to explore more about the way to control SCO behavior of transition metal complexes. Our calculated results show that the spin transition of these Fe{sup II} molecules is accompanied with charge transfer between the Fe atom and ligands. This causes change in the electrostatic energy ({Delta}U) as well as the total electronic energy of SCO molecules. Moreover, our calculated results demonstrate an important contribution of the interionic interactions to {Delta}U, and there is the relation between {Delta}U and the thermal hysteresis behavior of SCO molecules. These results should be helpful for developing new SCO molecules.

  10. Synthesis, structure and spectroscopic properties of an o-phthalate-bridged copper(II) chain complex

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Li, J.; Su, Q.; Wang, Q.; Wu, X.

    2000-01-01

    An o-phthalate-bridged copper(II) chain complex of {[Cu(2,2'-bipyridine)(μ-phthalate)H 2O]·3.5H 2O} n has been prepared and characterized by X-ray crystallography and UV-vis spectroscopy measurements. It crystallizes in the monoclinic system, space group P2 1/c, with a=9.9585(5), b=14.8312(8), c=13.6875(7) Å, β=104.868(1)° and Z=4. The copper(II) center is in 4+1 surrounding that can be described as square-pyramid. Each Cu(II) atom links by o-phthalate to form a waving chain. A network structure is assembled by chains via π-π interactions and water molecules are clathrated in the cavities. The UV-vis absorption spectrum of the title complex is also reported and explained perfectly by the scaling radial theory which was proposed by us.

  11. Structural mechanisms of the Ih–II and II → Ic transitions between the crystalline phases of aqueous ice

    SciTech Connect

    Zheligovskaya, E. A.

    2015-09-15

    Structural mechanisms are proposed for experimentally observed phase transitions between crystalline modifications of aqueous ice, Ih and II, as well as II and Ic. It is known that the Ih–II transition occurs with the conservation of large structural units (hexagonal channels) common for these ices. It is shown that the Ih → II transition may occur with the conservation of 5/6 of all hydrogen bonds in crystal, including all hydrogen bonds in the retained channels (3/4 of the total number of bonds in crystal) and 1/3 of the bonds between these channels (1/12 of the total number). The transformation of other hydrogen bonds between the retained channels leads to the occurrence of proton order in ice II. A structural mechanism is proposed to explain the transformation of single crystals of ice Ih either into single crystals of ice II or into crystalline twins of ice II with c axes rotated by 180° with respect to each other, which is often observed at the Ih → II transition. It is established that up to 7/12 of all hydrogen bonds are retained at the irreversible cooperative II → Ic transition.

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

    PubMed

    Aguado, Andrés; López, José M

    2010-09-01

    The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions. PMID:20831313

  13. Progress towards a precision measurement of the n=2 triplet P fine structure of atomic helium

    NASA Astrophysics Data System (ADS)

    Kato, K.; Fitzakerley, D. W.; George, M. C.; Vutha, A. C.; Storry, C. H.; Hessels, E. A.

    2016-05-01

    We report progress on the measurement of the J = 1 to J = 2 23 P fine-structure interval of atomic helium. The measurement uses a liquid-nitrogen-cooled DC discharge source of metastable helium and the atomic beam is laser cooled in the transverse directions. The atoms are excited to 23 P by a 1083-nm diode laser, and the fine-structure transition is driven by microwaves using the frequency-offset separated oscillatory fields technique. The transition is detected by further laser excitation to a Rydberg state, followed by Stark ionization. This work is supported by NSERC, CRC.

  14. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water

    PubMed Central

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P.; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-01-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry. PMID:26286479

  15. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water.

    PubMed

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-01-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry. PMID:26286479

  16. Atomic structure relaxation in nanocrystalline NiO studied by EXAFS spectroscopy: Role of nickel vacancies

    NASA Astrophysics Data System (ADS)

    Anspoks, A.; Kalinko, A.; Kalendarev, R.; Kuzmin, A.

    2012-11-01

    Nanocrystalline NiO samples have been studied using the Ni K-edge extended x-ray absorption fine structure (EXAFS) spectroscopy and recently developed modeling technique, combining classical molecular dynamics with ab initio multiple-scattering EXAFS calculations (MD-EXAFS). Conventional analysis of the EXAFS signals from the first two coordination shells of nickel revealed that (i) the second shell average distance R(Ni-Ni2) expands in nanocrystalline NiO compared to microcrystalline NiO, in agreement with overall unit cell volume expansion observed by x-ray diffraction; (ii) on the contrary, the first shell average distance R(Ni-O1) in nanocrystalline NiO shrinks compared to microcrystalline NiO; (iii) the thermal contribution into the mean-square relative displacement σ2 is close in both microcrystalline and nanocrystalline NiO and can be described by the Debye model; (iv) the static disorder is additionally present in nanocrystalline NiO in both the first Ni-O1 and second Ni-Ni2 shells due to nanocrystal structure relaxation. Within the MD-EXAFS method, the force-field potential models have been developed for nanosized NiO using as a criterion the agreement between the experimental and theoretical EXAFS spectra. The best solutions have been obtained for the 3D cubic-shaped nanoparticle models with nonzero Ni vacancy concentration Cvac: Cvac≈0.4-1.2% for NiO nanoparticles having the cube size of L≈3.6-4.2 nm and Cvac≈1.6-2.0% for NiO thin film composed of cubic nanograins with a size of L≈1.3-2.1 nm. Thus our results show that the Ni vacancies in nanosized NiO play important role in its atomic structure relaxation along with the size reduction effect.

  17. Synthesis, Characterization, Crystal Structure, and Biological Studies of a Cadmium(II) Complex with a Tridentate Ligand 4'-Chloro-2,2':6',2''-Terpyridine.

    PubMed

    Saghatforoush, L A; Valencia, L; Chalabian, F; Ghammamy, Sh

    2011-01-01

    A new Cd(II) complex with the ligand 4'-chloro-2,2'6',2''-terpyridine (Cltpy), [Cd(Cltpy)(I)(2)], has been synthesized and characterized by CHN elemental analysis, (1)H-NMR, (13)C-NMR, and IR spectroscopy and structurally analyzed by X-ray single-crystal diffraction. The single-crystal X-ray analyses show that the coordination number in complex is five with three terpyridine (Cltpy) N-donor atoms and two iodine atoms. The antibacterial activities of Cltpy and its Cd(II) complex are tested against different bacteria. PMID:21738495

  18. Spectroscopic investigation of the structure of complex compounds of Cu(II), Co(II), and Ni(II) with. cap alpha. - and. beta. -diketone

    SciTech Connect

    Krymova, N.M.; Ivanov, V.E.; Ostapkevich, N.A.

    1986-11-10

    In the reactions of Cu(II), Co(II), and Ni(II) chlorides with 2,3-butanedione and 2,4-pentanedione isonicotinoylhydrazones in neutral and weakly acid media complex compounds of the addition-product type are formed, but in an alkaline medium inner-complex compounds are formed. By methods of electronic and ESR spectroscopy it was shown that the Cu(II) complex compounds have a planar-square structure, the Ni(II) complexes are octrahedral, but the Co(II) complexes have a tetrahedral or distorted tetrahedral structure. In the spectrochemical series 2,3-butanedione and 2,4-pentanedione isonicotinoylhydrazones occupy positions between water and ammonia.

  19. Magnetic-field effects in transitions of X Li molecules (X: even isotopes of group II atoms)

    SciTech Connect

    Gopakumar, Geetha; Abe, Minori; Hada, Masahiko; Kajita, Masatoshi

    2011-10-15

    We analyze the Zeeman shift in the (v,N)=(0,0){yields}(1,0) transition frequency of X Li molecules (X: even isotopes of group II atoms), which is of interest in metrology. The Zeeman shift in the transition frequency between stretching states is found to be less than 1 mHz with a magnetic field of 1 G. X {sup 6}Li molecules are more advantageous than X {sup 7}Li molecules for measuring the transition frequency without the Zeeman shift because of the smaller g factor of the Li nuclear spin.

  20. Crystal structure and magnetic properties of NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl

    SciTech Connect

    Jin Tengteng; Liu Wei; Chen Shuang; Prots, Yurii; Schnelle, Walter; Zhao Jingtai; Kniep, Ruediger; Hoffmann, Stefan

    2012-08-15

    A new copper(II) oxide phosphate chloride, NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl], has been synthesized by flux synthesis. Single-crystal X-ray diffraction data show that the title compound crystallizes in the monoclinic system, space group P2{sub 1}/c (No. 14), with lattice parameters a=8.392(2) A, b=6.3960(10) A, c=16.670(2) A, {beta}=109.470(10) Degree-Sign , V=843.6(3) A{sup 3}, Z=4. The crystal structure is characterized by a complex chain of copper-centered polyhedra running along [0 1 0] which are connected by phosphate tetrahedra. The resulting three-dimensional polyhedra framework exhibits channels filled by additional copper and sodium atoms. Field and temperature dependent measurements of the specific heat and the magnetic susceptibility reveal low-dimensional magnetic behavior. The compound starts to decompose at 700 K under release of oxygen and evaporation of Cu{sup I}Cl as shown by simultaneous thermogravimetry and mass spectrometry. - Graphical abstract: The crystal structure of the new copper(II) phosphate chloride, NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl], exhibits linear chains of copper tetrahedra which show low-dimensional magnetic behavior proven by specific heat and magnetic susceptibility measurements. Highlights: Black-Right-Pointing-Pointer A new copper(II) oxide phosphate chloride, NaCu{sup II}[(Cu{sup II}{sub 3}O)(PO{sub 4}){sub 2}Cl], has been synthesized by flux synthesis. Black-Right-Pointing-Pointer The crystal structure comprises chains of Cu{sub 4}O tetrahedra. Black-Right-Pointing-Pointer Low-dimensional behavior has been proven by magnetic and specific heat measurements. Black-Right-Pointing-Pointer On heating, Cu{sup I}Cl and oxygen are released shown by simultaneous thermogravimetry and mass spectrometry.

  1. Theory of two-atom coherence in gases. II. Continuous-wave spectra

    NASA Astrophysics Data System (ADS)

    Ben-Reuven, Abraham

    1980-12-01

    General expressions are derived for the spectral line shapes of resonance absorption and scattering of coherent radiation in collision-broadened gases, taking into account effects of coherent excitation of two or more atoms (or molecules), as steady-state solutions of a hierarchy of master equations described in a previous publication (paper I). Coupling between the coherent motions of the atoms, provided by a Bethe-Salpeter-type effective interaction, in the binary-collision approximation, forms the essential mechanism for introducing cooperative coherent effects into the steady-state spectra. Explicit expressions are given for the effects of two-atom coherence in the binary-collision approximation, in which the Bloch-type dressed-atom self-energy superoperator is modified by the presence of collisions in which both atoms retain memory of their coherent propagation before the collision. The self-energies include the effects of resonance exchange symmetrization in self-broadening, and are renormalized by the coincidence of radiative transitions during the collisions. The impact (near-resonance) and the quasistatic (line-wing) limits of the applied-frequency detunings are discussed. In the quasistatic limit, coherent many-atom excitations become irrelevant; however, interactions of both collision partners with the radiation during the collision accounts for such phenomena as collision-induced absorption or radiative collisions. In the impact limit, the inclusion of the Bethe-Salpeter interactions allows for the appearance of two-atom resonances. Magnitude estimates of these effects are discussed. Effects of higher-rank (many-body) coherences are formally discussed with the help of a diagrammatic method, leading into implicit bootstrap equations that can be solved by iterative or other procedures.

  2. Synthesis, characterization and X-ray structural studies of four copper (II) complexes containing dinuclear paddle wheel structures

    PubMed Central

    2013-01-01

    Background Various dinuclear copper (II) complexes with octahedral geometry have been reported. The majority of these complexes contain N containing aromatic rings as axial ligands. There are also a few cases where the solvent used in the reaction occupies the axial position of the dinuclear copper (II) complex. This may occur by planned synthesis or some times by serendipity. Here we report some four copper (II) complexes containing solvent and or N containing heterocyclic ring as the axial ligand. Results Four compounds, each containing dinuclear Copper (II) units (with the most robust, frequently occurring paddle wheel structures) were synthesized and characterised by single crystal X-ray diffraction and by IR spectroscopy. The compounds 1 & 2 have the general formula Cu2(RCOO) 4(L)2 [(for (1) RCOO= 4-Chloro Benzoate, L= Isopropanol; for 2 RCOO= Benzoate, L= 2-Amino-4,6-dimethyl pyrimidine )] while 3 & 4 have the general formula, Cu2(RCOO) 4(S)2 Cu2(RCOO) 4(L)2 [RCOO=5-Chloro-thiophene-2-carboxylate L= 2-Amino-4,6-dimethyl pyrimidine, for 3 S= ethanol; for 4 S= methanol ]. A wide range of hydrogen bonds (of the O-H…O, N-H…O and N-H…N type) and π-π stacking interactions are present in the crystal structures. Conclusions All compounds contain the dinuclear units, in which two Cu (II) ions are bridged by four syn, syn-η1:η1:μ carboxylates, showing a paddle-wheel cage type with a distorted octahedral geometry. The compounds 1 &2 contain a single dimeric unit while 3 &4 contain two dimeric units. The structures 3 and 4 are very interesting co-crystals of two paddle wheel molecules. Also it is interesting to note that the compounds 3 &4 are isostructural with similar cell parameters. Both the compounds 3 &4 differ in the solvent molecule coordinated to copper in one of the dimeric units. In all the four compounds, each of the copper dimers has an inversion centre. Every copper has a distorted octahedral centre, formed by four oxygen atoms (from different

  3. Atomic structures and oxygen dynamics of CeO2 grain boundaries

    PubMed Central

    Feng, Bin; Sugiyama, Issei; Hojo, Hajime; Ohta, Hiromichi; Shibata, Naoya; Ikuhara, Yuichi

    2016-01-01

    Material performance is significantly governed by grain boundaries (GBs), a typical crystal defects inside, which often exhibit unique properties due to the structural and chemical inhomogeneity. Here, it is reported direct atomic scale evidence that oxygen vacancies formed in the GBs can modify the local surface oxygen dynamics in CeO2, a key material for fuel cells. The atomic structures and oxygen vacancy concentrations in individual GBs are obtained by electron microscopy and theoretical calculations at atomic scale. Meanwhile, local GB oxygen reduction reactivity is measured by electrochemical strain microscopy. By combining these techniques, it is demonstrated that the GB electrochemical activities are affected by the oxygen vacancy concentrations, which is, on the other hand, determined by the local structural distortions at the GB core region. These results provide critical understanding of GB properties down to atomic scale, and new perspectives on the development strategies of high performance electrochemical devices for solid oxide fuel cells. PMID:26838958

  4. Atomic structures and oxygen dynamics of CeO2 grain boundaries

    NASA Astrophysics Data System (ADS)

    Feng, Bin; Sugiyama, Issei; Hojo, Hajime; Ohta, Hiromichi; Shibata, Naoya; Ikuhara, Yuichi

    2016-02-01

    Material performance is significantly governed by grain boundaries (GBs), a typical crystal defects inside, which often exhibit unique properties due to the structural and chemical inhomogeneity. Here, it is reported direct atomic scale evidence that oxygen vacancies formed in the GBs can modify the local surface oxygen dynamics in CeO2, a key material for fuel cells. The atomic structures and oxygen vacancy concentrations in individual GBs are obtained by electron microscopy and theoretical calculations at atomic scale. Meanwhile, local GB oxygen reduction reactivity is measured by electrochemical strain microscopy. By combining these techniques, it is demonstrated that the GB electrochemical activities are affected by the oxygen vacancy concentrations, which is, on the other hand, determined by the local structural distortions at the GB core region. These results provide critical understanding of GB properties down to atomic scale, and new perspectives on the development strategies of high performance electrochemical devices for solid oxide fuel cells.

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

    A comparison is made of microstructures of droplets of Ni-Sn alloys rapidly solidified by gas atomization and in a glass emulsifying medium. Cooling rate of the gas atomized particles ranged from 10 to the 3rd to 10 to the 6th K/s depending on droplet diameter (20-230 microns). In the hypoeutectic alloy studied, /Ni-(25 wt pct Sn)/, most particles showed a dendritic structure. These same particles, melted and resolidified in a glass medium using DTA (Differential Thermal Analysis), showed undercoolings up to 280 K: the structures were dendritic at low undercoolings and nondendritic at undercoolings above 220 K. It is concluded that the gas atomized particles exhibited little or no undercooling before nucleation; the solidification time of the undercooled emulsified droplets is substantially less than that of gas atomized droplets, and the undercooling required to achieve nondendritic structure depends on sample size.

  6. Simple Nuclear Structure in Cd-129111 from Atomic Isomer Shifts

    NASA Astrophysics Data System (ADS)

    Yordanov, D. T.; Balabanski, D. L.; Bissell, M. L.; Blaum, K.; Budinčević, I.; Cheal, B.; Flanagan, K.; Frömmgen, N.; Georgiev, G.; Geppert, Ch.; Hammen, M.; Kowalska, M.; Kreim, K.; Krieger, A.; Meng, J.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Rajabali, M. M.; Papuga, J.; Schmidt, S.; Zhao, P. W.

    2016-01-01

    Isomer shifts have been determined in 111-129>Cd by high-resolution laser spectroscopy at CERN-ISOLDE. The corresponding mean square charge-radii changes, from the 1 /2+ and the 3 /2+ ground states to the 11 /2- isomers, have been found to follow a distinct parabolic dependence as a function of the atomic mass number. Since the isomers have been previously associated with simplicity due to the linear mass dependence of their quadrupole moments, the regularity of the isomer shifts suggests a higher order of symmetry affecting the ground states in addition. A comprehensive description assuming nuclear deformation is found to accurately reproduce the radii differences in conjunction with the known quadrupole moments. This intuitive interpretation is supported by covariant density functional theory.

  7. Atomic Models of Strong Solids Interfaces Viewed as Composite Structures

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  8. A dinuclear cadmium(II) Schiff base thiocyanato complex: crystal structure and fluorescence.

    PubMed

    Shit, Shyamapada; Sankolli, Ravish; Guru Row, Tayur N

    2014-01-01

    A new dinuclear cadmium(II) complex, [Cd(L)(NCS)]2 (1) has been synthesized using a potentially tetradentate Schiff base ligand HL, 2-((E)-(2-(diethylamino)ethylimino)methyl)-6-methoxyphenol, obtained by the condensation of 2-diethylaminoethylamine and o-vanillin, and characterized by different physicochemical techniques. Crystal structure of the title complex was unambiguously established by single crystal X-ray diffraction which reveals that metal centers are connected by bridging phenolato and chelating methoxy oxygen atoms of the coordinating Schiff bases and embedded in severely distorted octahedral geometries. Fluorescence properties of the ligand and its complex, studied at room temperature indicate that later may serve as strong fluorescent emitter. PMID:24664327

  9. Prediction of structural and mechanical properties of atom-decorated porous graphene via density functional calculations

    NASA Astrophysics Data System (ADS)

    Ansari, Reza; Ajori, Shahram; Malakpour, Sina

    2016-04-01

    The considerable demand for novel materials with specific properties has motivated the researchers to synthesize supramolecular nanostructures through different methods. Porous graphene is the first two-dimensional hydrocarbon synthesized quite recently. This investigation is aimed at studying the mechanical properties of atom-decorated (functionalized) porous graphene by employing density functional theory (DFT) calculation within both local density approximations (LDA) and generalized gradient approximations (GGA). The atoms are selected from period 3 of periodic table as well as Li and O atom from period 2. The results reveal that metallic atoms and noble gases are adsorbed physically on porous graphene and nonmetallic ones form chemical bonds with carbon atom in porous graphene structure. Also, it is shown that, in general, atom decoration reduces the values of mechanical properties such as Young's, bulk and shear moduli as well as Poisson's ratio, and this reduction is more considerable in the case of nonmetallic atoms (chemical adsorption), especially oxygen atoms, as compared to metallic atoms and noble gases (physical adsorption).

