Identification of light elements in silicon nitride by aberration-corrected scanning transmission electron microscopy.

PubMed

Idrobo, Juan C; Walkosz, Weronika; Klie, Robert F; Oğüt, Serdar

2012-12-01

In silicon nitride structural ceramics, the overall mechanical and thermal properties are controlled by the atomic and electronic structures at the interface between the ceramic grains and the amorphous intergranular films (IGFs) formed by various sintering additives. In the last ten years the atomic arrangements of heavy elements (rare-earths) at the Si(3)N(4)/IGF interfaces have been resolved. However, the atomic position of light elements, without which it is not possible to obtain a complete description of the interfaces, has been lacking. This review article details the authors' efforts to identify the atomic arrangement of light elements such as nitrogen and oxygen at the Si(3)N(4)/SiO(2) interface and in bulk Si(3)N(4) using aberration-corrected scanning transmission electron microscopy. Published by Elsevier B.V.

Classical And Quantum Rainbow Scattering From Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winter, H.; Schueller, A.; Busch, M.

2011-06-01

The structure of clean and adsorbate covered surfaces as well as of ultrathin films can be investigated by grazing scattering of fast atoms. We present two recent experimental techniques which allow one to study the structure of ordered arrangements of surface atoms in detail. (1) Rainbow scattering under axial surface channeling conditions, and (2) fast atom diffraction. Our examples demonstrate the attractive features of grazing fast atom scattering as a powerful analytical tool in studies on the structure of surfaces. We will concentrate our discussion on the structure of ultrathin silica films on a Mo(112) surface and of adsorbed oxygenmore » atoms on a Fe(110) surface.« less

Lattice Transparency of Graphene.

PubMed

Chae, Sieun; Jang, Seunghun; Choi, Won Jin; Kim, Youn Sang; Chang, Hyunju; Lee, Tae Il; Lee, Jeong-O

2017-03-08

Here, we demonstrated the transparency of graphene to the atomic arrangement of a substrate surface, i.e., the "lattice transparency" of graphene, by using hydrothermally grown ZnO nanorods as a model system. The growth behaviors of ZnO nanocrystals on graphene-coated and uncoated substrates with various crystal structures were investigated. The atomic arrangements of the nucleating ZnO nanocrystals exhibited a close match with those of the respective substrates despite the substrates being bound to the other side of the graphene. By using first-principles calculations based on density functional theory, we confirmed the energetic favorability of the nucleating phase following the atomic arrangement of the substrate even with the graphene layer present in between. In addition to transmitting information about the atomic lattice of the substrate, graphene also protected its surface. This dual role enabled the hydrothermal growth of ZnO nanorods on a Cu substrate, which otherwise dissolved in the reaction conditions when graphene was absent.

Local Atomic Arrangements and Band Structure of Boron Carbide.

PubMed

Rasim, Karsten; Ramlau, Reiner; Leithe-Jasper, Andreas; Mori, Takao; Burkhardt, Ulrich; Borrmann, Horst; Schnelle, Walter; Carbogno, Christian; Scheffler, Matthias; Grin, Yuri

2018-05-22

Boron carbide, the simple chemical combination of boron and carbon, is one of the best-known binary ceramic materials. Despite that, a coherent description of its crystal structure and physical properties resembles one of the most challenging problems in materials science. By combining ab initio computational studies, precise crystal structure determination from diffraction experiments, and state-of-the-art high-resolution transmission electron microscopy imaging, this concerted investigation reveals hitherto unknown local structure modifications together with the known structural alterations. The mixture of different local atomic arrangements within the real crystal structure reduces the electron deficiency of the pristine structure CBC+B 12 , answering the question about electron precise character of boron carbide and introducing new electronic states within the band gap, which allow a better understanding of physical properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-resolution imaging of silicene on an Ag(111) surface by atomic force microscopy

NASA Astrophysics Data System (ADS)

Onoda, Jo; Yabuoshi, Keisuke; Miyazaki, Hiroki; Sugimoto, Yoshiaki

2017-12-01

Silicene, a two-dimensional (2D) honeycomb arrangement of Si atoms, is expected to have better electronic properties than graphene and has been mostly synthesized on Ag surfaces. Although scanning tunneling microscopy (STM) has been used for visualizing its atomic structure in real space, the interpretation of STM contrast is not straightforward and only the topmost Si atoms were observed on the (4 ×4 ) silicene/Ag(111) surface. Here, we demonstrate that high-resolution atomic force microscopy (AFM) can resolve all constituent Si atoms in the buckled honeycomb arrangement of the (4 ×4 ) silicene. Site-specific force spectroscopy attributes the origin of the high-resolution AFM images to chemical bonds between the AFM probe apex and the individual Si atoms on the (4 ×4 ) silicene. A detailed analysis of the geometric parameters suggests that the pulling up of lower-buckled Si atoms by the AFM tip could be a key for high-resolution AFM, implying a weakening of the Si-Ag interactions at the interface. We expect that high-resolution AFM will also unveil atomic structures of edges and defects of silicene, or other emerging 2D materials.

Crystal structure refinement of ReSi1.75 with an ordered arrangement of silicon vacancies

NASA Astrophysics Data System (ADS)

Harada, Shunta; Hoshikawa, Hiroaki; Kuwabara, Kosuke; Tanaka, Katsushi; Okunishi, Eiji; Inui, Haruyuki

2011-08-01

The crystal structure and microstructure of ReSi1.75 were investigated by synchrotron X-ray diffraction combined with scanning transmission electron microscopy. ReSi1.75 contains an ordered arrangement of vacancies in Si sites in the underlying tetragonal C11b lattice of the MoSi2-type and the crystal structure is monoclinic with the space group Cm. Atomic positions of Si atoms near vacancies are considerably displaced from the corresponding positions in the parent C11b structure, and they exhibit anomalously large local thermal vibration accompanied by large values of atomic displacement parameter. There are four differently-oriented domains with two of them being related to each other by the 90° rotation about the c-axis of the underlying C11b lattice and the other two being their respective twins. The habit planes for domain boundaries observed experimentally are consistent with those predicted with ferroelastic theory.

Hydroxyl migration disorders the surface structure of hydroxyapatite nanoparticles

NASA Astrophysics Data System (ADS)

Cheng, Xiajie; Wu, Hong; Zhang, Li; Ma, Xingtao; Zhang, Xingdong; Yang, Mingli

2017-09-01

The surface structure of nano-hydroxyapatite (HAP) was investigated using a combined simulated annealing and molecular dynamics method. The stationary structures of nano-HAP with 4-7 nm in diameter and annealed under different temperatures were analyzed in terms of pair distribution function, structural factor, mean square displacement and atomic coordination number. The particles possess different structures from bulk crystal. A clear radial change in their atomic arrangements was noted. From core to surface the structures change from ordered to disordered. A three-shell model was proposed to describe the structure evolution of nano-HAP. Atoms in the core zone keep their arrangements as in crystal, while atoms in the surface shell are in short-range order and long-range disorder, adopting a typically amorphous structure. Atoms in the middle shell have small displacements and/or deflections but basically retain their original locations as in crystal. The disordered shell is about 1 nm in thickness, in agreement with experimental observations. The disordering mainly stems from hydroxyl migration during which hydroxyls move to the surface and bond with the exposed Ca ions, and their left vacancies bring about a rearrangement of nearby atoms. The disordering is to some extent different for particles unannealed under different temperatures, resulting from fewer number of migrated hydroxyls at lower temperatures. Particles with different sizes have similar surface structures, and their surface energy decreases with increasing size. Moreover, the surface energy is reduced by hydroxyl migration because the exposed Ca ions on the surface are ionically bonded with the migrated hydroxyls. Our calculations proposed a new structure model for nano-HAP, which indicates a surface structure with activities different from those without surface reorganization. This is particularly interesting because most bioactivities of biomaterials are dominated by their surface activity.

Incorporation of rare earth elements in titanite: Stabilization of the A2/a dimorph by creation of antiphase boundaries

USGS Publications Warehouse

Hughes, J.M.; Bloodaxe, E.S.; Hanchar, J.M.; Foord, E.E.

1997-01-01

The atomic arrangement of a natural rare-earth-rich titanite and two synthetic rare-earth-doped titanites have been refined in space group A2/a, and the atomic arrangement of an undoped P21/a synthetic titanite was also refined for comparison. Previous work has shown that titanite possesses a domain structure, with domains formed of like-displaced Ti atoms in the [100] octahedral chains. P21/a titanite results when the crystal is formed of a single domain, but as Ti-reversal sites occur in the octahedral chain the apparent A2/a structure results from the average of antiphase domains. Antiphase boundaries occur at O1, which is alternately overbonded or underbonded at the boundaries, depending on the displacement of the neighboring Ti atoms. Type 2 antiphase boundaries exist where two Ti atoms are displaced away from the intervening O1 atom and are energetically unfavorable because of underbonding of that O1 atom. However, substitution of a trivalent rare earth element in the adjacent Ca2+ site relieves that underbonding, favoring the creation of type 2 antiphase boundaries and stabilization of the A2/a dimorph. The results of high-precision crystal structure analyses demonstrate that rare earth substituents for Ca stabilize the A2/a dimorph at lower substitution levels than required for octahedral substitutions.

Thorium Copper Phosphides: More Diverse Metal-Phosphorus and Phosphorus-Phosphorus Interactions than U analogues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Geng Bang; Malliakas, Christos D.; Lin, Jian

To explore the chemical analogy between thorium and heavier actinides in soft anionic environments, three new thorium phosphides (ThCuP 2, beta-ThCu 2P 2, and ThCu 5P 3) have been prepared through solid-state reactions using CuI as a reaction promoter. The structure of ThCuP 2 can be described as a filled UTe 2-type with both dimeric P 2 4- and monomeric P 3- anions, in which Th is coordinated by eight P atoms in a bicapped trigonal prismatic arrangement and Cu is tetrahedrally coordinated by four P atoms. β-ThCu 2P 2 contains only P 3- anions and is isostructural with BaCumore » 2S 2. In this structure, Th is coordinated by seven P atoms in monocapped trigonal prismatic geometry and Cu is tetrahedrally coordinated by four P atoms. ThCu 5P 3 adopts the YCo 5P 3-type structure consisting of P 3- anions. This structure contains Th atoms coordinated by six P atoms in a trigonal prismatic arrangement and Cu atoms that are either tetrahedrally coordinated by four P atoms or square pyramidally coordinated by five P atoms. Electric resistivity measurements and electronic structure calculations on β-ThCu 2P 2 indicate a metal. These new compounds may be charge-balanced and formulated as Th 4+Cu +(P 2 4-) 1/2P 3-, Th 4+(Cu +) 2(P 3-) 2, and Th 4+(Cu +) 5(P 3-) 3, respectively. The structural, bonding, and property relationships between these Th compounds and related actinide and rare-earth phases are discussed. In conclusion, titled compounds display more diverse ion-ion interactions and different electronic structures from those in UCuP 2 and UCu 2P 2 that were synthesized under similar experimental conditions, suggesting divergence of thorium-phosphide chemistry from uranium-phosphide chemistry.« less

Thorium Copper Phosphides: More Diverse Metal-Phosphorus and Phosphorus-Phosphorus Interactions than U analogues

DOE PAGES

Jin, Geng Bang; Malliakas, Christos D.; Lin, Jian

2017-09-28

To explore the chemical analogy between thorium and heavier actinides in soft anionic environments, three new thorium phosphides (ThCuP 2, beta-ThCu 2P 2, and ThCu 5P 3) have been prepared through solid-state reactions using CuI as a reaction promoter. The structure of ThCuP 2 can be described as a filled UTe 2-type with both dimeric P 2 4- and monomeric P 3- anions, in which Th is coordinated by eight P atoms in a bicapped trigonal prismatic arrangement and Cu is tetrahedrally coordinated by four P atoms. β-ThCu 2P 2 contains only P 3- anions and is isostructural with BaCumore » 2S 2. In this structure, Th is coordinated by seven P atoms in monocapped trigonal prismatic geometry and Cu is tetrahedrally coordinated by four P atoms. ThCu 5P 3 adopts the YCo 5P 3-type structure consisting of P 3- anions. This structure contains Th atoms coordinated by six P atoms in a trigonal prismatic arrangement and Cu atoms that are either tetrahedrally coordinated by four P atoms or square pyramidally coordinated by five P atoms. Electric resistivity measurements and electronic structure calculations on β-ThCu 2P 2 indicate a metal. These new compounds may be charge-balanced and formulated as Th 4+Cu +(P 2 4-) 1/2P 3-, Th 4+(Cu +) 2(P 3-) 2, and Th 4+(Cu +) 5(P 3-) 3, respectively. The structural, bonding, and property relationships between these Th compounds and related actinide and rare-earth phases are discussed. In conclusion, titled compounds display more diverse ion-ion interactions and different electronic structures from those in UCuP 2 and UCu 2P 2 that were synthesized under similar experimental conditions, suggesting divergence of thorium-phosphide chemistry from uranium-phosphide chemistry.« less

Three-dimensional atomic arrangement around active/inactive dopant sites in boron-doped diamond

NASA Astrophysics Data System (ADS)

Kato, Yukako; Tsujikawa, Daichi; Hashimoto, Yusuke; Yoshida, Taisuke; Fukami, Shun; Matsuda, Hiroyuki; Taguchi, Munetaka; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

Boron-doped diamond has received significant attention as an advanced material for power devices owing to its high breakdown characteristics. To control the characteristics of diamond related to band conduction, it is essential to determine the atomic structure around dopants and to develop a method of controlling the atomic arrangement around dopants. We measured the photoelectron diffraction of a boron-doped diamond using a display-type ellipsoidal mesh analyzer to examine the dopant sites in heavily boron-doped diamond. The B 1s photoelectron spectrum shows two peaks for different chemical bonding sites. These two dopant sites were identified as the substitutional and interstitial sites in diamond.

Quantum Conductance in Metal Nanowires

NASA Astrophysics Data System (ADS)

Ugarte, Daniel

2004-03-01

Quantum Conductance in Metal Nanowires D. Ugarte Brazilian National Synchrotron Light Laboratory C.P. 6192, 13084-971 Campinas SP, Brazil. Electrical transport properties of metallic nanowires (NWs) have received great attention due to their quantum conductance behavior. Atomic scale wires can be generated by stretching metal contacts; during the elongation and just before rupture, the NW conductance shows flat plateaus and abrupt jumps of approximately a conductance quantum. In this experiments, both the NW atomic arrangement and conductance change simultaneously, making difficult to discriminate electronic and structural effects. In this work, the atomic structure of NWs was studied by time-resolved in situ experiments in a high resolution transmission electron microscope, while their electrical properties using an UHV mechanically controllable break junction (MCBJ). From the analysis of numerous HRTEM images and videos, we have deduced that metal (Au, Ag, Pt, etc.) junctions generated by tensile deformation are crystalline and free of defects. The neck structure is strongly dependent on the surface properties of the analyzed metal, this was verified by comparing different metal NWs (Au, Ag, Cu), which have similar atomic structure (FCC), but show very different faceting patterns. The correlation between the observed structural and transport properties of NW points out that the quantum conductance behavior is defined by preferred atomic arrangement at the narrowest constriction. In the case of magnetic (ex. Fe,Co,Ni) or quasi-magnetic (ex. Pd) wires, we have observed that one-atom-thick structures show a conductance of half the quantum as expected for a fully spin polarized current. This phenomenon seems to occur spontaneously for magnetic suspended atom-chains in zero magnetic field and at room temperature. These results open new opportunities for spin control in nanostructures. Funded by FAPESP, LNLS and CNPq.

Laser-induced transformation of graphitic materials to two-dimensional graphene-like structures at ambient conditions.

PubMed

Antonelou, Aspasia; Benekou, Vasiliki; Dracopoulos, Vasileios; Kollia, Mary; Yannopoulos, Spyros N

2018-06-27

Laser processing of carbon containing compounds towards the formation of graphene-based structures gains ground over the last years in view of the practicality that lasers offer against other conventional graphene preparation methods. The current work explores the viability of low-cost lasers, operating at ambient conditions, for the transformation of various graphitic materials to structures with graphene-like atomic arrangement. Starting materials are at two opposing sides. On one side stand typical graphite powder with Bernal stacking and strong sp2 character, while nanocrystalline or quasi-amorphous graphitic powders such as carbon black and activated carbon are also investigated. Electron microscopies are employed to observe post-irradiation morphological changes while Raman scattering identifies details on atomic arrangement. It is demonstrated that graphene-like structures can be prepared either by starting from a well-organized Bernal-stacked network or by irradiating the quasi-amorphous forms of nanocrystalline carbon. Mild structural changes in the former case pertain to increase of the interlayer spacing, which could possibly be rationalized by considering a mechanism based on Coulomb expansion. For less organized carbon structures, reorganization of the atomic arrangement with an appreciable sp3 to sp2 transformation is observed. The findings of this work confirm that laser processing at minimal chamber conditions demonstrate high potential for preparing high-quality graphene-based structures starting from low cost materials. The proposed method being easily scalable adaptable to current technological platforms is expected to be transformed to a viable and eco-friendly graphene production technology. © 2018 IOP Publishing Ltd.

Numerical study of the defect adamantine compound CuGaGeSe4

NASA Astrophysics Data System (ADS)

Shen, Kesheng; Zhang, Xianzhou; Lu, Hai; Jiao, Zhaoyong

2018-06-01

The electronic structure, elastic and optical properties of the defect adamantine compound CuGaGeSe4 in ? structure are systematically investigated using first-principles calculations. Through detailed calculation and comparison, we obtain three independent atomic arrangements and predict the most stable atomic arrangement according to the lattice constants and enthalpy formation energies. The elastic constants are calculated, which can be used to predict the axial thermal expansion coefficients accurately. The optical properties of compound CuGaGeSe4, including the dielectric function, refractive index and absorption spectrum, are depicted for a more intuitive understanding. Our calculated zero-frequency limits ɛ1(0) and n(0) are very close to the other theoretical values, which proves that our calculations are reliable.

Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.

PubMed

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

2014-02-01

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

Effect of edge defects on band structure of zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Wadhwa, Payal; Kumar, Shailesh; Dhilip Kumar, T. J.; Shukla, Alok; Kumar, Rakesh

2018-04-01

In this article, we report band structure studies of zigzag graphene nanoribbons (ZGNRs) on introducing defects (sp3 hybridized carbon atoms) in different concentrations at edges by varying the ratio of sp3 to sp2 hybridized carbon atoms. On the basis of theoretical analyses, bandgap values of ZGNRs are found to be strongly dependent on the relative arrangement of sp3 to sp2 hybridized carbon atoms at the edges for a defect concentration; so the findings would greatly help in understanding the bandgap of nanoribbons for their electronic applications.

Strong influence of off-site symmetry positions of hydrogen atoms in ScH3 hcp phases

NASA Astrophysics Data System (ADS)

Pakornchote, T.; Bovornratanaraks, T.; Vannarat, S.; Pinsook, U.

2016-01-01

We investigate the wave-like arrangements of H atoms around metal plane (Hm) in the ScH3 hcp phase by using the ab-initio method. We found that only P63 / mmc, P 3 bar c 1, P63cm and P63 phases are energetically favorable. The wave-like arrangement allows the off-site symmetry positions of the H atoms, and leads to substantial changes in the pair distribution between Sc and H atoms which are associating with the changes in the electronic structure in such a way that the total energy is lowering. The symmetry breaking from P63mmc is also responsible for the band gap opening. In the P63 structure, the calculated band gap is 0.823 eV and 1.223 eV using GGA and sX-LDA functionals, respectively. This band gap can be compared with 1.7 eV derived from the optical measurement and 1.55 eV from the HSE06 calculation. Thus, the broken symmetry structures can be viewed as Peierls distortion of the P63 / mmc structure. Furthermore, we found that only the P63 structure is dynamically stable, unlike YH3 where the P63cm structure is also stable. The stability of P63 comes from sufficiently strong interactions between two neighboring H atoms at their off-site symmetry positions, i.e. near the metal plane and near the tetragonal site. The P63 phonon density of states is in good agreement with the data from the neutron experiment.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

NASA Astrophysics Data System (ADS)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Atomic-Resolution Spectrum Imaging of Semiconductor Nanowires.

PubMed

Zamani, Reza R; Hage, Fredrik S; Lehmann, Sebastian; Ramasse, Quentin M; Dick, Kimberly A

2018-03-14

Over the past decade, III-V heterostructure nanowires have attracted a surge of attention for their application in novel semiconductor devices such as tunneling field-effect transistors (TFETs). The functionality of such devices critically depends on the specific atomic arrangement at the semiconductor heterointerfaces. However, most of the currently available characterization techniques lack sufficient spatial resolution to provide local information on the atomic structure and composition of these interfaces. Atomic-resolution spectrum imaging by means of electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) is a powerful technique with the potential to resolve structure and chemical composition with sub-angstrom spatial resolution and to provide localized information about the physical properties of the material at the atomic scale. Here, we demonstrate the use of atomic-resolution EELS to understand the interface atomic arrangement in three-dimensional heterostructures in semiconductor nanowires. We observed that the radial interfaces of GaSb-InAs heterostructure nanowires are atomically abrupt, while the axial interface in contrast consists of an interfacial region where intermixing of the two compounds occurs over an extended spatial region. The local atomic configuration affects the band alignment at the interface and, hence, the charge transport properties of devices such as GaSb-InAs nanowire TFETs. STEM-EELS thus represents a very promising technique for understanding nanowire physical properties, such as differing electrical behavior across the radial and axial heterointerfaces of GaSb-InAs nanowires for TFET applications.

Structural investigations in helium charged titanium films using grazing incidence XRD and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Wan, Chubin; Zhou, Xiaosong; Wang, Yuting; Li, Shina; Ju, Xin; Peng, Shuming

2014-01-01

The crystal structure and local atomic arrangements surrounding Ti atoms were determined for He-charged hexagonal close-packed (hcp) Ti films and measured at glancing angles by synchrotron radiation X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, respectively. The charged specimens were prepared by direct current magnetron sputtering with a He/Ar mixture. He atoms with a relatively medium concentration (He/Ti atomic ratio as high as 17 at.%) were incorporated evenly in the deposited films. XRD results showed the changes in the peak intensities in Ti films with different He contents. EXAFS Fourier Transform analysis indicated that the average Ti-Ti distance decreased significantly, and proved the existence of phase transition.

Theoretical predictions of a bucky-diamond SiC cluster.

PubMed

Yu, Ming; Jayanthi, C S; Wu, S Y

2012-06-15

A study of structural relaxations of Si(n)C(m) clusters corresponding to different compositions, different relative arrangements of Si/C atoms, and different types of initial structure, reveals that the Si(n)C(m) bucky-diamond structure can be obtained for an initial network structure constructed from a truncated bulk 3C-SiC for a magic composition corresponding to n = 68 and m = 79. This study was performed using a semi-empirical Hamiltonian (SCED-LCAO) since it allowed an extensive search of different types of initial structures. However, the bucky-diamond structure predicted by this method was also confirmed by a more accurate density functional theory (DFT) based method. The bucky-diamond structure exhibited by a SiC-based system represents an interesting paradigm where a Si atom can form three-coordinated as well as four-coordinated networks with carbon atoms and vice versa and with both types of network co-existing in the same structure. Specifically, the bucky-diamond structure of the Si(68)C(79) cluster consists of a 35-atom diamond-like inner core (four-atom coordinations) suspended inside a 112-atom fullerene-like shell (three-atom coordinations).

Atomic structure of nano voids in irradiated 3C-SiC

NASA Astrophysics Data System (ADS)

Lin, Yan-Ru; Chen, Liu-Gu; Hsieh, Cheng-Yo; Hu, Alice; Lo, Sheng-Chuan; Chen, Fu-Rong; Kai, Ji-Jung

2018-01-01

It is important to understand the atomic structure of defect clusters in SiC, a promising material for nuclear application. In this study, we have directly observed and identified nano voids in ion irradiated 3C-SiC at 800 °C, 20 dpa through ABF and HAADF STEM images. A quantitative method was used to analyze HAADF images in which atomic columns with a difference in the number of atoms could be identified and scattered intensities can be computed. Our result shows that these voids are composed of atomic vacancies in an octahedral arrangement. The density of the void was measured by STEM to be 9.2 × 1019m-3 and the size was ∼1.5 nm.

A thermally driven differential mutation approach for the structural optimization of large atomic systems

NASA Astrophysics Data System (ADS)

Biswas, Katja

2017-09-01

A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations. With just a population size of six systems, energetically very low structures are obtained. While each of the structures represents a distinctly different arrangement of the atoms, their properties, such as energy, distribution of rings, radial distribution function, coordination number, and distribution of bond angles, are very similar.

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

Chiral Gold Nanoclusters: Atomic Level Origins of Chirality.

PubMed

Zeng, Chenjie; Jin, Rongchao

2017-08-04

Chiral nanomaterials have received wide interest in many areas, but the exact origin of chirality at the atomic level remains elusive in many cases. With recent significant progress in atomically precise gold nanoclusters (e.g., thiolate-protected Au n (SR) m ), several origins of chirality have been unveiled based upon atomic structures determined by using single-crystal X-ray crystallography. The reported chiral Au n (SR) m structures explicitly reveal a predominant origin of chirality that arises from the Au-S chiral patterns at the metal-ligand interface, as opposed to the chiral arrangement of metal atoms in the inner core (i.e. kernel). In addition, chirality can also be introduced by a chiral ligand, manifested in the circular dichroism response from metal-based electronic transitions other than the ligand's own transition(s). Lastly, the chiral arrangement of carbon tails of the ligands has also been discovered in a very recent work on chiral Au 133 (SR) 52 and Au 246 (SR) 80 nanoclusters. Overall, the origins of chirality discovered in Au n (SR) m nanoclusters may provide models for the understanding of chirality origins in other types of nanomaterials and also constitute the basis for the development of various applications of chiral nanoparticles. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A beachhead on the island of stability

DOE PAGES

Oganessian, Yuri Ts.; Rykaczewski, Krzysztof P.

2015-01-01

Remember learning the periodic table of elements in high school? Our chemistry teachers explained that the chemical properties of elements come from the electronic shell structure of atoms. Furthermore, our physics teachers enriched that picture of the atomic world by introducing us to isotopes and the Segrè chart of nuclides, which arranges them by proton number Z and neutron number N.

Structure cristalline du composé intermétallique Ni18Ge12

PubMed Central

Kars, Mohammed; Herrero, Adrian Gómez; Roisnel, Thierry; Rebbah, Allaoua; Otero-Diáz, L. Carlos

2015-01-01

Single crystals of octa­deca­nickel dodeca­germanide were grown by chemical transport reaction. The inter­metallic compound crystallizes in a superstructure of the hexa­gonal NiAs type (B8 type). All atoms in the asymmetric unit lie on special positions except one Ni atom (two Ni atoms have site symmetry -6.. and another one has site symmetry .2. while the Ge atoms have site symmetries 32., m.. and 3..). In the structure, the Ni atoms are arranged in 11- or 13-vertex polyhedra (CN = 11–13). The coordination polyhedra of the Ge atoms are bicapped square anti­prisms (CN = 10) or 11-vertex polyhedra (CN = 11). The structure exhibits strong Ge⋯Ni inter­actions, but no close Ge⋯Ge contacts are observed. The Ni atoms with CN = 13 form infinite chains along [001] with an Ni—Ni distance of 2.491 (2) Å. PMID:25844198

Computational materials science: Think locally, act globally

NASA Astrophysics Data System (ADS)

Rabe, Karin M.

2002-11-01

New first-principles calculations reveal the range of atomic arrangements underlying the average crystallographic structure of a perovskite oxide, PZT. This work opens the door to understanding the exceptional physical behaviour of PZT and related systems.

Structure and superconductivity in the ternary silicide CaAlSi

NASA Astrophysics Data System (ADS)

Ma, Rong; Huang, Gui-Qin; Liu, Mei

2007-06-01

Using the linear response-linearized Muffin-tin orbital (LR-LMTO) method, we study the electronic band structure, phonon spectra, electron-phonon coupling and superconductivity for c-axis ferromagnetic-like (F-like) and antiferromagnetic-like (AF-like) structures in ternary silicide CaAlSi. The following conclusions are drawn from our calculations. If Al and Si atoms are assumed to arrange along the c axis in an F-like long-range ordering (-Al-Al-Al-and-Si-Si-Si-), one could obtain the ultrasoft B1g phonon mode and thus very strong electron-phonon coupling in CaAlSi. However, the appearance of imaginary frequency phonon modes indicates the instability of such a structure. For Al and Si atoms arranging along the c axis in an AF-like long-range ordering (-Al-Si-Al-), the calculated electron-phonon coupling constant is equal to 0.8 and the logarithmically averaged frequency is 146.8 K. This calculated result can correctly yield the superconducting transition temperature of CaAlSi by the standard BCS theory in the moderate electron-phonon coupling strength. We propose that an AF-like superlattice model for Al (or Si) atoms along the c direction may mediate the inconsistency estimated from theory and experiment, and explain the anomalous superconductivity in CaAlSi.

Role of Defects on Regioselectivity of Nano Pristine Graphene.

PubMed

Kudur Jayaprakash, Gururaj; Casillas, Norberto; Astudillo-Sánchez, Pablo D; Flores-Moreno, Roberto

2016-11-17

Here analytical Fukui functions based on density functional theory are applied to investigate the redox reactivity of pristine and defected graphene lattices. A carbon H-terminated graphene structure (with 96 carbon atoms) and a graphene defected surface with Stone-Wales rearrangement and double vacancy defects are used as models. Pristine sp 2 -hybridized, hexagonal arranged carbon atoms exhibit a symmetric reactivity. In contrast, common carbon atoms at reconstructed polygons in Stone-Wales and double vacancy graphene display large reactivity variations. The improved reactivity and the regioselectivity at defected graphene is correlated to structural changes that caused carbon-carbon bond length variations at defected zones.

Molecular structure of the dioctadecyldimethylammonium bromide (DODAB) bilayer.

PubMed

Jamróz, Dorota; Kepczynski, Mariusz; Nowakowska, Maria

2010-10-05

Dioctadecyldimethylammonium bromide (DODAB) is a double-chained quaternary ammonium surfactant that assembles in water into bilayer structures. This letter reports the molecular dynamics (MD) computer simulations of the DODAB bilayer at 25 °C. The simulations show that the surfactant membrane arranges spontaneously into the rippled phase (P(β)(')) at that temperature. The ordering within the chain fragment closest to the hydrophilic head (carbon atoms 1-5) is relatively low. It grows significantly for the carbon atoms located in the center of the membrane (atoms 6-17). The C6-C17 chain fragments are well aligned and tilted by ca. 15° with respect to the bilayer normal.

Predicting Catalytic Activity of Nanoparticles by a DFT-Aided Machine-Learning Algorithm.

PubMed

Jinnouchi, Ryosuke; Asahi, Ryoji

2017-09-07

Catalytic activities are often dominated by a few specific surface sites, and designing active sites is the key to realize high-performance heterogeneous catalysts. The great triumphs of modern surface science lead to reproduce catalytic reaction rates by modeling the arrangement of surface atoms with well-defined single-crystal surfaces. However, this method has limitations in the case for highly inhomogeneous atomic configurations such as on alloy nanoparticles with atomic-scale defects, where the arrangement cannot be decomposed into single crystals. Here, we propose a universal machine-learning scheme using a local similarity kernel, which allows interrogation of catalytic activities based on local atomic configurations. We then apply it to direct NO decomposition on RhAu alloy nanoparticles. The proposed method can efficiently predict energetics of catalytic reactions on nanoparticles using DFT data on single crystals, and its combination with kinetic analysis can provide detailed information on structures of active sites and size- and composition-dependent catalytic activities.

Atomic resolution study of the interfacial bonding at Si3N4/CeO2-δ grain boundaries

NASA Astrophysics Data System (ADS)

Walkosz, W.; Klie, R. F.; Öǧüt, S.; Borisevich, A.; Becher, P. F.; Pennycook, S. J.; Idrobo, J. C.

2008-08-01

Using a combination of atomic-resolution Z-contrast imaging and electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope, we examine the atomic and electronic structures at the interface between Si3N4 (101¯0) and CeO2-d intergranular film (IGF). Ce atoms are observed to segregate to the interface in a two-layer periodic arrangement, which is significantly different from the structure observed in a previous study. Our EELS experiments show (i) oxygen in direct contact with the terminating Si3N4 open-ring structures, (ii) a change in the Ce valence from a nominal oxidation state of +3 to almost +4 moving from the interface into the IGF, and (iii) a uniform concentration of Si in the film.

Structural paradox in submonolayer chlorine coverage on Au(111)

NASA Astrophysics Data System (ADS)

Zheltov, V. V.; Cherkez, V. V.; Andryushechkin, B. V.; Zhidomirov, G. M.; Kierren, B.; Fagot-Revurat, Y.; Malterre, D.; Eltsov, K. N.

2014-05-01

In this work, we present a combined low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT) study of chlorine adsorption on Au(111) at low coverages. Our STM study of Cl/Au(111) system has shown that at submonolayer coverages (θ < 0.1 ML) chlorine atoms form chainlike structures with abnormally short distances of 3.8 Å between them. Our DFT calculations have shown that chlorine atoms can interact with each other through distortion of the substrate and this indirect elastic interaction is strong enough to affect their arrangement in the chainlike structures.

Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

PubMed Central

Levin, Igor; Vanderah, Terrell

2008-01-01

The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure—a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale—the so-called “nanostructure problem”—at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem—an ultimate frontier in materials characterization—necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed “institute” would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3) developing and maintaining pertinent databases, and (4) providing necessary education and training. PMID:27096131

Metal-ligand bond directionality in the M2-NH3 complexes (M = Cu, Ag and Au)

NASA Astrophysics Data System (ADS)

Eskandari, K.; Ebadinejad, F.

2018-05-01

The metal-ligand bonds in the M2-NH3 complexes (M = Au, Ag and Cu) are directional and the M-M-N angles tend to be linear. Natural energy decomposition analysis (NEDA) and localised molecular orbital energy decomposition analysis (LMOEDA) approaches indicate that the metal-ligand bonds in these complexes are mainly electrostatic in nature, however, the electrostatic is not the cause of the linearity of M-M-N arrangements. Instead, NEDA shows that the charge transfer and core repulsion are mainly responsible for the directionality of these bonds. In the LMOEDA point of view, the repulsion term is the main reason for the linearity of these complexes. Interacting quantum atoms (IQA) analysis shows that inter-atomic and inter-fragment interactions favour the nonlinear arrangements; however, these terms are compensated by the atomic self-energies, which stabilise the linear structure.

An Example of Body-Centered Cubic Crystal Structure: The Atomium in Brussels as an Educative Tool for Introductory Materials Chemistry

ERIC Educational Resources Information Center

Pinto, Gabriel

2012-01-01

When students are introduced to the ways in which atoms are arranged in crystal structures, transposing the textbook illustrations into three-dimensional structures is difficult for some of them. To facilitate this transition, this article describes an approach to the study of the structure of solids through a well-known monument, the Atomium in…

Icosahedral quasicrystals as twins of cubic crystals containing large icosahedral clusters of atoms: The 1012-atom primitive cubic structure of Al(6)CuLi(3), the C-phase Al(37)Cu(3)Li(21)Mg(3), and GaMg(2)Zn(3).

PubMed

Pauling, L

1988-06-01

Single-grain precession x-ray diffraction photographs of Al(6)CuLi(3) have been successfully indexed on the basis of icosahedral twinning of cubic crystals with a 1012-atom primitive cubic unit with edge 25.70 A, giving support to the proposal that the so-called icosahedral quasicrystals are twins of crystals containing eight large icosahedral clusters in the beta-W arrangement. In this compound two of the clusters consist of 104 atoms and six consist of 136 atoms, with 24 atoms shared. The same structure is assigned to the C-phase, Al(37)Cu(3)Li(21)Mg(3), and to GaMg(2)Zn(3). A theory of icosahedral quasicrystals and amorphous metals is described.

Icosahedral quasicrystals as twins of cubic crystals containing large icosahedral clusters of atoms: The 1012-atom primitive cubic structure of Al6CuLi3, the C-phase Al37Cu3Li21Mg3, and GaMg2Zn3

PubMed Central

Pauling, Linus

1988-01-01

Single-grain precession x-ray diffraction photographs of Al6CuLi3 have been successfully indexed on the basis of icosahedral twinning of cubic crystals with a 1012-atom primitive cubic unit with edge 25.70 Å, giving support to the proposal that the so-called icosahedral quasicrystals are twins of crystals containing eight large icosahedral clusters in the β-W arrangement. In this compound two of the clusters consist of 104 atoms and six consist of 136 atoms, with 24 atoms shared. The same structure is assigned to the C-phase, Al37Cu3Li21Mg3, and to GaMg2Zn3. A theory of icosahedral quasicrystals and amorphous metals is described. PMID:16593929

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saito, M.; Suzuki, S.; Kimura, M.

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 twomore » 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.« less

Exotic chemical arrangements and magnetic moment evolution of NixPt1-x (0 ≤x≤ 1) nanoparticles

NASA Astrophysics Data System (ADS)

Mokkath, Junais Habeeb

2018-06-01

We present a systematic study on the chemical ordering pattern and the magnetic properties of NixPt1-x (0 ⩽ x≤ 1) nanoparticles having a size of 1.5 nm by means of an approach which combines basin hopping structure sampling technique and spin-polarized density functional theory. We found exotic chemical ordering patterns for different Ni/Pt ratios. In addition, we observed a sharp phase transition from non-magnetic to ferromagnetic behaviour around x = 67%. We show that this is a direct consequence of a unique atomic arrangement on the surface in which Ni atoms club together causing the strong Ni-Ni magnetic interaction. The observed magnetic properties are correlated to the electronic density of states.

1D chain formation by coadsorption of Pb and Bi on Cu(001): Determination using low energy electron diffraction

NASA Astrophysics Data System (ADS)

Kabiruzzaman, Md; Ahmed, Rezwan; Nakagawa, Takeshi; Mizuno, Seigi

2017-10-01

Coadsorption of two heavy metals, Pb and Bi, on Cu(001) at room temperature has been studied using low energy electron diffraction (LEED). c(4 × 4), c(2 × 2), and c(9√{ 2}×√{ 2}) phases are obtained at different coverages; here, we have determined the best-fit structure of c(4 × 4) phase. This structure can be described as a 1D substitutional chain arrangement of Pb and Bi atoms between the Cu rows along the [110] direction. The unit cell in the two-dimensional (2D) surface consists of one Bi atom, two Pb atoms, and four Cu atoms with one vacancy at the center. The optimal structure parameters demonstrate that Bi atoms are located at fourfold-hollow sites and that Pb atoms are laterally displaced by 0.78 Å from the fourfold-hollow site toward the vacancy. The reasons for the formation of the c(4 × 4) structure upon deposition of Pb and Bi on Cu(001) are discussed in comparison with a similar structure formed by the individual adsorption of Pb on the same substrate.

Theory versus experiment for a family of single-layer compounds with a similar atomic arrangement: (Tl,X )/Si(111 )√{3 }×√{3 }(X =Pb,Sn,Bi,Sb,Te,Se)

NASA Astrophysics Data System (ADS)

Matetskiy, A. V.; Kibirev, I. A.; Mihalyuk, A. N.; Eremeev, S. V.; Gruznev, D. V.; Bondarenko, L. V.; Tupchaya, A. Y.; Zotov, A. V.; Saranin, A. A.

2017-08-01

Two-dimensional compounds made of one monolayer of Tl and one-third monolayer of Pb, Bi, Te, or Se (but not of Sn or Sb) on Si(111) have been found to have a similar atomic arrangement which can be visualized as a √{3 }×√{3 } -periodic honeycomb network of chained Tl trimers with atoms of the second adsorbate occupying the centers of the honeycomb units. Structural and electronic properties of the compounds have been examined in detail theoretically using density functional theory (DFT) calculations and experimentally using low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), and angle-resolved photoelectron spectroscopy (ARPES) observations. It has been found that though structural parameters of the compounds are very similar for all species, the only common feature of their band structure is a considerable spin-splitting of the surface-state bands, while other basic electronic properties vary greatly with a change of species. The Tl-Pb compound is strongly metallic with two metallic surface-state bands; the Tl-Bi compound is also metallic but with a single metallic band; the Tl-Te and Tl-Se compounds appear to be insulators.

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akparov, V. Kh., E-mail: valery@akparov.ru; Timofeev, V. I., E-mail: tostars@mail.ru; Maghsoudi, N. N., E-mail: maghsudi@yahoo.com

2017-03-15

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and themore » acetate ion is different from that reported by Yoshimoto et al.« less

Dislocation structures of Σ3 {112} twin boundaries in face centered cubic metals

NASA Astrophysics Data System (ADS)

Wang, J.; Anderoglu, O.; Hirth, J. P.; Misra, A.; Zhang, X.

2009-07-01

High resolution transmission electron microscopy of nanotwinned Cu films revealed Σ3 {112} incoherent twin boundaries (ITBs), with a repeatable pattern involving units of three {111} atomic planes. Topological analysis shows that Σ3 {112} ITBs adopt two types of atomic structure with differing arrangements of Shockley partial dislocations. Atomistic simulations were performed for Cu and Al. These studies revealed the structure of the two types of ITBs, the formation mechanism and stability of the associated 9R phase, and the influence of stacking fault energies on them. The results suggest that Σ3 {112} ITBs may migrate through the collective glide of partial dislocations.

Crystal structure of the ternary silicide Gd2Re3Si5.

PubMed

Fedyna, Vitaliia; Kozak, Roksolana; Gladyshevskii, Roman

2014-12-01

A single crystal of the title compound, the ternary silicide digadolinium trirhenium penta-silicide, Gd2Re3Si5, was isolated from an alloy of nominal composition Gd20Re30Si50 synthesized by arc melting and investigated by X-ray single-crystal diffraction. Its crystal structure belongs to the U2Mn3Si5 structure type. All atoms in the asymmetric lie on special positions. The Gd site has site symmetry m..; the two Mn atoms have site symmetries m.. and 2.22; the three Si atoms have site symmetries m.., ..2 and 4.. . The coordination polyhedra of the Gd atoms have 21 vertices, while those of the Re atoms are cubo-octa-hedra and 13-vertex polyhedra. The Si atoms are arranged as tricapped trigonal prisms, bicapped square anti-prisms, or 11-vertex polyhedra. The crystal structure of the title compound is also related to the structure types CaBe2Ge2 and W5Si3. It can be represented as a stacking of Gd-centred polyhedra of composition [GdSi9]. The Re atoms form infinite chains with an Re-Re distance of 2.78163 (5) Å and isolated squares with an Re-Re distance of 2.9683 (6) Å.

Crystal structure of the ternary silicide Gd2Re3Si5

PubMed Central

Fedyna, Vitaliia; Kozak, Roksolana; Gladyshevskii, Roman

2014-01-01

A single crystal of the title compound, the ternary silicide digadolinium trirhenium penta­silicide, Gd2Re3Si5, was isolated from an alloy of nominal composition Gd20Re30Si50 synthesized by arc melting and investigated by X-ray single-crystal diffraction. Its crystal structure belongs to the U2Mn3Si5 structure type. All atoms in the asymmetric lie on special positions. The Gd site has site symmetry m..; the two Mn atoms have site symmetries m.. and 2.22; the three Si atoms have site symmetries m.., ..2 and 4.. . The coordination polyhedra of the Gd atoms have 21 vertices, while those of the Re atoms are cubo­octa­hedra and 13-vertex polyhedra. The Si atoms are arranged as tricapped trigonal prisms, bicapped square anti­prisms, or 11-vertex polyhedra. The crystal structure of the title compound is also related to the structure types CaBe2Ge2 and W5Si3. It can be represented as a stacking of Gd-centred polyhedra of composition [GdSi9]. The Re atoms form infinite chains with an Re—Re distance of 2.78163 (5) Å and isolated squares with an Re—Re distance of 2.9683 (6) Å. PMID:25552967

AFM Structural Characterization of Drinking Water Biofilm under Physiological Conditions

EPA Science Inventory

Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air...

Atomic structure of (111) SrTiO3/Pt interfaces

NASA Astrophysics Data System (ADS)

Schmidt, Steffen; Klenov, Dmitri O.; Keane, Sean P.; Lu, Jiwei; Mates, Thomas E.; Stemmer, Susanne

2006-03-01

Atomic resolution high-angle annular dark field (HAADF) imaging in scanning transmission electron microscopy was used to investigate the interface atomic structure of epitaxial, (111) oriented SrTiO3 films on epitaxial Pt electrodes grown on (0001) sapphire. The cube-on-cube orientation relationship of SrTiO3 on Pt was promoted by the use of a Ti adhesion layer underneath the Pt electrode. While a Ti-rich Pt surface was observed before SrTiO3 growth, HAADF images showed an atomically abrupt SrTiO3/Pt interface with no interfacial layers. The SrTiO3 films contained two twin variants that were related by a 180° rotation about the ⟨111⟩ surface normal. HAADF images showed two different interface atomic arrangements for the two twins. The role of Ti in promoting (111) epitaxy and the implications for the dielectric properties are discussed.

From toothpaste to topological insulators and materials for valleytronics: The journeys of fluorinated tin

NASA Astrophysics Data System (ADS)

Barraza-Lopez, Salvador; Rivero, Pablo; Yan, Jia-An; Garcia-Suarez, Victor Manuel; Ferrer, Jaime

2015-03-01

Tin fluoride has a vast literature. This material is stable in bulk form at room temperature and has commercial applications that include fluorinated toothpaste. Bulk tin fluoride has a pair of fluorine atoms bridging two tin atoms. In the recent past the electronic properties of 2D tin with honeycomb structure have been discussed thus generating a wealth of literature that emphasizes its non-topologically-trivial electronic properties due to the combination of a Dirac-like dispersion and a strong spin-orbit coupling given its large atomic mass. Nevertheless the stability of such freestanding structures has been contested recently. As it turns out, the most stable form of fluorinated tin does not possess a graphane-like structure either. In the most stable phase to be discussed here, fluorine atoms tilt away from (graphane-like) positions over/below tin atoms; in an atomistic arrangement similar to the one seen on their parent bulk structure. Electronic properties depend on atomistic coordination, and the most stable form of fluorinated tin does not possess non-trivial topological properties. Nevertheless it represents a new paradigm for valleytronics in 2D.

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.

Watching Silica's Dance: Imaging the Structure and Dynamics of the Atomic (Re-) Arrangements in 2D Glass

NASA Astrophysics Data System (ADS)

Muller, David

2014-03-01

Even though glasses are almost ubiquitous--in our windows, on our iPhones, even on our faces--they are also mysterious. Because glasses are notoriously difficult to study, basic questions like: ``How are the atoms arranged? Where and how do glasses break?'' are still under contention. We use aberration corrected transmission electron microscopy (TEM) to image the atoms in a new two-dimensional phase of silica glass - freestanding it becomes the world's thinnest pane of glass at only 3-atoms thick, and take a unique look into these questions. Using atom-by-atom imaging and spectroscopy, we are able to reconstruct the full structure and bonding of this 2D glass and identify it as a bi-tetrahedral layer of SiO2. Our images also strikingly resemble Zachariasen's original cartoon models of glasses, drawn in 1932. As such, our work realizes an 80-year-old vision for easily understandable glassy systems and introduces promising methods to test theoretical predictions against experimental data. We image atoms in the disordered solid and track their motions in response to local strain. We directly obtain ring statistics and pair distribution functions that span short-, medium-, and long-range order, and test these against long-standing theoretical predictions of glass structure and dynamics. We use the electron beam to excite atomic rearrangements, producing surprisingly rich and beautiful videos of how a glass bends and breaks, as well as the exchange of atoms at a solid/liquid interface. Detailed analyses of these videos reveal a complex dance of elastic and plastic deformations, phase transitions, and their interplay. These examples illustrate the wide-ranging and fundamental materials physics that can now be studied at atomic-resolution via transmission electron microscopy of two-dimensional glasses. Work in collaboration with: S. Kurasch, U. Kaiser, R. Hovden, Q. Mao, J. Kotakoski, J. S. Alden, A. Shekhawat, A. A. Alemi, J. P. Sethna, P. L. McEuen, A.V. Krasheninnikov, A. Srivastava, V. Skakalova, J. C. Meyer, and J.H. Smet. This work was supported by the NSF through the Cornell Center for Materials Research (NSF DMR-1120296).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laskowski, Lukasz, E-mail: lukasz.laskowski@kik.pcz.pl; Laskowska, Magdalena, E-mail: magdalena.laskowska@onet.pl; Jelonkiewicz, Jerzy, E-mail: jerzy.jelonkiewicz@kik.pcz.pl

The SBA-15 silica thin films containing copper ions anchored inside channels via propyl phosphonate groups are investigated. Such materials were prepared in the form of thin films, with hexagonally arranged pores, laying rectilinear to the substrate surface. However, in the case of our thin films, their free standing form allowed for additional research possibilities, that are not obtainable for typical thin films on a substrate. The structural properties of the samples were investigated by X-ray reflectometry, atomic force microscopy (AFM) and transmission electron microscopy (TEM). The molecular structure was examined by Raman spectroscopy supported by numerical simulations. Magnetic measurements (SQUIDmore » magnetometry and EPR spectroscopy) showed weak antiferromagnetic interactions between active units inside silica channels. Consequently, the pores arrangement was determined and the process of copper ions anchoring by propyl phosphonate groups was verified in unambiguous way. Moreover, the type of interactions between magnetic atoms was determined. - Highlights: • Functionalized free-standing SBA-15 thin films were synthesized for a first time. • Thin films synthesis procedure was described in details. • Structural properties of the films were thoroughly investigated and presented. • Magnetic properties of the novel material was investigated and presented.« less

Silicene on Ag(1 1 1): Geometric and electronic structures of a new honeycomb material of Si

NASA Astrophysics Data System (ADS)

Takagi, Noriaki; Lin, Chun-Liang; Kawahara, Kazuaki; Minamitani, Emi; Tsukahara, Noriyuki; Kawai, Maki; Arafune, Ryuichi

2015-02-01

Silicene, a two-dimensional honeycomb sheet consisting of Si atoms, has attracted much attention as a new low-dimensional material because it gains various fascinating characteristics originating from the combination of Dirac fermion features with spin-orbit coupling. The novel properties such as the quantum spin Hall effect and the compatibility with the current Si device technologies have fueled competition to realize the silicene. This review article focuses on the geometric and electronic structures of silicene grown on Ag(1 1 1) investigated by scanning tunneling microcopy (STM), low energy electron diffraction (LEED) and density functional theory (DFT) calculations. The silicene on Ag(1 1 1) takes locally-buckled structure in which the Si atoms are displaced perpendicularly to the basal plane. As a result, several superstructures such as 4 × 4,√{ 13 } ×√{ 13 } R 13.9 °, 4 /√{ 3 } × 4 /√{ 3 } , and etc. emerge. The atomic arrangement of the 4 × 4 silicene has been determined by STM, DFT calculations and LEED dynamical analysis, while the other superstructures remain to be fully-resolved. In the 4 × 4 silicene, Si atoms are arranged to form a buckled honeycomb structure where six Si atoms of 18 Si atoms in the unit cell are displaced vertically. The displacements lead to the vertical shift of the substrate Ag atoms, indicating the non-negligible coupling at the interface between the silicene layer and the substrate. The interface coupling significantly modifies the electronic structure of the 4 × 4 silicene. No Landau level sequences were observed by scanning tunneling spectroscopy (STS) with magnetic fields applied perpendicularly to the sample surface. The DFT calculations showed that the π and π∗ bands derived from the Si 3pz are hybridized with the Ag electronic states, leading to the drastic modification in the band structure and then the absence of Dirac fermion features together with the two-dimensionality in the electronic states. These findings demonstrate that the strong coupling at the interface causes the symmetry breaking for the 4 × 4 silicene and as a result the disappearance of Dirac fermion features. The geometric and electronic structures of other superstructures are also discussed.