  10. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

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

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

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

    SciTech Connect

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

    2014-05-05

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

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

    SciTech Connect

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

    2014-05-05

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

  13. Atomic structure and chemistry of human serum albumin

    NASA Technical Reports Server (NTRS)

    He, Xiao M.; Carter, Daniel C.

    1992-01-01

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

  14. Homochiral Cu(II) and Ni(II) malates with tunable structural features

    SciTech Connect

    Zavakhina, Marina S.; Samsonenko, Denis G.; Virovets, Alexander V.; Dybtsev, Danil N.; Fedin, Vladimir P.

    2014-02-15

    Four new homochiral metal–organic frameworks (MOFs) based on S-malate anions and N-donor linkers of different length have been prepared under solvothermal conditions. [Cu(mal)(bpy)]·H{sub 2}O (1), [Cu(mal)(bpe)]·2H{sub 2}O (2), [Ni(mal)(bpy)]·1.3CH{sub 3}OH (3) and [Ni(mal)(bpe)]·4H{sub 2}O (4) (mal=S-malate, bpy=4,4′-bipyridil, bpe=trans-1,2-bis(4-pyridyl)ethylene) were characterized by a number of analytical methods including powder X-ray diffraction, elemental, thermogravimetric analyses, IR spectroscopy. Compounds 1–3 were structurally characterized by X-ray crystallography. The absence of the chiral ligand racemization under synthetic conditions was unambiguously confirmed by polarimetry experiments. Compounds 1 and 2 contain metal-malate layered motives, connected by N-donor linkers and contribute to the family of isoreticular Cu(II) malates and tartrates [Cu(mal)L] and [Cu(tart)L], (tart=tartrate; L=ditopic rigid organic ligand). The Ni-based compounds 3 and 4 share 1D chiral (Ni(mal)) motives and possess novel type of the chiral framework, previously unknown for chiral carboxylates. The linear N-donor linkers connect these chiral chains, thus controlling the channel diameter and guest accessible volume of the homochiral structure, which exceeds 60 %. - Graphical abstract: Four new homochiral metal–organic frameworks are built from Ni{sup 2+} or Cu{sup 2+} cations, S-malate anions and N-donor linkers of different length, which controls the size of pores and guest accessible volume of the homochiral structure. Display Omitted - Highlights: • Four new homohiral metal–organic frameworks based on Ni{sup 2+} and Cu{sup 2+}. • Cu(II)–malate layers and Ni(II)–malate chains are connected by N-donor linkers. • N-donor linkers of different length control the size of pores.

  15. Synthesis, X-ray crystal structure and spectroscopy of a Werner-type host Co(II) complex, trans-bisisothiocyanatotetrakis( trans-4-styrylpyridine)cobalt(II)

    NASA Astrophysics Data System (ADS)

    Karunakaran, C.; Thomas, K. R. J.; Shunmugasundaram, A.; Murugesan, R.

    2000-05-01

    Single crystals of the title Co(II) complex, [Co(stpy) 4(NCS) 2] [stpy= trans-4-styrylpyridine] are prepared and characterized by elemental analysis, IR, and UV-visible spectroscopy and X-ray crystal structure determination. The complex crystallizes in the orthorhombic space group Pna2 1 with unit-cell parameters, a=32.058(3), b=15.362(5), c=9.818(5) Å, and Z=4. The structure consists of discrete monomeric units of [Co(stpy) 4(NCS) 2]. The equatorial positions of the Co(II) polyhedron are occupied by nitrogen atoms of the four stpy ligands and the axial positions are occupied by the nitrogen atoms of the two thiocyanate ions. The unit cell packing reveals interpenetration of styryl groups owing to conformational flexibility of phenyl and pyridyl rings in stpy ligands. Thus, it leads to efficient packing of the crystal lattice leaving no space available for guest inclusion. IR spectra reveal nitrogen coordination from stpy and terminal -NCS coordination of the thiocyanate group. The optical reflectance bands 475, 540 (shoulder) and 1022 nm suggest octahedral geometry in accordance with the X-ray data. However, the optical spectrum of acetonitrile solution shows an intense band at 615 nm and a weak shoulder at 570 nm suggesting participation of the solvent molecules in the coordination sphere. These bands indicate the presence of both tetrahedral and octahedral species in solution.

  16. NMR shielding constants for hydrogen guest molecules in structure II clathrates.

    PubMed

    Alavi, Saman; Ripmeester, J A; Klug, D D

    2005-08-01

    Proton NMR shielding constants and chemical shifts for hydrogen guests in small and large cages of structure II clathrates are calculated using density-functional theory and the gauge-invariant atomic-orbital method. Shielding constants are calculated at the B3LYP level with the 6-311++G(d,p) basis set. The calculated chemical shifts are corrected with a linear regression to reproduce the experimental chemical shifts of a set of standard molecules. The calculated chemical shifts of single hydrogen molecules in the small and large structure II cages are 4.94 and 4.84 ppm, respectively, which show that within the error range of the method the H2 guest molecules in the small and large cages cannot be distinguished. Chemical shifts are also calculated for double occupancy of the hydrogen guests in small cages, and double, triple, and quadruple occupancy in large cages. Multiple occupancy changes the chemical shift of the hydrogen guests by approximately 0.2 ppm. The relative effects of other guest molecules and the cage on the chemical shift are studied for the cages with multiple occupancies. PMID:16108623

  17. Kaonic atoms and in-medium K-N amplitudes II: Interplay between theory and phenomenology

    NASA Astrophysics Data System (ADS)

    Friedman, E.; Gal, A.

    2013-02-01

    A microscopic kaonic-atom optical potential VK-(1) is constructed, using the Ikeda-Hyodo-Weise NLO chiral K-N subthreshold scattering amplitudes constrained by the kaonic hydrogen SIDDHARTA measurement, and incorporating Pauli correlations within the Waas-Rho-Weise generalization of the Ericson-Ericson multiple-scattering approach. Good fits to kaonic atom data over the entire periodic table require additionally sizable K-NN-motivated absorptive and dispersive phenomenological terms, in agreement with our former analysis based on a post-SIDDHARTA in-medium chirally-inspired NLO separable model by Cieplý and Smejkal. Such terms are included by introducing a phenomenological potential VK-(2) and coupling it self-consistently to VK-(1). Properties of resulting kaonic atom potentials are discussed with special attention paid to the role of K--nuclear absorption and to the extraction of density-dependent amplitudes representing K- multi-nucleon processes.

  18. Structural changes of the oxygen-evolving complex in photosystem II during the catalytic cycle.

    PubMed

    Glöckner, Carina; Kern, Jan; Broser, Matthias; Zouni, Athina; Yachandra, Vittal; Yano, Junko

    2013-08-01

    The oxygen-evolving complex (OEC) in the membrane-bound protein complex photosystem II (PSII) catalyzes the water oxidation reaction that takes place in oxygenic photosynthetic organisms. We investigated the structural changes of the Mn4CaO5 cluster in the OEC during the S state transitions using x-ray absorption spectroscopy (XAS). Overall structural changes of the Mn4CaO5 cluster, based on the manganese ligand and Mn-Mn distances obtained from this study, were incorporated into the geometry of the Mn4CaO5 cluster in the OEC obtained from a polarized XAS model and the 1.9-Å high resolution crystal structure. Additionally, we compared the S1 state XAS of the dimeric and monomeric form of PSII from Thermosynechococcus elongatus and spinach PSII. Although the basic structures of the OEC are the same for T. elongatus PSII and spinach PSII, minor electronic structural differences that affect the manganese K-edge XAS between T. elongatus PSII and spinach PSII are found and may originate from differences in the second sphere ligand atom geometry. PMID:23766513

  19. Structural Changes of the Oxygen-evolving Complex in Photosystem II during the Catalytic Cycle*

    PubMed Central

    Glöckner, Carina; Kern, Jan; Broser, Matthias; Zouni, Athina; Yachandra, Vittal; Yano, Junko

    2013-01-01

    The oxygen-evolving complex (OEC) in the membrane-bound protein complex photosystem II (PSII) catalyzes the water oxidation reaction that takes place in oxygenic photosynthetic organisms. We investigated the structural changes of the Mn4CaO5 cluster in the OEC during the S state transitions using x-ray absorption spectroscopy (XAS). Overall structural changes of the Mn4CaO5 cluster, based on the manganese ligand and Mn-Mn distances obtained from this study, were incorporated into the geometry of the Mn4CaO5 cluster in the OEC obtained from a polarized XAS model and the 1.9-Å high resolution crystal structure. Additionally, we compared the S1 state XAS of the dimeric and monomeric form of PSII from Thermosynechococcus elongatus and spinach PSII. Although the basic structures of the OEC are the same for T. elongatus PSII and spinach PSII, minor electronic structural differences that affect the manganese K-edge XAS between T. elongatus PSII and spinach PSII are found and may originate from differences in the second sphere ligand atom geometry. PMID:23766513

  20. Structure determination of picolinato copper(II)-amine complexes

    NASA Astrophysics Data System (ADS)

    Mautner, Franz A.; Massoud, Salah S.

    2007-12-01

    Two series of Cu(II)-picolinato complexes of 1:1 and 3:2 Cu(II)-amine/picolinate namely [Cu(L 1)(pic)]ClO 4 and [Cu 3(L 2) 3(pic) 2(H 2O)](ClO 4) 4· xH 2O or [Cu 3(dpt) 3(pic) 2](ClO 4) 4, where pic = picolinate anion, L 1 = dien (diethylenetriamine), Et 2dien ( N, N-diethyldiethylenetriamine), Medpt (3,3'-diamino- N-methyldipropylamine), L 2 = pmedien ( N, N, N', N″, N″-pentamethyl-diethylenetriamine), TPA (tris(2-pyridylmethyl)amine), and dpt = dipropylenetriamine were synthesized and structurally characterized by electronic and IR spectroscopy. Single crystal X-ray diffraction analysis of the complex [Cu(dien)(pic)]ClO 4 ( 1) reveals its monomeric nature whereas for [Cu 3(pmedien) 3(pic) 2(H 2O)](ClO 4) 4·2H 2O ( 4), it was shown that the complex consists of two subunits of the mononuclear [Cu(pmedien)(pic)] + and the dinuclear [Cu 2(pmedien) 2(pic)(H 2O)] 3+ cations with the perchlorate as counter ions and lattice water molecules. In the mononuclear complexes of 1 and 4 the picolinato anions act as N, O-chelating ligands, whereas N, O, O'-picolinato bridges are observed in the dinuclear [Cu 2(pmedien) 2(pic)(H 2O)] 3+ cations of 4. The aqueous visible spectra of the complexes 1- 6 are consistent with five-coordinate Cu(II) species where distorted square pyramidal geometry (SP) was assigned for complexes 2- 5, trigonal bipyramidal geometry (TBP) for 6 and an intermediate geometry between SP and TBP for 1.

  1. Electronic structure investigation of atomic layer deposition ruthenium(oxide) thin films using photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Schaefer, Michael; Schlaf, Rudy

    2015-08-01

    Analyzing and manipulating the electronic band line-up of interfaces in novel micro- and nanoelectronic devices is important to achieve further advancement in this field. Such band alignment modifications can be achieved by introducing thin conformal interfacial dipole layers. Atomic layer deposition (ALD), enabling angstrom-precise control over thin film thickness, is an ideal technique for this challenge. Ruthenium (Ru0) and its oxide (RuO2) have gained interest in the past decade as interfacial dipole layers because of their favorable properties like metal-equivalent work functions, conductivity, etc. In this study, initial results of the electronic structure investigation of ALD Ru0 and RuO2 films via photoemission spectroscopy are presented. These experiments give insight into the band alignment, growth behavior, surface structure termination, and dipole formation. The experiments were performed in an integrated vacuum system attached to a home-built, stop-flow type ALD reactor without exposing the samples to the ambient in between deposition and analysis. Bis(ethylcyclopentadienyl)ruthenium(II) was used as precursor and oxygen as reactant. The analysis chamber was outfitted with X-ray photoemission spectroscopy (LIXPS, XPS). The determined growth modes are consistent with a strong growth inhibition situation with a maximum average growth rate of 0.21 Å/cycle for RuO2 and 0.04 Å/cycle for Ru.0 An interface dipole of up to -0.93 eV was observed, supporting the assumption of a strongly physisorbed interface. A separate experiment where the surface of a RuO film was sputtered suggests that the surface is terminated by an intermediate, stable, non-stoichiometric RuO2/OH compound whose surface is saturated with hydroxyl groups.

  2. Electronic structure investigation of atomic layer deposition ruthenium(oxide) thin films using photoemission spectroscopy

    SciTech Connect

    Schaefer, Michael E-mail: schlaf@mail.usf.edu; Schlaf, Rudy E-mail: schlaf@mail.usf.edu

    2015-08-14

    Analyzing and manipulating the electronic band line-up of interfaces in novel micro- and nanoelectronic devices is important to achieve further advancement in this field. Such band alignment modifications can be achieved by introducing thin conformal interfacial dipole layers. Atomic layer deposition (ALD), enabling angstrom-precise control over thin film thickness, is an ideal technique for this challenge. Ruthenium (Ru{sup 0}) and its oxide (RuO{sub 2}) have gained interest in the past decade as interfacial dipole layers because of their favorable properties like metal-equivalent work functions, conductivity, etc. In this study, initial results of the electronic structure investigation of ALD Ru{sup 0} and RuO{sub 2} films via photoemission spectroscopy are presented. These experiments give insight into the band alignment, growth behavior, surface structure termination, and dipole formation. The experiments were performed in an integrated vacuum system attached to a home-built, stop-flow type ALD reactor without exposing the samples to the ambient in between deposition and analysis. Bis(ethylcyclopentadienyl)ruthenium(II) was used as precursor and oxygen as reactant. The analysis chamber was outfitted with X-ray photoemission spectroscopy (LIXPS, XPS). The determined growth modes are consistent with a strong growth inhibition situation with a maximum average growth rate of 0.21 Å/cycle for RuO{sub 2} and 0.04 Å/cycle for Ru.{sup 0} An interface dipole of up to −0.93 eV was observed, supporting the assumption of a strongly physisorbed interface. A separate experiment where the surface of a RuO film was sputtered suggests that the surface is terminated by an intermediate, stable, non-stoichiometric RuO{sub 2}/OH compound whose surface is saturated with hydroxyl groups.

  3. Electronic structure and magnetic properties of substitutional transition-metal atoms in GaN nanotubes

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Shi, Jun-Jie

    2014-01-01

    The electronic structure and magnetic properties of the transition-metal (TM) atoms (Sc—Zn, Pt and Au) doped zigzag GaN single-walled nanotubes (NTs) are investigated using first-principles spin-polarized density functional calculations. Our results show that the bindings of all TM atoms are stable with the binding energy in the range of 6-16 eV. The Sc- and V-doped GaN NTs exhibit a nonmagnetic behavior. The GaN NTs doped with Ti, Mn, Ni, Cu and Pt are antiferromagnetic. On the contrary, the Cr-, Fe-, Co-, Zn- and Au-doped GaN NTs show the ferromagnetic characteristics. The Mn- and Co-doped GaN NTs induce the largest local moment of 4μB among these TM atoms. The local magnetic moment is dominated by the contribution from the substitutional TM atom and the N atoms bonded with it.

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

    NASA Astrophysics Data System (ADS)

    Ünlü, Pervin

    2010-07-01

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

  5. Imaging biological structures with the cryo atomic force microscope.

    PubMed Central

    Zhang, Y; Sheng, S; Shao, Z

    1996-01-01

    It has long been recognized that one of the major limitations in biological atomic force microscopy (AFM) is the softness of most biological samples, which are easily deformed or damaged by the AFM tip, because of the high pressure in the contact area, especially from the very sharp tips required for high resolution. Another is the molecular motion present at room temperature due to thermal fluctuation. Using an AFM operated in liquid nitrogen vapor (cryo-AFM), we demonstrate that cryo-AFM can be applied to a large variety of biological samples, from immunoglobulins to DNA to cell surfaces. The resolution achieved with cryo-AFM is much improved when compared with AFM at room temperature with similar specimens, and is comparable to that of cryo-electron microscopy on randomly oriented macromolecules. We will also discuss the technical problems that remain to be solved for achieving even higher resolution with cryo-AFM and other possible applications of this novel technique. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 PMID:8889193

  6. Regularities and symmetries in atomic structure and spectra

    NASA Astrophysics Data System (ADS)

    Pain, Jean-Christophe

    2013-09-01

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

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

    PubMed

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

    2014-07-28

    Most of the work done on the linear response kernel χ(r,r') has focussed on its atom-atom condensed form χAB. Our previous work [Boisdenghien et al., J. Chem. Theory Comput., 2013, 9, 1007] was the first effort to truly focus on the non-condensed form of this function for closed (sub)shell atoms in a systematic fashion. In this work, we extend our method to the open shell case. To simplify the plotting of our results, we average our results to a symmetrical quantity χ(r,r'). This allows us to plot the linear response kernel for all elements up to and including argon and to investigate the periodicity throughout the first three rows in the periodic table and in the different representations of χ(r,r'). Within the context of Spin Polarized Conceptual Density Functional Theory, the first two-dimensional plots of spin polarized linear response functions are presented and commented on for some selected cases on the basis of the atomic ground state electronic configurations. Using the relation between the linear response kernel and the polarizability we compare the values of the polarizability tensor calculated using our method to high-level values. PMID:24837234

  8. I.I. Rabi Prize Talk: Artificial gauge fields in multi-level atoms

    NASA Astrophysics Data System (ADS)

    Spielman, Ian

    2015-05-01

    We used Raman lasers to induce artificial gauge fields or spin-orbit coupling in the three-level system formed by the f=1 electronic ground state manifold of rubidium-87. In this colloquium I will report on two effects of this laser-coupling. I will explore the itinerant magnetic phases present in a spin-1 spin-orbit coupled atomic Bose-Einstein condensate (BEC); in this system, itinerant ferromagnetic order is stabilized by the spin-orbit coupling, vanishing in its absence. We first located a second-order phase transition that continuously stiffens until, at a tricritical point, it transforms into a first-order transition. These measurements are all in agreement with theory. We engineered a two-dimensional magnetic lattice in an elongated strip geometry, with effective per-plaquette flux about 4/3 times the flux quanta. We imaged the localized edge and bulk states of atomic Bose-Einstein condensates in this strip, with single lattice-site resolution along the narrow direction. Further, we observed both the skipping orbits of excited atoms traveling down our system's edges, analogues to edge magnetoplasmons in 2-D electron systems. Our lattice's long direction consisted of the sites of an optical lattice and its narrow direction consisted of the internal atomic spin states: a synthetic dimension.

  9. A solid phase extraction procedure for the determination of Cd(II) and Pb(II) ions in food and water samples by flame atomic absorption spectrometry.

    PubMed

    Daşbaşı, Teslima; Saçmacı, Şerife; Ülgen, Ahmet; Kartal, Şenol

    2015-05-01

    A relatively rapid, accurate and precise solid phase extraction method is presented for the determination of cadmium(II) and lead(II) in various food and water samples. Quantitation is carried out by flame atomic absorption spectrometry (FAAS). The method is based on the retention of the trace metal ions on Dowex Marathon C, a strong acid cation exchange resin. Some important parameters affecting the analytical performance of the method such as pH, flow rate and volume of the sample solution; type, concentration, volume, flow rate of the eluent; and matrix effects on the retention of the metal ions were investigated. Common coexisting ions did not interfere on the separation and determination of the analytes. The detection limits (3 σb) for Cd(II) and Pb(II) were found as 0.13 and 0.18 μg L(-1), respectively, while the limit of quantification values (10 σb) were computed as 0.43 and 0.60 μg L(-1) for the same sequence of the analytes. The precision (as relative standard deviation was lower than 4% at 5 μg L(-1) Cd(II) and 10 μg L(-1) Pb(II) levels, and the preconcentration factor was found to be 250. The accuracy of the proposed procedure was verified by analysing the certified reference materials, SPS-WW2 Batch 108 wastewater level 2 and INCT-TL-1 tea leaves, with the satisfactory results. In addition, for the accuracy of the method the recovery studies (⩾ 95%) were carried out. The method was applied to the determination of the analytes in the various natural waters (lake water, tap water, waste water with boric acid, waste water with H2SO4) and food samples (pomegranate flower, organic pear, radish leaf, lamb meat, etc.), and good results were obtained. While the food samples almost do not contain cadmium, they have included lead at low levels of 0.13-1.12 μg g(-1). PMID:25529724

  10. Synthesis of Calcium(II) Amidinate Precursors for Atomic Layer Deposition through a Redox Reaction between Calcium and Amidines.