Crystal structure of the co-crystal fac-tri-aqua-tris(thio-cyanato-κN)iron(III)-2,3-di-methyl-pyrazine (1/3).

PubMed

Kucheriv, Olesia I; Shylin, Sergii I; Ilina, Tetiana A; Dechert, Sebastian; Gural'skiy, Il'ya A

2015-04-01

In the crystal of the title compound, [Fe(NCS)3(H2O)3]·3C6H8N2, the Fe(III) cation is located on a threefold rotation axis and is coordinated by three N atoms of the thiocyanate anions and three water mol-ecules in a fac arrangement, forming a slightly distorted N3O3 octa-hedron. Stabilization within the crystal structure is provided by O-H⋯N hydrogen bonds; the H atoms from coordinating water mol-ecules act as donors to the N atoms of guest 2,3-di-methyl-pyrazine mol-ecules, leading to a three-dimensional supra-molecular framework.

AFM Structural Characterization of Drinking Water Biofilm ...

EPA Pesticide Factsheets

Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

A Capped Dipeptide Which Simultaneously Exhibits Gelation and Crystallization Behavior.

PubMed

Martin, Adam D; Wojciechowski, Jonathan P; Bhadbhade, Mohan M; Thordarson, Pall

2016-03-08

Short peptides capped at their N-terminus are often highly efficient gelators, yet notoriously difficult to crystallize. This is due to strong unidirectional interactions within fibers, resulting in structure propagation only along one direction. Here, we synthesize the N-capped dipeptide, benzimidazole-diphenylalanine, which forms both hydrogels and single crystals. Even more remarkably, we show using atomic force microscopy the coexistence of these two distinct phases. We then use powder X-ray diffraction to investigate whether the single crystal structure can be extrapolated to the molecular arrangement within the hydrogel. The results suggest parallel β-sheet arrangement as the dominant structural motif, challenging existing models for gelation of short peptides, and providing new directions for the future rational design of short peptide gelators.

Effect of the interface on the mechanical properties and thermal conductivity of bismuth telluride films

NASA Astrophysics Data System (ADS)

Lai, Tang-Yu; Wang, Kuan-Yu; Fang, Te-Hua; Huang, Chao-Chun

2018-02-01

Bismuth telluride (Bi2Te3) is a type of thermoelectric material used for energy generation that does not cause pollution. Increasing the thermoelectric conversion efficiency (ZT) is one of the most important steps in the development of thermoelectric components. In this study, we use molecular dynamics to investigate the mechanical properties and thermal conductivity of quintuple layers of Bi2Te3 nanofilms with different atomic arrangements at the interface and study the effects of varying layers, angles, and grain boundaries. The results indicate that the Bi2Te3 nanofilm perfect substrate has the ideal Young’s modulus and thermal conductivity, and the maximum yield stress is observed for a thickness of ∼90 Å. As the interface changed, the structural disorder of atomic arrangement affected the mechanical properties; moreover, the phonons encounter lattice disordered atomic region will produce scattering reduce heat conduction. The results of this investigation are helpful for the application of Bi2Te3 nanofilms as thermoelectric materials.

CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins

PubMed Central

Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

2014-01-01

Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function. PMID:24748753

Small size yet big action: a simple sulfate anion templated a discrete 78-nuclearity silver sulfur nanocluster with a multishell structure.

PubMed

Cheng, Li-Ping; Wang, Zhi; Wu, Qiao-Yu; Su, Hai-Feng; Peng, Tao; Luo, Geng-Geng; Li, Yan-An; Sun, Di; Zheng, Lan-Sun

2018-03-07

A discrete 78-nucleus silver-sulfur nanocluster with a sulfate-centered multishell structure was isolated and characterized. Its crystal structure revealed 18 and 60 Ag atoms in the inner and outer shell, respectively. The inner shell of 18-nuclearity Ag atoms is a very rare convex polyhedron featuring an elongated triangular orthobicupola. The incorporation of a sulfate anion and multishell arrangement in the nanocluster led to a dramatic decrease in the band gap (E g = 1.40 eV). Our study showed that simple anions can also induce the formation of high-nuclearity silver clusters with excellent optical properties.

Structure formation in Ag-X (X = Au, Cu) alloys synthesized far-from-equilibrium

NASA Astrophysics Data System (ADS)

Elofsson, V.; Almyras, G. A.; Lü, B.; Garbrecht, M.; Boyd, R. D.; Sarakinos, K.

2018-04-01

We employ sub-monolayer, pulsed Ag and Au vapor fluxes, along with deterministic growth simulations, and nanoscale probes to study structure formation in miscible Ag-Au films synthesized under far-from-equilibrium conditions. Our results show that nanoscale atomic arrangement is primarily determined by roughness build up at the film growth front, whereby larger roughness leads to increased intermixing between Ag and Au. These findings suggest a different structure formation pathway as compared to the immiscible Ag-Cu system for which the present study, in combination with previously published data, reveals that no significant roughness is developed, and the local atomic structure is predominantly determined by the tendency of Ag and Cu to phase-separate.

Identification of Complex Carbon Nanotube Structures

NASA Technical Reports Server (NTRS)

Han, Jie; Saini, Subhash (Technical Monitor)

1998-01-01

A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

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.

Crystallinity of tellurium capping and epitaxy of ferromagnetic topological insulator films on SrTiO 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Jihwey; Soh, Yeong-Ah; Aeppli, Gabriel

2015-06-30

Thin films of topological insulators are often capped with an insulating layer since topological insulators are known to be fragile to degradation. However, capping can hinder the observation of novel transport properties of the surface states. To understand the influence of capping on the surface states, it is crucial to understand the crystal structure and the atomic arrangement at the interfaces. Here, we use x-ray diffraction to establish the crystal structure of magnetic topological insulator Cr-doped (Bi,Sb) 2Te 3 (CBST) films grown on SrTiO 3 (1 1 1) substrates with and without a Te capping layer. We find that bothmore » the film and capping layer are single crystal and that the crystal quality of the film is independent of the presence of the capping layer, but that x-rays cause sublimation of the CBST film, which is prevented by the capping layer. Our findings show that the different transport properties of capped films cannot be attributed to a lower crystal quality but to a more subtle effect such as a different electronic structure at the interface with the capping layer. Our results on the crystal structure and atomic arrangements of the topological heterostructure will enable modelling the electronic structure and design of topological heterostructures.« less

Fullerenes formation in flames

NASA Technical Reports Server (NTRS)

Howard, Jack B.

1993-01-01

Fullerenes are composed of carbon atoms arranged in approximately spherical or ellipsoidal cages resembling the geodesic domes designed by Buckminster Fuller, after whom the molecules were named. The approximately spherical fullerene, which resembles a soccer ball and contains sixty atoms (C60), is called buckminsterfullerene. The fullerene containing seventy carbon atoms (C70) is approximately ellipsoidal, similar to a rugby ball. Fullerenes were first detected in 1985, in carbon vapor produced by laser evaporation of graphite. The closed shell structure, which has no edge atoms vulnerable to reaction, was proposed to explain the observed high stability of certain carbon clusters relative to that of others at high temperatures and in the presence of an oxidizing gas.

First-principles study of the solid solution of hydrogen in lanthanum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schoellhammer, Gunther; Herzig, Peter; Wolf, Walter

2011-09-01

Results from first-principles investigations of the energetical, structural, electronic, and vibrational properties of model structures probing the metal-rich region of the lanthanum-hydrogen system, i.e., the region of the solid solution of hydrogen in lanthanum, are presented. We have studied the site preference and the ordering tendency of hydrogen atoms interstitially bonded in close-packed lanthanum. Spatially separated hydrogen atoms have turned out to exhibit an energetical preference for the occupation of octahedral interstitial sites at low temperature. Indications for a reversal of the site preference in favor of the occupation of tetrahedral interstitial sites at elevated temperature have been found. Linearmore » arrangements consisting of pairs of octahedrally and/or tetrahedrally coordinated hydrogen atoms collinearly bonded to a central lanthanum atom have turned out to be energetically favorable structure elements. Further stabilization is achieved if such hydrogen pairs are in turn linked together so that extended chains of La-H bonds are formed. Pair formation and chain linking counteract the energetical preference for octahedral coordination observed for separated hydrogen atoms.« less

Free RCK arrangement in Kch, a putative escherichia coli potassium channel, as suggested by electron crystallography.

PubMed

Kuang, Qie; Purhonen, Pasi; Jegerschöld, Caroline; Koeck, Philip J B; Hebert, Hans

2015-01-06

The ligand-gated potassium channels are stimulated by various kinds of messengers. Previous studies showed that ligand-gated potassium channels containing RCK domains (the regulator of the conductance of potassium ion) form a dimer of tetramer structure through the RCK octameric gating ring in the presence of detergent. Here, we have analyzed the structure of Kch, a channel of this type from Escherichia coli, in a lipid environment using electron crystallography. By combining information from the 3D map of the transmembrane part of the protein and docking of an atomic model of a potassium channel, we conclude that the RCK domains face the solution and that an RCK octameric gating ring arrangement does not form under our crystallization condition. Our findings may be applied to other potassium channels that have an RCK gating ring arrangement. Copyright © 2015 Elsevier Ltd. All rights reserved.

Photoelectron Holographic Atomic Arrangement Imaging of Cleaved Bimetal-intercalated Graphite Superconductor Surface

PubMed Central

Matsui, Fumihiko; Eguchi, Ritsuko; Nishiyama, Saki; Izumi, Masanari; Uesugi, Eri; Goto, Hidenori; Matsushita, Tomohiro; Sugita, Kenji; Daimon, Hiroshi; Hamamoto, Yuji; Hamada, Ikutaro; Morikawa, Yoshitada; Kubozono, Yoshihiro

2016-01-01

From the C 1s and K 2p photoelectron holograms, we directly reconstructed atomic images of the cleaved surface of a bimetal-intercalated graphite superconductor, (Ca, K)C8, which differed substantially from the expected bulk crystal structure based on x-ray diffraction (XRD) measurements. Graphene atomic images were collected in the in-plane cross sections of the layers 3.3 Å and 5.7 Å above the photoelectron emitter C atom and the stacking structures were determined as AB- and AA-type, respectively. The intercalant metal atom layer was found between two AA-stacked graphenes. The K atomic image revealing 2 × 2 periodicity, occupying every second centre site of C hexagonal columns, was reconstructed, and the Ca 2p peak intensity in the photoelectron spectra of (Ca, K)C8 from the cleaved surface was less than a few hundredths of the K 2p peak intensity. These observations indicated that cleavage preferentially occurs at the KC8 layers containing no Ca atoms. PMID:27811975

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

DOE PAGES

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs; ...

2018-05-25

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural Network Approach for Characterizing Structural Transformations by X-Ray Absorption Fine Structure Spectroscopy

NASA Astrophysics Data System (ADS)

Timoshenko, Janis; Anspoks, Andris; Cintins, Arturs; Kuzmin, Alexei; Purans, Juris; Frenkel, Anatoly I.

2018-06-01

The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its in situ changes directly from the x-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from a body-centered to a face-centered cubic arrangement of iron atoms. This method is attractive for a broad range of materials and experimental conditions.

Discovery of superconductivity in quasicrystal.

PubMed

Kamiya, K; Takeuchi, T; Kabeya, N; Wada, N; Ishimasa, T; Ochiai, A; Deguchi, K; Imura, K; Sato, N K

2018-01-11

Superconductivity is ubiquitous as evidenced by the observation in many crystals including carrier-doped oxides and diamond. Amorphous solids are no exception. However, it remains to be discovered in quasicrystals, in which atoms are ordered over long distances but not in a periodically repeating arrangement. Here we report electrical resistivity, magnetization, and specific-heat measurements of Al-Zn-Mg quasicrystal, presenting convincing evidence for the emergence of bulk superconductivity at a very low transition temperature of [Formula: see text] K. We also find superconductivity in its approximant crystals, structures that are periodic, but that are very similar to quasicrystals. These observations demonstrate that the effective interaction between electrons remains attractive under variation of the atomic arrangement from periodic to quasiperiodic one. The discovery of the superconducting quasicrystal, in which the fractal geometry interplays with superconductivity, opens the door to a new type of superconductivity, fractal superconductivity.

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

Self-consistent self-interaction corrected density functional theory calculations for atoms using Fermi-Löwdin orbitals: Optimized Fermi-orbital descriptors for Li-Kr

NASA Astrophysics Data System (ADS)

Kao, Der-you; Withanage, Kushantha; Hahn, Torsten; Batool, Javaria; Kortus, Jens; Jackson, Koblar

2017-10-01

In the Fermi-Löwdin orbital method for implementing self-interaction corrections (FLO-SIC) in density functional theory (DFT), the local orbitals used to make the corrections are generated in a unitary-invariant scheme via the choice of the Fermi orbital descriptors (FODs). These are M positions in 3-d space (for an M-electron system) that can be loosely thought of as classical electron positions. The orbitals that minimize the DFT energy including the SIC are obtained by finding optimal positions for the FODs. In this paper, we present optimized FODs for the atoms from Li-Kr obtained using an unbiased search method and self-consistent FLO-SIC calculations. The FOD arrangements display a clear shell structure that reflects the principal quantum numbers of the orbitals. We describe trends in the FOD arrangements as a function of atomic number. FLO-SIC total energies for the atoms are presented and are shown to be in close agreement with the results of previous SIC calculations that imposed explicit constraints to determine the optimal local orbitals, suggesting that FLO-SIC yields the same solutions for atoms as these computationally demanding earlier methods, without invoking the constraints.

Electronic Structure of Two-Dimensional Hydrocarbon Networks of sp2 and sp3 C Atoms

NASA Astrophysics Data System (ADS)

Fujii, Yasumaru; Maruyama, Mina; Wakabayashi, Katsunori; Nakada, Kyoko; Okada, Susumu

2018-03-01

Based on density functional theory with the generalized gradient approximation, we have investigated the geometric and electronic structures of two-dimensional hexagonal covalent networks consisting of oligoacenes and fourfold coordinated hydrocarbon atoms, which are alternately arranged in a hexagonal manner. All networks were semiconductors with a finite energy gap at the Γ point, which monotonically decreased with the increase of the oligoacene length. As a result of a Kagome network of oligoacene connected through sp3 C atoms, the networks possess peculiar electron states in their valence and conduction bands, which consist of a flat dispersion band and a Dirac cone. The total energy of the networks depends on the oligoacene length and has a minimum for the network comprising naphthalene.

Atomic structures of Ruddlesden-Popper faults in LaCoO3/SrRuO3 multilayer thin films induced by epitaxial strain

NASA Astrophysics Data System (ADS)

Wang, Wei; Zhang, Hui; Shen, Xi; Guan, Xiangxiang; Yao, Yuan; Wang, Yanguo; Sun, Jirong; Yu, Richeng

2018-05-01

In this paper, scanning transmission electron microscopy is used to study the microstructures of the defects in LaCoO3/SrRuO3 multilayer films grown on the SrTiO3 substrates, and these films have different thickness of SrRuO3 (SRO) layers. Several types of Ruddlesden-Popper (R.P.) faults at an atomic level are found, and these chemical composition fluctuations in the growth process are induced by strain fields originating from the film-film and film-substrate lattice mismatches. Furthermore, we propose four types of structural models based on the atomic arrangements of the R.P. planar faults, which severely affect the functional properties of the films.

Atomic Resolution Study of the Interfacial Bonding at Si3N4/CeO2-δ Grain Boundaries

NASA Astrophysics Data System (ADS)

Klie, Robert F.; Walkosz, Weronika; Ogut, Serdar; Borisevich, A.; Becher, Paul F.; Pennycook, Steve J.; Idrobo, Juan C.

2008-03-01

Using a combination of atomic resolution Z-contrast imaging and electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope, we examine the atomic and electronic structures at the interface between Si3N4 (10 10) and CeO2-δ inter-granular film (IGF). Ce atoms are observed to segregate to the interface in a two-layer periodic arrangement, which is significantly different compared to the structure observed in a previous study. Our EELS experiments show that (i) oxygen is present at the interface in direct contact with the terminating Si3N4 open-ring structures, (ii) the Ce valence state changes from +3 to +4 in going from the interface into the IGF, and (iii) while the N concentration decreases away from the Si3N4 grains into the IGF, the Si concentration remains uniform across the whole width of the IGF. Possible reasons for these observed structural and electronic variations at the interface and their implications for future studies on Si3N4/rare-earth oxide interfaces are briefly discussed.

Annealing induced atomic rearrangements on (Ga,In) (N,As) probed by hard X-ray photoelectron spectroscopy and X-ray absorption fine structure.

PubMed

Ishikawa, Fumitaro; Higashi, Kotaro; Fuyuno, Satoshi; Morifuji, Masato; Kondow, Masahiko; Trampert, Achim

2018-04-13

We study the effects of annealing on (Ga 0.64 ,In 0.36 ) (N 0.045 ,As 0.955 ) using hard X-ray photoelectron spectroscopy and X-ray absorption fine structure measurements. We observed surface oxidation and termination of the N-As bond defects caused by the annealing process. Specifically, we observed a characteristic chemical shift towards lower binding energies in the photoelectron spectra related to In. This phenomenon appears to be caused by the atomic arrangement, which produces increased In-N bond configurations within the matrix, as indicated by the X-ray absorption fine structure measurements. The reduction in the binding energies of group-III In, which occurs concomitantly with the atomic rearrangements of the matrix, causes the differences in the electronic properties of the system before and after annealing.

The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies.

PubMed

Hawelek, L; Brodka, A; Dore, J C; Honkimaki, V; Burian, A

2013-11-13

The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

Structural building principles of complex face-centered cubic intermetallics.

PubMed

Dshemuchadse, Julia; Jung, Daniel Y; Steurer, Walter

2011-08-01

Fundamental structural building principles are discussed for all 56 known intermetallic phases with approximately 400 or more atoms per unit cell and space-group symmetry F43m, Fd3m, Fd3, Fm3m or Fm3c. Despite fundamental differences in chemical composition, bonding and electronic band structure, their complex crystal structures show striking similarities indicating common building principles. We demonstrate that the structure-determining elements are flat and puckered atomic {110} layers stacked with periodicities 2p. The atoms on this set of layers, which intersect each other, form pentagon face-sharing endohedral fullerene-like clusters arranged in a face-centered cubic packing (f.c.c.). Due to their topological layer structure, all these crystal structures can be described as (p × p × p) = p(3)-fold superstructures of a common basic structure of the double-diamond type. The parameter p, with p = 3, 4, 7 or 11, is determined by the number of layers per repeat unit and the type of cluster packing, which in turn are controlled by chemical composition.

12. General Arrangement Plan, Building 189D, U.S. Atomic Energy Commission, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. General Arrangement Plan, Building 189-D, U.S. Atomic Energy Commission, General Electric Company, Dwg. No. H-1-11068, 1958. - D-Reactor Complex, Deaeration Plant-Refrigeration Buildings, Area 100-D, Richland, Benton County, WA

Nanoscale structure in AgSbTe2 determined by diffuse elastic neutron scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Specht, Eliot D; Ma, Jie; Delaire, Olivier A

2015-01-01

Diffuse elastic neutron scattering measurements confirm that AgSbTe2 has a hierarchical structure, with defects on length scales from nanometers to microns. While scattering from mesoscale structure is consistent with previously-proposed structures in which Ag and Sb order on a NaCl lattice, more diffuse scattering from nanoscale structure suggests a structural rearrangement in which hexagonal layers form a combination of (ABC), (ABA), and (AAB) stacking sequences. The AgCrSe2 structure is the best-fitting model for the local atomic arrangements.

Biomolecular Chemistry of Isopropyl Fibrates

PubMed Central

Rath, Niharika; Kotheimer, Amenda; Miller, Chad; Zeller, Matthias; Rath, Nigam P.

2012-01-01

Isopropyl 2-[4-(4-chlorobenzoyl)-phenoxy]-2-methylpropanoic acid and isopropyl 2-(4-chlorophenoxy)-2-methylpropanoate, also known as fenofibrate and isopropyl clofibrate, are hypolipidemic agents of the fibrate family. In a previously reported triclinic structure of fenofibrate (polymorph I) the methyl groups of the isopropyl moiety (iPr) are located symmetrically about the carboxylate group. We report a new monoclinic form (polymorph II) of fenofibrate and a first structural description of isopropyl clofibrate, and in these the methyl groups are placed asymmetrically about the carboxylate group. In particular the dihedral (torsion) angle between the hydrogen atom on the secondary C and the C atom of the carboxyl group makes a 2.74° angle about the ester O-C bond in the symmetric fenofibrate structure of polymorph I, whereas the same dihedral angle is 45.94° in polymorph II and -30.9° in the crystal structure of isopropyl clofibrate. Gas phase DFT geometry minimizations of fenofibrate and isopropyl clofibrate result in lowest energy conformations for both molecules with a value of about ± 30° for this same angle between the O=C-O-C plane and the C-H bond of the iPr group. A survey of crystal structures containing an iPr ester group reveals that the asymmetric conformation is predominant. Although the hydrogen atom on the secondary C atom of the isopropyl group is located at a comparable distance from the carbonyl oxygen in the symmetric and asymmetric fenofibrate (2.52 and 2.28 Å) and the isopropyl clofibrate (2.36 Å) structures, this hydrogen atom participates in a puckered five membered ring arrangement in the latter two that is unlike the planar arrangement found in symmetric fenofibrate (polymorph I). Polar molecular surface area (PSA) values indicate fenofibrate and isopropyl clofibrate are less able to act as acceptors of hydrogen bonds than their corresponding acid derivatives. Surface area calculations show dynamic polar molecular surface area (PSAd) values of the iPr esters of the fibrates are lower than those of their acids, implying that the fibrates have better membrane permeability and a higher absorbability and hence are better prodrugs when these agents need to be orally administered. PMID:22246648

Doping of Semiconducting Atomic Chains

NASA Technical Reports Server (NTRS)

Toshishige, Yamada; Kutler, Paul (Technical Monitor)

1997-01-01

Due to the rapid progress in atom manipulation technology, atomic chain electronics would not be a dream, where foreign atoms are placed on a substrate to form a chain, and its electronic properties are designed by controlling the lattice constant d. It has been shown theoretically that a Si atomic chain is metallic regardless of d and that a Mg atomic chain is semiconducting or insulating with a band gap modified with d. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along the chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of dopant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Atomically resolved scanning force studies of vicinal Si(111)

NASA Astrophysics Data System (ADS)

Pérez León, Carmen; Drees, Holger; Wippermann, Stefan Martin; Marz, Michael; Hoffmann-Vogel, Regina

2017-06-01

Well-ordered stepped semiconductor surfaces attract intense attention owing to the regular arrangements of their atomic steps that makes them perfect templates for the growth of one-dimensional systems, e.g., nanowires. Here, we report on the atomic structure of the vicinal Si (111 ) surface with 10∘ miscut investigated by a joint frequency-modulation scanning force microscopy (FM-SFM) and ab initio approach. This popular stepped surface contains 7 ×7 -reconstructed terraces oriented along the Si (111 ) direction, separated by a stepped region. Recently, the atomic structure of this triple step based on scanning tunneling microscopy (STM) images has been subject of debate. Unlike STM, SFM atomic resolution capability arises from chemical bonding of the tip apex with the surface atoms. Thus, for surfaces with a corrugated density of states such as semiconductors, SFM provides complementary information to STM and partially removes the dependency of the topography on the electronic structure. Our FM-SFM images with unprecedented spatial resolution on steps coincide with the model based on a (7 7 10 ) orientation of the surface and reveal structural details of this surface. Two different FM-SFM contrasts together with density functional theory calculations explain the presence of defects, buckling, and filling asymmetries on the surface. Our results evidence the important role of charge transfers between adatoms, restatoms, and dimers in the stabilisation of the structure of the vicinal surface.

The ground state of two-dimensional silicon

NASA Astrophysics Data System (ADS)

Borlido, Pedro; Rödl, Claudia; Marques, Miguel A. L.; Botti, Silvana

2018-07-01

We perform ab initio structure-prediction calculations of the low-energy crystal structures of two-dimensional silicon. Besides the well-known silicene and a few other allotropes proposed earlier in the literature, we discover a wealth of new phases with interesting properties. In particular, we find that the ground state of two-dimensional silicon is an unreported structure formed by a honeycomb lattice with dumbbell atoms arranged in a zigzag pattern. This material, that we call zigzag dumbbell silicene, is 218 meV/atom more stable than silicene and displays a quasi-direct band gap of around 1.11 eV, with a very dispersive electron band. These properties should make it easier to synthesize than silicene and interesting for a wealth of opto-electronic applications.

The atomic arrangement of iimoriite-(Y), Y2(SiO4)(CO3)

USGS Publications Warehouse

Hughes, J.M.; Foord, E.E.; Jai-Nhuknan, J.; Bell, J.M.

1996-01-01

Iimoriite-(Y) from Bokan Mountain, Prince of Wales Island, Alaska has been studied using single-crystal X-ray-diffraction techniques. The mineral, ideally Y2(SiO4)(CO3), crystallizes in space group P1, with a 6.5495(13), b 6.6291(14), c 6.4395(11)A??, ?? 116.364(15), ?? 92.556(15) and ?? 95.506(17)??. The atomic arrangement has been solved and refined to an R value of 0.019. The arrangement of atoms consists of alternating (011) slabs of orthosilicate groups and carbonate groups, with no sharing of oxygen atoms between anionic complexes in adjacent slabs. Y1 atoms separate adjacent tetrahedra along [100] within the orthosilicate slab, and Y2 atoms separate adjacent carbonate groups along [100] within the carbonate slab. Adjacent orthosilicate and carbonate slabs are linked in (100) by bonding Y atoms from each slab to oxygen atoms of adjacent slabs, in the form of YO8 polyhedra. The Y1 atoms exist in Y12O14 dimers in the orthosilicate slab, and the Y2 atoms exist in continuous [011] ribbons of edge-sharing Y2O8 polyhedra in the carbonate slab.