    PubMed

    Kim, Sang Bok; Yang, Chuanxi; Powers, Tamara; Davis, Luke M; Lou, Xiabing; Gordon, Roy G

    2016-08-22

    We have prepared two new Ca(II) amidinates, which comprise a new class of ALD precursors. The syntheses proceed by a direct reaction between Ca metal and the amidine ligands in the presence of ammonia. Bis(N,N'-diisopropylformamidinato)calcium(II) (1) and bis(N,N'-diisopropylacetamidinato)calcium(II) (2) adopt dimeric structures in solution and in the solid state. X-ray crystallography revealed asymmetry in one of the bridging ligands to afford the structure [(η(2) -L)Ca(μ-η(2) :η(2) -L)(μ-η(2) :η(1) -L)Ca(η(2) -L)]. These amidinate complexes showed unprecedentedly high volatility as compared to the widely employed and commercially available Ca(II) precursor, [Ca3 (tmhd)6 ]. In CaS ALD with 1 and H2 S, the ALD window was approximately two times wider and lower in temperature by about 150 °C than previously reported with [Ca3 (tmhd)6 ] and H2 S. Complexes 1 and 2, with their excellent volatility and thermal stability (up to at least 350 °C), are the first homoleptic Ca(II) amidinates suitable for use as ALD precursors. PMID:27351794

  11. Deformation of chlorin rings in the Photosystem II crystal structure.

    PubMed

    Saito, Keisuke; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo; Ishikita, Hiroshi

    2012-05-29

    The crystal structure of Photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed deformations of chlorin rings in the chlorophylls for the first time. We investigated the degrees of chlorin ring deformation and factors that contributed to them in the PSII crystal structure, using a normal-coordinate structural decomposition procedure. The out-of-plane distortion of the P(D1) chlorin ring can be described predominantly by a large "doming mode" arising from the axial ligand, D1-His198, as well as the chlorophyll side chains and PSII protein environment. In contrast, the deformation of P(D2) was caused by a "saddling mode" arising from the D2-Trp191 ring and the doming mode arising from D2-His197. Large ruffling modes, which were reported to lower the redox potential in heme proteins, were observed in P(D1) and Chl(D1), but not in P(D2) and Chl(D2). Furthermore, as P(D1) possessed the largest doming mode among the reaction center chlorophylls, the corresponding bacteriochlorophyll P(L) possessed the largest doming mode in bacterial photosynthetic reaction centers. However, the majority of the redox potential shift in the protein environment was determined by the electrostatic environment. The difference in the chlorin ring deformation appears to directly refer to the difference in "the local steric protein environment" rather than the redox potential value in PSII. PMID:22568617

  12. Novel functionalization of Ti-V alloy and Ti-II using atomic layer deposition for improved surface wettability.

    PubMed

    Patel, Sweetu; Butt, Arman; Tao, Qian; Rossero A, Jorge Iván; Royhman, Dmitry; Sukotjo, Cortino; Takoudis, Christos G

    2014-03-01

    Surface wettability characteristics of commercially pure titanium (CP-Ti/Ti-II) and titanium Grade 5 alloy (Ti-6Al-4V/Ti-V) with 10nm-thick atomic layer deposited (ALD) TiO2 from Tetrakis DiEthyl Amino Titanium and water vapor were studied in conjunction with cleaning steps before and after the ALD treatment. The wettability characteristics of rough Ti-II and Ti-V samples were investigated after each step, that is, as received, after de-ionized (DI) water rinse followed by N2 drying, sonication in methanol, ALD treatment, and post-ALD DI water rinse. Samples without ALD or cleaning treatments were hydrophobic to variable extents, depending on exposure to different environments, surface impurities, roughness, and aging. Surface treatments reported in the literature resulted in hydrophilic/hydrophobic surfaces likely due to organic and/or inorganic impurities. In this study, (i) it is established that it is critically important to probe surface wettability after each substrate treatment; (ii) both Ti-II and Ti-V surfaces are found to become more hydrophilic after each one of the sequential treatments used; and (iii) independently of the initial wettability characteristics of Ti-II and Ti-V surfaces, the aforementioned treatments result in a water contact angle well below 10°, which is an important factor in cellular response. X-ray photoelectron spectroscopy of ALD titania films indicated trace impurities in them. Grazing incidence X-ray diffraction suggested amorphous ALD TiO2 at 200 °C; anatase TiO2 was obtained with as little as 5 min annealing at 600 °C in nitrogen. PMID:24384144

  13. Structural and luminescence studies of nickel(II) and copper(II) complexes with (1R,2R)-cyclohexanediamine derived unsymmetric Schiff base.

    PubMed

    Barwiolek, Magdalena; Szlyk, Edward; Muzioł, Tadeusz M; Lis, Tadeusz

    2011-11-01

    Unsymmetrical Schiff base obtained by the condensation reaction of (1R,2R)(-)cyclohexanediamine with 2-hydroxybenzaldehyde and 2-hydroxynaphthaldehyde was used as a ligand for copper(II) and nickel(II). The ligand and complexes were characterized by circular dichroism (CD), UV-VIS, fluorescence, IR and (1)H (NOE diff), NOESY and (13)C NMR (ligand) spectra. The X-ray crystal structures solved for (1R,2R)(-)chxn(salH)(naftalH) and Cu(II)(1R,2R)(-)chxn(sal)(naftal) revealed tetrahedral distortion of coordination sphere in the solid phase. The [Cu(1R,2R)(-)chxn(sal)(naftal)]·0.5EtOH·1.25H(2)O complex crystallized in the monoclinic chiral C2 space group with two molecules in the asymmetric unit as well as disordered ethanol and water molecules. For both molecules Cu(II) ions were found in square-planar environments and adopts conformation described as "semi-open armed", because of distinctly oriented arms according to cyclohexane ring defined by three torsion angles. The thin layers of the ligands, copper(II) and nickel(II) complexes were deposited on Si(111) by a spin coating method and characterized with scanning electron microscopy SEM/EDS and fluorescence spectra. The ligand layers exhibit the most intensive fluorescence band at 498 nm, which can be assigned to emission transition π* → n of Schiff base ligand. For copper(II) layers the most intensive band from intraligand transition at 550 nm was observed. The highest intensity band was registered for the layer obtained when rotation speed was 1000 rpm and time 20 s. The nickel(II) complex layers fluorescence spectra exhibit an intensive band at 564 nm. The emission maxima of the copper(II) and nickel(II) complexes are shifted towards longer wavelength in comparison to the free ligand layers. CD spectra of the complexes in solution are characteristic for tetrahedral planar distortion of the chelate ring. The (1)H NMR NOE diff were measured and the position of the nearest hydrogen atoms in the cyclohexane and

  14. Atomic Structure and Phase Transformations in Pu Alloys

    SciTech Connect

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

    2008-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

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

  17. First-principles calculation of atomic forces and structural distortions in strongly correlated materials.

    PubMed

    Leonov, I; Anisimov, V I; Vollhardt, D

    2014-04-11

    We introduce a novel computational approach for the investigation of complex correlated electron materials which makes it possible to evaluate interatomic forces and, thereby, determine atomic displacements and structural transformations induced by electronic correlations. It combines ab initio band structure and dynamical mean-field theory and is implemented with the linear-response formalism regarding atomic displacements. We apply this new technique to explore structural transitions of prototypical correlated systems such as elemental hydrogen, SrVO3, and KCuF3. PMID:24765993

  18. Structure stabilities and transitions in polyhedral metal nanocrystals: An atomic-bond-relaxation approach

    NASA Astrophysics Data System (ADS)

    Zhang, Ai; Zhu, Ziming; He, Yan; Ouyang, Gang

    2012-04-01

    We present an atomic-bond-relaxation (ABR) method to illustrate a deeper insight on structure stabilities and transitions of metal nanocrystals with polyhedral structure based on the thermodynamic consideration. It has been found that the end effects in polyhedral nanocrystals induced by the atoms located at edges, side facets, and vertexes play the dominant roles for their structure performances. The theoretical predictions are well consistent with the experimental measurements and simulations, which suggest the ABR model can be an effective method to understand solid-solid phase transition of polyhedral metal nanocrystals.

  19. Atomic structure and electronic properties of Ni3Al(111) and (011) surfaces

    NASA Astrophysics Data System (ADS)

    Jurczyszyn, L.; Krupski, A.; Degen, S.; Pieczyrak, B.; Kralj, M.; Becker, C.; Wandelt, K.

    2007-07-01

    We present results of theoretical studies of the structural and electronic properties of (111) and (011) surfaces of paramagnetic Ni3Al alloy. Atomic and electronic structures of these surfaces have been obtained from the density-functional calculations performed with the use of plane wave basis set. Our ab initio calculations show that for all considered surfaces, the topmost Al atoms are located above Ni atoms, and the structural parameters of relaxed surface systems well correspond to experimental data provided by earlier low-energy electron-diffraction measurements. The details of the calculated electronic structure of Ni3Al(111) in the vicinity of the Fermi level were compared with the results of scanning tunneling spectroscopy (STS) measurements which we have performed for this system, and a good agreement has been found between the calculated local-density-of-states distributions and the shape of obtained STS spectra.

  20. Structure and Chemistry of Atomic Clusters from Supersonic Beams.

    NASA Astrophysics Data System (ADS)

    Yang, Shi-He.

    A tandem time-of-flight (TOF) apparatus was designed to study the structure and chemistry of cold transition metal cluster ions from supersonic beams. By means of a photodissociation laser fluence dependence technique, binding energies of Nb_{rm x }^{+} (x = 2 - 20), Co_{rm x}^{+ } (x = 4 - 20) and etc. were found to generally increase with cluster size. The desorption energies of Nb_{rm x}N _2^{+} (x = 2 - 17) and Nb_{rm x} CO^{+} (x = 2 - 10) also increase with cluster size with some oscillations similar to the size dependent reactivities of these clusters. Photodetachment studies revealed that electron affinities of copper clusters increase with cluster size with a sharp even/odd alternation. Unlike other noble metals, Ag_{rm x}^ {-} clusters display two competing processes: photodissociation and photodetachment. Relative reactivities of cluster ions of Nb, Co, Ag, and etc. have been measured using a fast flow cluster reactor, displaying a similar function of cluster size to that of the neutrals. In addition, preliminary photoelectron experiments have been performed on Cu_{ rm x}^{-} and Nb _{rm x}^{-}. A magnetic Time-of-flight ultraviolet photoelectron spectrometer (MTOFUPS) has been developed to study electronic structures of cold metal and semiconductor cluster anions prepared in supersonic beams. Application of this spectrometer to carbon clusters with a F_2 laser (7.9 eV) allowed their electron affinities and UPS patterns to be measured,demonstrating a remarkable structural evolution of these clusters: Chains (C_2^{ -}-C_9^{-} ) - Rings (C_{10}^ {-}-C_{29}^ {-}) - Cages (C_{38 }^{-}-C_{84 }^{-}). In particular, the UPS of C_{60}^{-} is in excellent agreement with the CNDO/S calculation, providing a striking spectral evidence for the highly symmetric icosahedral soccer ball structure--Buckminsterfullerene. For comparison, the UPS of Si_ {rm x}^{-} and Ge_{rm x}^{ -} are presented. Unlike carbon clusters which prefer structures of low dimensionality, these

  1. Chemical Structure and Properties: A Modified Atoms-First, One-Semester Introductory Chemistry Course

    ERIC Educational Resources Information Center

    Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jakubowski, Henry V.; McKenna, Anna G.; McIntee, Edward J.; Jones, T. Nicholas; Fazal, M. A.; Peterson, Alicia A.

    2015-01-01

    A one-semester, introductory chemistry course is described that develops a primarily qualitative understanding of structure-property relationships. Starting from an atoms-first approach, the course examines the properties and three-dimensional structure of metallic and ionic solids before expanding into a thorough investigation of molecules. In…

  2. Energy losses of fast heavy multiply charged structural ions in collisions with complex atoms

    NASA Astrophysics Data System (ADS)

    Matveev, V. I.; Sidorov, D. B.

    2007-07-01

    A nonperturbatve theory of energy losses of fast heavy multiply charged structural ions in collisions with neutral complex atoms is elaborated with allowance for simultaneous excitations of ionic and atomic electron shells. Formulas for the effective deceleration that are similar to the well-known Bethe-Bloch formulas are derived. By way of example, the energy lost by partially stripped U q+ ions (10 ≤ q ≤ 70) colliding with argon atoms and also the energy lost by Au, Pb, and Bi ions colliding with various targets are calculated. The results of calculation are compared with experimental data.

  3. Determining Chemically and Spatially Resolved Atomic Profile of Low Contrast Interface Structure with High Resolution

    PubMed Central

    Nayak, Maheswar; Pradhan, P. C.; Lodha, G. S.

    2015-01-01

    We present precise measurements of atomic distributions of low electron density contrast at a buried interface using soft x-ray resonant scattering. This approach allows one to construct chemically and spatially highly resolved atomic distribution profile upto several tens of nanometer in a non-destructive and quantitative manner. We demonstrate that the method is sensitive enough to resolve compositional differences of few atomic percent in nano-scaled layered structures of elements with poor electron density differences (0.05%). The present study near the edge of potential impurities in soft x-ray range for low-Z system will stimulate the activity in that field. PMID:25726866

  4. Determining chemically and spatially resolved atomic profile of low contrast interface structure with high resolution.

    PubMed

    Nayak, Maheswar; Pradhan, P C; Lodha, G S

    2015-01-01

    We present precise measurements of atomic distributions of low electron density contrast at a buried interface using soft x-ray resonant scattering. This approach allows one to construct chemically and spatially highly resolved atomic distribution profile upto several tens of nanometer in a non-destructive and quantitative manner. We demonstrate that the method is sensitive enough to resolve compositional differences of few atomic percent in nano-scaled layered structures of elements with poor electron density differences (0.05%). The present study near the edge of potential impurities in soft x-ray range for low-Z system will stimulate the activity in that field. PMID:25726866

  5. Synthesis, characterization, crystal structure and antimicrobial studies of a novel Cu(II) complex based on itaconic acid and nicotinamide

    NASA Astrophysics Data System (ADS)

    Tella, Adedibu C.; Owalude, Samson O.; Ajibade, Peter A.; Simon, Nzikahyel; Olatunji, Sunday J.; Abdelbaky, Mohammed S. M.; Garcia-Granda, Santiago

    2016-12-01

    A novel complex was synthesized from Cu(II), nicotinamide and itaconic acid and is formulated as [Cu(C5H4O4)2(C6H6N2O)2(H2O)2·2(H2O)] (1). The compound was characterized by elemental analysis, FTIR spectroscopy, UV-Vis and single crystal X-ray diffraction. The complex crystallizes in the triclinic P-1 space group, with a = 7.5111(2) Å, b = 9.8529(3) Å, c = 10.5118(4) Å, α = 116.244(3)°, β = 90.291(3)°, γ = 103.335(3)°, V = 673.81(4) Å3, Z = 1.The octahedral geometry around the copper(II) ion is of the form CuN2O4 consisting of two molecules of nicotinamide acting as monodentate ligand through the nitrogen atoms, two molecules itaconate ligand and two coordinated water molecules each coordinating through the oxygen atoms. The structure of 1 showed infinite chains build up linking the molecules together via strong Osbnd H⋯O and Nsbnd H⋯O intermolecular hydrogen bonds generating a two dimensional network sheet along c axis. The antimicrobial study of the synthesized complex 1 was investigated and showed higher antibacterial activity against all the organisms comparing with Copper(II) nicotinamide 2 and Copper(II) itaconate 3.

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  7. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Wu, X.; Sha, W.

    2008-12-01

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.

  8. Synthesis, crystal structure and antifungal activity of a divalent cobalt(II) complex with uniconazole.

    PubMed

    Zhang, Yao; Li, Jie; Ren, Guoyu; Qin, Baofu; Ma, Haixia

    2016-06-01

    Azole compounds have attracted commercial interest due to their high bactericidal and plant-growth-regulating activities. Uniconazole [or 1-(4-chlorophenyl)-4,4-dimethyl-2-(1H-1,2,4-triazol-1-yl)pent-1-en-3-ol] is a highly active 1,2,4-triazole fungicide and plant-growth regulator with low toxicity. The pharmacological and toxicological properties of many drugs are modified by the formation of their metal complexes. Therefore, there is much interest in exploiting the coordination chemistry of triazole pesticides and their potential application in agriculture. However, reports of complexes of uniconazole are rare. A new cobalt(II) complex of uniconazole, namely dichloridotetrakis[1-(4-chlorophenyl)-4,4-dimethyl-2-(1H-1,2,4-triazol-1-yl-κN(4))pent-1-en-3-ol]cobalt(II), [CoCl2(C15H18ClN3O)4], was synthesized and structurally characterized by element analysis, IR spectrometry and X-ray single-crystal diffraction. The crystal structural analysis shows that the Co(II) atom is located on the inversion centre and is coordinated by four uniconazole and two chloride ligands, forming a distorted octahedral geometry. The hydroxy groups of an uniconazole ligands of adjacent molecules form hydrogen bonds with the axial chloride ligands, resulting in one-dimensional chains parallel to the a axis. The complex was analysed for its antifungal activity by the mycelial growth rate method. It was revealed that the antifungal effect of the title complex is more pronounced than the effect of fungicide uniconazole for Botryosphaeria ribis, Wheat gibberellic and Grape anthracnose. PMID:27256696

  9. Structural Preferences in Phosphanylthiolato Platinum(II) Complexes

    PubMed Central

    Duran, Josep; Real, Julio; Benet‐Buchholz, Jordi; Solà, Miquel

    2015-01-01

    Abstract The transition‐metal complexes of heterotopic phosphanylthiolato ligands are useful in various reactions which depend on the stereochemistry of the complexes. Bis‐chelate complex [Pt(SCH2CH2PPh2‐κ2 P,S)2] (1) was obtained in good yields by direct base‐free substitution reaction of the corresponding phosphanylthiol (HSCH2CH2PPh2) with K2PtCl4 or by oxidative addition of the same phosphanylthiol to Pt(PPh3)4. In agreement with the antisymbiosis rule, complex 1 shows a cis‐P,P arrangement in solid state crystallizing in the monoclinic system (C2/c). Density functional theory (DFT) calculations on 1 reveal the right characteristics for the preferred cis‐P,P arrangement, rationalizing its formation. Direct base‐free reaction of [PtCl2(1,5‐cyclooctadiene)] with one equivalent of the same phosphanylthiol produce the trinuclear complex [PtCl(μ‐SCH2CH2PPh2‐κ2 P,S)]3 (2) instead of the binuclear structure common in palladium and nickel derivatives. Crystals of 2 are triclinic (P 1‾ ) showing a sulfur‐bridging edge‐sharing cyclic trinuclear complex with square‐planar coordination geometry around the platinum atoms and a Pt3S3 cycle in skew‐boat conformation. This preference for the trinuclear structure was rationalized mechanistically and through conceptual DFT. PMID:27308212

  10. Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

    PubMed Central

    Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

    2012-01-01

    Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their population was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed. PMID:22312477

  11. Structure and dynamics of dinucleosomes assessed by atomic force microscopy.

    PubMed

    Filenko, Nina A; Palets, Dmytro B; Lyubchenko, Yuri L

    2012-01-01

    Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their population was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed. PMID:22312477

  12. Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

    DOE PAGESBeta

    Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

    2012-01-01

    Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their populationmore » was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.« less

  13. Structure of magnetic resonance in 87Rb atoms

    NASA Astrophysics Data System (ADS)

    Kozlov, A. N.; Zibrov, S. A.; Zibrov, A. A.; Yudin, V. I.; Taichenachev, A. V.; Yakovlev, V. P.; Tsygankov, E. A.; Zibrov, A. S.; Vassiliev, V. V.; Velichansky, V. L.

    2016-05-01

    Magnetic resonance at the F g = 1 rightleftarrows F e = 1 transition of the D 1 line in 87Rb has been studied with pumping and detection by linearly polarized radiation and detection at the double frequency of the radiofrequency field. The intervals of allowed values of the static and alternating magnetic fields in which magnetic resonance has a single maximum have been found. The structure appearing beyond these intervals has been explained. It has been shown that the quadratic Zeeman shift is responsible for the three-peak structure of resonance; the radiofrequency shift results in the appearance of additional extrema in resonance, which can be used to determine the relaxation constant Γ2. The possibility of application in magnetometry has been discussed.

  14. Structure and stability of a silicon cluster on sequential doping with carbon atoms

    NASA Astrophysics Data System (ADS)

    AzeezullaNazrulla, Mohammed; Joshi, Krati; Israel, S.; Krishnamurty, Sailaja

    2016-02-01

    SiC is a highly stable material in bulk. On the other hand, alloys of silicon and carbon at nanoscale length are interesting from both technological as well fundamental view point and are being currently synthesized by various experimental groups (Truong et. al., 2015 [26]). In the present work, we identify a well-known silicon cluster viz., Si10 and dope it sequentially with carbon atoms. The evolution of electronic structure (spin state and the structural properties) on doping, the charge redistribution and structural properties are analyzed. It is interesting to note that the ground state SiC clusters prefer to be in the lowest spin state. Further, it is seen that carbon atoms are the electron rich centres while silicon atoms are electron deficient in every SiC alloy cluster. The carbon-carbon bond lengths in alloy clusters are equivalent to those seen in fullerene molecules. Interestingly, the carbon atoms tend to aggregate together with silicon atoms surrounding them by donating the charge. As a consequence, very few Si-Si bonds are noted with increasing concentrations of C atoms in a SiC alloy. Physical and chemical stability of doped clusters is studied by carrying out finite temperature behaviour and adsorbing O2 molecule on Si9C and Si8C2 clusters, respectively.

  15. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems

    NASA Astrophysics Data System (ADS)

    Li, Jun; Jiang, Bin; Guo, Hua

    2013-11-01

    A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resulting in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations.

  16. Photoassociation of a cold-atom-molecule pair. II. Second-order perturbation approach

    SciTech Connect

    Lepers, M.; Vexiau, R.; Bouloufa, N.; Dulieu, O.; Kokoouline, V.

    2011-04-15

    The electrostatic interaction between an excited atom and a diatomic ground-state molecule in an arbitrary rovibrational level at large mutual separations is investigated with a general second-order perturbation theory, in the perspective of modeling the photoassociation between cold atoms and molecules. We find that the combination of quadrupole-quadrupole and van der Waals interactions competes with the rotational energy of the dimer, limiting the range of validity of the perturbative approach to distances larger than 100 Bohr radii. Numerical results are given for the long-range interaction between Cs and Cs{sub 2}, showing that the photoassociation is probably efficient for any Cs{sub 2} rotational energy.

  17. The electrostatic potential generated by topological atoms. II. Inverse multipole moments.

    PubMed

    Rafat, M; Popelier, P L A

    2005-11-22

    Quantum chemical topology defines finite atoms, whose bounded electron density generates a well-defined electrostatic potential. A multipole expansion based on spherical tensors provides a potential that is formally convergent outside the divergence sphere. Part I of this series [P. L. A. Popelier and M. Rafat, Chem. Phys. Lett.376, 148 (2003)] showed that a continuous multipole expansion expands the convergence region, thereby allowing the electrostatic potential to be evaluated at short range. Here, we propose a different method, based on "inverse" multipole moments, enabling an expansion that converges everywhere. These moments are defined by inverse (i.e., negative) powers of the magnitude of the position vector describing the electron density inside the atom. We illustrate this technique on nitrogen in N(2), oxygen in H(2)O, and oxygen in the phenolic group of the amino acid tyrosine. The proposed method constitutes a considerable advance over the method presented in Part I. PMID:16351236

  18. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems

    SciTech Connect

    Li, Jun; Jiang, Bin; Guo, Hua

    2013-11-28

    A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resulting in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations.

  19. Synthesis and crystal structure of oxalato-bridged dicopper(II) complex with reduced imino nitroxide radicals

    NASA Astrophysics Data System (ADS)

    Li, Licun; Liao, Daizheng; Bai, Lingjun; Jiang, Zonghui; Yan, Shiping

    2001-07-01

    A new oxalato-bridged dicopper(II) complex [Cu 2(μ-C 2O 4)(Him2-py) 2(NO 3) 2]CH 3OH has been synthesized and its crystal structure determined by X-ray diffraction methods. The imino nitroxide 2-(2'-pyridyl)-4,4,5,5-tetramethyl-4,5-dihydro-1 H-imidazolyl-1-oxyl(im2-py) is reduced in the reaction to yield 2-(2'-pyridyl)-4,4,5,5-tetramethyl-4,5-dihydro-1 H-imidazolyl-1-hydroxy(Him2-py). The structure consists of centrosymmetric [Cu 2(μ-C 2O 4)(Him2-py) 2(NO 3) 2] and one solvent methanol molecule. Each Cu(II) ion is in a distorted tetragonal pyramid environment: two nitrogen atoms from Him2-py, two oxygen atoms from the oxalate ion in the basal plane and one oxygen atom from the nitrato group in the axial position.

  20. Inelastic scattering in atom-diatomic molecule collisions. II - Effect of rotation on vibrational transition

    NASA Technical Reports Server (NTRS)

    Stallcop, J. R.

    1975-01-01

    Rotational and vibrational transitions in a diatomic molecule caused by collisions with an atom are analyzed by a semiclassical method for conditions where the rotational transitions can be handled well by the sudden approximation and the vibrational transitions belong to the adiabatic regime. The contribution to the vibrational transition probability from the correction, which takes the finite value of the spacing between rotational energy levels into account, is examined.-

  1. Synthesis, Structure, and Reactivity of Co(II) and Ni(II) PCP Pincer Borohydride Complexes

    PubMed Central

    2015-01-01

    The 15e square-planar complexes [Co(PCPMe-iPr)Cl] (2a) and [Co(PCP-tBu)Cl] (2b), respectively, react readily with NaBH4 to afford complexes [Co(PCPMe-iPr)(η2-BH4)] (4a) and [Co(PCP-tBu)(η2-BH4)] (4b) in high yields, as confirmed by IR spectroscopy, X-ray crystallography, and elemental analysis. The borohydride ligand is symmetrically bound to the cobalt center in η2-fashion. These compounds are paramagnetic with effective magnetic moments of 2.0(1) and 2.1(1) μB consistent with a d7 low-spin system corresponding to one unpaired electron. None of these complexes reacted with CO2 to give formate complexes. For structural and reactivity comparisons, we prepared the analogous Ni(II) borohydride complex [Ni(PCPMe-iPr)(η2-BH4)] (5) via two different synthetic routes. One utilizes [Ni(PCPMe-iPr)Cl] (3) and NaBH4, the second one makes use of the hydride complex [Ni(PCPMe-iPr)H] (6) and BH3·THF. In both cases, 5 is obtained in high yields. In contrast to 4a and 4b, the borohydride ligand is asymmetrically bound to the nickel center but still in an η2-mode. [Ni(PCPMe-iPr)(η2-BH4)] (5) loses readily BH3 at elevated temperatures in the presence of NEt3 to form 6. Complexes 5 and 6 are both diamagnetic and were characterized by a combination of 1H, 13C{1H}, and 31P{1H} NMR, IR spectroscopy, and elemental analysis. Additionally, the structure of these compounds was established by X-ray crystallography. Complexes 5 and 6 react with CO2 to give the formate complex [Ni(PCPMe-iPr)(OC(C=O)H] (7). The extrusion of BH3 from [Co(PCPMe-iPr)(η2-BH4)] (4a) and [Ni(PCPMe-iPr)(η2-BH4)] (5) with the aid of NH3 to yield the respective hydride complexes [Co(PCPMe-iPr)H] and [Ni(PCPMe-iPr)H] (6) and BH3NH3 was investigated by DFT calculations showing that formation of the Ni hydride is thermodynamically favorable, whereas the formation of the Co(II) hydride, in agreement with the experiment, is unfavorable. The electronic structures and the bonding of the borohydride ligand in [Co

  2. Student perception and conceptual development as represented by student mental models of atomic structure

    NASA Astrophysics Data System (ADS)

    Park, Eun Jung

    The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced

  3. Homochiral Cu(II) and Ni(II) malates with tunable structural features

    NASA Astrophysics Data System (ADS)

    Zavakhina, Marina S.; Samsonenko, Denis G.; Virovets, Alexander V.; Dybtsev, Danil N.; Fedin, Vladimir P.

    2014-02-01

    Four new homochiral metal-organic frameworks (MOFs) based on S-malate anions and N-donor linkers of different length have been prepared under solvothermal conditions. [Cu(mal)(bpy)]·H2O (1), [Cu(mal)(bpe)]·2H2O (2), [Ni(mal)(bpy)]·1.3CH3OH (3) and [Ni(mal)(bpe)]·4H2O (4) (mal=S-malate, bpy=4,4‧-bipyridil, bpe=trans-1,2-bis(4-pyridyl)ethylene) were characterized by a number of analytical methods including powder X-ray diffraction, elemental, thermogravimetric analyses, IR spectroscopy. Compounds 1-3 were structurally characterized by X-ray crystallography. The absence of the chiral ligand racemization under synthetic conditions was unambiguously confirmed by polarimetry experiments. Compounds 1 and 2 contain metal-malate layered motives, connected by N-donor linkers and contribute to the family of isoreticular Cu(II) malates and tartrates [Cu(mal)L] and [Cu(tart)L], (tart=tartrate; L=ditopic rigid organic ligand). The Ni-based compounds 3 and 4 share 1D chiral {Ni(mal)} motives and possess novel type of the chiral framework, previously unknown for chiral carboxylates. The linear N-donor linkers connect these chiral chains, thus controlling the channel diameter and guest accessible volume of the homochiral structure, which exceeds 60 %.

  4. Phase Diagrams and Electronic Structure of II-VI Alloys

    NASA Astrophysics Data System (ADS)

    de Gironcoli, Stefano

    1998-03-01

    Among II-VI wide-gap semiconductor solid solutions, Zn_xMg_1-xS_ySe_1-y alloy is the most studied for its potential applications in the blue-green light-emitter technology. In spite of this enormous technological interest little is known about its fundamental thermodynamical and structural properties. In this work the structural and thermodynamical properties of the Zn_xMg_1-xS_ySe_1-y solid solutions are determined by a combination of the computational alchemy (S. de Gironcoli, P. Giannozzi, and S. Baroni, Phys. Rev. Lett. 66), 2116 (1991); N. Marzari, S. de Gironcoli, and S. Baroni, Phys. Rev. Lett. 72, 4001 (1994). and the cluster expansion (S.-H. Wei, L. G. Ferreira, and A. Zunger, Phys. Rev. B 41), 8240 (1990). methods with Monte Carlo simulations. We determine the phase diagram of the alloy and show that the system is completely mixible at the tipical growth temperatures and phase separates at lower temperatures into two or three phases. The homogeneous phase is characterized by a large amount of short-range order occurring among first-nearest neighbors. Electronic-structure calculations, performed extending the special quasi-random structures approach (A. Zunger, S.-H. Wei, L. G. Ferreira, and J. E. Bernard, Phys. Rev. Lett. 65), 353 (1990). to the quaternary alloy case, indicate that the energy gap of the alloy is rather sensitive to this short-range order.

  5. The Factor Structure of the CIBS-II-Readiness Assessment

    ERIC Educational Resources Information Center

    Gotch, Chad M.; French, Brian F.

    2011-01-01

    The Brigance Comprehensive Inventory of Basic Skills-II (CIBS-II)-Readiness form is a diagnostic battery intended for children aged 5 and 6 years. The CIBS-II-Readiness is a new version of the CIBS-Revised-Readiness and includes updated normative information on a larger representative sample in comparison to the CIBS-Revised-Readiness. Empirical…

  6. A new trinuclear zinc(II) complex and a heptacoordinated mononuclear cadmium(II) complex with a pyrimidine derived Schiff base ligand: Syntheses, crystal structures, photoluminescence and DFT calculations

    NASA Astrophysics Data System (ADS)

    Das, Kinsuk; Jana, Atanu; Konar, Saugata; Chatterjee, Sudipta; Mondal, Tapan Kumar; Barik, Anil Kumar; Kar, Susanta Kumar

    2013-09-01

    The new N6 donor hexadentate Schiff base 2,4-bis [2-(pyridine-2-ylmethylidene) hydrazinyl] pyrimidine (L), its trinuclear Zn(II) complex, [Zn3(L)2Cl6] (1) and mononuclear heptacoordinate Cd(II) complex [Cd(L)(H2O)2](ClO4)2 (2) have been synthesised and characterised by crystallographically and spectroscopically. Complex 1 is featured by the triangular arrangement of three zinc atoms where the neighbouring Zn atoms are linked via half portion (N3 chromophore) of the same ligand molecule. In 1, the ligand molecules behave as hexadentate ones (employing both pyrimidine nitrogen atoms as active donor centres) to create the octahedral environment around Zn(II). The central and terminal Zn(II) atom has N6 and N3Cl3 chromophores respectively. In 2 the same ligand (L) behaves as pentadentate one (ignoring one pyrimidine nitrogen in the coordination process) to produce a pentagonal bipyramidal geometry with two apical water molecules. The geometries of both complexes were optimised in the singlet state by DFT method. The TDDFT calculations have been done on the optimised geometries to understand the electronic structure and spectral transition in the complexes. Complex 1 exhibits intraligand 1(π → π*) fluorescence in aqueous methanol solvent at room temperature.

  7. Access to a Cu(II)-O-Cu(II) motif: spectroscopic properties, solution structure, and reactivity.

    PubMed

    Haack, Peter; Kärgel, Anne; Greco, Claudio; Dokic, Jadranka; Braun, Beatrice; Pfaff, Florian F; Mebs, Stefan; Ray, Kallol; Limberg, Christian

    2013-10-30

    We report a complex with a rare Cu(II)-O-Cu(II) structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a Cu(II)-O-Cu(II) species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol, and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu-X-Cu moieties. A Cu(I) precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV-vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV-vis spectroscopy, HR-ESI mass spectrometry, and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction, all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu-O-Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV-vis absorptions of 5

  8. Crystal structures and Hirshfeld surface analysis calculations of mercury(II) complexes with a diiminopyridine ligand

    NASA Astrophysics Data System (ADS)

    Hosseini, Seyed Ali; Mahmoudi, Ghodrat; Garczarek, Piotr; Hazendonk, Paul; Abedi, Marjan; Servati Gargari, Masoumeh

    2016-02-01

    The reaction of a diiminopyridine ligand, N,N‧-bis(phenyl(pyridin-2-yl)methylene)propane-1,3-diamine (L), with mercury(II) salts gave two complexes namely [Hg(L)Cl]·0.5[Hg2Cl6] (1) and [Hg(L)(μ-I)HgI3] (2), which were characterized by XRD, NMR and FTIR. The crystal structure of 1 consists of discrete units of [Hg(L)CI]+cations and [Hg2C16]2- anions in the ratio 2:1. The coordination of mercury in the cation is approximately square pyramidal (sp), the metal center is chelated in a tetradentate manner by the ligand and further coordinated by one chlorine atom. In 2 the packing can be described as units of μ-I-connected square pyramidal (sp) and tetrahedral Hg complexes. The sp coordination around the metal atom is defined by the N4 donor set of the ligand and one bridging iodide. The hydrogen-chlorine donor-accepter interactions in 1 stabilize an infinite 1-D chain; however, such interactions were not observed in 2. Analysis of their Hirshfeld surfaces indicates that the molecules in 1 and 2 are packed predominately by means of van der Waals forces, 'edge to face' aromatic ring packing and weak C-H··X donor-acceptor interactions.

  9. Fractional Band Filling in an Atomic Chain Structure

    NASA Astrophysics Data System (ADS)

    Crain, J. N.; Kirakosian, A.; Altmann, K. N.; Bromberger, C.; Erwin, S. C.; McChesney, J. L.; Lin, J.-L.; Himpsel, F. J.

    2003-05-01

    A new chain structure of Au is found on stepped Si(111) which exhibits a 1/4-filled band and a pair of ≥1/2-filled bands with a combined filling of 4/3. Band dispersions and Fermi surfaces for Si(553)-Au are obtained by photoemission and compared to that of Si(557)-Au. The dimensionality of both systems is determined using a tight binding fit. The fractional band filling makes it possible to preserve metallicity in the presence of strong correlations.

  10. Synthesis, structure and electrochemical behavior of a 3D crystalline copper(II) metal-organic framework

    NASA Astrophysics Data System (ADS)

    Bai, Hong-Ye; Fan, Wei-Qiang; Liu, Chun-Bo; Shi, Wei-Dong; Yan, Yong-Sheng

    2014-05-01

    Using an flexible amide-type tripodal ligand N,N‧,N″-tris(3-pyridyl)-1,3,5-benzenetricarboxamide (L) and 1,4-benzenedicarboxylic acid (H2bdc), a three-dimensional copper(II) metal-organic framework (MOF) formulated as [Cu(bdc)(L)]n has been hydrothermally synthesized and structurally characterized by IR, elemental, X-ray single-crystal diffraction and thermal analysis. The complex crystallizes in the triclinic, space group P - 1, a = 8.891(2) Å, b = 11.760(2) Å, c = 15.348(3) Å, α = 96.73(3)°, β = 105.96(3)°, γ = 106.47(3)°, V = 1446.2(5) Å3, Mr = 666.10, Dc = 1.530 g/cm3, Z = 2, F(000) = 682, GOOF = 1.0560, μ(MoKα) = 0.817 mm-1, R = 0.0366 and wR = 0.0885. The structural analyses reveal that the title compound consists of one Cu(II) atom, two halves of bdc, and one L ligand. Each Cu(II) atom is linked by two bdc ligands and three L ligands to form a three-dimensional network. In addition, the electrochemical behavior of title compound has been studied. CCDC No. 990526.

  11. Computational structural investigation of select II-VI compounds and radtkeite (alpha-mercury(3) sulfur(2) chlorine iodine)

    NASA Astrophysics Data System (ADS)

    Sellepack, Steven Matthew

    2000-12-01

    Computational modeling of novel materials is an increasingly powerful tool being used in the development of advanced materials and their device applications. This course of study has been undertaken to discern: (1) the present state of computational simulation of materials; (2) the present ability of computational hardware and software to model new materials; and (3) the ability to apply computational modeling to a relatively poorly studied solid state system, namely mercury(II) chalcogenide halides. Initial interest in this system was fostered by the reported tubular growth of radtkeite (alpha-Hg3S2ClI), which can display a tubular crystal habit tens of micrometers long and micrometers in diameter. To validate that the structures and energies of mercury(II) chalcogenides could be accurately modeled the pressure induced phase transitions in the HgS system were studied using ab initio DF (density functional) calculations. Select MS (M = Ca, Ba, Zn, Cd, Hg, S) compounds were modeled in the cinnabar and zinc-blende structures to discern that they could be accurately modeled. A qualitative description of the MS compounds in the cinnabar structure is provided along with reasoning concerning their relative stability. Three possible radtkeite structures were identified using a brute force methodology of powder x-ray diffraction pattern simulation and then modeled using A initio DF calculations. The cell based upon the gamma-Hg3S 2Cl2 structure was deemed as the best match. This study has validated that computational methods can be used for structural prediction of mercury(II) chalcogenides and chalcogenide halides, however certain methods produced unacceptable results. Materials application statement. This study seeks to discern halogen interactions within II--VI semiconducting materials, namely the mercury(II) chalcogenides. The strategy and methodology of the research will be to invoke computer simulations. The ultimate goal being the correlation of atomic to bulk scale

  12. Tensegrity II. How structural networks influence cellular information processing networks

    NASA Technical Reports Server (NTRS)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

  13. Structure-activity relationships of glutamate carboxypeptidase II (GCPII) inhibitors.

    PubMed

    Ferraris, D V; Shukla, K; Tsukamoto, T

    2012-01-01

    Glutamate carboxypeptidase II (GCPII, EC 3.4.17.21) is a zinc metallopeptidase that hydrolyzes N-acetylaspartylglutamate (NAAG) into N-acetylaspartate (NAA) and glutamate in the nervous system. Inhibition of GCPII has the potential to reduce extracellular glutamate and represents an opportune target for treating neurological disorders in which excess glutamate is considered pathogenic. Furthermore, GCPII was found to be identical to a tumor marker, prostate-specific membrane antigen (PSMA), and has drawn significant interest as a diagnostic and/or therapeutic target in oncology. Over the past 15 years, tremendous efforts have been made in the discovery of potent GCPII inhibitors, particularly those with phosphorus-, urea- and thiol-based zinc binding groups. In addition, significant progress has been made in understanding the three-dimensional structural characteristics of GCPII in complex with various ligands. The purpose of this review article is to analyze the structure-activity relationships (SAR) of GCPII inhibitors reported to date, which are classified on the basis of their zinc-binding group. SAR and crystallographic data are evaluated in detail for each of these series to highlight the future challenges and opportunities to identify clinically viable GCPII inhibitors. PMID:22304717

  14. Structure/Function/Dynamics of Photosystem II Plastoquinone Binding Sites

    PubMed Central

    Lambreva, Maya D.; Russo, Daniela; Polticelli, Fabio; Scognamiglio, Viviana; Antonacci, Amina; Zobnina, Veranika; Campi, Gaetano; Rea, Giuseppina

    2014-01-01

    Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as bio-sensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed. PMID:24678671

  15. Extended X-ray absorption fine structure study of mixed-ligand copper(II) complexes having analogous structures

    NASA Astrophysics Data System (ADS)

    Gaur, Abhijeet; Shrivastava, B. D.; Srivastava, Krishna; Prasad, J.