Structure of Se-Te glasses studied using neutron, X-ray diffraction and reverse Monte Carlo modelling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Itoh, Keiji, E-mail: itoh@okayama-u.ac.jp; Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494

Pulsed neutron diffraction and synchrotron X-ray diffraction measurements were performed on Se{sub 100-x}Te{sub x} bulk glasses with x=10, 20, 30 and 40. The coordination numbers obtained from the diffraction results demonstrate that Se and Te atoms are twofold coordinated and the glass structure is formed by the chain network. The three-dimensional structure model for Se{sub 60}Te{sub 40} glass obtained by using reverse Monte Carlo modelling shows that the alternating arrangements of Se and Te atoms compose the major part of the chain clusters but several other fragments such as Se{sub n} chains and Te-Te dimers are also present in largemore » numbers. The chain clusters have geometrically disordered forms and the interchain atomic order is different from those in the crystal structures of trigonal Se and trigonal Te. - Graphical abstract: Coordination environment in Se{sub 60}Te{sub 40} glass.« less

Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

NASA Astrophysics Data System (ADS)

Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

2017-05-01

Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

Atomic and electronic structure of Mo6S9-xIx nanowires

NASA Astrophysics Data System (ADS)

Meden, A.; Kodre, A.; Padeznik Gomilsek, J.; Arcon, I.; Vilfan, I.; Vrbanic, D.; Mrzel, A.; Mihailovic, D.

2005-09-01

Moybdenum-based subnanometre diameter nanowires are easy to synthesize and disperse, and they exhibit a variety of functional properties in which they are superior to other one-dimensional materials. However, further progress in the understanding of physical properties and the development of new and specific applications have so far been impeded by the fact that their structure was not accurately known. Here we report on a combination of systematic x-ray diffraction and extended x-ray absorption fine structure experiments, and first-principles theoretical structure calculations, which are used to determine the atomic skeletal structure of individual Mo6S9-xIx (MoSIx) nanowires, their packing arrangement within bundles and their electronic band structure. From this work we conclude that the variations in functional properties appear to arise from different stoichiometry, not skeletal structure. A supplementary data file is available from http://stacks.iop.org/0957-4484/16/1578

Inherent structures of crystalline pentacene

NASA Astrophysics Data System (ADS)

Della Valle, Raffaele Guido; Venuti, Elisabetta; Brillante, Aldo; Girlando, Alberto

2003-01-01

Using a quasi-Monte Carlo scheme, we search the potential energy surface of crystalline pentacene to sample its local minima, which represent the "inherent" structures, i.e., the possible configurations of mechanical equilibrium. The system is described in terms of rigid molecules interacting through a standard atom-atom potential model. Several hundreds of distinct minima are encountered, with a surprising variety of structural arrangements. We find that deep minima are easily accessible because they exhibit a favorable energy distribution and their attraction basins tend to be wide. Thanks to these features of the potential surface, the localization the global minimum becomes entirely feasible, allowing reliable a priori predictions of the crystallographic structures. The results for pentacene are very satisfactory. In fact, the two deepest minima correspond to the structures of the two known experimental polymorphs, which are described correctly. Further polymorphs are also likely to exist.

Low energy electron diffraction and low energy electron microscopy microspot I/V analysis of the (4 x 4)O structure on Ag(111): surface oxide or reconstruction?

PubMed

Reichelt, R; Günther, S; Wintterlin, J; Moritz, W; Aballe, L; Mentes, T O

2007-10-07

A low energy electron diffraction (LEED) I/V analysis was performed of the (4 x 4) oxygen structure on Ag(111). Two data sets were used, one recorded with a conventional LEED system and a second with a low energy electron microscope (LEEM). The data sets agree well with each other, demonstrating that I/V structure analyses can be performed with the same quality with LEEM as with conventional LEED. The structure obtained confirms the recently proposed model that involves a reconstruction of the Ag(111) surface. Previous models based on a thin layer of Ag(2)O that had been accepted for more than 30 years are disproved. The reconstruction model contains two units of six triangularly arranged Ag atoms and a stacking fault in one half of the unit cell. The six O atoms per unit cell occupy sites in the trenches between the Ag(6) triangles. Small lateral displacements of the Ag atoms lift the mirror symmetry of the structure, leading to two nonequivalent groups of O atoms. The atoms of both groups are located approximately 0.5 Angstrom below the top Ag layer, on fourfold positions with respect to the top layer Ag atoms. Ag-O distances between 2.05 and 2.3 Angstrom are found. The oxygen atoms exhibit large static or dynamic displacements of up to 0.3 Angstrom at 300 K.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolmatov, Dima; Zhernenkov, Mikhail; Zav’yalov, Dmitry

Here in this work we report on terahertz phononic excitations in 2D gold nanoparticle arrays in a water matrix through a series of large-scale molecular dynamics simulations. For the first time, we observe acoustic Dirac-like crossings in H (H 2O) atomic (molecular) networks which emerge due to an intraband phononic scattering. These crossings are the phononic fingerprints of ice-like arrangements of H (H 2O) atomic (molecular) networks at nanometer scale. We reveal how phononic excitations in metallic nanoparticles and the water matrix reciprocally impact on one another providing the mechanism for the THz phononics manipulation via structural engineering. In addition,more » we show that by tuning the arrangement of 2D gold nanoparticle assemblies the Au phononic polarizations experience sub-terahertz hybridization (Kohn anomaly) due to surface electron-phonon relaxation processes. This opens the way for the sound control and manipulation in soft matter metamaterials at nanoscale.« less

Scalable quantum computer architecture with coupled donor-quantum dot qubits

DOEpatents

Schenkel, Thomas; Lo, Cheuk Chi; Weis, Christoph; Lyon, Stephen; Tyryshkin, Alexei; Bokor, Jeffrey

2014-08-26

A quantum bit computing architecture includes a plurality of single spin memory donor atoms embedded in a semiconductor layer, a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, wherein a first voltage applied across at least one pair of the aligned quantum dot and donor atom controls a donor-quantum dot coupling. A method of performing quantum computing in a scalable architecture quantum computing apparatus includes arranging a pattern of single spin memory donor atoms in a semiconductor layer, forming a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, applying a first voltage across at least one aligned pair of a quantum dot and donor atom to control a donor-quantum dot coupling, and applying a second voltage between one or more quantum dots to control a Heisenberg exchange J coupling between quantum dots and to cause transport of a single spin polarized electron between quantum dots.

Quantitative Phase Analysis of Plasma-Treated High-Silica Materials

NASA Astrophysics Data System (ADS)

Kosmachev, P. V.; Abzaev, Yu. A.; Vlasov, V. A.

2018-06-01

The paper presents the X-ray diffraction (XRD) analysis of the crystal structure of SiO2 in two modifications, namely quartzite and quartz sand before and after plasma treatment. Plasma treatment enables the raw material to melt and evaporate after which the material quenches and condenses to form nanoparticles. The Rietveld refinement method is used to identify the lattice parameters of SiO2 phases. It is found that after plasma treatment SiO2 oxides are in the amorphous state, which are modeled within the microcanonical ensemble. Experiments show that amorphous phases are stable, and model X-ray reflection intensities approximate the experimental XRD patterns with fine precision. Within the modeling, full information is obtained for SiO2 crystalline and amorphous phases, which includes atom arrangement, structural parameters, atomic population of silicon and oxygen atoms in lattice sites.

[7,13-Bis(2-aminobenzyl)-1,4,10-trioxa-7,13-diazacyclopentadecane]diisothiocyanatobarium(II).

PubMed

Avecilla, Fernando; Esteban, David; Platas-Iglesias, Carlos; De Blas, Andres; Rodríguez-Blas, Teresa

2003-01-01

The X-ray crystal structure of the title complex, [Ba(NCS)(2)(C(24)H(36)N(4)O(3))], indicates that the Ba(II) cation is nine-coordinate in the solid state, being fully encapsulated by the organic receptor ligand. The receptor adopts a syn arrangement, with both pendant arms oriented on the same side of the crown moiety. The distance between the two amine N atoms is 3.911 (12) A, while the pivotal N atoms are 5.322 (10) A apart.

Superconductivity of ternary silicide with the AlB(2)-type structure Sr(Ga(0.37),Si(0.63))(2).

PubMed

Imai, M; Abe, E; Ye, J; Nishida, K; Kimura, T; Honma, K; Abe, H; Kitazawa, H

2001-08-13

A ternary silicide Sr(Ga(0.37),Si(0.63))(2) was synthesized by a floating zone method. Electron diffraction and powder x-ray diffraction measurements indicate that the silicide has the AlB(2)-type structure with the lattice constants of a = 4.1427(6) A and c = 4.7998(9) A, where Si and Ga atoms are arranged in a chemically disordered honeycomb lattice and Sr atoms are inercalated between them. The silicide is isostructural with the high-temperature superconductor MgB(2) reported recently. Electrical resistivity and dc magnetization measurements revealed that it is a type-II superconductor with onset temperature of 3.5 K.

Topological defect formation in rotating binary dipolar Bose–Einstein condensate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xiao-Fei, E-mail: xfzhang@ntsc.ac.cn; University of Chinese Academy of Sciences, Beijing 100049; Department of Engineering Science, University of Electro-Communications, Tokyo 182-8585

We investigate the topological defects and spin structures of a rotating binary Bose–Einstein condensate, which consists of both dipolar and scalar bosonic atoms confined in spin-dependent optical lattices, for an arbitrary orientation of the dipoles with respect to their plane of motion. Our results show that the tunable dipolar interaction, especially the orientation of the dipoles, can be used to control the direction of stripe phase and its related half-vortex sheets. In addition, it can also be used to obtain a regular arrangement of various topological spin textures, such as meron, circular and cross disgyration spin structures. We point outmore » that such topological defects and regular arrangement of spin structures arise primarily from the long-range and anisotropic nature of dipolar interaction and its competition with the spin-dependent optical lattices and rotation. - Highlights: • Effects of both strength and orientation of the dipoles are discussed. • Various topological defects can be formed in different parameter regions. • Present one possible way to obtain regular arrangements of spin textures.« less

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms

PubMed Central

Olson, Wilma K.

2014-01-01

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides. PMID:24791158

Synthesis, Structure, Te Alloying, and Physical Properties of CuSbS 2

DOE PAGES

Hobbis, Dean; Wei, Kaya; Wang, Hsin; ...

2017-10-30

Materials with very low thermal conductivities continue to be of interest for a variety of applications. In this paper, we synthesized CuSbS 2 employing a mechanical alloying technique in order to investigate its physical properties. The trigonal pyramid arrangement of the S atoms around the Sb atoms allows for lone-pair electron formation that results in very low thermal conductivity. Finally, in addition to thermal properties, the structural, electrical, and optical properties, as well as compositional stability measurements, are also discussed. CuSbS 1.8Te 0.2 was similarly synthesized and characterized in order to compare its structural and transport properties with that ofmore » CuSbS 2, in addition to investigating the effect of Te alloying on these properties.« less

Synthesis, Structure, Te Alloying, and Physical Properties of CuSbS 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hobbis, Dean; Wei, Kaya; Wang, Hsin

Materials with very low thermal conductivities continue to be of interest for a variety of applications. In this paper, we synthesized CuSbS 2 employing a mechanical alloying technique in order to investigate its physical properties. The trigonal pyramid arrangement of the S atoms around the Sb atoms allows for lone-pair electron formation that results in very low thermal conductivity. Finally, in addition to thermal properties, the structural, electrical, and optical properties, as well as compositional stability measurements, are also discussed. CuSbS 1.8Te 0.2 was similarly synthesized and characterized in order to compare its structural and transport properties with that ofmore » CuSbS 2, in addition to investigating the effect of Te alloying on these properties.« less

Structure of the Si(111)-(5×2)-Au Surface

NASA Astrophysics Data System (ADS)

Abukawa, Tadashi; Nishigaya, Yoshiki

2013-01-01

The structure of the Si(111)-(5×2)-Au surface, one of the long-standing problems in surface science, has been solved by means of Weissenberg reflection high-energy electron diffraction. The arrangement of the Au atoms and their positions with respect to the substrate were determined from a three-dimensional Patterson function with a lateral resolution of 0.3 Å based on a large amount of diffraction data. The new structural model consists of six Au atoms in a 5×2 unit, which agrees with the recently confirmed Au coverage of 0.6 ML [I. Barke , Phys. Rev. B 79, 155301 (2009).PRBMDO1098-0121]. The model has a distinct ×2 periodicity, and includes a Au dimer. The model is also compatible with previously obtained STM images.

Metastability and structural polymorphism in noble metals: the role of composition and metal atom coordination in mono- and bimetallic nanoclusters.

PubMed

Sanchez, Sergio I; Small, Matthew W; Bozin, Emil S; Wen, Jian-Guo; Zuo, Jian-Min; Nuzzo, Ralph G

2013-02-26

This study examines structural variations found in the atomic ordering of different transition metal nanoparticles synthesized via a common, kinetically controlled protocol: reduction of an aqueous solution of metal precursor salt(s) with NaBH₄ at 273 K in the presence of a capping polymer ligand. These noble metal nanoparticles were characterized at the atomic scale using spherical aberration-corrected scanning transmission electron microscopy (C(s)-STEM). It was found for monometallic samples that the third row, face-centered-cubic (fcc), transition metal [(3M)-Ir, Pt, and Au] particles exhibited more coherently ordered geometries than their second row, fcc, transition metal [(2M)-Rh, Pd, and Ag] analogues. The former exhibit growth habits favoring crystalline phases with specific facet structures while the latter samples are dominated by more disordered atomic arrangements that include complex systems of facets and twinning. Atomic pair distribution function (PDF) measurements further confirmed these observations, establishing that the 3M clusters exhibit longer ranged ordering than their 2M counterparts. The assembly of intracolumn bimetallic nanoparticles (Au-Ag, Pt-Pd, and Ir-Rh) using the same experimental conditions showed a strong tendency for the 3M atoms to template long-ranged, crystalline growth of 2M metal atoms extending up to over 8 nm beyond the 3M core.

Near-edge X-ray absorption spectra for metallic Cu and Mn

NASA Astrophysics Data System (ADS)

Greaves, G. N.; Durham, P. J.; Diakun, G.; Quinn, P.

1981-11-01

The measurement of X-ray absorption fine structure of metals- both in the extended region (EXAFS) as well as in the near edge region (XANES)-has been widely discussed (see refs 1-6 for Cu and refs 7-9 for Mn). The recent availability of intense X-ray fluxes from storage rings has usually been exploited for EXAFS leaving the XANES often with poorer resolution than earlier work performed on conventional sources (for example, compare the near edge structure for copper in ref. 1 with refs 3 or 6). In addition, whilst the theory and analysis of EXAFS is relatively well-established2,10, a theory for the strong scattering regime near to the absorption edge has only recently been developed11. We report here the first high resolution XANES spectra for Cu and Mn which were performed at the SRS storage ring at Daresbury. Although both metals have close-packed structures consisting of atoms of similar size their local atomic structure is different in detail. Significant differences are found in their respective XANES reflecting the senstivity of this region of the X-ray absorption fine structure to the local atomic structure. Spectra for the two metals have been analysed using the new multiple scattering formalism. This is a real space calculation and unlike a conventional band structure approach it does not require structural periodicity but works from the local arrangement of atoms.

CIT-7, a crystalline, molecular sieve with pores bounded by 8 and 10-membered rings

DOE PAGES

Schmidt, Joel E.; Xie, Dan; Rea, Thomas; ...

2015-01-23

A new crystalline molecular sieve, denoted CIT-7, is synthesized using an imidazolium-based diquaternary organic structure directing agent (OSDA). The framework structure is determined from a combination of rotation electron diffraction and synchrotron X-ray powder diffraction data. The structure has 10 crystallographically unique tetrahedral atoms (T-atoms) in the unit cell, and can be described as an ordered arrangement of the [4 25 46 2] mtw building unit and a previously unreported [4 45 2] building unit. The framework contains a 2-dimensional pore system that is bounded by 10 T-atom rings (10-ring, 5.1 Å × 6.2 Å opening) that are connected withmore » oval 8-rings (2.9 Å × 5.5 Å opening) through medium-sized cavities (~7.9 Å) at the channel intersections. CIT-7 can be synthesized over a broad range of compositions including pure-silica and heteroatom, e.g., aluminosilicate and titanosilicate, containing variants.« less

Effect of atomic-arrangement matching on La{sub 2}O{sub 3}/Ge heterostructures for epitaxial high-k-gate-stacks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanashima, T., E-mail: kanashima@ee.es.osaka-u.ac.jp; Zenitaka, M.; Kajihara, Y.

2015-12-14

We demonstrate a high-quality La{sub 2}O{sub 3} layer on germanium (Ge) as an epitaxial high-k-gate-insulator, where there is an atomic-arrangement matching condition between La{sub 2}O{sub 3}(001) and Ge(111). Structural analyses reveal that (001)-oriented La{sub 2}O{sub 3} layers were grown epitaxially only when we used Ge(111) despite low growth temperatures less than 300 °C. The permittivity (k) of the La{sub 2}O{sub 3} layer is roughly estimated to be ∼19 from capacitance-voltage (C-V) analyses in Au/La{sub 2}O{sub 3}/Ge structures after post-metallization-annealing treatments, although the C-V curve indicates the presence of carrier traps near the interface. By using X-ray photoelectron spectroscopy analyses, we findmore » that only Ge–O–La bonds are formed at the interface, and the thickness of the equivalent interfacial Ge oxide layer is much smaller than that of GeO{sub 2} monolayer. We discuss a model of the interfacial structure between La{sub 2}O{sub 3} and Ge(111) and comment on the C-V characteristics.« less

Structure and cation ordering in La 2UO 6, Ce 2UO 6, LaUO 4, and CeUO 4 by first principles calculations

DOE PAGES

Casillas-Trujillo, Luis; Xu, H.; McMurray, Jake W.; ...

2016-07-06

In the present work, we have used density functional theory (DFT) and DFT+U to investigate the crystal structure and phase stability of four model compounds in the Ln 2O 3-UO 2-UO 3 ternary oxide system: La2UO 6, Ce 2UO 6, LaUO 4, CeUO 4, due to the highly-correlated nature of the f-electrons in uranium. We have considered both hypothetical ordered compounds and compounds in which the cations randomly occupy atomic sites in a fluorite-like lattice. We determined that ordered compounds are stable and are energetically favored compared to disordered configurations, though the ordering tendencies are weak. To model and analyzemore » the structures of these complex oxides, we have used supercells based on a layered atomic model. In the layer model, the supercell is composed of alternating planes of anions and cations. We have considered two different ordering motifs for the cations, namely single species (isoatomic) cation layers versus mixed species cation layers. Energy differences between various ordered cationic arrangements were found to be small. This may have implications regarding radiation stability, since cationic arrangements should be able to change under irradiation with little cost in energy.« less

Cd4As2Br3

PubMed Central

Kars, Mohammed; Roisnel, Thierry; Dorcet, Vincent; Rebbah, Allaoua; Otero-Diáz, L. Carlos

2014-01-01

Single crystals of Cd4As2Br3 (tetra­cadmium biarsenide tri­bromide) were grown by a chemical transport reaction. The structure is isotypic with the members of the cadmium and mercury pnictidohalides family with general formula M 4 A 2 X 3 (M = Cd, Hg; A = P, As, Sb; X = Cl, Br, I) and contains two independent As atoms on special positions with site symmetry -3 and two independent Cd atoms, of which one is on a special position with site symmetry -3. The Cd4As2Br3 structure consists of AsCd4 tetra­hedra sharing vertices with isolated As2Cd6 octa­hedra that contain As–As dumbbells in the centre of the octahedron. The Br atoms are located in the voids of this three-dimensional arrangement and bridge the different polyhedra through Cd⋯Br contacts. PMID:24764933

Stereochemistry of silicon in oxygen-containing compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serezhkin, V. N., E-mail: Serezhkin@samsu.ru; Urusov, V. S.

2017-01-15

Specific stereochemical features of silicon in oxygen-containing compounds, including hybrid silicates with all oxygen atoms of SiO{sub n} groups ({sub n} = 4, 5, or 6) entering into the composition of organic anions or molecules, are described by characteristics of Voronoi—Dirichlet polyhedra. It is found that in rutile-like stishovite and post-stishovite phases with the structures similar to those of СаСl{sub 2}, α-PbO{sub 2}, or pyrite FeS{sub 2}, the volume of Voronoi—Dirichlet polyhedra of silicon and oxygen atoms decreases linearly with pressure increasing to 268 GPa. Based on these results, the possibility of formation of new post-stishovite phases is shown, namely,more » the fluorite-like structure (transition predicted at ~400 GPa) and a body-centered cubic lattice with statistical arrangement of silicon and oxygen atoms (~900 GPa).« less

High pressure–low temperature phase diagram of barium: Simplicity versus complexity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Desgreniers, Serge; Tse, John S., E-mail: John.Tse@usask.ca; State Key Laboratory of Superhard Materials, Jilin University, 130012 Changchun

2015-11-30

Barium holds a distinctive position among all elements studied upon densification. Indeed, it was the first example shown to violate the long-standing notion that high compression of simple metals should preserve or yield close-packed structures. From modest pressure conditions at room temperature, barium transforms at higher pressures from its simple structures to the extraordinarily complex atomic arrangements of the incommensurate and self-hosting Ba-IV phases. By a detailed mapping of the pressure/temperature structures of barium, we demonstrate the existence of another crystalline arrangement of barium, Ba-VI, at low temperature and high pressure. The simple structure of Ba-VI is unlike that ofmore » complex Ba-IV, the phase encountered in a similar pressure range at room temperature. First-principles calculations predict Ba-VI to be stable at high pressure and superconductive. The results illustrate the complexity of the low temperature-high pressure phase diagram of barium and the significant effect of temperature on structural phase transformations.« less

Spin-interaction effects for ultralong-range Rydberg molecules in a magnetic field

NASA Astrophysics Data System (ADS)

Hummel, Frederic; Fey, Christian; Schmelcher, Peter

2018-04-01

We investigate the fine and spin structure of ultralong-range Rydberg molecules exposed to a homogeneous magnetic field. Each molecule consists of a 87Rb Rydberg atom the outer electron of which interacts via spin-dependent s - and p -wave scattering with a polarizable 87Rb ground-state atom. Our model includes also the hyperfine structure of the ground-state atom as well as spin-orbit couplings of the Rydberg and ground-state atom. We focus on d -Rydberg states and principal quantum numbers n in the vicinity of 40. The electronic structure and vibrational states are determined in the framework of the Born-Oppenheimer approximation for varying field strengths ranging from a few up to hundred Gauss. The results show that the interplay between the scattering interactions and the spin couplings gives rise to a large variety of molecular states in different spin configurations as well as in different spatial arrangements that can be tuned by the magnetic field. This includes relatively regularly shaped energy surfaces in a regime where the Zeeman splitting is large compared to the scattering interaction but small compared to the Rydberg fine structure, as well as more complex structures for both weaker and stronger fields. We quantify the impact of spin couplings by comparing the extended theory to a spin-independent model.

Structural investigations in helium implanted cubic zirconia using grazing incidence XRD and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Kuri, G.; Degueldre, C.; Bertsch, J.; Döbeli, M.

2010-06-01

The crystal structure and local atom arrangements surrounding Zr atoms were determined for a helium implanted cubic stabilized zirconia (CSZ) using X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, respectively, measured at glancing angles. The implanted specimen was prepared at a helium fluence of 2 × 10 16 cm -2 using He + beams at two energies (2.54 and 2.74 MeV) passing through a 8.0 μm Al absorber foil. XRD results identified the formation of a new rhombohedral phase in the helium embedded layer, attributed to internal stress as a result of expansion of the CSZ-lattice. Zr K-edge EXAFS data suggested loss of crystallinity in the implanted lattice and disorder of the Zr atoms environment. EXAFS Fourier transforms analysis showed that the average first-shell radius of the Zr sbnd O pair in the implanted sample was slightly larger than that of the CSZ standard. Common general disorder features were explained by rhombohedral type short-range ordered clusters. The average structural parameters estimated from the EXAFS data of unimplanted and implanted CSZ are compared and discussed. Potential of EXAFS as a local probe of atomic-scale structural modifications induced by helium implantation in CSZ is demonstrated.

Raman spectroscopy as a tool to investigate the structure and electronic properties of carbon-atom wires

PubMed Central

Milani, Alberto; Tommasini, Matteo; Russo, Valeria; Li Bassi, Andrea; Lucotti, Andrea; Cataldo, Franco

2015-01-01

Summary Graphene, nanotubes and other carbon nanostructures have shown potential as candidates for advanced technological applications due to the different coordination of carbon atoms and to the possibility of π-conjugation. In this context, atomic-scale wires comprised of sp-hybridized carbon atoms represent ideal 1D systems to potentially downscale devices to the atomic level. Carbon-atom wires (CAWs) can be arranged in two possible structures: a sequence of double bonds (cumulenes), resulting in a 1D metal, or an alternating sequence of single–triple bonds (polyynes), expected to show semiconducting properties. The electronic and optical properties of CAWs can be finely tuned by controlling the wire length (i.e., the number of carbon atoms) and the type of termination (e.g., atom, molecular group or nanostructure). Although linear, sp-hybridized carbon systems are still considered elusive and unstable materials, a number of nanostructures consisting of sp-carbon wires have been produced and characterized to date. In this short review, we present the main CAW synthesis techniques and stabilization strategies and we discuss the current status of the understanding of their structural, electronic and vibrational properties with particular attention to how these properties are related to one another. We focus on the use of vibrational spectroscopy to provide information on the structural and electronic properties of the system (e.g., determination of wire length). Moreover, by employing Raman spectroscopy and surface enhanced Raman scattering in combination with the support of first principles calculations, we show that a detailed understanding of the charge transfer between CAWs and metal nanoparticles may open the possibility to tune the electronic structure from alternating to equalized bonds. PMID:25821689

Resonance fluorescence microscopy via three-dimensional atom localization

NASA Astrophysics Data System (ADS)

Panchadhyayee, Pradipta; Dutta, Bibhas Kumar; Das, Nityananda; Mahapatra, Prasanta Kumar

2018-02-01

A scheme is proposed to realize three-dimensional (3D) atom localization in a driven two-level atomic system via resonance fluorescence. The field arrangement for the atom localization involves the application of three mutually orthogonal standing-wave fields and an additional traveling-wave coupling field. We have shown the efficacy of such field arrangement in tuning the spatially modulated resonance in all directions. Under different parametric conditions, the 3D localization patterns originate with various shapes such as sphere, sheets, disk, bowling pin, snake flute, flower vase. High-precision localization is achieved when the radiation field detuning equals twice the combined Rabi frequencies of the standing-wave fields. Application of a traveling-wave field of suitable amplitude at optimum radiation field detuning under symmetric standing-wave configuration leads to 100% detection probability even in sub-wavelength domain. Asymmetric field configuration is also taken into consideration to exhibit atom localization with appreciable precision compared to that of the symmetric case. The momentum distribution of the localized atoms is found to follow the Heisenberg uncertainty principle under the validity of Raman-Nath approximation. The proposed field configuration is suitable for application in the study of atom localization in an optical lattice arrangement.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalsi, Deepti; Rayaprol, S.; Siruguri, V.

We report the crystallographic properties of RE{sub 2}NiGe{sub 3} (RE=La, Ce) synthesized by arc melting. Rietveld refinement on the powder neutron diffraction (ND) data suggest both compounds are isostructural and crystallize in the non-centrosymmetric Er{sub 2}RhSi{sub 3} type structure having hexagonal space group P6{sup ¯}2c. In the crystal structure of RE{sub 2}NiGe{sub 3}, two dimensional arrangements of nickel and germanium atoms lead to the formation of hexagonal layers with rare earth atoms sandwiched between them. Magnetic susceptibility measurements performed in low fields exhibit antiferromagnetic ordering in cerium compound around (T{sub o}=) 3.2 K. Neutron diffraction measurements at 2.8 K (i.e.,more » at T« less

Structure characterization, photoluminescence and dielectric properties of a new hybrid compound containing chlorate anions of zincate (II)

NASA Astrophysics Data System (ADS)

Lassoued, Mohamed Saber; Abdelbaky, Mohammed S. M.; Ben Soltan, Wissem; Lassoued, Abdelmajid; Ammar, Salah; Gadri, Abdellatif; Ben Salah, Abdelhamid; García-Granda, Santiago

2018-04-01

A new hybrid compound, bis (2-aminophenylenamonium) tetrachlorozincate (II), was synthesized and formulated as (C6H9N2)2ZnCl4. Its crystal structure was solved by single crystal X-ray diffraction reveling that compound crystallizes in the monoclinic system, space group C2/c (N°: 15) with cell parameters a = 7.4957(4) Å, b = 25.6837(15) Å, c = 9.4041(5) Å, β = 94.35(0)°, V = 1805.23(45) Å3. Their atomic arrangement can be described as an alternation of inorganic and organic layers, [ZnCl4]2- tetrahedral anions and 2-aminophenylenamonium cations. The cohesion of the atomic arrangement is ensured by hydrogen bonds (strong Nsbnd H⋯N and weak Nsbnd H⋯Cl) and π-π stacking interactions between identical antiparallel organic moieties. In optical transmission and photoluminescence measurements, this material exhibit two absorption bands (253 and 316 nm) and a strong emission line (390 nm), while the thermal analysis disclosed a phase transition at 420-445 K previously to the sample decomposition at 476 K. Finally, electrical measurements were performed to discuss the phase-transition mechanism.

Wet-chemical synthesis of nanoscale iron boride, XAFS analysis and crystallisation to α-FeB.

PubMed

Rades, Steffi; Kornowski, Andreas; Weller, Horst; Albert, Barbara

2011-06-20

The reaction of lithium tetrahydridoborate and iron bromide in high boiling ether as reaction medium produces an ultrafine, pyrophoric and magnetic precipitate. X-ray and electron diffraction proved the product to be amorphous. According to X-ray absorption fine structure spectroscopy (XAFS) the precipitate has FeB structure up to nearly two coordination spheres around an iron absorber atom. Transmission electron microscopy (TEM) confirms the ultrafine powder to be nanoscale. Subsequent annealing at 450 °C causes the atoms to arrange in a more distinct FeB structure, and further thermal treatment to 1050 °C extends the local structure to the α-modification of FeB. Between 1050 °C and 1500 °C α-FeB is transformed into β-FeB. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

AAuAl (A = Ca, Sc, and Ti): Peierls Distortion, Atomic Coloring, and Structural Competition

DOE PAGES

Pham, Joyce; Miller, Gordon J.

2018-04-02

Using density functional theory, the crystal structure variation of AAuAl (A = Ca, Sc, and Ti) from orthorhombic Co 2Si-type to distorted hexagonal Fe 2P-type and then Ni 2In-type structures is shown to correlate with their electronic structures and valence electron counts, sizes of the active metals A, and site preferences for Au and Al atoms, which are arranged to maximize Au–Al nearest neighbor contacts. An evaluation of chemical pressure imposed by the varying A metals using total energy vs volume calculations indicates that larger unit cell volumes favor the orthorhombic structure, whereas smaller volumes favor the hexagonal structures. Themore » electronic origin of the Mg 2Ga-type crystal structure of ScAuAl, refined as a distorted Fe 2P-type supercell doubled along the c-axis, indicates a Peierls-type distortion mechanism of the Au chains along the c-axis.« less

Observation of Structure of Surfaces and Interfaces by Synchrotron X-ray Diffraction: Atomic-Scale Imaging and Time-Resolved Measurements

NASA Astrophysics Data System (ADS)

Wakabayashi, Yusuke; Shirasawa, Tetsuroh; Voegeli, Wolfgang; Takahashi, Toshio

2018-06-01

The recent developments in synchrotron optics, X-ray detectors, and data analysis algorithms have enhanced the capability of the surface X-ray diffraction technique. This technique has been used to clarify the atomic arrangement around surfaces in a non-contact and nondestructive manner. An overview of surface X-ray diffraction, from the historical development to recent topics, is presented. In the early stage of this technique, surface reconstructions of simple semiconductors or metals were studied. Currently, the surface or interface structures of complicated functional materials are examined with sub-Å resolution. As examples, the surface structure determination of organic semiconductors and of a one-dimensional structure on silicon are presented. A new frontier is time-resolved interfacial structure analysis. A recent observation of the structure and dynamics of the electric double layer of ionic liquids, and an investigation of the structural evolution in the wettability transition on a TiO2 surface that utilizes a newly designed time-resolved surface diffractometer, are presented.

AAuAl (A = Ca, Sc, and Ti): Peierls Distortion, Atomic Coloring, and Structural Competition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Joyce; Miller, Gordon J.

Using density functional theory, the crystal structure variation of AAuAl (A = Ca, Sc, and Ti) from orthorhombic Co 2Si-type to distorted hexagonal Fe 2P-type and then Ni 2In-type structures is shown to correlate with their electronic structures and valence electron counts, sizes of the active metals A, and site preferences for Au and Al atoms, which are arranged to maximize Au–Al nearest neighbor contacts. An evaluation of chemical pressure imposed by the varying A metals using total energy vs volume calculations indicates that larger unit cell volumes favor the orthorhombic structure, whereas smaller volumes favor the hexagonal structures. Themore » electronic origin of the Mg 2Ga-type crystal structure of ScAuAl, refined as a distorted Fe 2P-type supercell doubled along the c-axis, indicates a Peierls-type distortion mechanism of the Au chains along the c-axis.« less

Effects of the c-Si/a-SiO2 interfacial atomic structure on its band alignment: an ab initio study.

PubMed

Zheng, Fan; Pham, Hieu H; Wang, Lin-Wang

2017-12-13

The crystalline-Si/amorphous-SiO 2 (c-Si/a-SiO 2 ) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO 2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containing Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO 2 , was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO 2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO 2 and c-Si/a-SiO 2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV.

Effects of the c-Si/a-SiO 2 interfacial atomic structure on its band alignment: an ab initio study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Fan; Pham, Hieu H.; Wang, Lin-Wang

The crystalline-Si/amorphous-SiO 2 (c-Si/a-SiO 2) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO 2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here in this study, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containingmore » Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO 2, was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO 2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO 2 and c-Si/a-SiO 2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV« less

Effects of the c-Si/a-SiO 2 interfacial atomic structure on its band alignment: an ab initio study

DOE PAGES

Zheng, Fan; Pham, Hieu H.; Wang, Lin-Wang

2017-11-13

The crystalline-Si/amorphous-SiO 2 (c-Si/a-SiO 2) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO 2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here in this study, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containingmore » Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO 2, was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO 2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO 2 and c-Si/a-SiO 2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV« less

Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2014-01-01

The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.

The magic triangle goes MAD: experimental phasing with a bromine derivative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beck, Tobias, E-mail: tbeck@shelx.uni-ac.gwdg.de; Gruene, Tim; Sheldrick, George M.

2010-04-01

5-Amino-2, 4, 6-tribromoisophthalic acid is used as a phasing tool for protein structure determination by MAD phasing. It is the second representative of a novel class of compounds for heavy-atom derivatization that combine heavy atoms with amino and carboxyl groups for binding to proteins. Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2, 4, 6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups andmore » one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br K edge was successfully carried out. Radiation damage to the bromine–carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.« less

Crystal Structure and Crystal Chemistry of Some Common REE Minerals and Nanpingite

NASA Astrophysics Data System (ADS)

Ni, Yunxiang

1995-01-01

Part I. Crystal structure and crystal chemistry of fluorocarbonate minerals. The crystal structure of bastnasite-(Ce) have been solved in P-62c and refined to R = 0.018. The structure is composed of (001) (CeF) layers interspersed with (CO_3) layers in a 1:1 ratio. The Ce atom is coordinated in rm CeO_6F_3 polyhedra. The atomic arrangement of synchysite-(Ce) has been solved and refined to R = 0.036 with a monoclinic space group C2/c. It possesses a (001) layer structure, with layers of (Ca) and (CeF) separated by layers of carbonate groups. The layers stack in a manner analogous to C2/c muscovite. Polytypism similar to the micas may exist in synchysite. The crystal structures of cordylite-(Ce) have been solved in P6 _3/mmc and refined to R = 0.023. The structure and chemical formula are different from those deduced by Oftedal. The formula is rm MBaCe_2(CO _3)_4F, where M is rm Na^+, Ca^{2+}_{1/2 }+ O_{1/2}, or any solution. The presence of (NaF) layer in the structure is the key difference from the Oftedal's structure. This redefinition of the chemical formula and crystal structure of cordylite will be proposed to IMA-CNMMN. Part II. Crystal structure and crystal chemistry of monazite-xenotime series. Monazite is monoclinic, P2 _1/n, and xenotime is isostructural with zircon (I4_1/amd). Both atomic arrangements are based on (001) chains of intervening phosphate tetrahedra and RE polyhedra, with a REO_8 polyhedron in xenotime that accommodates HRE (Tb - Lu) and a REO_9 polyhedron in monazite that preferentially incorporates LRE (La - Gd). As the structure "transforms" from xenotime to monazite, the crystallographic properties are comparable along the (001) chains, with structural adjustments of 2.2 A along (010) to accommodate the different size RE atoms. Part III. Crystal structure of nanpingite-2M _2, the Cs end-member of muscovite. The crystal structure of nanpingite has been refined to R = 0.058. Compared to K^+ in muscovite, the largest interlayer Cs^+ in nanpingite increases (001) separation between adjacent 2:1 layers, but has little effect on the dimensions in (001). The existence of rare 2M_2 polytype in nanpingite is attributed to this large layer separation, which minimizes the repulsion of the superimposed (along (001)) basal oxygens in neighboring tetrahedral layers.

Multiscale structural changes of atomic order in severely deformed industrial aluminum

NASA Astrophysics Data System (ADS)

Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

2016-02-01

The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

Crystal structure of fac-aquatricarbonyl[(S)-valin-ato-κ(2) N,O]-rhenium(I).

PubMed

Piletska, Kseniia O; Domasevitch, Kostiantyn V; Shtemenko, Alexander V

2016-04-01

In the mol-ecule of the title compound, [Re(C5H10NO2)(CO)3(H2O)], the Re(I) atom adopts a distorted octa-hedral coordination sphere defined by one aqua and three carbonyl ligands as well as one amino N and one carboxyl-ate O atom of the chelating valinate anion. The carbonyl ligands are arranged in a fac-configuration around the Re(I) ion. In the crystal, an intricate hydrogen-bonding system under participation of two O-H, two N-H and one C-H donor groups and the carboxyl-ate and carbonyl O atoms as acceptor groups contribute to the formation of a three-dimensional supra-molecular network.

4-(4-Meth­oxy­phen­yl)-2-methyl­but-3-yn-2-ol

PubMed Central

Eissmann, Frank; Kafurke, Uwe; Weber, Edwin

2010-01-01

The mol­ecular structure of the title compound, C12H14O2, features a nearly coplanar arrangement including the aromatic ring, the C C—C group and the ether O atom. The maximum deviation from the least-squares plane of these ten atoms is 0.0787 (8) Å for the ether O atom. In the crystal, mol­ecules are connected via O—H⋯O hydrogen bonds (involving the hy­droxy O atom both as hydrogen-bond donor and acceptor) and weaker (ar­yl)C—H⋯π(ar­yl) contacts, leading to the formation of strands running parallel to the b axis. Further stabilization results from weaker (meth­yl)C—H⋯π(acetyl­ene) inter­actions between different strands. PMID:21588063

Terasonic Excitations in 2D Gold Nanoparticle Arrays in a Water Matrix as Revealed by Atomistic Simulations

DOE PAGES

Bolmatov, Dima; Zhernenkov, Mikhail; Zav’yalov, Dmitry; ...

2016-08-19

Here in this work we report on terahertz phononic excitations in 2D gold nanoparticle arrays in a water matrix through a series of large-scale molecular dynamics simulations. For the first time, we observe acoustic Dirac-like crossings in H (H 2O) atomic (molecular) networks which emerge due to an intraband phononic scattering. These crossings are the phononic fingerprints of ice-like arrangements of H (H 2O) atomic (molecular) networks at nanometer scale. We reveal how phononic excitations in metallic nanoparticles and the water matrix reciprocally impact on one another providing the mechanism for the THz phononics manipulation via structural engineering. In addition,more » we show that by tuning the arrangement of 2D gold nanoparticle assemblies the Au phononic polarizations experience sub-terahertz hybridization (Kohn anomaly) due to surface electron-phonon relaxation processes. This opens the way for the sound control and manipulation in soft matter metamaterials at nanoscale.« less

Structure-function insights of membrane and soluble proteins revealed by electron crystallography.

PubMed

Dreaden, Tina M; Devarajan, Bharanidharan; Barry, Bridgette A; Schmidt-Krey, Ingeborg

2013-01-01

Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.

Deciphering chemical order/disorder and material properties at the single-atom level.

PubMed

Yang, Yongsoo; Chen, Chien-Chun; Scott, M C; Ophus, Colin; Xu, Rui; Pryor, Alan; Wu, Li; Sun, Fan; Theis, Wolfgang; Zhou, Jihan; Eisenbach, Markus; Kent, Paul R C; Sabirianov, Renat F; Zeng, Hao; Ercius, Peter; Miao, Jianwei

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

Extended x-ray absorption fine structure study of phase transitions in the piezoelectric perovskite K0.5Na0.5NbO3

NASA Astrophysics Data System (ADS)

Kodre, A.; Tellier, J.; Arčon, I.; Malič, B.; Kosec, M.

2009-06-01

Following an x-ray diffraction study of phase transitions of the piezoelectric perovskite K0.5Na0.5NbO3 the structural changes of the material are studied using extended x-ray absorption fine structure analysis, whereby the neighborhood of Nb atom is determined in the temperature range of monoclinic, tetragonal, and cubic phases. Within the entire range Nb atom is displaced from the center of the octahedron of its immediate oxygen neighbors, as witnessed by the splitting of Nb-O distance. The model shows high prevalence of the displacement in the (111) crystallographic direction of the simple perovskite cell. The corresponding splitting of the Nb-Nb distance is negligible. There is no observable disalignment of the linear Nb-O-Nb bonds from the ideal cubic arrangement, judging from the intensity of the focusing of the photoelectron wave on the Nb-Nb scattering path by the interposed oxygen atom. As a general result, the phase transitions are found as an effect of the long-range order, while the placement of the atoms in the immediate vicinity remains largely unaffected.

Atomic Scale Analysis of the Enhanced Electro- and Photo-Catalytic Activity in High-Index Faceted Porous NiO Nanowires

NASA Astrophysics Data System (ADS)

Shen, Meng; Han, Ali; Wang, Xijun; Ro, Yun Goo; Kargar, Alireza; Lin, Yue; Guo, Hua; Du, Pingwu; Jiang, Jun; Zhang, Jingyu; Dayeh, Shadi A.; Xiang, Bin

2015-02-01

Catalysts play a significant role in clean renewable hydrogen fuel generation through water splitting reaction as the surface of most semiconductors proper for water splitting has poor performance for hydrogen gas evolution. The catalytic performance strongly depends on the atomic arrangement at the surface, which necessitates the correlation of the surface structure to the catalytic activity in well-controlled catalyst surfaces. Herein, we report a novel catalytic performance of simple-synthesized porous NiO nanowires (NWs) as catalyst/co-catalyst for the hydrogen evolution reaction (HER). The correlation of catalytic activity and atomic/surface structure is investigated by detailed high resolution transmission electron microscopy (HRTEM) exhibiting a strong dependence of NiO NW photo- and electrocatalytic HER performance on the density of exposed high-index-facet (HIF) atoms, which corroborates with theoretical calculations. Significantly, the optimized porous NiO NWs offer long-term electrocatalytic stability of over one day and 45 times higher photocatalytic hydrogen production compared to commercial NiO nanoparticles. Our results open new perspectives in the search for the development of structurally stable and chemically active semiconductor-based catalysts for cost-effective and efficient hydrogen fuel production at large scale.

Invited Article: Autonomous assembly of atomically perfect nanostructures using a scanning tunneling microscope.

PubMed

Celotta, Robert J; Balakirsky, Stephen B; Fein, Aaron P; Hess, Frank M; Rutter, Gregory M; Stroscio, Joseph A

2014-12-01

A major goal of nanotechnology is to develop the capability to arrange matter at will by placing individual atoms at desired locations in a predetermined configuration to build a nanostructure with specific properties or function. The scanning tunneling microscope has demonstrated the ability to arrange the basic building blocks of matter, single atoms, in two-dimensional configurations. An array of various nanostructures has been assembled, which display the quantum mechanics of quantum confined geometries. The level of human interaction needed to physically locate the atom and bring it to the desired location limits this atom assembly technology. Here we report the use of autonomous atom assembly via path planning technology; this allows atomically perfect nanostructures to be assembled without the need for human intervention, resulting in precise constructions in shorter times. We demonstrate autonomous assembly by assembling various quantum confinement geometries using atoms and molecules and describe the benefits of this approach.

Structures Self-Assembled Through Directional Solidification

NASA Technical Reports Server (NTRS)

Dynys, Frederick W.; Sayir, Ali

2005-01-01

Nanotechnology has created a demand for new fabrication methods with an emphasis on simple, low-cost techniques. Directional solidification of eutectics (DSE) is an unconventional approach in comparison to low-temperature biomimetic approaches. A technical challenge for DSE is producing microstructural architectures on the nanometer scale. In both processes, the driving force is the minimization of Gibb's free energy. Selfassembly by biomimetic approaches depends on weak interaction forces between organic molecules to define the architectural structure. The architectural structure for solidification depends on strong chemical bonding between atoms. Constituents partition into atomic-level arrangements at the liquid-solid interface to form polyphase structures, and this atomic-level arrangement at the liquid-solid interface is controlled by atomic diffusion and total undercooling due to composition (diffusion), kinetics, and curvature of the boundary phases. Judicious selection of the materials system and control of the total undercooling are the keys to producing structures on the nanometer scale. The silicon-titanium silicide (Si-TiSi2) eutectic forms a rod structure under isothermal cooling conditions. At the NASA Glenn Research Center, directional solidification was employed along with a thermal gradient to promote uniform rods oriented with the thermal gradient. The preceding photomicrograph shows the typical transverse microstructure of a solidified Si-TiSi2 eutectic composition. The dark and light gray regions are Si and TiSi2, respectively. Preferred rod orientation along the thermal gradient was poor. The ordered TiSi2 rods have a narrow distribution in diameter of 2 to 3 m, as shown. The rod diameter showed a weak dependence on process conditions. Anisotropic etch behavior between different phases provides the opportunity to fabricate structures with high aspect ratios. The photomicrographs show the resulting microstructure after a wet chemical etch and a dry plasma etch. The wet chemical etches the silicon away, exposing the TiSi2 rods, whereas plasma etching preferentially etches the Si-TiSi2 interface to form a crater. The porous architectures are applicable to fabricating microdevices or creating templates for part fabrication. The porous rod structure can serve as a platform for fabricating microplasma devices for propulsion or microheat exchangers and for fabricating microfilters for miniatured chemical reactors. Although more work is required, self-assembly from DSE can have a role in microdevice fabrication.

Directing Matter: Toward Atomic-Scale 3D Nanofabrication.

PubMed

Jesse, Stephen; Borisevich, Albina Y; Fowlkes, Jason D; Lupini, Andrew R; Rack, Philip D; Unocic, Raymond R; Sumpter, Bobby G; Kalinin, Sergei V; Belianinov, Alex; Ovchinnikova, Olga S

2016-06-28

Enabling memristive, neuromorphic, and quantum-based computing as well as efficient mainstream energy storage and conversion technologies requires the next generation of materials customized at the atomic scale. This requires full control of atomic arrangement and bonding in three dimensions. The last two decades witnessed substantial industrial, academic, and government research efforts directed toward this goal through various lithographies and scanning-probe-based methods. These technologies emphasize 2D surface structures, with some limited 3D capability. Recently, a range of focused electron- and ion-based methods have demonstrated compelling alternative pathways to achieving atomically precise manufacturing of 3D structures in solids, liquids, and at interfaces. Electron and ion microscopies offer a platform that can simultaneously observe dynamic and static structures at the nano- and atomic scales and also induce structural rearrangements and chemical transformation. The addition of predictive modeling or rapid image analytics and feedback enables guiding these in a controlled manner. Here, we review the recent results that used focused electron and ion beams to create free-standing nanoscale 3D structures, radiolysis, and the fabrication potential with liquid precursors, epitaxial crystallization of amorphous oxides with atomic layer precision, as well as visualization and control of individual dopant motion within a 3D crystal lattice. These works lay the foundation for approaches to directing nanoscale level architectures and offer a potential roadmap to full 3D atomic control in materials. In this paper, we lay out the gaps that currently constrain the processing range of these platforms, reflect on indirect requirements, such as the integration of large-scale data analysis with theory, and discuss future prospects of these technologies.

Directing Matter: Toward Atomic-Scale 3D Nanofabrication

DOE PAGES

Jesse, Stephen; Borisevich, Albina Y.; Fowlkes, Jason D.; ...

2016-05-16

Here we report that enabling memristive, neuromorphic, and quantum based computing as well as efficient mainstream energy storage and conversion technologies requires next generation of materials customized at the atomic scale. This requires full control of atomic arrangement and bonding in three dimensions. The last two decades witnessed substantial industrial, academic, and government research efforts directed towards this goal through various lithographies and scanning probe based methods. These technologies emphasize 2D surface structures, with some limited 3D capability. Recently, a range of focused electron and ion based methods have demonstrated compelling alternative pathways to achieving atomically precise manufacturing of 3Dmore » structures in solids, liquids, and at interfaces. Electron and ion microscopies offer a platform that can simultaneously observe dynamic and static structures at the nano and atomic scales, and also induce structural rearrangements and chemical transformation. The addition of predictive modeling or rapid image analytics and feedback enables guiding these in a controlled manner. Here, we review the recent results that used focused electron and ion beams to create free-standing nanoscale 3D structures, radiolysis and the fabrication potential with liquid precursors, epitaxial crystallization of amorphous oxides with atomic layer precision, as well as visualization and control of individual dopant motion within a 3D crystal lattice. These works lay the foundation for new approaches to directing nanoscale level architectures and offer a potential roadmap to full 3D atomic control in materials. Lastly, in this perspective we lay out the gaps that currently constrain the processing range of these platforms, reflect on indirect requirements, such as the integration of large scale data analysis with theory, and discuss future prospects of these technologies.« less

From carbon nanotubes to carbon atomic chains

NASA Astrophysics Data System (ADS)

Casillas García, Gilberto; Zhang, Weijia; José-Yacamán, Miguel

2010-10-01

Carbyne is a linear allotrope of carbon. It is formed by a linear arrangement of carbon atoms with sp-hybridization. We present a reliable and reproducible experiment to obtain these carbon atomic chains using few-layer-graphene (FLG) sheets and a HRTEM. First the FLG sheets were synthesized from worm-like exfoliated graphite and then drop-casted on a lacey-carbon copper grid. Once in the TEM, two holes are opened near each other in a FLG sheet by focusing the electron beam into a small spot. Due to the radiation, the carbon atoms rearrange themselves between the two holes and form carbon fibers. The beam is concentrated on the carbon fibers in order excite the atoms and induce a tension until multi wall carbon nanotube (MWCNT) is formed. As the radiation continues the MWCNT breaks down until there is only a single wall carbon nanotube (SWCNT). Then, when the SWCNT breaks, an atomic carbon chain is formed, lasts for several seconds under the radiation and finally breaks. This demonstrates the stability of this carbon structure.