    2013-02-01

    X-ray absorption fine structure spectra have been studied at the Cu K-edge in five mixed-ligand copper(II) complexes, viz., [Cu(L-glu)(bipy)] 1, [Cu(L-glu)(phen) (H2O)].3H2O 2, [Cu(L-tyro)(bipy)(ClO4)].2H2O 3, [Cu(L-phen)(bipy)(H2O)] (ClO4) 4, and [Cu(L-tyro)(phen)(H2O)] (ClO4).1.5H2O 5 (where L-glu = L-glutamate dianion, L-tyro = L-tyrosinate anion, bipy = 2,2'-bipyridine, and phen =1,10-phenanthroline), having essentially the same structure. The crystallographic data are available for all the complexes using which five theoretical models have been generated. Firstly, extended X-ray absorption fine structure (EXAFS) data of each complex has been analyzed using its own theoretical model and the results obtained are found to be comparable with the crystallographic results. Then, the EXAFS data of each complex has been analyzed using the theoretical models of the remaining four of these complexes. For each complex, the structural parameters obtained by fitting EXAFS data with theoretical models of the four remaining complexes have been found to be comparable with those obtained by fitting its own theoretical model. Thus, it has been found that if the crystal structure is not available for a complex, then the crystal structure of similar or analogous complex can be used satisfactorily for generating the theoretical model for the EXAFS data analysis of that complex, even if different ligands are attached to the central metal atom. On the basis of EXAFS data analysis, the coordination geometries around the central metal ions in these complexes have been depicted.

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

    SciTech Connect

    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.

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

    PubMed

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

    2013-05-24

    To describe the microscopic properties of matter, quantum mechanics uses wave functions, whose structure and time dependence is governed by the Schrödinger equation. In atoms the charge distributions described by the wave function are rarely observed. The hydrogen atom is unique, since it only has one electron and, in a dc electric field, the Stark Hamiltonian is exactly separable in terms of parabolic coordinates (η, ξ, φ). As a result, the microscopic wave function along the ξ coordinate that exists in the vicinity of the atom, and the projection of the continuum wave function measured at a macroscopic distance, share the same nodal structure. In this Letter, we report photoionization microscopy experiments where this nodal structure is directly observed. The experiments provide a validation of theoretical predictions that have been made over the last three decades. PMID:23745864

  18. Theoretical investigations of the structures and electronic spectra of Zn(II) and Ni(II) complexes with cyclohexylamine-N-dithiocarbamate

    NASA Astrophysics Data System (ADS)

    Yu, Xiaohan; Wang, Na; He, Hongqing; Wang, Li

    2014-03-01

    The ground-state structures of two ligands cyclohexylamine-N-dithiocarbamate (L) and PPh3 and four complexes [Zn(L)2] (A), [Ni(L)2] (B), [Zn(L)2PPh3] (C), and [Ni(L)2PPh3] (D) are optimized by M06, B3LYP, and B3PW91 methods with the same mixed basis set. As compared with the experimental data of other complexes containing the Ni-P bond, the result obtained by M06/6-31+G(d)-LANL2DZ method is finally regarded as accurate and reliable for this project. Based on the optimized geometries, the compositions of molecular orbitals are analyzed and the absorption spectra are simulated. When one more ligand PPh3 is coordinated, the lowest-lying transition energy presents red-shift; while it shows blue-shift when the metal coordination center change from Ni to Zn with the same ligands. The detailed transition characters related with the absorption spectrum are assigned. In all the key transitions, it is hard to find the contribution from Zn atom. On the contrary, the d orbital of Ni atom contributes a lot for the HOMO and LUMO of complexes B and D. Consequently, the transition characters of Zn(II) and Ni(II) complexes are different.

  19. Theoretical investigations of the structures and electronic spectra of Zn(II) and Ni(II) complexes with cyclohexylamine-N-dithiocarbamate.

    PubMed

    Yu, Xiaohan; Wang, Na; He, Hongqing; Wang, Li

    2014-03-25

    The ground-state structures of two ligands cyclohexylamine-N-dithiocarbamate (L) and PPh3 and four complexes [Zn(L)2] (A), [Ni(L)2] (B), [Zn(L)2PPh3] (C), and [Ni(L)2PPh3] (D) are optimized by M06, B3LYP, and B3PW91 methods with the same mixed basis set. As compared with the experimental data of other complexes containing the Ni-P bond, the result obtained by M06/6-31+G(d)-LANL2DZ method is finally regarded as accurate and reliable for this project. Based on the optimized geometries, the compositions of molecular orbitals are analyzed and the absorption spectra are simulated. When one more ligand PPh3 is coordinated, the lowest-lying transition energy presents red-shift; while it shows blue-shift when the metal coordination center change from Ni to Zn with the same ligands. The detailed transition characters related with the absorption spectrum are assigned. In all the key transitions, it is hard to find the contribution from Zn atom. On the contrary, the d orbital of Ni atom contributes a lot for the HOMO and LUMO of complexes B and D. Consequently, the transition characters of Zn(II) and Ni(II) complexes are different. PMID:24316543

  20. Structure-property-relationship of p-toluidinium tetrachloromercurate(II)

    SciTech Connect

    Dinesh; Kumar, Mukesh; Dalela, S.

    2014-04-24

    The single crystals of p-toluidinium tetrachloromercurate(II) hybrid materials have been grown with perfect crystal of size 0.35 × 0.30 × 0.27 mm. The hybrid material is exposed to X-rays for 3D intensity data which is used to refine the crystal structure upto reliability-factor of 0.034. The phenyl ring has planar conformation with skeletal torsion angle of 0.003(6)° and the aromatic ring (C1-C6) forms an angle of 78.7(1)° to the plane of inorganic layer. The N-H...Cl hydrogen bonded tetramer pattern is observed in p-toluidinium tetrachloromercurate(II) and the two tetramer layers are separated by a distance of 3.925(6)Å and the minimum distance between two mercury atoms is 4.112(1)Å which is quite larger for any metallophilic interaction. The inorganic layers form zig-zag ribbons which are separated by a distance of 12.987(5)Å.

  1. Synthesis, Crystal structure, and Hirshfeld Surface Analysis of a New Mixed Ligand Copper(II) Complex.

    PubMed

    Shit, Shyamapada; Marschner, Christoph; Mitra, Samiran

    2016-01-01

    A new mixed ligand copper(II) complex, [Cu(2,4-pydc)(pic)(H(2)O)]∙H(2)O (1) (where 2,4-pydc = pyridine-2,4-dicarboxylate, pic = 2-picolylamine) has been synthesized and characterized by elemental analysis, FT-IR and UV-Vis spectroscopic and thermogravimetric methods. Single crystal X-ray diffraction analysis reveals that copper(II) atom in the title complex adopts distorted square pyramidal geometry. Structural characterization also reveals that interplay of O-H···O, N-H···O, C-H···O, and C-H···π interactions between lattice and coordinated water and ligands significantly contribute to the crystal packing leading to the formation and strengthening of three dimensional supramolecular assembly. Hirshfeld surface analysis employing 3D molecular surface contours and 2D fingerprint plots have been used to analyze intermolecular interactions present in the solid state of the crystal. PMID:26970797

  2. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    PubMed Central

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-01-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature. PMID:27220411

  3. Atomic-scale study of lateral graphene/h-BN hybrid structure

    NASA Astrophysics Data System (ADS)

    Lee, Jaekwang; Park, Jewook; Li, An-Ping; Yoon, Mina

    2014-03-01

    Recently, atomically sharp 1D interfaces have been successfully implemented in lateral graphene/hexagonal boron nitride (h-BN) hybrid structures. Graphene/h-BN interfaces are of particular interest, because their bandgap and magnetic properties can be engineered by controlling the arrangement of nonmagnetic B, C and N atoms. Despite the enormous interest in graphene/h-BN, there has been very limited experimental success in determining the local atomic structure of the graphene/h-BN interface. Here, using state-of-the-art scanning tunneling microscopy, we report the direct and precise observation of a graphene/h-BN interface bonding structure at the atomic scale. Based on the detailed atomic structure, first-principles density-functional calculations show that graphene zigzag edge states and the h-BN polarity are strongly coupled to each other near the interface and induce spatial modulation of physical properties along the lateral direction. In addition, we investigate how the d-orbitals of metal surfaces (Cu (111), Cu (001)) and the pi-orbital of graphene/h-BN hybridize and predict resulting modification of the electronic properties of graphene/h-BN. This research was conducted at the CNMS, which is sponsored at ORNL by the Office of Basic Energy Sciences, U.S. Department of Energy. We acknowledge partial support provided by a Laboratory Directed Research and Development award (#7004).

  4. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures.

    PubMed

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-01-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature. PMID:27220411

  5. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    NASA Astrophysics Data System (ADS)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  6. Materials by Design-A Perspective From Atoms to Structures.

    PubMed

    Buehler, Markus J

    2013-02-01

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

  7. Photonic band gap response of structurally modified non-close-packed inverse opals by template directed multilayer atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Graugnard, Elton; Gaillot, Davy P.; King, Jeffrey S.; Summers, Christopher J.

    2006-04-01

    We report the controllable and tunable fabrication of structurally modified non-close-packed inverse shell opals using multi-layer atomic layer deposition and present a model and simulation algorithm to calculate the structural parameters critical to fabrication. This powerful, flexible and unique technique enables opal inversion, structural modification and backfilling and was applied to the fabrication of TiO II non-close-packed inverse opals. Using successive conformal backfilling it was possible to tune the Bragg peak over 600 nm and enhance the Bragg peak width by >50%. Additionally, band structure calculations, using dielectric functions approximating the true network topology, were used to predict the optical properties during the fabrication process. 3D finite-difference-time-domain results predict experimentally achievable structures with a complete band gap as large as 7.2%. Additionally, the refractive index requirement was predicted to decrease from 3.3 in an 86% infiltrated inverse shell opal to 3.0 in an optimized non-close-packed inverse shell opal. It was also shown for these structures that the complete photonic band gap peak can be statically tuned by over 70% by increasing the backfilled thickness.

  8. The Latent Symptom Structure of the Beck Depression Inventory-II in Outpatients with Major Depression

    ERIC Educational Resources Information Center

    Quilty, Lena C.; Zhang, K. Anne; Bagby, R. Michael

    2010-01-01

    The Beck Depression Inventory-II (BDI-II) is a self-report instrument frequently used in clinical and research settings to assess depression severity. Although investigators have examined the factor structure of the BDI-II, a clear consensus on the best fitting model has not yet emerged, resulting in different recommendations regarding how to best…

  9. The Factor Structure of the Beck Depression Inventory-II: An Evaluation

    ERIC Educational Resources Information Center

    Vanheule, Stijn; Desmet, Mattias; Groenvynck, Hans; Rosseel, Yves; Fontaine, Johnny

    2008-01-01

    The Beck Depression Inventory-II (BDI-II) is a frequently used scale for measuring depressive severity. BDI-II data (404 clinical; 695 nonclinical adults) were analyzed by means of confirmatory factor analysis to test whether the factor structure model with a somatic-affective and cognitive component of depression, formulated by Beck and…

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

    SciTech Connect

    Pennycook, S.J.; Chisholm, M.F.; Nellist, P.D.; Browning, N.D.; Wallis, D.J.; Dickey, E.C.

    1996-12-31

    It is over 100 y since Lord Rayleigh first showed the differences between coherent and incoherent imaging in the light microscope, pointing out the advantages of the latter for resolution and image interpretation. The annular detector in the high-resolution STEM provides the same advantages for electrons, allowing incoherent imaging at atomic resolution, with image contrast strongly dependent on atomic number (Z). Since incoherent imaging has no phase problem, these Z-contrast images may be directly inverted to given the (projected) atomic positions. A maximum entropy method avoids false detail associated with direct deconvolution, and gives atomic coordinates to an accuracy of {+-}0.1{Angstrom}. Electron energy loss spectroscopy can provide valuable complementary information on light element bonding and the presence of impurities in specific atomic planes selected from the image. Together, these techniques have revealed some surprisingly complex interfacial structures. For surface studies, the 1.3{Angstrom} probe of the VG Microscopes HB603U STEM provides sufficient penetration and contrast to image single Pt and Rh atoms on {gamma}-alumina supports. Such images reveal preferred atomic configurations and allow possible surface adsorption sites to be deduced.

  11. Rotational excitation of symmetric top molecules by collisions with atoms. II - Infinite order sudden approximation

    NASA Technical Reports Server (NTRS)

    Green, S.

    1979-01-01

    The infinite order sudden (IOS) approximation is extended to rotational excitation of symmetric tops by collisions with atoms. After development of a formalism for 'primitive' or 'one-ended' tops, proper parity-adapted linear combinations describing real rotors are considered and modifications needed for asymmetric rigid rotors are noted. The generalized spectroscopic relaxation cross sections are discussed. IOS calculations for NH3-He and H2CO-He are performed and compared with more accurate calculations, and the IOS approximation is found to provide a reasonably accurate description.

  12. Crystal structures of bis(cyanido)bis(N,N Prime -diethylthiourea-{kappa}S) mercury(II) and bis(cyanido)bis(N,N Prime -dipropylthiourea-{kappa}S) mercury(II)

    SciTech Connect

    Ahmad, Saeed Sadaf, Haseeba; Altaf, Muhammad; Stoeckli-Evans, Helen; Seerat-ur-Rehman; Bashir, Sarfaraz Ahmed

    2013-09-15

    Two mercury(II) complexes containing cyanide and, N,N Prime -diethylthiourea (detu) and N,N Prime -dipropylthiourea (dprtu) ligands, [(detu){sub 2}Hg(CN){sub 2}] (1) and [(dprtu){sub 2}Hg(CN){sub 2}] (2), respectively, have been prepared and characterized by X-ray crystallography. In the both complexes Hg atom lies on a 2-fold rotation axis, and is coordinated to the sulfur atoms of two thiourea ligands and to two cyanide carbon atoms. Both have a distorted tetrahedral environment with bond angles about the Hg atoms in the range of 93.41(4) Degree-Sign -146.75(19) Degree-Sign . In the crystal structures symmetry related molecules are linked via N-H-N hydrogen bonds resulting in the formation of a two-dimensional network in 1, while in 2 a double stranded one-dimensional chain is formed.

  13. A new nano-scale manganese (II) coordination polymer constructed from semicarbazone Schiff base and dicyanamide ligands: Synthesis, crystal structure and DFT calculations

    NASA Astrophysics Data System (ADS)

    Farhadi, Saeed; Mahmoudi, Farzaneh; Simpson, Jim

    2016-03-01

    A new nano-structured Mn(II) coordination polymer [Mn(HL)(dca)(Cl)]n(1), [HL= Pyridine-2-carbaldehyde semicarbazone, dca= dicyanamide] has been synthesized by a sonochemical method and has been characterized by scanning electron microscopy, X-ray powder diffraction elemental analysis and IR spectroscopy. Single crystals of compound 1 was synthesized by slow evaporation method and was structurally characterised by single crystal X-ray diffraction. The single crystal structure shows one dimensional zig-zag chains with end-to-end dicyanamide-bridged ligand. A distorted octahedral geometry around the Mn2+centers was achieved by NNO atoms from HL, two nitrogen atoms of dicyanamide and one chlorine atom. Also for more details, the structure of 1, has been optimized by density functional theory (DFT calculations).

  14. Structure studies of Ni(II) complexes with picolinaldehyde N-oxide thiosemicarbazone

    NASA Astrophysics Data System (ADS)

    Qing, Yu; Hua, Deng Ji; Gang, Zhu Li; Qing, Zhang Xiu; Dong, Bian He; Hong, Liang

    2006-08-01

    Two nickel(II) complexes [Ni(Hpiotsc) 2(NO 3) 2] ( 1), [Ni(Hpiotsc) 2(NO 3) 2]·H 2O ( 2) were synthesized and characterized by single crystal X-ray diffraction, IR, and thermal analyses. The geometry of the nickel(II) atom in two complexes is a distorted octahedron with ONS atoms of two neutral ligands. The antimicrobial activities of complex 1 were evaluated by the MIC (minimum inhibitory concentration) against five bacteria. The six-coordinate complex 1 did not inhibit the growth of the test organisms.

  15. Ab initio prediction of protein structure with both all-atom and simplified force fields

    NASA Astrophysics Data System (ADS)

    Scheraga, Harold

    2004-03-01

    Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.

  16. Atomic calculations and search for variation of the fine-structure constant in quasar absorption spectra

    NASA Astrophysics Data System (ADS)

    Dzuba, V. A.; Flambaum, V. V.

    A brief review of the search for variation of the fine structure constant in quasar absorption spectra is presented. Special consideration is given to the role of atomic calculations in the analysis of the observed data. A range of methods which allow to perform calculations for atoms or ions with different electron structure and which cover practically all periodic table of elements is discussed. Critical compilation of the results of the calculations as well as a review of the most recent results of the analysis are presented.

  17. The Atomic-to-Molecular Transition: Anatomy of a Forming Molecular Cloud. (Part II: Diffuse OH with Parkes)

    NASA Astrophysics Data System (ADS)

    Dawson, Joanne; Mcclure-Griffiths, Naomi; Jones, Paul; Dickey, John; Cunningham, Maria; Jones, Courtney

    2011-10-01

    The condensation of molecular clouds from the atomic ISM is a key link in the lifecycle of material in galactic systems, but one that remains poorly observationally constrained. This project will obtain HI, OH and CO line data at parsec and sub-parsec resolutions in order to form a comprehensive picture of the anatomy of a region in which this atomic-molecular transition is occurring. This combination of complementary tracers will reveal the medium throughout this evolutionary process, providing an unparalleled dataset for comparison with theoretical models, and allowing the testing of key predictions such as structure formation size scales and the degree of interpenetration of the molecular and atomic phases. This proposal requests 25 hours to obtain sensitive diffuse OH 18cm line data with Parkes, in order to bridge the gap between the fully atomic and molecular regimes probed by HI and CO. This data will be used to estimate the mass fraction of transition-state gas, investigate its global distribution, and will provide short-spacing correction to high-resolution ATCA data. This document comprises one of a set of three observing proposals submitted this semester as part of this project.

  18. Synthesis and structural characterization of zinc(II) and cobalt(II) complexes based on multidentate hydrazone ligands

    NASA Astrophysics Data System (ADS)

    Li, Li; Zhang, Yuan Zhuo; Liu, E.; Yang, Chengxiong; Golen, James A.; Rheingold, Arnold L.; Zhang, Guoqi

    2016-04-01

    Two multidentate Schiff base ligands containing a hydrazone unit have been synthesized and investigated for zinc(II) and cobalt(II) coordination chemistry. The reactions of the 4-pyridyl derived hydrazone ligand HL1 with zinc(II) or cobalt(II) salts gave three mononuclear complexes that were structurally characterized by X-ray diffraction analysis. The results revealed that the ligand could adopt different coordination modes when various counter anions were employed. While in the case that zinc dichloride was used as a metal salt a neutral mononuclear mono-ligand complex was formed, the deprotonation of hydrazone occurred when zinc(II) or cobalt(II) nitrate were present and two new isostructural mononuclear bis-ligand complexes were isolated. Modification of the hydrazone ligand with oxygen donors was found to have a significant impact on the ligand reactivity, and a similar reaction of H2L2 with cobalt(II) nitrate gave a protonated product of H2L2 without the incorporation of cobalt(II), which features a one-dimensional hydrogen-bonded network in the solid state.

  19. Breit–Pauli atomic structure calculations for Fe XI

    SciTech Connect

    Aggarwal, Sunny Singh, Jagjit; Mohan, Man

    2013-11-15

    Energy levels, oscillator strengths, and transition probabilities are calculated for the lowest-lying 165 energy levels of Fe XI using configuration-interaction wavefunctions. The calculations include all the major correlation effects. Relativistic effects are included in the Breit–Pauli approximation by adding mass-correction, Darwin, and spin–orbit interaction terms to the non-relativistic Hamiltonian. For comparison with the calculated ab initio energy levels, we have also calculated the energy levels by using the fully relativistic multiconfiguration Dirac–Fock method. The calculated results are in close agreement with the National Institute of Standards and Technology compilation and other available results. New results are predicted for many of the levels belonging to the 3s3p{sup 4}3d and 3s3p{sup 3}3d{sup 2} configurations, which are very important in astrophysics, relevant, for example, to the recent observations by the Hinode spacecraft. We expect that our extensive calculations will be useful to experimentalists in identifying the fine structure levels in their future work.

  20. Atomic calligraphy: the direct writing of nanoscale structures using a microelectromechanical system.

    PubMed

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

    2013-07-10

    We present a microelectromechanical system (MEMS) based method for the resist-free patterning of nanostructures. Using a focused ion beam to customize larger MEMS machines, we fabricate apertures with features less than 50 nm in diameter on plates that can be moved with nanometer precision over an area greater than 20 × 20 μm(2). Depositing thermally evaporated gold atoms though the apertures while moving the plate results in the deposition of nanoscale metal patterns. Adding a shutter positioned micrometers above the aperture enables high speed control of not only where but also when atoms are deposited. With this shutter, different-sized apertures can be opened and closed selectively for nanostructure fabrication with features ranging from nano- to micrometers in scale. The ability to evaporate materials with high precision, and thereby fabricate circuits and structures in situ, enables new kinds of experiments based on the interactions of a small number of atoms and eventually even single atoms. PMID:23782403

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  2. Atomic and electronic structure of the corundum (0001) surface: comparison with surface spectroscopies

    NASA Astrophysics Data System (ADS)

    Puchin, V. E.; Gale, J. D.; Shluger, A. L.; Kotomin, E. A.; Günster, J.; Brause, M.; Kempter, V.

    1997-01-01

    The electronic structure and geometry of the Al-terminated corundum (0001) surface were studied using a slab model within the ab-initio Hartree-Fock technique. The distance between the top Al plane and the next O basal plane is found to be considerably reduced on relaxation (by 0.57 Å, i.e. by 68% of the corresponding interlayer distance in the bulk). An interpretation of experimental photoelectron spectra (UPS He I) and metastable impact electron spectra (MIES) is given using the calculated total density of states of the slab and the projections to the atoms, atomic orbitals, and He 1s floating atomic orbital at different positions above the surface. Calculated projected densities of states exhibit a strong dependence on the relaxation of surface atoms. The good agreement of simulated and experimental UPS and MIES spectra supports the correctness of calculated surface relaxation.

  3. The CHX Beamline at NSLS-II: a Tool to probe Structure and Dynamics in Soft-Condensed Matter

    NASA Astrophysics Data System (ADS)

    Fluerasu, Andrei; Wiegart, Lutz

    2012-02-01

    The Coherent Hard X-ray (CHX) beamline currently under construction at NSLS-II (Brookhaven National Laboratory) will serve as an optimized tool for the study of structure and dynamics in soft condensed matter. The unprecedented coherent flux will enable the study of dynamics in soft matter systems down to microsecond time scales via X-ray Photon Correlation Spectroscopy (XPCS). The available scattering geometries such as (GI)SAXS and (GI)WAXS can be used in a simultaneous fashion to collect static and dynamic scattering information on length scales ranging from supramolecular assemblies to atomic distances.

  4. Atomic and molecular effects on spherically convergent ion flow. II. Multiple molecular species

    NASA Astrophysics Data System (ADS)

    Emmert, Gilbert A.; Santarius, John F.

    2010-01-01

    A theoretical model for the effect of molecular interactions on the flow of molecular ions in spherically convergent geometry where the inner grid (cathode) is at a large negative potential and the outer grid (anode) is grounded has been developed. The model assumes a weakly ionized deuterium plasma composed of D+, D2+, and D3+ ions that interact with the dominant background gas (D2). The interactions included are charge exchange, ionization, and dissociative processes. The formalism developed includes the bouncing motion of the ions in the electrostatic well and sums over all generations of subsequent ions produced by atomic and molecular processes. This leads to a set of two coupled Volterra integral equations, which are solved numerically. From the solution of the Volterra equations, one can obtain quantities of interest, such as the energy spectra of the ions and fast neutral atoms and molecules, and the fusion reaction rate. To provide an experimental test, the model is applied to inertial electrostatic devices and the calculated neutron production rate is compared to previously reported measurements for one University of Wisconsin inertial electrostatic confinement device [D. C. Donovan et al., Fusion Sci. Technol. 56, 507 (2009)]. The results show general agreement with the experimental results, but significant differences remain to be resolved.

  5. Atomic structure, alloying behavior, and magnetism in small Fe-Pt clusters

    NASA Astrophysics Data System (ADS)

    Chittari, Bheema Lingam; Kumar, Vijay

    2015-09-01

    We report results of the atomic structure, alloying behavior, and magnetism in F emP tn(m +n =2 -10 ) clusters using projector augmented wave (PAW) pseudopotential method and spin-polarized generalized gradient approximation (GGA) for the exchange-correlation energy. These results are compared with those obtained by using HCTH exchange-correlation functional and LANL2DZ basis set in the Gaussian program and the overall trends are found to be similar. As in bulk Fe-Pt alloys, clusters with equal composition of Fe and Pt have the largest binding energy and the largest heat of nanoalloy formation for a given number of atoms in the cluster. There are some deviations due to the different symmetries in clusters and in cases where the total number of atoms is odd. The lowest energy isomers tend to maximize bonds between unlike atoms with Fe (Pt) atoms occupying high (low) coordination sites in the core (surface) of the cluster. The binding energy, heat of formation, and the second order difference of the total energy show F e2P t2 , F e4P t4 , and F e4P t6 clusters to be the most stable ones among the different clusters we have studied. The magnetic moments on Fe atoms are high in Pt-rich clusters as well as in small Fe-rich clusters and decrease as the aggregation of Fe atoms and the cluster size increases. The maximum value of the magnetic moments on Fe atoms is ˜3.8 μB , whereas for Pt atoms it is 1 μB. These are quite high compared with the values for bulk Fe as well as bulk FePt and F e3Pt phases while bulk Pt is nonmagnetic. There is significant charge transfer from those Fe atoms that interact directly with Pt atoms. We discuss the hybridization between the electronic states of Pt and Fe atoms as well as the variation in the magnetic moments on Fe and Pt atoms. Our results provide insight into the understanding of the nanoalloy behavior of Fe-Pt and we hope that this would help to design Fe based nanoalloys and their assemblies with high magnetic moments for

  6. Crystal structure of bis­(N,N,N′,N′-tetra­methyl­guanidinium) tetra­chlorido­cuprate(II)

    PubMed Central

    Ndiaye, Mamadou; Samb, Abdoulaye; Diop, Libasse; Maris, Thierry

    2016-01-01

    In the structure of the title salt, (C5H14N3)2[CuCl4], the CuII atom in the anion lies on a twofold rotation axis. The tetra­chlorido­cuprate(II) anion adopts a flattened tetra­hedral coordination environment and inter­acts electrostatically with the tetra­methyl­guanidinium cation. The crystal packing is additionally consolidated through N—H⋯Cl and C—H⋯Cl hydrogen bonds, resulting in a three-dimensional network structure. PMID:27555960

  7. Water in Photosystem II: structural, functional and mechanistic considerations.

    PubMed

    Linke, Katrin; Ho, Felix M

    2014-01-01

    Water is clearly important for the functioning of Photosystem II (PSII). Apart from being the very substrate that needs to be transported in this water oxidation enzyme, water is also vital for the transport of protons to and from the catalytic center as well as other important co-factors and key residues in the enzyme. The latest crystal structural data of PSII have enabled detailed analyses of the location and possible function of water molecules in the enzyme. Significant progress has also been made recently in the investigation of channels and pathways through the protein complex. Through these studies, the mechanistic significance of water for PSII is becoming increasingly clear. An overview and discussion of key aspects of the current research on water in PSII is presented here. The role of water in three other systems (aquaporin, bacteriorhodopsin and cytochrome P450) is also outlined to illustrate further points concerning the central significance that water can have, and potential applications of these ideas for continued research on PSII. It is advocated that water be seen as an integral part of the protein and far from a mere solvent. PMID:23978393

  8. Structural Preferences in Phosphanylthiolato Platinum(II) Complexes

    PubMed Central

    Duran, Josep; Real, Julio; Benet‐Buchholz, Jordi; Solà, Miquel

    2016-01-01

    Abstract Invited for this month's cover picture are the groups of Prof. Alfonso Polo and Dr. Albert Poater at the Universitat de Girona, as well as their collaborators from the Universitat Autònoma de Barcelona and the Institute of Chemical Research of Catalonia. The cover picture shows phosphanylthiolate ligand coordination on a platinum(II) center to give only the bischelate cis ‐P,P isomer when the ligand/Pt ratio is 2, whereas a trinuclear unexpected complex is achieved with a ligand/Pt ratio of 1. Here, the synthesis and structural determination is combined with density functional theory (DFT) calculations to rationalize the reaction mechanistically and through conceptual DFT. The exciting point of this study is that it opens the door to test new experimental pathways to monitor the preferred cis or trans arrangement of bidentate ligands to platinum. (Legend: H‐white, C‐black, P‐purple, S‐yellow, Cl‐green, Pt‐blue.) For more details, see the Full Paper on p. 51 ff. PMID:27308218

  9. The meloxicam complexes of Co(II) and Zn(II): Synthesis, crystal structures, photocleavage and in vitro DNA-binding

    NASA Astrophysics Data System (ADS)

    Sanatkar, Tahereh Hosseinzadeh; Hadadzadeh, Hassan; Simpson, Jim; Jannesari, Zahra

    2013-10-01

    Two neutral mononuclear complexes of Co(II) and Zn(II) with the non-steroidal anti-inflammatory drug meloxicam (H2mel, 4-hydroxy-2-methyl-N-(5-methyl-2-thiazolyl)-2H-1,2-benzothiazine-3-carboxammide-1,1-dioxide), [Co(Hmel)2(EtOH)2] (1), and [Zn(Hmel)2(EtOH)2] (2), were synthesized and characterized by elemental analysis, IR and UV-Vis spectroscopy and their solid-state structures were studied by single-crystal diffraction. The complexes have a distorted octahedral geometry around the metal atom. The experimental data indicate that the meloxicam acts as a deprotonated bidentate ligand (through the amide oxygen and the nitrogen atom of the thiazolyl ring) in the complexes, and a strong intramolecular hydrogen bond between the amide N-H function and the enolate O atom stabilizes the ZZZ conformation of meloxicam ligands. Absorption, fluorescence spectroscopy and cyclic voltammetry have been used to investigate the binding of the complexes with fish sperm DNA (FS-DNA). Additionally, the photocleavage studies have been also used to investigate the binding of the complexes with plasmid DNA. The interaction of the complexes with DNA was monitored by a blue shift and hyperchromism in the UV-Vis spectra attributed to an electrostatic binding mode. A competitive study with ethidium bromide (EB) has shown that the complexes can displace the DNA-bound EB indicating that they bind to DNA in strong competition with EB. The experimental results show that the complexes can cleave pUC57 plasmid DNA.

  10. Charge-state-dependent energy loss of slow ions. II. Statistical atom model

    NASA Astrophysics Data System (ADS)

    Wilhelm, Richard A.; Möller, Wolfhard

    2016-05-01

    A model for charge-dependent energy loss of slow ions is developed based on the Thomas-Fermi statistical model of atoms. Using a modified electrostatic potential which takes the ionic charge into account, nuclear and electronic energy transfers are calculated, the latter by an extension of the Firsov model. To evaluate the importance of multiple collisions even in nanometer-thick target materials we use the charge-state-dependent potentials in a Monte Carlo simulation in the binary collision approximation and compare the results to experiment. The Monte Carlo results reproduce the incident charge-state dependence of measured data well [see R. A. Wilhelm et al., Phys. Rev. A 93, 052708 (2016), 10.1103/PhysRevA.93.052708], even though the experimentally observed charge exchange dependence is not included in the model.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  12. Atomic Structure and Charge Density Waves of Blue Bronze by Variable Temperature Scanning Tunneling Microscopy

    SciTech Connect

    Nikiforov,M.; Isakovic, A.; Bonnell, D.

    2007-01-01

    Blue bronze (K{sub 0.3}MoO{sub 3}) has been the focus of a number of scattering, transport, scanning tunneling microscopy (STM), and theoretical studies that have provided insight into the relation between atomic structure and charge-density wave (CDW) formation. However, the full extent of a relation of the CDWs to the atomic lattice and the microscopic origin of CDW pinning are still not completely resolved. In this study STM is used to distinguish the atomic structure and CDWs at the (20{bar 1}) surface. Within the STM's spatial resolution, the CDWs are incommensurate with the lattice at midrange temperatures and approach commensurability at low temperatures. Incommensurate CDWs are present on the surface and the degree of the incommensurability between blue bronze lattice and CDW lattice agree well with those determined from bulk scattering techniques.

  13. Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging

    NASA Astrophysics Data System (ADS)

    Giordano, V. M.; Ruta, B.

    2016-01-01

    Understanding and controlling physical aging, that is, the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, here for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization.

  14. Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging

    PubMed Central

    Giordano, V. M.; Ruta, B

    2016-01-01

    Understanding and controlling physical aging, that is, the spontaneous temporal evolution of out-of-equilibrium systems, represents one of the greatest tasks in material science. Recent studies have revealed the existence of a complex atomic motion in metallic glasses, with different aging regimes in contrast with the typical continuous aging observed in macroscopic quantities. By combining dynamical and structural synchrotron techniques, here for the first time we directly connect previously identified microscopic structural mechanisms with the peculiar atomic motion, providing a broader unique view of their complexity. We show that the atomic scale is dominated by the interplay between two processes: rearrangements releasing residual stresses related to a cascade mechanism of relaxation, and medium range ordering processes, which do not affect the local density, likely due to localized relaxations of liquid-like regions. As temperature increases, a surprising additional secondary relaxation process sets in, together with a faster medium range ordering, likely precursors of crystallization. PMID:26787443

  15. Atomic and electronic structures of lattice mismatched Cu2O/TiO2 interfaces

    NASA Astrophysics Data System (ADS)

    Wang, Shuzhi; Kavaipatti, Balasubramaniam; Kim, Sung-Joo; Pan, Xiaoqing; Ramesh, Ramamoorthy; Ager, Joel W.; Wang, Lin-Wang

    2014-05-01

    Heterojunction interfaces between metal oxides are often highly lattice mismatched. The atomic and electronic structures of such interfaces, however, are not well understood. We have synthesized Cu2O/TiO2 heterojunction thin films with 13% lattice mismatch and studied the interface via experimental methods and large-scale density function theory calculations of supercells containing ˜1300 atoms. We find that an interface of epitaxial quality is formed via a coincidence site lattice of 8 Cu2O unit cells matching 9 TiO2 unit cells. Calculations reveal the existence of a dislocation core of the O sublattices at the interface and a random arrangement of one layer of interfacial Cu atoms. The interfacial electronic structure is found to be mostly determined by the interfacial Cu distribution, rather than by the O dislocation core. The conduction band minimum and valence band maximum states are spatially separated, and there is no strongly localized state near the core.

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

    SciTech Connect

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

    2014-12-02

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

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

    SciTech Connect

    Kim, Min-Geun; Jang, Hong-Lae; Cho, Seonho

    2013-05-01

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

  18. Identification of ordered atomic structures of Ba on the Si(100) surface

    NASA Astrophysics Data System (ADS)

    Fan, W. C.; Ignatiev, A.

    1991-08-01

    Three long-range ordered atomic structures of (2 × 3), (1 × 2) and (2 × 4) phases have been observed by low-energy electron-diffraction (LEED) in the Ba/Si(100) surface at submonolayer Ba coverages (θ < 1 ML). The relationship between the observed phases for Ba on the Si(100) surface have been described as a function of Ba coverage and anneal temperature. Possible models of the surface atomic structures for the ordered phases are proposed by assuming Ba atomic chains in the Ba overlayer. A diffuse c(4 × 4)-like pattern has also been observed in the Ba/Si(100) system at high Ba exposure (> 2 ML), which might result from Ba diffusion and possible formation of a barium suicide.

  19. Insights into the structure-activity relationships of chiral 1,2-diaminophenylalkane platinum(II) anticancer derivatives.

    PubMed

    Berger, Gilles; Fusaro, Luca; Luhmer, Michel; Czapla-Masztafiak, Joanna; Lipiec, Ewelina; Szlachetko, Jakub; Kayser, Yves; Fernandes, Daniel L A; Sá, Jacinto; Dufrasne, François; Bombard, Sophie

    2015-07-01

    The structure-activity relationships of chiral 1,2-diaminophenylalkane platinum(II) anticancer derivatives are studied, including interactions with telomeric- and genomic-like DNA sequences, the pKa of their diaqua species, structural properties obtained from DFT calculations and resonant X-ray emission spectroscopy. The binding modes of the compounds to telomeric sequences were elucidated, showing no major differences with conventional cis-platinum(II) complexes like cisplatin, supporting that the cis-square planar geometry governs the binding of small Pt(II) complexes to G4 structures. Double-stranded DNA platination kinetics and acid-base constants of the diaqua species of the compounds were measured and compared, highlighting a strong steric dependence of the DNA-binding kinetics, but independent to stereoisomerism. Structural features of the compounds are discussed on the basis of dispersion-corrected DFT, showing that the most active series presents conformers for which the platinum atom is well devoid of steric hindrance. If reactivity indices derived from conceptual DFT do not show evidences for different reactivity between the compounds, RXES experiments provide new insight into the availability of platinum orbitals for binding to nucleophiles. PMID:25982100

  20. Structural diversity in mercury(II) coordination complexes with asymmetrical hydrazone-based ligands derived from pyridine

    NASA Astrophysics Data System (ADS)

    Masoumi, Asad; Servati Gargari, Masoumeh; Mahmoudi, Ghodrat; Miroslaw, Barbara; Therrien, Bruno; Abedi, Marjan; Hazendonk, Paul

    2015-05-01

    Three novel Hg(II) complexes 1-3 of asymmetrical hydrazone-pyridine based ligands, L1-L3, with distinct coordination structures have been prepared and characterized by a single crystal X-ray diffraction, elemental and thermal analysis, and IR spectroscopy. The complexes form either discrete units with one (1) or two (2) organic ligands, or one-dimensional polymers (3). Hence the ligands can be regarded as chelating (1), mono-dentate (2) or bridging (3) agents. The mercury center is essentially neutralized in each complex by two iodide anions. The coordination in complexes 2 and 3 adopts deformed tetrahedral shapes. In contrast the Hg(II) cation in complex 1 binds three coplanar ligating atoms (O,N,N) and, as with pincer ligands, its coordination polyhedron is supplemented with two I- anions in apical positions. The structural diversity in these complexes is strongly influenced by the position of N atom in pyridine derived moieties. The crystal structure is stabilized by N/O-H⋯N/O/I hydrogen bonds and π⋯π interactions.