Doping Scheme in Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Toshishige, Yamada

1997-01-01

Due to the dramatic reduction in MOS size, there appear many unwanted effects. In these small devices, the number of dopant atoms in the channel is not macroscopic and electrons may suffer significantly different scattering from device to device since the spatial distribution of dopant atoms is no longer regarded as continuous. This prohibits integration, while it is impossible to control such dopant positions within atomic scale. A fundamental solution is to create electronics with simple but atomically precise structures, which could be fabricated with recent atom manipulation technology. All the constituent atoms are placed as planned, and then the device characteristics are deviation-free, which is mandatory for integration. Atomic chain electronics belongs to this category. Foreign atom chains or arrays form devices, and they are placed on the atomically flat substrate surface. We can design the band structure and the resultant Fermi energy of these structures by manipulating the lattice constant. Using the tight-binding theory with universal parameters, it has been predicted that isolated Si chains and arrays are metallic, Mg chains are insulating, and Mg arrays have metallic and insulating phases [1]. The transport properties along a metallic chain have been studied, emphasizing the role of the contact to electrodes [2]. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along die chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of pant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Two- and three-dimensional growth of Bi on i -Al-Pd-Mn studied using medium-energy ion scattering

NASA Astrophysics Data System (ADS)

Noakes, T. C. Q.; Bailey, P.; McConville, C. F.; Draxler, M.; Walker, M.; Brown, M. G.; Hentz, A.; Woodruff, D. P.; Lograsso, T. A.; Ross, A. R.; Smerdon, J. A.; Leung, L.; McGrath, R.

2010-11-01

Recent work on the growth of thin metal films on quasicrystalline substrates has indicated the formation of so-called “magic height” islands with multiples of 4 atomic layers (AL) arising as a result of quantum size effects, which lead to enhanced stability. Here the results of a study are reported of Bi deposition on i -Al-Pd-Mn using medium-energy ion scattering to characterize the island thickness and the structural arrangement of Bi atoms within the islands. In addition, data were taken from annealed surfaces after Bi cluster desorption to leave a single aperiodic monolayer of Bi at the surface. Scattered-ion energy spectra from the Bi islands are consistent with a single Bi monolayer covered with mainly 4 AL islands for both 1.8 and 3.2 monolayer equivalent coverages but with some occupation of 2 and 8 Al islands as well. The angular dependence of the scattered-ion intensity (“blocking curve”) from Bi has been compared with simulations for various models of both rhombohedral Bi and a distorted “black-phosphorus”-like structure. The data demonstrate bilayer formation within the Bi islands. In the case of the aperiodic Bi monolayer, the blocking curves from substrate scattering are found to be inconsistent with two high-symmetry sites on the quasicrystalline surface that theory indicates are energetically favorable but do not exclude the formation of pentagonal arrangements of Bi atoms as seen in other recent experimental work.

Atomic and electronic basis for the serrations of refractory high-entropy alloys

NASA Astrophysics Data System (ADS)

Wang, William Yi; Shang, Shun Li; Wang, Yi; Han, Fengbo; Darling, Kristopher A.; Wu, Yidong; Xie, Xie; Senkov, Oleg N.; Li, Jinshan; Hui, Xi Dong; Dahmen, Karin A.; Liaw, Peter K.; Kecskes, Laszlo J.; Liu, Zi-Kui

2017-06-01

Refractory high-entropy alloys present attractive mechanical properties, i.e., high yield strength and fracture toughness, making them potential candidates for structural applications. Understandings of atomic and electronic interactions are important to reveal the origins for the formation of high-entropy alloys and their structure-dominated mechanical properties, thus enabling the development of a predictive approach for rapidly designing advanced materials. Here, we report the atomic and electronic basis for the valence-electron-concentration-categorized principles and the observed serration behavior in high-entropy alloys and high-entropy metallic glass, including MoNbTaW, MoNbVW, MoTaVW, HfNbTiZr, and Vitreloy-1 MG (Zr41Ti14Cu12.5Ni10Be22.5). We find that the yield strengths of high-entropy alloys and high-entropy metallic glass are a power-law function of the electron-work function, which is dominated by local atomic arrangements. Further, a reliance on the bonding-charge density provides a groundbreaking insight into the nature of loosely bonded spots in materials. The presence of strongly bonded clusters and weakly bonded glue atoms imply a serrated deformation of high-entropy alloys, resulting in intermittent avalanches of defects movement.

Double-atomic layer of Tl on Si(111): Atomic arrangement and electronic properties

NASA Astrophysics Data System (ADS)

Mihalyuk, Alexey N.; Bondarenko, Leonid V.; Tupchaya, Alexandra Y.; Gruznev, Dimitry V.; Chou, Jyh-Pin; Hsing, Cheng-Rong; Wei, Ching-Ming; Zotov, Andrey V.; Saranin, Alexander A.

2018-02-01

Metastable double-atomic layer of Tl on Si(111) has recently been found to display interesting electric properties, namely superconductivity below 0.96 K and magnetic-field-induced transition into an insulating phase intermediated by a quantum metal state. In the present work, using a set of experimental techniques, including low-energy electron diffraction, scanning tunneling microscopy, angle-resolved photoelectron spectroscopy, in a combination with density-functional-theory calculations, we have characterized atomic and electronic properties of the Tl double layer on Si(111). The double Tl layer has been concluded to contain ∼ 2.4 monolayer of Tl. A top Tl layer has a '1 × 1' basic structure and displays 6 × 6 moiré pattern which originates from various residence sites of Tl atoms. Upon cooling below ∼ 140 K, the 6 × 6 moiré pattern changes to that having a 6√{ 3} × 6√{ 3} periodicity. However, the experimentally determined electron band dispersions show a 1 × 1 periodicity. The calculated band structure unfolded into the 1 × 1 surface Brillouin zone reproduces well the main features of the photoelectron spectra.

Crystal structure of ammonium/potassium trans-bis­(N-methyl­iminodi­acetato-κ3 O,N,O′)chromate(III) from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2016-01-01

The structure of the title compound, [(NH4)0.8K0.2][Cr(C5H7NO4)2] (C5H7NO4 is methyl­iminodi­acetate; mida), has been determined from synchrotron data. The CrIII atom is located on a centre of symmetry and is coordinated by two N atoms and four O atoms of two facially arranged tridentate mida ligands, displaying a slightly distorted octa­hedral coordination environment. The Cr—N and mean Cr—O bond lengths are 2.0792 (14) and 1.958 (14) Å, respectively. The cation site is located on a twofold rotation axis and shows occupational disorder, being occupied by ammonium and potassium cations in a 0.8:0.2 ratio. In the crystal, inter­molecular hydrogen bonds involving the N—H groups of the ammonium cation as donor and the two non-coordinating O atoms of the carboxyl­ate group as acceptor groups consolidate the three-dimensional packing. PMID:27536411

Synthesis, crystal structure and optical properties of a new fluorocarbonate with an interesting sandwich-like structure.

PubMed

Tang, Changcheng; Jiang, Xingxing; Guo, Shu; Xia, Mingjun; Liu, Lijuan; Wang, Xiaoyang; Lin, Zheshuai; Chen, Chuangtian

2018-05-08

A new fluorocarbonate, Na3Zn2(CO3)3F, was synthesized using a subcritical hydrothermal method. Na3Zn2(CO3)3F crystallizes in the space group C2/c with a sandwich-like framework in which the stacked [Zn(CO3)]∞ layers are connected with one another by bridging F atoms and [CO3] groups alternately. Interestingly, each Zn atom is surrounded by one F atom and four O atoms, forming a distorted [ZnO4F] trigonal bipyramid, which is observed for the first time in the carbonate system. Na3Zn2(CO3)3F has high transparency in a wide spectral region ranging from UV to mid IR with a short ultraviolet absorption edge (∼213 nm). First-principles calculations revealed that Na3Zn2(CO3)3F possesses a large birefringence (Δn = 0.11, λ = 589 nm), which is mainly contributed by the coplanar arrangement of [CO3] groups in the ab plane. Na3Zn2(CO3)3F might find applications as a UV birefringence crystal.

Diverse carrier mobility of monolayer BNC_x: A combined density functional theory and Boltzmann transport theory study.

PubMed

Wu, Tao; Deng, Kaiming; Deng, Wei-Qiao; Lu, Ruifeng

2017-09-19

BNCX monolayer as a kind of two-dimensional material has numerous chemical atomic ratios and arrangements with different electronic structures. Via calculations on the basis of density functional theory and Boltzmann transport theory under deformation potential approximation, the band structures and carrier mobilities of BNCX (x=1,2,3,4) nanosheets are systematically investigated. The calculated results show that BNC2-1 is a material with very small band gap (0.02 eV) among all the structures while other BNCX monolayers are semiconductors with band gap ranging from 0.51 to 1.32 eV. The carrier mobility of BNCX varies considerably from tens to millions of cm2 V-1 s-1. For BNC2-1, the hole mobility and electron mobility along both x and y directions can reach 105 orders of magnitude, which is similar to the carrier mobility of graphene. Besides, all studied BNCX monolayers obviously have anisotropic hole mobility and electron mobility. In particular, for semiconductor BNC4, its hole mobility along y direction and electron mobility along x direction unexpectedly reach 106 orders of magnitude, even higher than that of graphene. Our findings suggest that BNCX layered materials with proper ratio and arrangement of carbon atoms will possess desirable charge transport properties, exhibiting potential applications in nanoelectronic devices. © 2017 IOP Publishing Ltd.

Local Structure Analysis and Interface Layer Effect of Phase-Change Recording Material Using Actual Media

NASA Astrophysics Data System (ADS)

Nakai, Tsukasa; Yoshiki, Masahiko; Satoh, Yasuhiro; Ashida, Sumio

2008-07-01

The influences of the interface layer on crystal structure, the local atomic arrangement, and the electronic and chemical structure of a GeBiTe (GBT) phase-change recording material have been investigated using X-ray diffraction (XRD), X-ray absorption fine structure (XAFS), and hard X-ray photoelectron spectroscopy (HX-PES) methods using actual rewritable high-speed HD DVD media without special sample processing. XRD results showed that the crystal structure of laser-crystallized GBT alloy in the actual HD DVD media is the same as that of GeSbTe (GST) alloy, which has a NaCl-type structure. No differences between samples with and without interface layers were found. The lattice constant of GBT is larger than that of GST. Bi increases the lattice constant of GST with respect to the Bi substitution ratio of Sb. According to HX-PES, the DOS of in the recording film amorphous state with an interface layer is closer to that of the crystalline state than the recording film without an interface layer. From XAFS results, clear differences between amorphous (Amo.) and crystalline states (Cry.) were observed. The interatomic distance of amorphous recording material is independent of the existence of an interface layer. On the other hand, the coordination number varied slightly due to the presence of the interface layer. Therefore, the electronic state of the recording layer changes because of the interface layer, although the local structure changes only slightly except for the coordination number. Combining these results, we conclude that the interface layer changes the electronic state of the recording layer and promotes crystallization, but only affects the local structure of the atomic arrangement slightly.

The Kelvin-Thomson Atom. Part 2: The Many-Electron Atoms

ERIC Educational Resources Information Center

Walton, Alan J.

1977-01-01

Presents part two of a two-part article describing the Kelvin-Thomson atom. This part discusses the arrangement of electrons within the atom and examines some of the properties predicted for elements in the Kelvin-Thomson model. (SL)

Atomic force microscope characterization of self-assembly behaviors of cyclo[8] pyrrole on solid substrates

NASA Astrophysics Data System (ADS)

Xu, Hai; Zhao, Siqi; Xiong, Xiang; Jiang, Jinzhi; Xu, Wei; Zhu, Daoben; Zhang, Yi; Liang, Wenjie; Cai, Jianfeng

2017-04-01

Cyclo [8] pyrrole (CP) is a porphyrin analogue containing eight α-conjugated pyrrole units which are arranged in a nearly coplanar conformation. The π-π interactions between CP molecules lead to regular aggregations through a solution casting process. Using tapping mode atomic force microscope (AFM), we investigated the morphology of self-assembled aggregates formed by deposition of different CP solutions on different substrates. We found that in the n-butanol solution, nanofibrous structures could be formed on the silicon or mica surface. Interestingly, on the highly oriented pyrolytic graphite (HOPG) surface, or silicon and mica surface with a toluene solution, only irregular spherical structures were identified. The difference in the nanomorphology may be attributed to distinct interactions between molecule-molecule, molecule-solvent and molecule-substrate.

Potential-specific structure at the hematite-electrolyte interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

McBriarty, Martin E.; Stubbs, Joanne; Eng, Peter

The atomic-scale structure of interfaces between metal oxides and aqueous electrolytes controls their catalytic, geochemical, and corrosion behavior. Measurements that probe these interfaces in situ provide important details of ion and solvent arrangements, but atomically precise structural models do not exist for common oxide-electrolyte interfaces far from equilibrium. Using a novel cell, we measured the structure of the hematite (a-Fe 2O 3) (110more » $$\\bar{2}$$)-electrolyte interface under controlled electrochemical bias using synchrotron crystal truncation rod X ray scattering. At increasingly cathodic potentials, charge-compensating protonation of surface oxygen groups increases the coverage of specifically bound water while adjacent water layers displace outwardly and became disordered. Returning to open circuit potential leaves the surface in a persistent metastable protonation state. The flux of current and ions at applied potential is thus regulated by a unique interfacial electrolyte environment, suggesting that electrical double layer models should be adapted to the dynamically changing interfacial structure far from equilibrium.« less

Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

PubMed

Sturgis, James N; Niederman, Robert A

2008-01-01

Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

Crystal structure of a new polar borate Na{sub 2}Ce{sub 2}[BO{sub 2}(OH)][BO{sub 3}]{sub 2} · H{sub 2}O with isolated boron triangles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Topnikova, A. P.; Belokoneva, E. L., E-mail: elbel@geol.msu.ru; Dimitrova, O. V.

2016-11-15

Crystals of a new polar borate Na{sub 2}Ce{sub 2}[BO{sub 2}(OH)][BO{sub 3}]{sub 2} · H{sub 2}O were prepared by hydrothermal synthesis. The crystals are orthorhombic, a = 7.2295(7) Å, b = 11.2523(8) Å, c = 5.1285(6) Å, Z = 2, sp. gr. C2mm (Amm2), R = 0.0253. The formula of the compound was derived from the structure determination. The Ce and Na atoms are coordinated by nine and six O atoms, respectively. The Ce position is split, and a small amount of Ce is incorporated into the Na1 site with the isomorphous substitution for Na. The anionic moieties exist as isolatedmore » BO{sub 3} and BO{sub 2}(OH) triangles. The planes of the BO{sub 2}(OH) triangles with mm2 symmetry are parallel to the ab plane. The planes of the BO{sub 3} triangles with m symmetry are perpendicular to the ab plane and are rotated in a diagonal way. The splitting of the Ce positions and the polar arrangement of the BO{sub 2}(OH) triangles, water molecules, and Na atoms are observed along the polar a axis. The new structure is most similar to the new borate NaCa{sub 4}[BO{sub 3}]{sub 3} (sp. gr. Ama2), in which triangles of one type are arranged in a polar fashion along the c axis. Weak nonlinear-optical properties of both polar borates are attributed to the quenching of the second-harmonic generation due to the mutually opposite orientation of two-thirds of B triangles in the unit cell.« less

Structure of 1-butylpyridinium tetrafluoroborate ionic liquid: quantum chemistry and molecular dynamic simulation studies.

PubMed

Sun, Hui; Qiao, Baofu; Zhang, Dongju; Liu, Chengbu

2010-03-25

Density functional theory (DFT) calculations combined with molecular dynamic (MD) simulations have been performed to show in detail the structure characteristic of 1-butylpyridinium tetrafluoroborate ([BPy(+)][BF(4)(-)]), a representative of pyridinium-based ionic liquids (ILs). It is found that the relative stability for ion pair configurations is synergically determined by the electrostatic attractions and the H-bond interactions between the ions of opposite charge. [BPy(+)][BF(4)(-)] IL possesses strong long-range ordered structure with cations and anions alternately arranging. The spatial distributions of anions and cations around the given cations are clearly shown, and T-shaped orientation is indicated to play a key role in the interaction between two pyridine rings. DFT calculations and MD simulations uniformly suggest that the H-bonds of the fluorine atoms with the hydrogen atoms on the pyridine rings are stronger than those of the fluorine atoms with the butyl chain hydrogens. The present results can offer useful information for understanding the physicochemical properties of [BPy(+)][BF(4)(-)] IL and further designing new pyridinium-based ILs.

Identification of the Structure Model of the Si(111)-(5×2)-Au Surface

NASA Astrophysics Data System (ADS)

Shirasawa, Tetsuroh; Voegeli, Wolfgang; Nojima, Takehiro; Iwasawa, Yusaku; Yamaguchi, Yudai; Takahashi, Toshio

2014-10-01

The atomic structure of the Si(111)-(5×2)-Au surface, a periodic gold chain on the silicon surface, has been a long-debated issue in surface science. The recent three candidates, the so-called Erwin-Barke-Himpsel (EBH) model [S. C. Erwin, I. Barke, and F. J. Himpsel, Phys. Rev. B 80, 155409 (2009)], the Abukawa-Nishigaya (AN) model [T. Abukawa and Y. Nishigaya, Phys. Rev. Lett. 110, 036102 (2013)], and the Kwon-Kang (KK) model [S. G. Kwon and M. H. Kang, Phys. Rev. Lett. 113, 086101 (2014)] that has one additional Au atom than the EBH model are tested by surface x-ray diffraction data. A two-dimensional Patterson map constructed from the in-plane diffraction intensities rejects the AN model and prefers the KK model over the EBH model. On the basis of the arrangement of Au obtained from the Patterson map, all the reconstructed Si atoms, such as the so-called honeycomb chain structure, are directly imaged out by utilizing a holographic method. The KK model reproduces out-of-plane diffraction data as well.

On the influence of tetrahedral covalent-hybridization on electronic band structure of topological insulators from first principles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, X. M.; Xu, G. Z.; Liu, E. K.

Based on first-principles calculations, we investigate the influence of tetrahedral covalent-hybridization between main-group and transition-metal atoms on the topological band structures of binary HgTe and ternary half-Heusler compounds, respectively. Results show that, for the binary HgTe, when its zinc-blend structure is artificially changed to rock-salt one, the tetrahedral covalent-hybridization will be removed and correspondingly the topologically insulating band character lost. While for the ternary half-Heusler system, the strength of covalent-hybridization can be tuned by varying both chemical compositions and atomic arrangements, and the competition between tetrahedral and octahedral covalent-hybridization has been discussed in details. As a result, we found thatmore » a proper strength of tetrahedral covalent-hybridization is probably in favor to realizing the topologically insulating state with band inversion occurring at the Γ point of the Brillouin zone.« less

Imaging quasiperiodic electronic states in a synthetic Penrose tiling

NASA Astrophysics Data System (ADS)

Collins, Laura C.; Witte, Thomas G.; Silverman, Rochelle; Green, David B.; Gomes, Kenjiro K.

2017-06-01

Quasicrystals possess long-range order but lack the translational symmetry of crystalline solids. In solid state physics, periodicity is one of the fundamental properties that prescribes the electronic band structure in crystals. In the absence of periodicity and the presence of quasicrystalline order, the ways that electronic states change remain a mystery. Scanning tunnelling microscopy and atomic manipulation can be used to assemble a two-dimensional quasicrystalline structure mapped upon the Penrose tiling. Here, carbon monoxide molecules are arranged on the surface of Cu(111) one at a time to form the potential landscape that mimics the ionic potential of atoms in natural materials by constraining the electrons in the two-dimensional surface state of Cu(111). The real-space images reveal the presence of the quasiperiodic order in the electronic wave functions and the Fourier analysis of our results links the energy of the resonant states to the local vertex structure of the quasicrystal.

Imaging quasiperiodic electronic states in a synthetic Penrose tiling.

PubMed

Collins, Laura C; Witte, Thomas G; Silverman, Rochelle; Green, David B; Gomes, Kenjiro K

2017-06-22

Quasicrystals possess long-range order but lack the translational symmetry of crystalline solids. In solid state physics, periodicity is one of the fundamental properties that prescribes the electronic band structure in crystals. In the absence of periodicity and the presence of quasicrystalline order, the ways that electronic states change remain a mystery. Scanning tunnelling microscopy and atomic manipulation can be used to assemble a two-dimensional quasicrystalline structure mapped upon the Penrose tiling. Here, carbon monoxide molecules are arranged on the surface of Cu(111) one at a time to form the potential landscape that mimics the ionic potential of atoms in natural materials by constraining the electrons in the two-dimensional surface state of Cu(111). The real-space images reveal the presence of the quasiperiodic order in the electronic wave functions and the Fourier analysis of our results links the energy of the resonant states to the local vertex structure of the quasicrystal.

Decoupling of epitaxial graphene via gold intercalation probed by dispersive Raman spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pillai, P. B., E-mail: p.pillai@sheffield.ac.uk, E-mail: m.desouza@sheffield.ac.uk; DeSouza, M., E-mail: p.pillai@sheffield.ac.uk, E-mail: m.desouza@sheffield.ac.uk; Narula, R.

Signatures of a superlattice structure composed of a quasi periodic arrangement of atomic gold clusters below an epitaxied graphene (EG) layer are examined using dispersive Raman spectroscopy. The gold-graphene system exhibits a laser excitation energy dependant red shift of the 2D mode as compared to pristine epitaxial graphene. The phonon dispersions in both the systems are mapped using the experimentally observed Raman signatures and a third-nearest neighbour tight binding electronic band structure model. Our results reveal that the observed excitation dependent Raman red shift in gold EG primarily arise from the modifications of the phonon dispersion in gold-graphene and showsmore » that the extent of decoupling of graphene from the underlying SiC substrate can be monitored from the dispersive nature of the Raman 2D modes. The intercalated gold atoms restore the phonon band structure of epitaxial graphene towards free standing graphene.« less

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

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

PubMed

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

2008-10-14

The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS(2) nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS(2) nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism.

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langkilde, Annette E., E-mail: annette.langkilde@sund.ku.dk; Morris, Kyle L.; Serpell, Louise C.

The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-raymore » crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.« less

Production of an ordered (B2) CuPd nanoalloy by low-temperature annealing under hydrogen atmosphere.

PubMed

Yamauchi, Miho; Tsukuda, Tatsuya

2011-05-14

CuPd (1/1) nanoalloys composed of disordered body-centered-cubic crystals (crystal size = 1.6 nm) were prepared by synchronous reduction of Cu and Pd precursor ions with NaBH(4). In situ XRD measurement revealed that Cu and Pd atoms in the CuPd nanoalloys are arranged into an ordered B2 structure under exposure to H(2) (5 kPa) at 373 K. Ordering of Cu and Pd atoms over a longer distance (up to 3.6 nm) was achieved by annealing the nanoalloys for a longer time under a H(2) atmosphere.

1-Do-decyl-indoline-2,3-dione.

PubMed

Qachchachi, Fatima-Zahrae; Ouazzani Chahdi, Fouad; Misbahi, Houria; Bodensteiner, Michael; El Ammari, Lahcen

2014-02-01

The structure of the title compound, C20H29NO2, is isotypic to that of its homologue 1-octylindoline-2,3-dione. The indoline ring and the two carbonyl-group O atoms are approximately coplanar, the largest deviation from the mean plane being 0.0760 (10) Å. The mean plane through the fused-ring system is nearly perpendicular to the mean plane passing through the 1-dodecyl chain [dihedral angle = 77.69 (5)°]. All C atoms of the dodecyl group are in an anti-periplanar arrangement. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming a three-dimensional network.

Characterization of Carbon Nanotube Reinforced Nickel

NASA Technical Reports Server (NTRS)

Gill, Hansel; Hudson, Steve; Bhat, Biliyar; Munafo, Paul M. (Technical Monitor)

2002-01-01

Carbon nanotubes are cylindrical molecules composed of carbon atoms in a regular hexagonal arrangement. If nanotubes can be uniformly dispersed in a supporting matrix to form structural materials, the resulting structures could be significantly lighter and stronger than current aerospace materials. Work is currently being done to develop an electrolyte-based self-assembly process that produces a Carbon Nanotube/Nickel composite material with high specific strength. This process is expected to produce a lightweight metal matrix composite material, which maintains it's thermal and electrical conductivities, and is potentially suitable for applications such as advanced structures, space based optics, and cryogenic tanks.

From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.

PubMed

Zheng, Jianping; Birktoft, Jens J; Chen, Yi; Wang, Tong; Sha, Ruojie; Constantinou, Pamela E; Ginell, Stephan L; Mao, Chengde; Seeman, Nadrian C

2009-09-03

We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 A resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

CIT-7, a crystalline, molecular sieve with pores bounded by 8 and 10-membered rings† †Electronic supplementary information (ESI) available: Details of the synthesis and characterization of all materials as well as details on the synchrotron and RED data collection and structure determination, including the cif file. See DOI: 10.1039/c4sc03935a Click here for additional data file.