  1. Structural Diversity of Copper(II) Complexes with 9-Deazahypoxanthine and Their in Vitro SOD-Like Activity

    PubMed Central

    Gáliková, Jana; Trávníček, Zdeněk

    2015-01-01

    Two structurally different copper(II) complexes of the compositions [{Cu(9dhx)(H2O)3}2(µ-SO4)2] (1) and [Cu(9dhx)2(H2O)2(NO3)2]·H2O (2), involving 9-deazahypoxanthine (9dhx; 6-oxo-9-deazapurine; 9-deazahypoxanthine), have been prepared and characterized by elemental analysis, infrared and electronic spectroscopy, electrospray ionisation (ESI) mass spectrometry, thermogravimetric (TG) and differential thermal (DTA) analyses, and cyclic voltammetry. The X-ray structures of complexes 1 and [Cu(9dhx)2(H2O)2(NO3)2] (2a) revealed the distorted octahedral geometry in the vicinity of the copper(II) atoms, with the NO5 and N2O4 donor set, respectively. In the dimeric compound 1, the {Cu(9dhx)(H2O)3}2 units are bridged by sulfate groups with the Cu···Cu separation being 5.3446(2) Å. In both structures the 9dhx ligands are coordinated through the N3 atoms of the pyrimidine moieties. The SOD-like activity of complexes 1 and 2 was evaluated in vitro showing moderate effect, with the IC50 values equal to 18.20, and 53.33 μM, respectively. PMID:26184182

  2. Structural Diversity of Copper(II) Complexes with 9-Deazahypoxanthine and Their in Vitro SOD-Like Activity.

    PubMed

    Gáliková, Jana; Trávníček, Zdeněk

    2015-01-01

    Two structurally different copper(II) complexes of the compositions [{Cu(9dhx)(H2O)3}2(µ-SO4)2] (1) and [Cu(9dhx)2(H2O)2(NO3)2]·H2O (2), involving 9-deazahypoxanthine (9dhx; 6-oxo-9-deazapurine; 9-deazahypoxanthine), have been prepared and characterized by elemental analysis, infrared and electronic spectroscopy, electrospray ionisation (ESI) mass spectrometry, thermogravimetric (TG) and differential thermal (DTA) analyses, and cyclic voltammetry. The X-ray structures of complexes 1 and [Cu(9dhx)2(H2O)2(NO3)2] (2a) revealed the distorted octahedral geometry in the vicinity of the copper(II) atoms, with the NO5 and N2O4 donor set, respectively. In the dimeric compound 1, the {Cu(9dhx)(H2O)3}2 units are bridged by sulfate groups with the Cu···Cu separation being 5.3446(2) Å. In both structures the 9dhx ligands are coordinated through the N3 atoms of the pyrimidine moieties. The SOD-like activity of complexes 1 and 2 was evaluated in vitro showing moderate effect, with the IC50 values equal to 18.20, and 53.33 μM, respectively. PMID:26184182

  3. Structure, spectroscopy, and theory calculations of mononuclear mixed-ligand copper(II) complex with malonate and 2-propylimidazole, [Cu(mal)(PIM) 2(H 2O)

    NASA Astrophysics Data System (ADS)

    Peng, Xian; Cui, Guang-Hua; Li, De-Jie; Wu, Shang-Zhuo; Yu, Ya-Mei

    2010-05-01

    A mononuclear copper(II) complex, [Cu(mal)(PIM) 2(H 2O)] (1) [mal = malonate dianion, PIM = 2-propylimidazole] has been synthesized and characterized by elemental analysis, IR, UV-Vis, TG-DTA, and single crystal X-ray diffraction. The center Cu(II) atom in the complex has a distorted square-pyramidal geometry, being coordinated by two nitrogen atoms and three oxygen atoms. Density Functional Theory (DFT) with the B3LYP method and time-dependent DFT calculations were performed to provide insight into the structural, electronic, and electronic spectroscopic properties of the complex 1, and the UV-Vis spectrum of the title compound has been discussed on this basis. All the absorption bands in UV-Vis spectrum are mostly π/( P, σ) → d x2-y2 ligand-to-metal charge transfer (LMCT) transition, together with partial d → d ligand field (LF) transition.

  4. Synthesis, crystal structure, and spectroscopic and thermal properties of the polymeric compound catena-poly[[bis(2,4-dichlorobenzoato)zinc(II)]-μ-isonicotinamide].

    PubMed

    Homzová, Katarína; Györyová, Katarína; Koman, Marián; Melník, Milan; Juhászová, Žofia

    2015-09-01

    Zinc(II) carboxylates with O-, S- and N-donor ligands are interesting for their structural features, as well as for their antibacterial and antifungal activities. The one-dimensional zinc(II) coordination complex catena-poly[[bis(2,4-dichlorobenzoato-κO)zinc(II)]-μ-isonicotinamide-κ(2)N(1):O], [Zn(C7H3Cl2O2)2(C6H6N2O)]n, has been prepared and characterized by IR spectroscopy, single-crystal X-ray analysis and thermal analysis. The tetrahedral ZnO3N coordination about the Zn(II) cation is built up by the N atom of the pyridine ring, an O atom of the carbonyl group of the isonicotinamide ligand and two O atoms of two dichlorobenzoate ligands. Isonicotinamide serves as a bridge between tetrahedra, with a Zn···Zn distance of 8.8161 (7) Å. Additionally, π-π interactions between the planar benzene rings contribute to the stabilization of the extended structure. The structure is also stabilized by intermolecular hydrogen bonds between the amino and carboxylate groups of the ligands, forming a two-dimensional network. During thermal decomposition of the complex, isonicotinamide, dichlorobenzene and carbon dioxide were evolved. The final solid product of the thermal decomposition heated up to 1173 K was metallic zinc. PMID:26322615

  5. Crystal structure of anhydrous poly[bis-(μ2-sarcosinato-κ(3) O,N:O')copper(II)].

    PubMed

    Butcher, Ray J; Brewer, Greg; Zemba, Matthew

    2014-10-01

    The title compound, [Cu(C3H6NO2)2] n , is a bis-complex of the anion of sarcosine (N-methyl-glycine). The asymmetric unit consists of a copper(II) ion, located on a center of inversion, and one mol-ecule of the uninegative sarcosinate anion. The copper(II) ion exhibits a typical Jahn-Teller distorted [4 + 2] coordination geometry. The four shorter equatorial bonds are to the nitro-gen and carboxyl-ate O atoms of two sarcosinate anions, and the longer axial bonds are to carboxyl-ate O atoms of neighboring complexes. The overall structure is made up from two chains formed by these longer axial Cu-O bonds, one extending parallel to [011] and the other parallel to [0-11]. Each one-dimensional array is connected by the equatorial bridging moieties to the chains on either side, creating an extended two-dimensional framework parallel to (100). There is a single inter-molecular hydrogen-bonding inter-action within the sheets between the amino NH group and an O atom of an adjacent mol-ecule. PMID:25484653

  6. Crystal structure of anhydrous poly[bis­(μ2-sarcosinato-κ3 O,N:O′)copper(II)

    PubMed Central

    Butcher, Ray J.; Brewer, Greg; Zemba, Matthew

    2014-01-01

    The title compound, [Cu(C3H6NO2)2]n, is a bis-complex of the anion of sarcosine (N-methyl­glycine). The asymmetric unit consists of a copper(II) ion, located on a center of inversion, and one mol­ecule of the uninegative sarcosinate anion. The copper(II) ion exhibits a typical Jahn–Teller distorted [4 + 2] coordination geometry. The four shorter equatorial bonds are to the nitro­gen and carboxyl­ate O atoms of two sarcosinate anions, and the longer axial bonds are to carboxyl­ate O atoms of neighboring complexes. The overall structure is made up from two chains formed by these longer axial Cu—O bonds, one extending parallel to [011] and the other parallel to [0-11]. Each one-dimensional array is connected by the equatorial bridging moieties to the chains on either side, creating an extended two-dimensional framework parallel to (100). There is a single inter­molecular hydrogen-bonding inter­action within the sheets between the amino NH group and an O atom of an adjacent mol­ecule. PMID:25484653

  7. Three-Dimensional Imaging of the Local Structure of Materials at Atomic Resolution by Electron Tomography

    NASA Astrophysics Data System (ADS)

    Zhu, Chun

    Electron tomography was originally developed in 1968, and has been primarily applied to determine the three-dimensional (3D) structure of biological systems. In the last decade, the application of electron tomography in materials science and nanoscience has revived due to the utilization of scanning transmission electron microscopy (STEM) in the high-angle annular dark-field (HAADF) mode, and a highest resolution of ˜1 nm3 has been achieved. However, improving the resolution from ˜1 nm 3 to the atomic level remains a challenging task, which requires new tomographic reconstruction algorithms, better projection alignment methods, state-of-the-art STEM instruments, and more accurate data-acquisition procedures. In this thesis, important progress has been made in all these four areas. First, a novel tomographic method, termed equally sloped tomography (EST), was developed and allows the 3D image reconstruction of tilt series with a limited number projections and a "missing wedge" (i.e. specimens cannot usually be tilted beyond +/-70°). Second, an alignment method which can be used to align the projections of a tilt series at atomic-level resolution was developed based on center of mass. Finally, by using a Titan 80-300 STEM instrument at the California NanoSystems Institute, UCLA, more accurate data acquisition procedures were developed and a number of tomographic tilt series of atomic resolution projections from different nanoparticles have been obtained. With all these combinations, the 3D structure of a 10 nm gold nanoparticle was determined at 2.4 A resolution, the highest resolution ever achieved in any general tomography method. More recently, this novel electron tomography method has been applied to observe nearly all the atoms in a Pt nanoparticle, and imaged for the first time the 3D core structure of edge and screw dislocations at atomic resolution. Furthermore, through numerical simulations the feasibility of determining the 3D atomic structure of

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

    SciTech Connect

    Saito, M.; Suzuki, S. . E-mail: ssuzuki@tagen.tohoku.ac.jp; Kimura, M.; Suzuki, T.; Kihira, H.; Waseda, Y.

    2005-11-15

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

  9. An iron(II) diketonate-diamine complex as precursor for thin film fabrication by atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Bratvold, Jon E.; Carraro, Giorgio; Barreca, Davide; Nilsen, Ola

    2015-08-01

    A new divalent Fe precursor has been explored for deposition of iron-containing thin films by atomic layer deposition and molecular layer deposition (ALD/MLD). The Fe(II) β-diketonate-diamine complex, Fe(hfa)2TMEDA, (hfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionate, TMEDA = N,N,N‧,N‧-tetramethylethylenediamine) can be handled in air, and sublimation at 60 °C ensures a satisfactory vaporization rate. The reactivity of the precursor does not allow for direct reaction with water as co-reactant. Nevertheless, it reacts with carboxylic acids, resulting in organic-inorganic hybrid materials, and with ozone, yielding α-Fe2O3. The divalent oxidation state of iron was maintained during deposition when oxalic acid was used as co-reactant, demonstrating the first preservation of Fe(II) from precursor to film during an MLD process. A self-saturating growth mode was proven by in situ quartz crystal microbalance (QCM) measurements, and the films were further characterized by grazing incidence X-ray diffraction (GIXRD), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS).

  10. Current State of Web Sites in Science Education--Focus on Atomic Structure.

    ERIC Educational Resources Information Center

    Tuvi, Inbal; Nachmias, Rafi

    2001-01-01

    Explores to what extent the web's advanced graphical tools and computational power are implemented in science education. Focuses on the pedagogical and technological characteristics of web sites attempting to teach the subject of atomic structure. (Contains 33 references.) (Author/YDS)

  11. Supporting Students in Learning with Multiple Representation to Improve Student Mental Models on Atomic Structure Concepts

    ERIC Educational Resources Information Center

    Sunyono; Yuanita, L.; Ibrahim, M.

    2015-01-01

    The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…

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

    ERIC Educational Resources Information Center

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

    2013-01-01

    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 physics textbooks published in Korea based on the eight criteria developed in previous research. The result of this study shows that Korean general…

  13. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    PubMed Central

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-01-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of ‘high-Q perp’ reflections. PMID:27437112

  14. Compensation of logarithmic corrections in calculating the fine structure of levels in hydrogen-like atoms

    SciTech Connect

    Boikova, N. A. Tyukhtyaev, Yu. N.; Faustov, R. N.

    2011-01-15

    Special features of the quasipotential approach to calculating logarithmic (in the fine-structure constant) contributions to the fine splitting of energy levels in hydrogen-like atoms are analyzed. The boundaries of the region of applicability of the Fell technique are indicated, and the order of corrections beyond this region is estimated.

  15. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    PubMed Central

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  16. The role of bridged structures in the mechanism of the reaction between chlorine atom and ethylene

    NASA Astrophysics Data System (ADS)

    Braña, P.; Menéndez, B.; Fernández, T.; Sordo, J. A.

    2000-08-01

    The potential energy surface for the reaction between a chlorine atom and ethylene was extensively explored by using ab initio methodologies. Two different routes for the 1,2 migration of the chlorine atom were identified. One of them involves a C 2v ( 2B 2) transition structure (TS sb) that directly connects two equivalent structures (P and P') of the 2-chloroethyl radical with the chlorine atom attached either to C1 (P) or to C2 (P') carbon atoms in ethylene (shuttling motion). In the second pathway, the 2-chloroethyl radical (P) coverts into a C 2v ( 2A 1) intermediate (I add) through a C s ( 2A') transition structure (TS add ). Then I add leads to the 2-chloroethyl radical (P') through a transition structure equivalent to TS add (TS add' ). The `indirect shuttling motion' described along this latter route is notably lower in energy and allows one to rationalize some mechanistic aspects experimentally observed in reactions involving haloethyl radicals.

  17. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms.

    PubMed

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J; Le Thi Thu, Huong; Torres, F Javier; Zambrano, Cesar H; Muñiz Olite, Jorge L; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel's Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  18. The Structure of the Atom: Teacher's Guide Levels A, B, and C. Preliminary Limited Edition.

    ERIC Educational Resources Information Center

    Cambridge Physics Outlet, Woburn, MA. Education Programs Dept.

    This is a two-part curriculum package for teaching the structure of atoms. The first part--the Teacher's Guide--contains information necessary for using the equipment in a typical classroom including learning goals, vocabulary, math skills, and sample data for each activity. The second part of the package consists of photocopy masters for a set of…

  19. Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms

    NASA Astrophysics Data System (ADS)

    Ji, Chen; Hernandez, Oscar Javier; Nevo Dinur, Nir; Bacca, Sonia; Barnea, Nir

    2016-03-01

    We present calculations of nuclear structure effects to the Lamb shift in light muonic atoms. We adopt a modern ab-initio approach by combining state-of-the-art nuclear potentials with the hyperspherical harmonics method. Our calculations are instrumental to the determination of nuclear charge radii in the Lamb shift measurements, which will shed light on the proton radius puzzle.

  20. Synthesis, structural characterization and in vitro biological screening of some homoleptic copper(II) complexes with substituted guanidines.

    PubMed

    Murtaza, Ghulam; Rauf, Muhammad Khawar; Badshah, Amin; Ebihara, Masahiro; Said, Muhammad; Gielen, Marcel; de Vos, Dick; Dilshad, Erum; Mirza, Bushra

    2012-02-01

    A series of homoleptic copper(II) complexes (1a-8a) with N,N',N″-trisubstituted guanidines, [Cu(II){PhCONHC(NHR)NPh}(2)] (where R = phenyl (1a), n-butyl (2a), sec-butyl (3a), cyclohexyl (4a), 1-naphthyl (5a), 2,4-dichlorophenyl (6a), 3,4-dichlorophenyl (7a), and 3,5-dichlorophenyl (8a)) have been synthesized and characterized by elemental analyses, FT-IR, UV-visible, (1)H and (13)C NMR spectroscopy, and single crystal X-ray diffraction analysis. The X-ray crystal structures revealed that the complexes 2a and 4a are mononuclear in the solid state and that the geometry around the copper atom is nearly square planar. In both the cases, N,N',N″-trisubstituted guanidine ligands have been coordinated to the Cu(II) through the oxygen and nitrogen atoms. The synthesized guanidines and their complexes were initially screened for their anti-microbial activities, and Brine Shrimps Lethality assay. The complexes were also screened for in vitro cytotoxicity activity in human cell lines carcinomas A498, EVSAT, H226, IGROV, M19, MCF-7 and WIDR. The results show a moderate level of cytotoxicity against these seven human cancer cell lines as compared with standard chemotherapeutic drugs. PMID:22177420

  1. Synthesis, structure, and biological evaluation of a copper(ii) complex with fleroxacin and 1,10-phenanthroline.

    PubMed

    Xiao, Ying; Wang, Qing; Huang, Yanmei; Ma, Xiangling; Xiong, Xinnuo; Li, Hui

    2016-07-01

    A novel mixed-ligand Cu(ii) complex combined with the quinolone drug fleroxacin and 1,10-phenanthroline was synthesized in this work. The crystal structure of the complex was characterized via X-ray crystallography, which was the first reported single crystal complex of fleroxacin. Results showed that Cu(ii) was coordinated through pyridone oxygen and one carboxylate oxygen atom of fleroxacin, as well as two nitrogen atoms from 1,10-phenanthroline. Various characterization methods, including Fourier transform infrared, elementary analysis, thermogravimetry, and X-ray powder diffraction, were applied. The Cu(ii)-quinolone complex exhibited favorable biological activities, and was proved to be capable of transforming supercoiled PUC19 DNA into nicked form under hydrolytic conditions. The obtained pseudo-Michaelis-Menten kinetic parameter was 12.64 h(-1), which corresponded to a million-fold rate enhancement in DNA cleavage. In addition, the interaction capacity of the complex with human serum albumin (HSA) was investigated. The results demonstrated a moderately intense combination between HSA and the complex. The complex evidently quenched the fluorescence of HSA. Approximately 19.2% of the quenching was attributed to Förster resonance energy transfer (FRET), whereas the rest was caused by ground-state complex formation (molar ratio of HSA : complex = 1 : 2). The energy of the complex was excited during FRET, which increased the fluorescence of the complex by approximately 18%. PMID:27301999

  2. Atomic Structure Study of the Quantum Spin-ice Pyrochlore Yb2Ti2O7

    NASA Astrophysics Data System (ADS)

    Mostaed, Ali; Balakrishnan, Geetha; Lees, Martin; Beanland, Richard; Microscopy Team; Superconductivity; Magnetism Team

    The quantum spin-ice candidate Yb2Ti2O7 (YTO) lies on the boundary between a number of competing magnetic ground states. Features in the low-temperature specific heat capacity are found to vary in sharpness and temperature depending on materials processing. It has been suggested that these changes in the magnetic ground state could be influenced by several factors, including the degree of cation stuffing, changes in oxygen occupancy and/or vacancies. In the present work, the structures of three different YTO samples, grown by the optical floating zone technique and that exhibit quite different heat capacity behaviour, have been studied by annular dark field scanning transmission microscopy (ADF-STEM). We show that the detailed intensity distribution around the visible atomic columns is sensitive to the presence of nearby atoms of low atomic number (in this case oxygen), even though they are not directly visible in the images. To the best of our knowledge, this is the first time that oxygen columns with a distance of ~30 pm have been distinguished in ADF-STEM images. Furthermore, by comparing atomic columns with different configurations of nearby oxygen atoms, we are able to distinguish between the different YTO samples Finally, the ADF data for the crystal that exhibits no specific heat anomaly shows signs of the substitution of Yb atoms on Ti sites, supporting the view that the magnetic ground state of YTO is extremely sensitive to disorder.