PubMed Central

Schmidt, Joel E.; Xie, Dan; Rea, Thomas

2015-01-01

A new crystalline molecular sieve, denoted CIT-7, is synthesized using an imidazolium-based diquaternary organic structure directing agent (OSDA). The framework structure is determined from a combination of rotation electron diffraction and synchrotron X-ray powder diffraction data. The structure has 10 crystallographically unique tetrahedral atoms (T-atoms) in the unit cell, and can be described as an ordered arrangement of the [425462] mtw building unit and a previously unreported [4452] building unit. The framework contains a 2-dimensional pore system that is bounded by 10 T-atom rings (10-ring, 5.1 Å × 6.2 Å opening) that are connected with oval 8-rings (2.9 Å × 5.5 Å opening) through medium-sized cavities (∼7.9 Å) at the channel intersections. CIT-7 can be synthesized over a broad range of compositions including pure-silica and heteroatom, e.g., aluminosilicate and titanosilicate, containing variants. PMID:29163872

Mn induced 1 × 2 reconstruction in the τ-MnAl(0 0 1) surface

NASA Astrophysics Data System (ADS)

Guerrero-Sánchez, J.; Takeuchi, Noboru

2018-05-01

We report on first principles total energy calculations to describe the structural, electronic and magnetic properties of MnAl(0 0 1) surfaces. We have concentrated in structural models having 1 × 1 and 1 × 2 periodicities, since recent experiments of the similar MnGa(0 0 1) surface have found 1 × 1 and 1 × 2 reconstructions. Our calculations show the existence of two stable structures for different ranges of chemical potential. A 1 × 1 surface is stable for Al-rich conditions, whereas a Mn-induced 1 × 2 reconstruction appears after increasing the Mn chemical potential up to Mn-rich conditions. It is important to notice that experimentally, Mn rich conditions are important for improved magnetic properties. The Mn layers in both structures have ferromagnetic arrangements, but they are aligned antiferromagnetically with the almost no magnetic Al atoms. Moreover, the on top Mn atoms, which produce the 1 × 2 reconstruction, align antiferromagnetically with the second layer Mn atoms. These findings are similar to those obtained experimentally in MnGa thin films grown by molecular beam epitaxy. Therefore, this method could also be used to grow the proposed MnAl films.

Invited Article: Autonomous assembly of atomically perfect nanostructures using a scanning tunneling microscope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Celotta, Robert J., E-mail: robert.celotta@nist.gov, E-mail: joseph.stroscio@nist.gov; Hess, Frank M.; Rutter, Gregory M.

2014-12-15

A major goal of nanotechnology is to develop the capability to arrange matter at will by placing individual atoms at desired locations in a predetermined configuration to build a nanostructure with specific properties or function. The scanning tunneling microscope has demonstrated the ability to arrange the basic building blocks of matter, single atoms, in two-dimensional configurations. An array of various nanostructures has been assembled, which display the quantum mechanics of quantum confined geometries. The level of human interaction needed to physically locate the atom and bring it to the desired location limits this atom assembly technology. Here we report themore » use of autonomous atom assembly via path planning technology; this allows atomically perfect nanostructures to be assembled without the need for human intervention, resulting in precise constructions in shorter times. We demonstrate autonomous assembly by assembling various quantum confinement geometries using atoms and molecules and describe the benefits of this approach.« less

Stability and electronic properties of Gex(BN)y monolayers

NASA Astrophysics Data System (ADS)

Freitas, A.; Machado, L. D.; Tromer, R. M.; Bezerra, C. G.; Azevedo, S.

2017-10-01

In this work, we employ ab initio simulations to propose a new class of monolayers with stoichiometry Gex(BN)y . These monolayers belong to a family of 2D materials combining B, N and group IV atoms, such as BxCyNz and SixByNz . We calculated the formation energy for ten atomic arrangements, and found that it increases when the number of Bsbnd Ge and Nsbnd Ge bonds increases, and decreases when the number of Bsbnd N and Gesbnd Ge bonds increases. We found that the lowest energy monolayer presented a Ge2 BN stoichiometry, and maximized the number of Bsbnd N and Gesbnd Ge bonds. This structure also presented mixed sp2 and sp3 bonds and out-of-plane buckling. Moreover, it remained stable in our ab initio molecular dynamics simulations carried out at T = 300 K. The calculated electronic properties revealed that Gex(BN)y monolayers might present conductor or semiconductor behavior, with band gaps ranging from 0.0 to 0.74 eV, depending on atomic arrangement. Tunable values of band gap can be useful in applications. In optoelectronics, for instance, this property might be employed to control absorbed light wavelengths. Our calculations add a new class of monolayers to the increasing library of 2D materials.

Solving the nanostructure problem: exemplified on metallic alloy nanoparticles

NASA Astrophysics Data System (ADS)

Petkov, Valeri; Prasai, Binay; Ren, Yang; Shan, Shiyao; Luo, Jin; Joseph, Pharrah; Zhong, Chuan-Jian

2014-08-01

With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called ``nanostructure problem'' from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized PdxNi100-x particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now.With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called ``nanostructure problem'' from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized PdxNi100-x particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modeling results. See DOI: 10.1039/c4nr01633e

Topologically Allowed Nonsixfold Vortices in a Sixfold Multiferroic Material: Observation and Classification

DOE PAGES

Cheng, Shaobo; Li, Jun; Han, Myung-Geun; ...

2017-04-05

Here, we report structural transformation of sixfold vortex domains into two-, four-, and eightfold vortices via a different type of topological defect in hexagonal manganites. Combining high-resolution electron microscopy and Landau-theory-based numerical simulations, we also investigate the remarkable atomic arrangement and the intertwined relationship between the vortex structures and the topological defects. The roles of their displacement field, formation temperature, and nucleation sites are revealed. All conceivable vortices in the system are topologically classified using homotopy group theory, and their origins are identified.

Structure determination of helical filaments by solid-state NMR spectroscopy

PubMed Central

Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

2016-01-01

The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

Full multiple-scattering calculations on silicates and oxides at the Al K edge

NASA Astrophysics Data System (ADS)

Cabaret, Delphine; Sainctavit, Philippe; Ildefonse, Philippe; Flank, Anne-Marie

1996-05-01

We present full multiple-scattering calculations at the aluminium K edge that we compare with experiments for four crystalline silicates and oxide minerals. In the different minerals aluminium atoms are either fourfold or sixfold coordinated to oxygen atoms in Al sites that are poorly symmetric. The calculations are based on different choices of one-electron potentials according to aluminium coordinations and crystallographic structures of the compounds. Hence it is possible to determine how the near-edge spectral features are a sensitive probe of the effective potential seen by the photoelectron in the molecular environment. The purpose of this work is to determine on the one hand the relation between Al K-edge spectral features and the geometrical arrangements around the aluminium sites, and on the other hand the electronic structure of the compounds.

Experimental Study into the Stability of Whitlockite and Hydroxylapatite in Basaltic Magmas

NASA Technical Reports Server (NTRS)

McCubbin, F. M.; Barnes, J. J.; Vander Kaaden, K. E.; Srinivasan, P.; Whitson, E. S.; Turner, A.; Reppart, J. J.

2018-01-01

Apatite (Ca5(PO4)3(F,Cl,OH)), merrillite (Ca18Na2Mg2(PO4)14), and whitlockite (Ca9(Mg,Fe(2+))(PO4)6[PO3(OH)]) are the primary phosphate minerals found in most planetary materials including rocks from Earth, Moon, Mars, and asteroids. For many years, the terms merrillite and whitlockite have been used interchangeably in the meteorite literature. Much of the confusion regarding the relationship between terrestrial and extraterrestrial 'whitlockite' is based on the presence or absence of hydrogen in the mineral structure. Whitlockite has approximately 8500 ppm H2O, and the term 'merrillite' has been adopted to identify the hydrogen-free form of whitlockite. The atomic structures of merrillite and whitlockite were examined in detail by Hughes et al.. On Earth, whitlockite has been found in rocks from evolved pegmatitic systems and in some mantle rocks. Furthermore, terrestrial whitlockite has been shown to have some merrillite component. For the meteoritic and lunar materials that have been investigated, merrillite appears to be far more common than whitlockite, and it has been proposed that the whitlockite component is unique to terrestrial samples. There are some reports of 'whitlockite' in the meteorite literature; however, these may represent misidentifications of merrillite because there have been no reports of extraterrestrial whitlockite that have been verified through crystal structural studies or analyzed for their H contents. Hughes et al. reported the atomic arrangement of lunar merrillite and demonstrated that the phase is similar to meteoritic merrillite and, predictably, devoid of hydrogen. In a follow-up study, Hughes et al. reported the atomic arrangements of two natural samples of whitlockite, one synthetic whitlockite, and samples of synthetic whitlockite that were heated at 500 C or 1050 C for 24 h. The crystal chemistry and crystal structures of the phases were compared, and it was discovered that the latter treatment resulted in the dehydrogenation of whitlockite to form merrillite.

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

PubMed Central

Nasica-Labouze, Jessica; Meli, Massimiliano; Derreumaux, Philippe; Colombo, Giorgio; Mousseau, Normand

2011-01-01

The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided. PMID:21625573

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

PubMed

Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

2016-12-13

Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

Synthesis, Crystal Structure, and Topology-Symmetry Analysis of a New Modification of NaIn[IO3]4

NASA Astrophysics Data System (ADS)

Belokoneva, E. L.; Karamysheva, A. S.; Dimitrova, O. V.; Volkov, A. S.

2018-01-01

Crystals of new iodate NaIn[IO3]4 were prepared by the hydrothermal synthesis. The unit cell parameters are a = 7.2672(2) Å, b = 15.2572(6) Å, c = 15.0208(6) Å, β = 101.517(3)°, sp. gr. P21/ c. The formula was determined during the structure determination and refinement of a twinned crystal based on a set of reflections from the atomic planes of the major individual. The refinement with anisotropic displacement parameters was performed for both twin components to the final R factor of 0.050. The In and Na atoms are in octahedral coordination formed by oxygen atoms. The oxygen octahedra are arranged into columns by sharing edges, and the columns are connected by isolated umbrella-like [IO3]- groups to form layers. The new structure is most similar to the isoformular iodate NaIn[IO3]4, which crystallizes in the same sp. gr. P21/ c and is structurally similar, but has a twice smaller unit cell and is characterized by another direction of the monoclinic axis. The structural similarity and difference between the two phases were studied by topologysymmetry analysis. The formation of these phases is related to different combinations of identical one-dimensional infinite chains of octahedra.

Predicting RNA 3D structure using a coarse-grain helix-centered model

PubMed Central

Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

2015-01-01

A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. PMID:25904133

Structure of Li5AlS4 and comparison with other lithium-containing metal sulfides

NASA Astrophysics Data System (ADS)

Lim, Hanjin; Kim, Sung-Chul; Kim, Jaegyeom; Kim, Young-Il; Kim, Seung-Joo

2018-01-01

Lithium aluminum sulfide (Li5AlS4) was synthesized by solid state reaction, and its crystal structure was characterized by ab initio structure determination on the basis of powder neutron diffraction (ND) data. Li5AlS4 was found to have monoclinic unit cell (space group, P21/m) with the lattice parameters: a = 6.8583(4) Å, b = 7.8369(4) Å, c = 6.2488(4) Å, and β = 90.333(4)°. This structure is built from a hexagonal close-packed (hcp) arrangement of sulfur atoms with a stacking sequence of …ABAB…. The hcp sulfide lattice consists of two different double-sulfide layers alternately stacked along the c-axis. Between the first pair of sulfur layers all the tetrahedral interstices (T+ and T- sites) are filled with lithium and aluminum atoms. All octahedral interstices between the second pair of sulfur layers are occupied by the remaining lithium atoms. The structure of Li5AlS4 is compared with those of various lithium-containing metal sulfides like Li2FeS2, NaLiMS2 (M = Zn, Cd), Li4GeS4, LiM‧S2 (M‧ = Al, Ga, In) and γ-Li3PS4. Each sulfide represents a specific distribution of lithium atoms in the lattice depending on how the octahedral and tetrahedral interstitial sites are filled. The low ionic conductivity of Li5AlS4 (9.7 × 10-9 S cm-1 at 323 K) relative to other sulfides may be due to the highly-ordered distribution of the lithium atoms in the layered structure and the lack of adjacent void spaces that can be used for lithium ion hopping.

Effect of gradual ordering of Ge/Sb atoms on chemical bonding: A proposed mechanism for the formation of crystalline Ge2Sb2Te5

NASA Astrophysics Data System (ADS)

Singh, Janpreet; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

2018-04-01

Using first principle calculations, we study the atomic arrangement and bonding mechanism in the crystalline phase of Ge2Sb2Te5 (GST). It is found that the stability of GST depends on the gradual ordering of Ge/Sb atoms. The configurations with different concentration of Ge/Sb in layers have been analyzed by the partial density of state, electron localization function and Bader charge distribution. The s and p-states of Ge atom alter with different stacking configurations but there is no change in Sb and Te atom states. Our findings show that the bonding between Ge-Te is not only responsible for the stability of GST alloy but can also predict which composition can show generic features of phase change material. As the number of Ge atoms near to vacancy layer decreases, Ge donates more charge. A growth model has been proposed for the formation of crystalline phase which justifies the structure models proposed in the literature.

Simulation of a 3D MOT-Optical Molasses Hybrid for Potassium-41 Atoms

NASA Astrophysics Data System (ADS)

Peterson, W. A.; Wrubel, Jonathan

2017-04-01

We report a design and numerical model for a 3D magneto-optical trap (MOT)-optical molasses hybrid for potassium-41 atoms. In this arrangement, the usual quadrupole magnetic field is replaced by an octupole field. The octupole field has a central region of very low magnetic field where our simulations show that the atoms experience an optical molasses, resulting in sub-doppler cooling not possible in a quadrupole MOT. The simulations also show that the presence of the magneto-optical trapping force at the edge of the cooling beams provides a restoring force which cycles atoms through the molasses region. We plan to use this hybrid trap to directly load a far off-resonance optical dipole trap. Because the atoms are recycled for multiple passes through the molasses, we expect a higher phase-space density of atoms loaded into the dipole trap. Similar hybrid cooling schemes should be relevant for lithium-6 and lithium-7, which also have poorly resolved D2 hyperfine structure. Research Corporation for Science Advancement, Cottrell College Science Award.

Assembly and microscopic characterization of DNA origami structures.

PubMed

Scheible, Max; Jungmann, Ralf; Simmel, Friedrich C

2012-01-01

DNA origami is a revolutionary method for the assembly of molecular nanostructures from DNA with precisely defined dimensions and with an unprecedented yield. This can be utilized to arrange nanoscale components such as proteins or nanoparticles into pre-defined patterns. For applications it will now be of interest to arrange such components into functional complexes and study their geometry-dependent interactions. While commonly DNA nanostructures are characterized by atomic force microscopy or electron microscopy, these techniques often lack the time-resolution to study dynamic processes. It is therefore of considerable interest to also apply fluorescence microscopic techniques to DNA nanostructures. Of particular importance here is the utilization of novel super-resolved microscopy methods that enable imaging beyond the classical diffraction limit.

Templated Synthesis of Single-Walled Carbon Nanotubes with Specific Structure.

PubMed

Yang, Feng; Wang, Xiao; Li, Meihui; Liu, Xiyan; Zhao, Xiulan; Zhang, Daqi; Zhang, Yan; Yang, Juan; Li, Yan

2016-04-19

Single-walled carbon nanotubes (SWNTs) have shown great potential in various applications attributed to their unique structure-dependent properties. Therefore, the controlled preparation of chemically and structurally pristine SWNTs is a crucial issue for their advanced applications (e.g., nanoelectronics) and has been a great challenge for two decades. Epitaxial growth from well-defined seeds has been shown to be a promising strategy to control the structure of SWNTs. Segments of carbon nanotubes, including short pipes from cutting of preformed nanotubes and caps from opening of fullerenes or cyclodehydrogenation of polycyclic hydrocarbon precursors, have been used as the seeds to grow SWNTs. Single-chirality SWNTs were obtained with both presorted chirality-pure SWNT segments and end caps obtained from polycyclic hydrocarbon molecules with designed structure. The main challenges of nanocarbon-segment-seeded processes are the stability of the seeds, yield, and efficiency. Catalyst-mediated SWNT growth is believed to be more efficient. The composition and morphology of the catalyst nanoparticles have been widely reported to affect the chirality distribution of SWNTs. However, chirality-specific SWNT growth is hard to achieve by alternating catalysts. The specificity of enzyme-catalyzed reactions brings us an awareness of the essentiality of a unique catalyst structure for the chirality-selective growth of SWNTs. Only catalysts with the desired atomic arrangements in their crystal planes can act as structural templates for chirality-specific growth of SWNTs. We have developed a new family of catalysts, tungsten-based intermetallic compounds, which have high melting points and very special crystal structures, to facilitate the growth of SWNTs with designed chirality. By the use of W6Co7 catalysts, (12,6) SWNTs were directly grown with purity higher than 92%. Both high-resolution transmission electron microscopy measurements and density functional theory simulations show that the selective growth of (12,6) tubes is due to a good structural match between the carbon atom arrangement around the nanotube circumference and the metal atom arrangement of (0 0 12) planes in the catalyst. Similarly, (16,0) SWNTs exhibit a good structural match to the (116) planes of the W6Co7 catalyst. By optimization of the chemical vapor deposition (CVD) conditions, zigzag (16,0) SWNTs, which are generally known as a kinetically unfavorable species in CVD growth, were obtained with a purity of ∼80%. Generally speaking, the chirality-specific growth of SWNTs is realized by the cooperation of two factors: the structural match between SWNTs and the catalysts makes the growth of SWNTs with specific chirality thermodynamically favorable, and further manipulation of the CVD conditions results in optimized growth kinetics for SWNTs with this designed chirality. We expect that this advanced epitaxial growth strategy will pave the way for the ultimate goal of chirality-specified growth of SWNTs and will also be applicable in the controlled preparation of other nanomaterials.

Chemical contrast in STM imaging of transition metal aluminides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duguet, T.; Thiel, Patricia A.

2012-08-01

The present manuscript reviews recent scanning tunnelling microscopy (STM) studies of transition metal (TM) aluminide surfaces. It provides a general perspective on the contrast between Al atoms and TM atoms in STM imaging. A general trend is the much stronger bias dependence of TM atoms, or TM-rich regions of the surface. This dependence can be attenuated by the local chemical arrangements and environments. Al atoms can show a stronger bias dependence when their chemical environment, such as their immediate subsurface, is populated with TM. All this is well explained in light of combined results of STM and both theoretical andmore » experimental electronic and crystallographic structure determinations. Since STM probes the Fermi surface, the electronic structure in the vicinity of the Fermi level (EF) is essential for understanding contrast and bias dependence. Hence, partial density of states provides information about the TM d band position and width, s–p–d hybridization or interactions, or charge transfer between constituent elements. In addition, recent developments in STM image simulations are very interesting for elucidating chemical contrast at Al–TM alloy surfaces, and allow direct atomic identification, when the surface does not show too much disorder. Overall, we show that chemically-specific imaging is often possible at these surfaces.« less

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Perilla, Juan R.; Schulten, Klaus

2017-07-01

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.

Atomic quantum corrals for Bose-Einstein condensates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong Hongwei; Kavli Institute for Theoretical Physics China, Chinese Academy of Sciences, Beijing 100190; Wu Biao

2010-11-15

We consider the dynamics of Bose-Einstein condensates in a corral-like potential. Compared to the electronic quantum corrals, the atomic quantum corrals have the advantages of allowing direct and convenient observation of the wave dynamics, together with adjustable interaction strength. Our numerical study shows that these advantages not only allow exploration of the rich dynamical structures in the density distribution but also make the corrals useful in many other aspects. In particular, the corrals for atoms can be arranged into a stadium shape for the experimental visualization of quantum chaos, which has been elusive with electronic quantum corrals. The density correlationmore » is used to describe quantitatively the dynamical quantum chaos. Furthermore, we find that the interatomic interaction can greatly enhance the dynamical quantum chaos, for example, inducing a chaotic behavior even in circle-shaped corrals.« less

Free-energy landscape of the villin headpiece in an all-atom force field.

PubMed

Herges, Thomas; Wenzel, Wolfgang

2005-04-01

We investigate the landscape of the internal free-energy of the 36 amino acid villin headpiece with a modified basin hopping method in the all-atom force field PFF01, which was previously used to predictively fold several helical proteins with atomic resolution. We identify near native conformations of the protein as the global optimum of the force field. More than half of the twenty best simulations started from random initial conditions converge to the folding funnel of the native conformation, but several competing low-energy metastable conformations were observed. From 76,000 independently generated conformations we derived a decoy tree which illustrates the topological structure of the entire low-energy part of the free-energy landscape and characterizes the ensemble of metastable conformations. These emerge as similar in secondary content, but differ in tertiary arrangement.

Study of crystallization mechanisms of Fe nanoparticle

NASA Astrophysics Data System (ADS)

Kien, P. H.; Trang, G. T. T.; Hung, P. K.

2017-06-01

In this paper, the nanoparticle (NP) Fe was investigated by means of molecular dynamics simulation. The crystallization mechanism was studied through the time evolution of crystal cluster and potential energies of different atom types. The simulation shows that the NP was crystallized into bcc crystal structure when it was annealed at 900 K for long times. At early stage of the annealing, small nuclei form in different places of NP and dissolve for short times. After long times some nuclei form and gather nearby which create the stable clusters in the core of NP. After that the crystal clusters grow in the direction to cover the core and then to spread into the surface of NP. Analyzing the energies of different type atoms, we found that the crystal growth is originated from specific atomic arrangement in the boundary region of crystal clusters.

Microstructural evolution and micromechanical properties of gamma-irradiated Au ball bonds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yusoff, Wan Yusmawati Wan, E-mail: yusmawati@upnm.edu.my; Ismail, Roslina, E-mail: roslina.ismail@ukm.my; Jalar, Azman, E-mail: azmn@ukm.my

2014-07-01

The effect of gamma radiation on the mechanical and structural properties of gold ball bonds was investigated. Gold wires from thermosonic wire bonding were exposed to gamma rays from a Cobalt-60 source at a low dose (5 Gy). The load–depth curve of nanoindentation for the irradiated gold wire bond has an apparent staircase shape during loading compared to the as-received sample. The hardness of the specimens calculated from the nanoindentation shows an increase in value from 0.91 to 1.09 GPa for specimens after exposure. The reduced elastic modulus for irradiated specimens significantly increased as well, with values from 75.18 tomore » 98.55 GPa. The change in intrinsic properties due to gamma radiation was investigated using dual-focused ion beam and high-resolution transmission electron microscope analysis. The dual-focused ion beam and high-resolution transmission electron microscope images confirmed the changes in grain structure and the presence of dislocations. The scanning electron microscope micrographs of focused ion beam cross sections showed that the grain structure of the gold became elongated and smaller after exposure to gamma rays. Meanwhile, high-resolution transmission electron microscopy provided evidence that gamma radiation induced dislocation of the atomic arrangement. - Highlights: • Nanoindentation technique provides a detailed characterisation of Au ball bond. • P–h curve of irradiated Au ball bond shows an apparent pop-in event. • Hardness and reduced modulus increased after exposure. • Elongated and smaller grain structure in irradiated specimens • Prevalent presence of dislocations in the atomic arrangement.« less

Fusion of multichannel local and global structural cues for photo aesthetics evaluation.

PubMed

Luming Zhang; Yue Gao; Zimmermann, Roger; Qi Tian; Xuelong Li

2014-03-01

Photo aesthetic quality evaluation is a fundamental yet under addressed task in computer vision and image processing fields. Conventional approaches are frustrated by the following two drawbacks. First, both the local and global spatial arrangements of image regions play an important role in photo aesthetics. However, existing rules, e.g., visual balance, heuristically define which spatial distribution among the salient regions of a photo is aesthetically pleasing. Second, it is difficult to adjust visual cues from multiple channels automatically in photo aesthetics assessment. To solve these problems, we propose a new photo aesthetics evaluation framework, focusing on learning the image descriptors that characterize local and global structural aesthetics from multiple visual channels. In particular, to describe the spatial structure of the image local regions, we construct graphlets small-sized connected graphs by connecting spatially adjacent atomic regions. Since spatially adjacent graphlets distribute closely in their feature space, we project them onto a manifold and subsequently propose an embedding algorithm. The embedding algorithm encodes the photo global spatial layout into graphlets. Simultaneously, the importance of graphlets from multiple visual channels are dynamically adjusted. Finally, these post-embedding graphlets are integrated for photo aesthetics evaluation using a probabilistic model. Experimental results show that: 1) the visualized graphlets explicitly capture the aesthetically arranged atomic regions; 2) the proposed approach generalizes and improves four prominent aesthetic rules; and 3) our approach significantly outperforms state-of-the-art algorithms in photo aesthetics prediction.

Diverse carrier mobility of monolayer BNC x : a combined density functional theory and Boltzmann transport theory study.

PubMed

Wu, Tao; Deng, Kaiming; Deng, Weiqiao; Lu, Ruifeng

2017-10-19

BNC x monolayer as a kind of two-dimensional material has numerous chemical atomic ratios and arrangements with different electronic structures. Via calculations on the basis of density functional theory and Boltzmann transport theory under deformation potential approximation, the band structures and carrier mobilities of BNC x (x  =  1,2,3,4) nanosheets are systematically investigated. The calculated results show that BNC 2 -1 is a material with very small band gap (0.02 eV) among all the structures while other BNC x monolayers are semiconductors with band gap ranging from 0.51 eV to 1.32 eV. The carrier mobility of BNC x varies considerably from tens to millions of cm 2 V -1 s -1 . For BNC 2 -1, the hole mobility and electron mobility along both x and y directions can reach 10 5 orders of magnitude, which is similar to the carrier mobility of graphene. Besides, all studied BNC x monolayers obviously have anisotropic hole mobility and electron mobility. In particular, for semiconductor BNC 4 , its hole mobility along the y direction and electron mobility along the x direction unexpectedly reach 10 6 orders of magnitude, even higher than that of graphene. Our findings suggest that BNC x layered materials with the proper ratio and arrangement of carbon atoms will possess desirable charge transport properties, exhibiting potential applications in nanoelectronic devices.