  3. Spontaneous emission of a photon: Wave-packet structures and atom-photon entanglement

    SciTech Connect

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

    2005-09-15

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

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

    NASA Astrophysics Data System (ADS)

    Barke, I.; Rügheimer, T. K.; Zheng, Fan; Himpsel, F. J.

    2007-10-01

    This work has three main themes: (1) fabricate atomically precise nanostructures at surfaces, particularly nanowires consisting of atom chains; (2) explore the behavior of one-dimensional electrons in atomic chains; (3) find the fundamental limits of data storage using an atomic scale memory. Semiconductor surfaces lend themselves towards self-assembly, because the broken covalent bonds create elaborate reconstruction patterns to minimize the surface energy. An example is the large 7 × 7 unit cell on Si(1 1 1), which can be used as building block. On semiconductors, the surface electrons completely de-couple from the substrate, as long as their energy lies in the band gap. Angle-resolved photoemission reveals surprising features, such as a fractional band filling and a spin-splitting at a non-magnetic surface. An interesting by-product is a memory structure with self-assembled tracks that are five atom rows wide and store a bit by the presence or absence of a single silicon atom. This toy memory is used to test the fundamental limits of data storage and to see how storage on silicon compares to storage in DNA.

  5. Segregation and temperature effect on the atomic structure of Bi30Ga70 liquid alloy

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

    We investigate the structure of liquid monotectic alloy Bi30Ga70 above and below the critical point. The three-dimensional structure at 265 °C is modelled by means of the reverse Monte Carlo simulation technique using neutron and x-ray diffraction experimental data. It is shown that atomic segregation on the short-range scale exists in the liquid Bi30Ga70 slightly above the critical temperature (TC = 262 °C). We present also the structure factors of Bi30Ga70 liquid alloy under the critical point at 240 and 230 °C obtained with neutron diffraction to highlight the temperature effect in the atomic structure.

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

    PubMed

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

    2009-06-17

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

  7. Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study

    SciTech Connect

    Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

    2014-04-01

    The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  8. Synthesis, magnetic, thermal and structural properties of Co(II), Ni(II) and Cu(II) complexes containing isophthalato ligands

    NASA Astrophysics Data System (ADS)

    Rogan, Jelena; Poleti, Dejan; Karanović, Ljiljana; Jagličić, Zvonko

    2011-01-01

    A series of novel ternary Co(II), Ni(II) and Cu(II) complexes containing 2,2'-dipyridylamine (dipya), 2,2'-bipyridine (bipy), and 1,10-phenanthroline (phen), as aromatic diamine ligands, and dianion of isophthalic acid (ipht) have been prepared by ligand exchange reactions from diluted H 2O/EtOH solutions. The complexes were characterized by elemental analysis, IR spectroscopy, magnetic susceptibility measurements and TG and DSC analysis. Three complexes, Cu(dipya)(ipht)·H 2O ( 1), Co(dipya)(ipht)·2H 2O ( 2) and Cu(ipht)(phen)·2H 2O ( 5) are polymeric with bis-monodentate ipht, while the other two complexes M(bipy)(ipht)·4H 2O, M dbnd Co(II) ( 3) and Ni(II) ( 4), contain ipht as a counter ion. All Co(II) and Ni(II) complexes are (pseudo)octahedral, while Cu(II) complexes have square-pyramidal or distorted octahedral geometry. The variable temperature magnetic susceptibility measurements showed very weak antiferromagnetic behaviour for all complexes. Dehydration processes, decomposition mechanisms and thermal stability of 1- 5 are assumed. One complex from the above series, [Ni(bipy)(H 2O) 4](ipht) ( 4), and one additional complex, [Co(bipy)(ipht)] n ( 6), are obtained as single-crystals and their structures are determined from X-ray diffraction data. In both structures M(II) centers are in deformed octahedral environment and they are linked by hemi-ipht ligands ( 4) and two different bridging ipht ligands ( 6). Three-dimensional networks in 4 and 6 are governed by strong noncovalent interactions. The cations and ipht anions in 4 are connected by hydrogen bonds building double layers parallel to ab-plane that are further packed by π- π interactions. In 6 double chains extending along b-axis are strengthened by interchain π- π interactions constructing a three-dimensional framework.

  9. Synthesis, structural, spectral (FT-IR, FT-Ra, and UV-Vis), thermal, and density functional studies on p-methylaniline complexes of Mn(II), Co(II), and Ni(II) bromides

    NASA Astrophysics Data System (ADS)

    Bardakçı, Tayyibe; Altun, Ahmet; Golcuk, Kurtulus; Kumru, Mustafa

    2015-11-01

    Transition metal complexes of the form MBr2L2, where M = Mn(II), Co(II) and Ni(II); L = p-methylaniline, were prepared and characterized by elemental and thermogravimetric analyses, magnetic moment measurements, and UV-vis, FT-IR and FT-Raman spectral studies. Geometries, spin-state energetics, and vibrational spectra of the complexes were obtained at the B3LYP/def2-TZVP level. The present experimental and theoretical data suggest 5-coordinate polymeric bromide bridged structure for the Mn complex, distorted tetrahedral structure for the Co complex, and distorted octahedral coordination site for the Ni complex. The experimental FT-IR and FT-Raman bands of the complexes were assigned based on the computational results expressed in terms of internal coordinates with percent potential energy distributions. The vibrational spectra suggest that the coordination occurs via nitrogen atom of p-methylaniline. The thermal characteristics of the complexes indicate that their decompositions start through p-methylaniline.

  10. Detection of O I and Si II far-infrared fine-structure emission from Alpha Orionis

    NASA Technical Reports Server (NTRS)

    Haas, Michael R.; Glassgold, Alfred E.

    1993-01-01

    We have detected forbidden O I 63 micron and forbidden Si II 35 micron emission from the oxygen-rich, M2 lab supergiant, Alpha Orionis (Betelgeuse). The forbidden O I line flux is 2.4 +/- 0.2 x 10 exp -18 W/sq cm, and the forbidden Si II line flux is 0.9 +/- 0.4 x 10 exp -18 W/sq cm. These fluxes are consistent with the thermal model of Rodgers and Glassgold (1991), which indicates that the emission arises in dense, warm gas in Alpha Ori's inner envelope and implies that nearly all of the available O and Si is in atomic form. This is the first reported detection of FIR, fine-structure emission from the inner or transition region of a circumstellar envelope, where molecules and dust are expected to form.

  11. Generation of atomic four-body statistical potentials derived from the delaunay tessellation of protein structures.

    PubMed

    Masso, Majid

    2012-01-01

    Delaunay tessellation of the atomic coordinates for a crystallographic protein structure yields an aggregate of non-overlapping and space-filling irregular tetrahedral simplices. The vertices of each simplex objectively identify a quadruplet of nearest neighbor atoms in the protein. Here we apply Delaunay tessellation to 1417 high-resolution structures of single chains that share low sequence identity, for the purpose of determining the relative frequencies of occurrence for all possible nearest neighbor atomic quadruplet types. Alternative distributions are explored by varying two fundamental parameters: atomic alphabet selection and cutoff length for admissible simplex edges. The distributions are then converted to four-body potential functions by implementing the inverted Boltzmann principle, which requires calculating the distribution of the reference state. Two alternative definitions for the reference state are presented, which introduces a third parameter, and we derive and compare an array of such potential functions. These knowledge-based statistical potentials based on higher-order interactions complement and generalize the more commonly encountered atom-pair potentials, for which a number of approaches are described in the literature. PMID:23367374

  12. Electronic structures and magnetic properties of rare-earth-atom-doped BNNTs

    NASA Astrophysics Data System (ADS)

    Ren, Juan; Zhang, Ning-Chao; Wang, Peng; Ning, Chao; Zhang, Hong; Peng, Xiao-Juan

    2016-04-01

    Stable geometries, electronic structures, and magnetic properties of (8,0) and (4,4) single-walled BN nanotubes (BNNTs) doped with rare-earth (RE) atoms are investigated using the first-principles pseudopotential plane wave method with density functional theory (DFT). The results show that these RE atoms can be effectively doped in BNNTs with favorable energies. Because of the curvature effect, the values of binding energy for RE-atom-doped (4,4) BNNTs are larger than those of the same atoms on (8,0) BNNTs. Electron transfer between RE-5 d, 6 s, and B-2 p, N-2 p orbitals was also observed. Furthermore, electronic structures and magnetic properties of BNNTs can be modified by such doping. The results show that the adsorption of Ce, Pm, Sm, and Eu atoms can induce magnetization, while no magnetism is observed when BNNTs are doped with La. These results are useful for spintronics applications and for developing magnetic nanostructures.

  13. Molecular structure of mononuclear azido- and dicyanamido-Cu(II) complexes

    NASA Astrophysics Data System (ADS)

    Mautner, Franz A.; Landry, Christine N.; Gallo, August A.; Massoud, Salah S.

    2007-06-01

    A new series of mononuclear azido- and dicyanamido-Cu(II) complexes, [Cu(L)(N 3)]ClO 4 where L = pdpa { N-(2-aminopropyl)- N, N-bis(2-pyridylmethyl)amine}, Me 3tren {tris( N-methyl-2-aminoethyl)amine} and Me 6trien (1,1,4,7,10,10-hexamethyltriethylenetetraamine) and Cu(L)(C 2N 3) 2 with L = pmedien ( N, N, N', N″, N″-pentamethyldiethylenetriamine) and Me 2dpt ( N, N-dimethyldipropyltriamine) were synthesized and structurally characterized by electronic and IR spectroscopy as well as by X-ray. Single crystal X-ray diffraction analysis of the complexes [Cu(pdpa)(N 3)]ClO 4 ( 1), [Cu(Me 3tren)(N 3)]ClO 4 ( 2) and [Cu(pmedien)(C 2N 3) 2] ( 3) reveals their monomeric nature. The structures of the complexes 1 and 2 derived from the blocking tripod tetraamines pdpa and Me 3tren consist of isolated [Cu(L)(N 3)] + cations and ClO4- counter ions. The copper centers are penta-coordinated by the four N of the amine ligands with the monodentate azido ligand occupying the apical site in distorted trigonal bipyramidal (TBP) geometry. Complex 1 exhibits π-π stacking interaction between the pyridyl groups. In the neutral complex 3, where the blocking ligand, pmedien is a linear tridentate amine the penta-coordinate geometry of the complex was achieved by the three planar amine- N and two terminal nitrile- N atoms from the two dicyanamide groups; one N in the basal position from the first dicyanamido group and one N at the apical position from the second group. The coordination polyhedron around the copper center may be described as an axially elongated square pyramidal (SP). The visible spectra of the complexes in aqueous solutions are in complete agreement with the assigned X-ray geometry around the Cu(II) centers.

  14. Self-consistent QM/MM methodologies for structural refinement of photosystem II and other macromolecules of biological interest

    SciTech Connect

    Batista, Enrique R; Sproviero, Eduardo M; Newcomer, Michael; Gascon, Jose A; Batista, Victor S

    2008-01-01

    The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins and nucleic acids. However, there some instances in which the limitations of either the MM (lack of a proper electronic description) or QM (limited to a few number of atoms) methods prevent a proper description of the system. To address this issue, we review here our approach to fine-tune the structure of biological systems using post-QM/MM refinements. These protocols are based on spectroscopy data, and/or partitioning of the system to extend the QM description to a larger region of a protein. We illustrate these methodologies through applications to several biomolecules, which were pre-optimized at the QM/MM level and then further refined using postQM/MM refinement methodologies: mod(QM/MM), which refines the atomic charges of the residues included in the MM region accounting for polarization effects; mod(QM/MM)-opt that partition the MM region in smaller parts and optimizes each part in an iterative. self-consistent way, and the Polarized-Extended X-Ray Absorption Fine Structure (P-EXAFS) fitting procedure, which fine-tune the atomic coordinates to reproduce experimental polarized EXAFS spectra. The first two techniques were applied to the guanine quadruplex. while the P-EXAFS refinement was applied to the oxygen evolving complex of photosystem II.

  15. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates

    PubMed Central

    Radisky, Evette S.; Lee, Justin M.; Lu, Chia-Jung Karen; Koshland, Daniel E.

    2006-01-01

    Atomic resolution structures of trypsin acyl-enzymes and a tetrahedral intermediate analog, along with previously solved structures representing the Michaelis complex, are used to reconstruct events in the catalytic cycle of this classic serine protease. Structural comparisons provide insight into active site adjustments involved in catalysis. Subtle motions of the catalytic serine and histidine residues coordinated with translation of the substrate reaction center are seen to favor the forward progress of the acylation reaction. The structures also clarify the attack trajectory of the hydrolytic water in the deacylation reaction. PMID:16636277

  16. Nanoscale structure and atomic disorder in the iron-based chalcogenides

    NASA Astrophysics Data System (ADS)

    Lal Saini, Naurang

    2013-02-01

    The multiband iron-based superconductors have layered structure with a phase diagram characterized by a complex interplay of charge, spin and lattice excitations, with nanoscale atomic structure playing a key role in their fundamental electronic properties. In this paper, we briefly review nanoscale structure and atomic disorder in iron-based chalcogenide superconductors. We focus on the Fe(Se,S)1-xTex (11-type) and K0.8Fe1.6Se2 (122-type) systems, discussing their local structure obtained by extended x-ray absorption fine structure. Local structure studies on the Fe(Se,S)1-xTex system reveal clear nanoscale phase separation characterized by coexisting components of different atomic configurations, similar to the case of random alloys. In fact, the Fe-Se/S and Fe-Te distances in the ternary Fe(Se,S)1-xTex are found to be closer to the respective distances in the binary FeSe/FeS and FeTe systems, showing significant divergence of the local structure from the average one. The observed features are characteristic of ternary random alloys, indicating breaking of the local symmetry in these materials. On the other hand, K0.8Fe1.6Se2 is known for phase separation in an iron-vacancy ordered phase and an in-plane compressed lattice phase. The local structure of these 122-type chalcogenides shows that this system is characterized by a large local disorder. Indeed, the experiments suggest a nanoscale glassy phase in K0.8Fe1.6Se2, with the superconductivity being similar to the granular materials. While the 11-type structure has no spacer layer, the 122-type structure contains intercalated atoms unlike the 1111-type REFeAsO (RE = rare earth) oxypnictides, having well-defined REO spacer layers. It is clear that the interlayer atomic correlations in these iron-based superconducting structures play an important role in structural stability as well as superconductivity and magnetism.

  17. Local Structure of Cu in Cs8Na16Cu5Ge131 Type II Clathrate

    SciTech Connect

    Mansour, A.; Beekman, M; Wong-Ng, W; Nolas, G

    2008-01-01

    We have used X-ray absorption spectroscopy (XAS) to investigate the local structure of Cu and Ge in the Cs8Na16Cu5Ge131 type II clathrate. We show that the local structure parameters for Ge (coordination number and distances) are consistent with those derived on the basis of XRD investigation of Cs8Na16Ge136. The EXAFS data suggest that Cu either randomly substitutes for Ge on the clathrate framework or preferentially on the 96g site but not preferentially on the 32e or 8a sites (Wyckoff notation). Furthermore, we find that the Cu-Ge distance is smaller than the Ge-Ge distance by 0.13 Angstroms, indicating a local distortion around the Cu atoms. The estimated degrees of disorder for Cu-Ge and Ge-Ge interactions indicate the Cu-Ge clathrate framework to be relatively stiff, while those for Na-Ge and Cs-Ge interactions corroborate previous observations of strong thermal disorder of the alkali guests in these materials. Our XAS results offer insight into the site substitution of Cu in this material, information unattainable from X-ray diffraction due to the lack of scattering contrast between Cu and Ge.

  18. Synthesis, structure, spectroscopic and electrochemical properties of bis(histamine-saccharinate) copper(II) complex

    NASA Astrophysics Data System (ADS)

    Bulut, İclal; Uçar, İbrahim; Karabulut, Bünyamin; Bulut, Ahmet

    2007-05-01

    Crystal structure of [Cu(hsm) 2(sac) 2] (hsm is histamine and sac is saccharinate) complex has been determined by X-ray diffraction analyses and its magnetic environment has been identified by electron paramagnetic resonance (EPR) technique. The title complex crystallizes in the monoclinic system, space group P 21/ c with a = 7.4282(4), b = 22.5034(16), c = 8.3300(5) Å, β = 106.227(4)°, V = 1336.98(14) Å 3, and Z = 2. The structure consist of discrete [Cu(hsm) 2(sac) 2] molecules in which the copper ion is centrosymmetrically coordinated by two histamine ligands forming an equatorial plane [Cu-N hsm = 2.024(2) and Cu-N hsm = 2.0338(18) Å]. Two N atoms from the saccharinate ligands coordinate on the elongated axial positions with Cu-N sac being 2.609(5) Å. The complex is also characterized by spectroscopic (IR, UV/Vis) and thermal (TG, and TDA) methods. The cyclic voltammogram of the title complex investigated in DMSO (dimethylsulfoxide) solution exhibits only metal centred electroactivity in the potential range - 1.25-1.5 V versus Ag/AgCl reference electrode. The molecular orbital bond coefficients of Cu(II) ion in d 9 state is also calculated by using EPR and optical absorption parameters.

  19. Synthesis, structure, and spectroscopic properties of ortho-metalated platinum(II) complexes

    SciTech Connect

    Mdleleni, M.M.; Bridgewater, J.S.; Watts, R.J.; Ford, P.C.

    1995-04-26

    The ortho-metalated Pt(II) complexes Pt(ppy)(CO)Cl (1), Pt(ptpy)(CO)Cl (2), and Pt(ppy)(Hppy)Cl (3) (where ppy and ptpy are respectively the ortho-C-deprotonated forms of 2-phenylpyridine and 2-p-tolylpyridine and Hppy is 2-phenylpyridine) have been prepared. The CO ligand is coordinated trans to the nitrogen atom of the ortho-metalated ligand and exerts a strong trans effect resulting in a relatively long Pt-N bond [2.114(19) {angstrom}]. This structure shows both the bidentate ppy ligand and the monodentate Hppy with the nitrogens of these ligands trans to each other. The UV/vis electronic absorption spectra of 1-3 have intense bands in the near-UV region ({approximately}375 nm) which have been assigned as metal to ligand charge transfer (MLCT) transitions, and higher energy bands were assigned as ligand-centered transitions. Each complex exhibits relatively long-lived structured emissions in the solid state at ambient temperature and at 77 K and 77 K glassy toluene solutions. These emissions are proposed to originate from triplet MLCT states. Notably, in solution both the lifetime and spectrum of 2 proved to be a function of the concentration, a phenomenon interpreted in terms of the propensity of square planar d{sup 8} complexes to oligomerize. In contrast, the more sterically hindered complex 3 displayed no such tendency toward oligomerization.

  20. Infrared image recognition based on structure sparse and atomic sparse parallel

    NASA Astrophysics Data System (ADS)

    Wu, Yalu; Li, Ruilong; Xu, Yi; Wang, Liping

    2015-12-01

    Use the redundancy of the super complete dictionary can capture the structural features of the image effectively, can achieving the effective representation of the image. However, the commonly used atomic sparse representation without regard the structure of the dictionary and the unrelated non-zero-term in the process of the computation, though structure sparse consider the structure feature of dictionary, the majority coefficients of the blocks maybe are non-zero, it may affect the identification efficiency. For the disadvantages of these two sparse expressions, a weighted parallel atomic sparse and sparse structure is proposed, and the recognition efficiency is improved by the adaptive computation of the optimal weights. The atomic sparse expression and structure sparse expression are respectively, and the optimal weights are calculated by the adaptive method. Methods are as follows: training by using the less part of the identification sample, the recognition rate is calculated by the increase of the certain step size and t the constraint between weight. The recognition rate as the Z axis, two weight values respectively as X, Y axis, the resulting points can be connected in a straight line in the 3 dimensional coordinate system, by solving the highest recognition rate, the optimal weights can be obtained. Through simulation experiments can be known, the optimal weights based on adaptive method are better in the recognition rate, weights obtained by adaptive computation of a few samples, suitable for parallel recognition calculation, can effectively improve the recognition rate of infrared images.