Diverse carrier mobility of monolayer BNC x : a combined density functional theory and Boltzmann transport theory study

NASA Astrophysics Data System (ADS)

Wu, Tao; Deng, Kaiming; Deng, Weiqiao; Lu, Ruifeng

2017-11-01

BNC x monolayer as a kind of two-dimensional material has numerous chemical atomic ratios and arrangements with different electronic structures. Via calculations on the basis of density functional theory and Boltzmann transport theory under deformation potential approximation, the band structures and carrier mobilities of BNC x (x  =  1,2,3,4) nanosheets are systematically investigated. The calculated results show that BNC2-1 is a material with very small band gap (0.02 eV) among all the structures while other BNC x monolayers are semiconductors with band gap ranging from 0.51 eV to 1.32 eV. The carrier mobility of BNC x varies considerably from tens to millions of cm2 V-1 s-1. For BNC2-1, the hole mobility and electron mobility along both x and y directions can reach 105 orders of magnitude, which is similar to the carrier mobility of graphene. Besides, all studied BNC x monolayers obviously have anisotropic hole mobility and electron mobility. In particular, for semiconductor BNC4, its hole mobility along the y direction and electron mobility along the x direction unexpectedly reach 106 orders of magnitude, even higher than that of graphene. Our findings suggest that BNC x layered materials with the proper ratio and arrangement of carbon atoms will possess desirable charge transport properties, exhibiting potential applications in nanoelectronic devices.

Crystal structure of hexa­kis­(urea-κO)chromium(III) dichromate bromide monohydrate from synchrotron X-ray data

PubMed Central

Moon, Dohyun; Tanaka, Shinnosuke; Akitsu, Takashiro; Choi, Jong-Ha

2015-01-01

The title bromide salt, [Cr{CO(NH2)2}6](Cr2O7)Br·H2O, is isotypic to the corresponding chloride salt. Within the complex cation, the CrIII atom is coordinated by six O atoms of six urea ligands, displaying a slightly distorted octa­hedral coordination environment. The Cr—O bond lengths involving the urea ligands are in the range 1.9534 (13)–1.9776 (12) Å. The Cr2O7 2− anion has a nearly staggered conformation, with a bridging angle of 130.26 (10)°. The individual components are arranged in rows extending parallel to [100]. The Br− anion links the complex cation, as well as the solvent water mol­ecule, through N—H⋯Br and O—H⋯Br hydrogen-bonding inter­actions. The supra­molecular architecture also includes N—H⋯O and O—H⋯O hydrogen bonding between urea N—H and water O—H donor groups and the O atoms of the Cr2O7 2− anion as acceptor atoms, leading to a three-dimensional network structure. PMID:26594505

Atomic spin-chain realization of a model for quantum criticality

NASA Astrophysics Data System (ADS)

Toskovic, R.; van den Berg, R.; Spinelli, A.; Eliens, I. S.; van den Toorn, B.; Bryant, B.; Caux, J.-S.; Otte, A. F.

2016-07-01

The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum computing and spintronic devices; on the other hand, they can be used as fundamental building blocks for the realization of textbook many-body quantum models, illustrating key concepts such as quantum phase transitions, topological order or frustration as a function of system size. Here, we use low-temperature scanning tunnelling microscopy to construct arrays of magnetic atoms on a surface, designed to behave like spin-1/2 XXZ Heisenberg chains in a transverse field, for which a quantum phase transition from an antiferromagnetic to a paramagnetic phase is predicted in the thermodynamic limit. Site-resolved measurements on these finite-size realizations reveal a number of sudden ground state changes when the field approaches the critical value, each corresponding to a new domain wall entering the chains. We observe that these state crossings become closer for longer chains, suggesting the onset of critical behaviour. Our results present opportunities for further studies on quantum behaviour of many-body systems, as a function of their size and structural complexity.

Crystal structure of fac-tri-carbonyl-chlorido-bis-(4-hy-droxy-pyridine)-rhenium(I)-pyridin-4(1H)-one (1/1).

PubMed

Argibay-Otero, Saray; Carballo, Rosa; Vázquez-López, Ezequiel M

2017-10-01

The asymmetric unit of the title compound, [ReCl(C 5 H 5 NO) 2 (CO) 3 ]·C 5 H 5 NO, contains one mol-ecule of the complex fac -[ReCl(4-pyOH) 2 (CO) 3 ] (where 4-pyOH represents 4-hy-droxy-pyridine) and one mol-ecule of pyridin-4(1 H )-one (4-HpyO). In the mol-ecule of the complex, the Re atom is coordinated to two N atoms of the two 4-pyOH ligands, three carbonyl C atoms, in a facial configuration, and the Cl atom. The resulting geometry is slightly distorted octa-hedral. In the crystal structure, both fragments are associated by hydrogen bonds; two 4-HpyO mol-ecules bridge between two mol-ecules of the complex using the O=C group as acceptor for two different HO- groups of coordinated 4-pyOH from two neighbouring metal complexes. The resulting square arrangements are extented into infinite chains by hydrogen bonds involving the N-H groups of the 4-HpyO mol-ecule and the chloride ligands. The chains are further stabilized by π-stacking inter-actions.

1-Do­decyl­indoline-2,3-dione

PubMed Central

Qachchachi, Fatima-Zahrae; Ouazzani Chahdi, Fouad; Misbahi, Houria; Bodensteiner, Michael; El Ammari, Lahcen

2014-01-01

The structure of the title compound, C20H29NO2, is isotypic to that of its homologue 1-octylindoline-2,3-dione. The indoline ring and the two carbonyl-group O atoms are approximately coplanar, the largest deviation from the mean plane being 0.0760 (10) Å. The mean plane through the fused-ring system is nearly perpendicular to the mean plane passing through the 1-dodecyl chain [dihedral angle = 77.69 (5)°]. All C atoms of the dodecyl group are in an anti­periplanar arrangement. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds, forming a three-dimensional network. PMID:24764928

Construction and validation of an atomic model for bacterial TSPO from electron microscopy density, evolutionary constraints, and biochemical and biophysical data.

PubMed

Hinsen, Konrad; Vaitinadapoule, Aurore; Ostuni, Mariano A; Etchebest, Catherine; Lacapere, Jean-Jacques

2015-02-01

The 18 kDa protein TSPO is a highly conserved transmembrane protein found in bacteria, yeast, animals and plants. TSPO is involved in a wide range of physiological functions, among which the transport of several molecules. The atomic structure of monomeric ligand-bound mouse TSPO in detergent has been published recently. A previously published low-resolution structure of Rhodobacter sphaeroides TSPO, obtained from tubular crystals with lipids and observed in cryo-electron microscopy, revealed an oligomeric structure without any ligand. We analyze this electron microscopy density in view of available biochemical and biophysical data, building a matching atomic model for the monomer and then the entire crystal. We compare its intra- and inter-molecular contacts with those predicted by amino acid covariation in TSPO proteins from evolutionary sequence analysis. The arrangement of the five transmembrane helices in a monomer of our model is different from that observed for the mouse TSPO. We analyze possible ligand binding sites for protoporphyrin, for the high-affinity ligand PK 11195, and for cholesterol in TSPO monomers and/or oligomers, and we discuss possible functional implications. Copyright © 2014 Elsevier B.V. All rights reserved.

Antitumor activity of 3,4-ethylenedioxythiophene derivatives and quantitative structure-activity relationship analysis

NASA Astrophysics Data System (ADS)

Jukić, Marijana; Rastija, Vesna; Opačak-Bernardi, Teuta; Stolić, Ivana; Krstulović, Luka; Bajić, Miroslav; Glavaš-Obrovac, Ljubica

2017-04-01

The aim of this study was to evaluate nine newly synthesized amidine derivatives of 3,4- ethylenedioxythiophene (3,4-EDOT) for their cytotoxic activity against a panel of human cancer cell lines and to perform a quantitative structure-activity relationship (QSAR) analysis for the antitumor activity of a total of 27 3,4-ethylenedioxythiophene derivatives. Induction of apoptosis was investigated on the selected compounds, along with delivery options for the optimization of activity. The best obtained QSAR models include the following group of descriptors: BCUT, WHIM, 2D autocorrelations, 3D-MoRSE, GETAWAY descriptors, 2D frequency fingerprint and information indices. Obtained QSAR models should be relieved in elucidation of important physicochemical and structural requirements for this biological activity. Highly potent molecules have a symmetrical arrangement of substituents along the x axis, high frequency of distance between N and O atoms at topological distance 9, as well as between C and N atoms at topological distance 10, and more C atoms located at topological distances 6 and 3. Based on the conclusion given in the QSAR analysis, a new compound with possible great activity was proposed.

Structure and method for controlling band offset and alignment at a crystalline oxide-on-semiconductor interface

DOEpatents

McKee, Rodney A.; Walker, Frederick J.

2003-11-25

A crystalline oxide-on-semiconductor structure and a process for constructing the structure involves a substrate of silicon, germanium or a silicon-germanium alloy and an epitaxial thin film overlying the surface of the substrate wherein the thin film consists of a first epitaxial stratum of single atomic plane layers of an alkaline earth oxide designated generally as (AO).sub.n and a second stratum of single unit cell layers of an oxide material designated as (A'BO.sub.3).sub.m so that the multilayer film arranged upon the substrate surface is designated (AO).sub.n (A'BO.sub.3).sub.m wherein n is an integer repeat of single atomic plane layers of the alkaline earth oxide AO and m is an integer repeat of single unit cell layers of the A'BO.sub.3 oxide material. Within the multilayer film, the values of n and m have been selected to provide the structure with a desired electrical structure at the substrate/thin film interface that can be optimized to control band offset and alignment.

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed Central

Pollanen, M. S.; Markiewicz, P.; Bergeron, C.; Goh, M. C.

1994-01-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures. Images Figure 1 PMID:8178938

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed

Pollanen, M S; Markiewicz, P; Bergeron, C; Goh, M C

1994-05-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

PubMed Central

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradeca­bromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome. PMID:23385464

Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liu, Feng-xiang; Liu, Rang-su; Hou, Zhao-yang; Liu, Hai-Rong; Tian, Ze-an; Zhou, Li-li

2009-02-01

The rapid solidification processes of Al 50Mg 50 liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method—cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, …. The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Polymeric Cd(II), trinuclear and mononuclear Ni(II) complexes of 5-methyl-4-phenyl-1,2,4-triazole-3-thione: Synthesis, structural characterization, thermal behaviour, fluorescence properties and antibacterial activity

NASA Astrophysics Data System (ADS)

Bharty, M. K.; Paswan, S.; Dani, R. K.; Singh, N. K.; Sharma, V. K.; Kharwar, R. N.; Butcher, R. J.

2017-02-01

Syntheses of a polymeric Cd(II) complex, [Cd(mptt)2]n (1), a trinuclear Ni(II) complex, [Ni3(μ-mptt)4(μ-H2O)2(H2O)2(ttfa)2]·3H2O (2) and a mononuclear Ni(II) complex [Ni(mptt)2(en)2] (3) have been performed using the ligand 5-methyl-4-phenyl-1,2,4-triazole-3-thione (Hmptt) and nickel(II)/cadmium(II) salts {ttfa = thenoyltrifluroacetonate). The ligand and the complexes have been characterized by various physicochemical methods in addition to their single crystal X-ray structure. The Cd centre in complex 1 adopts a distorted tetrahedral geometry with one sulfur atom and two mptt ligands provide three nitrogen atoms from three triazole units. The sulfur atom of the ligand binds covalently and overall the ligand acts as uninigative N,S/N,N bidentate moiety. The polymeric structure of complex 1 results from the N atoms of the neighboring triazole units coordinating with the Cd(II) centre. The three Ni(II) centres in the trinuclear Ni(II) complex 2 form a linear arrangement and all have six coordinated arrangements. The middle Ni(II) binds with four deprotonated triazole ring nitrogens and two water molecules form two bridges. The terminal Ni(II) centres bind through two thenoyl oxygens, two triazole nitrogens and water molecules that formed bridges with the middle Ni centre. In complex 3, the nickel(II) centre is covalently bonded through two deprotonated triazole ring nitrogens from two ligand moieties and other four sites are occupied by four nitrogens from two bidentate en ligands. Thermogravimetric analyses (TGA) of the complexes indicated for NiO as the final residue. The bioefficacy of the ligand and complexes 2 and 3 have been examined against the growth of bacteria to evaluate their anti-microbial potential. Complex 2 showed high antibacterial activity as compared to the ligand and complex 3. Complexes 1, 2 and 3 are fluorescent materials with maximum emissions at 425, 421 and 396 nm at an excitation wavelength of 323, 348 and 322 nm, respectively.

MgCu metallic glass

NASA Astrophysics Data System (ADS)

Durandurdu, Murat

2018-03-01

We generate an amorphous MgCu model using the rapid solidification of the melt through a first-principles molecular dynamics approach within a generalised gradient approximation and reveal, for the first time, its structural features and mechanical properties in details. The liquid and glassy MgCu are found to acquire slightly distinct local structures. Yet in both forms of MgCu, most Cu atoms have a tendency to form the ideal and defective icosahedrons while Mg atoms are arranged in complex configurations. The mean coordination number of Cu and Mg at 300 K is 11.31 and 13.73, respectively. The short-range order of MgCu glass is projected to be different than the known crystalline MgCu and Mg2Cu phases. The mechanical properties of MgCu glass and the CsCl-type MgCu crystal are computed and compared. On the basis of the enthalpy analyses, a possible pressure-induced crystallisation of the MgCu glass into a CsCl-type structure is proposed to occur at around 11 GPa.

Monoatomic and dimer Mn adsorption on the Au(111) surface from first principles

NASA Astrophysics Data System (ADS)

Muñoz, Francisco; Romero, Aldo H.; Mejía-López, Jose; Morán-López, J. L.

2011-05-01

A theoretical study based on the density functional theory of the adsorption of Mn monomers and dimers on a Au-(111) surface is presented. As necessary preliminary steps, the bulk and clean surface electronic structure are calculated, which agree well with previous reports. Then, the electronic structure of the Mn adatom, chemisorbed on four different surface geometries, is analyzed. It is found that the most stable geometry is when the Mn atom is chemisorbed on threefold coordinated sites. Using this geometry for a single adatom a second Mn atom is chemisorbed and the most stable dimer geometrical structure is calculated. The lowest-energy configuration corresponds to the molecule lying parallel to the surface, adsorbed on two topological equivalent threefold coordinated sites. It is also found that the lowest-energy magnetic configuration corresponds to the antiferromagnetic arrangement with individual magnetic moments of 4.64μB. Finally, it is concluded that the dimer is not stable and should fragment at the surface.

Ab initio studies of isolated boron substitutional defects in graphane

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Chetty, N.

2017-10-01

We have systematically studied energetics, structural and electronic properties of different configurations of the B atoms substituting C-H pairs located on a single hexagonal ring in a graphane system using the first-principles density functional theory (DFT). A total number of 12 distinct B dopants configurations were identified and characterized. Based on the formation energy analysis, we found that relative stability of B dopants depends greatly on the defect configurations. Our results suggest that the B substitutions prefer to be distributed randomly but avoiding the formation of homo-elemental B-B bonds in a graphane system, at any concentration. Generally, the values of band gap decrease as the number of B dopants increases, but the low energy configurations have large band gaps compared to those that have homo-elemental bonds. As a result, the band gap of graphane can be fine tuned through the change in the structural arrangement of B atoms. The adequate control of the electronic structure of graphane through doping should be essential for technological device applications.

A near atomic structure of the active human apoptosome

PubMed Central

Cheng, Tat Cheung; Hong, Chuan; Akey, Ildikó V; Yuan, Shujun; Akey, Christopher W

2016-01-01

In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease. DOI: http://dx.doi.org/10.7554/eLife.17755.001 PMID:27697150

Structure and magnetism of new rare-earth-free intermetallic compounds: Fe 3+xCo 3-xTi 2 (0 ≤ x ≤ 3)

DOE PAGES

Balasubramanian, Balamurugan; Das, Bhaskar; Nguyen, Manh Cuong; ...

2016-11-28

Here, we report the fabrication of a set of new rare-earth-free magnetic compounds, which form the Fe 3Co 3Ti 2-type hexagonal structure with P-6m2 symmetry. Neutron powder diffraction shows a significant Fe/Co anti-site mixing in the Fe 3Co 3Ti 2 structure, which has a strong effect on the magnetocrystalline anisotropy as revealed by first-principle calculations. Increasing substitution of Fe atoms for Co in the Fe 3Co 3Ti 2 lattice leads to the formation of Fe 4Co 2Ti 2, Fe 5CoTi, and Fe 6Ti 2 with significantly improved permanent-magnet properties. A high magnetic anisotropy (13.0 Mergs/cm 3) and saturation magnetic polarizationmore » (11.4 kG) are achieved at 10 K by altering the atomic arrangements and decreasing Fe/Co occupancy disorder.« less

Imaging atomic-level random walk of a point defect in graphene

NASA Astrophysics Data System (ADS)

Kotakoski, Jani; Mangler, Clemens; Meyer, Jannik C.

2014-05-01

Deviations from the perfect atomic arrangements in crystals play an important role in affecting their properties. Similarly, diffusion of such deviations is behind many microstructural changes in solids. However, observation of point defect diffusion is hindered both by the difficulties related to direct imaging of non-periodic structures and by the timescales involved in the diffusion process. Here, instead of imaging thermal diffusion, we stimulate and follow the migration of a divacancy through graphene lattice using a scanning transmission electron microscope operated at 60 kV. The beam-activated process happens on a timescale that allows us to capture a significant part of the structural transformations and trajectory of the defect. The low voltage combined with ultra-high vacuum conditions ensure that the defect remains stable over long image sequences, which allows us for the first time to directly follow the diffusion of a point defect in a crystalline material.

Self-assembly of a binodal metal-organic framework exhibiting a demi-regular lattice.

PubMed

Yan, Linghao; Kuang, Guowen; Zhang, Qiushi; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2017-10-26

Designing metal-organic frameworks with new topologies is a long-standing quest because new topologies often accompany new properties and functions. Here we report that 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene molecules coordinate with Cu atoms to form a two-dimensional framework in which Cu adatoms form a nanometer-scale demi-regular lattice. The lattice is articulated by perfectly arranged twofold and threefold pyridyl-Cu coordination motifs in a ratio of 1 : 6 and features local dodecagonal symmetry. This structure is thermodynamically robust and emerges solely when the molecular density is at a critical value. In comparison, we present three framework structures that consist of semi-regular and regular lattices of Cu atoms self-assembled out of 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene and trispyridylbenzene molecules. Thus a family of regular, semi-regular and demi-regular lattices can be achieved by Cu-pyridyl coordination.

A new fundamental type of conformational isomerism

NASA Astrophysics Data System (ADS)

Canfield, Peter J.; Blake, Iain M.; Cai, Zheng-Li; Luck, Ian J.; Krausz, Elmars; Kobayashi, Rika; Reimers, Jeffrey R.; Crossley, Maxwell J.

2018-06-01

Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term `akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Computational Investigation of Graphene-Carbon Nanotube-Polymer Composite

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Roth, Michael; Todde, Guido; Subramanian, Gopinath; Shukla, Manoj; Univ of Southern Mississippi Collaboration; US Army Engineer Research; Development Center 3909 Halls Ferry Road Vicksburg, MS 39180, USA Collaboration

Graphene is a single atom thick two dimensional carbon sheet where sp2 -hybridized carbon atoms are arranged in a honeycomb structure. The functionalization of graphene and carbon nanotubes (CNTs) with polymer is a route for developing high performance nanocomposite materials. We study the interfacial interactions among graphene, CNT, and Nylon 6 polymer using computational methods based on density functional theory (DFT) and empirical force-field. Our DFT calculations are carried out using Quantum-ESPRESSO electronic structure code with van der Waals functional (vdW-DF2), whereas the empirical calculations are performed using LAMMPS with the COMPASS force-field. Our results demonstrated that the interactions between (8,8) CNT and graphene, and between CNT/graphene and Nylon 6 consist mostly of van der Waals type. The computed Young's moduli indicated that the mechanical properties of carbon nanostructures are enhanced by their interactions with polymer. The presence of Stone-Wales (SW) defects lowered the Young's moduli of carbon nanostructures.

Cohesive Relations for Surface Atoms in the Iron-Technetium Binary System

DOE PAGES

Taylor, Christopher D.

2011-01-01

Iron-technetium alloys are of relevance to the development of waste forms for disposition of radioactive technetium-99 obtained from spent nuclear fuel. Corrosion of candidate waste forms is a function of the local cohesive energy () of surface atoms. A theoretical model for calculating is developed. Density functional theory was used to construct a modified embedded atom (MEAM) potential for iron-technetium. Materials properties determined for the iron-technetium system were in good agreement with the literature. To explore the relationship between local structure and corrosion, MEAM simulations were performed on representative iron-technetium alloys and intermetallics. Technetium-rich phases have lower , suggesting thatmore » these phases will be more noble than iron-rich ones. Quantitative estimates of based on numbers of nearest neighbors alone can lead to errors up to 0.5 eV. Consequently, atomistic corrosion simulations for alloy systems should utilize physics-based models that consider not only neighbor counts, but also local compositions and atomic arrangements.« less

Single-Layer Limit of Metallic Indium Overlayers on Si(111).

PubMed

Park, Jae Whan; Kang, Myung Ho

2016-09-09

Density-functional calculations are used to identify one-atom-thick metallic In phases grown on the Si(111) surface, which have long been sought in quest of the ultimate two-dimensional (2D) limit of metallic properties. We predict two metastable single-layer In phases, one sqrt[7]×sqrt[3] phase with a coverage of 1.4 monolayer (ML; here 1 ML refers to one In atom per top Si atom) and the other sqrt[7]×sqrt[7] phase with 1.43 ML, which indeed agree with experimental evidences. Both phases reveal quasi-1D arrangements of protruded In atoms, leading to 2D-metallic but anisotropic band structures and Fermi surfaces. This directional feature contrasts with the free-electron-like In-overlayer properties that are known to persist up to the double-layer thickness, implying that the ultimate 2D limit of In overlayers may have been achieved in previous studies of double-layer In phases.

In-plane heterostructures of graphene and hexagonal boron nitride with controlled domain sizes

NASA Astrophysics Data System (ADS)

Liu, Zheng; Ma, Lulu; Shi, Gang; Zhou, Wu; Gong, Yongji; Lei, Sidong; Yang, Xuebei; Zhang, Jiangnan; Yu, Jingjiang; Hackenberg, Ken P.; Babakhani, Aydin; Idrobo, Juan-Carlos; Vajtai, Robert; Lou, Jun; Ajayan, Pulickel M.

2013-02-01

Graphene and hexagonal boron nitride (h-BN) have similar crystal structures with a lattice constant difference of only 2%. However, graphene is a zero-bandgap semiconductor with remarkably high carrier mobility at room temperature, whereas an atomically thin layer of h-BN is a dielectric with a wide bandgap of ~5.9 eV. Accordingly, if precise two-dimensional domains of graphene and h-BN can be seamlessly stitched together, hybrid atomic layers with interesting electronic applications could be created. Here, we show that planar graphene/h-BN heterostructures can be formed by growing graphene in lithographically patterned h-BN atomic layers. Our approach can create periodic arrangements of domains with size ranging from tens of nanometres to millimetres. The resulting graphene/h-BN atomic layers can be peeled off the growth substrate and transferred to various platforms including flexible substrates. We also show that the technique can be used to fabricate two-dimensional devices, such as a split closed-loop resonator that works as a bandpass filter.

Atomic resolution of Lithium Ions in LiCoO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao-Horn, Yang; Croguennec, Laurence; Delmas, Claude

2003-03-18

LiCoO2 is the most common lithium storage material for lithium rechargeable batteries, used widely to power portable electronic devices such as laptop computers. Lithium arrangements in the CoO2 framework have a profound effect on the structural stability and electrochemical properties of LixCoO2 (0 < x < 1), however, probing lithium ions has been difficult using traditional X-ray and neutron diffraction techniques. Here we have succeeded in simultaneously resolving columns of cobalt, oxygen, and lithium atoms in layered LiCoO2 battery material using experimental focal series of LiCoO2 images obtained at sub-Angstrom resolution in a mid-voltage transmission electron microscope. Lithium atoms aremore » the smallest and lightest metal atoms, and scatter electrons only very weakly. We believe our observations of lithium to be the first by electron microscopy, and that they show promise to direct visualization of the ordering of lithium and vacancy in LixCoO2.« less

Atomically thin gallium layers from solid-melt exfoliation

PubMed Central

Kochat, Vidya; Samanta, Atanu; Zhang, Yuan; Bhowmick, Sanjit; Manimunda, Praveena; Asif, Syed Asif S.; Stender, Anthony S.; Vajtai, Robert; Singh, Abhishek K.; Tiwary, Chandra S.; Ajayan, Pulickel M.

2018-01-01

Among the large number of promising two-dimensional (2D) atomic layer crystals, true metallic layers are rare. Using combined theoretical and experimental approaches, we report on the stability and successful exfoliation of atomically thin “gallenene” sheets on a silicon substrate, which has two distinct atomic arrangements along crystallographic twin directions of the parent α-gallium. With a weak interface between solid and molten phases of gallium, a solid-melt interface exfoliation technique is developed to extract these layers. Phonon dispersion calculations show that gallenene can be stabilized with bulk gallium lattice parameters. The electronic band structure of gallenene shows a combination of partially filled Dirac cone and the nonlinear dispersive band near the Fermi level, suggesting that gallenene should behave as a metallic layer. Furthermore, it is observed that the strong interaction of gallenene with other 2D semiconductors induces semiconducting to metallic phase transitions in the latter, paving the way for using gallenene as promising metallic contacts in 2D devices. PMID:29536039

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

High-emission cold cathode

DOEpatents

Mancebo, L.

1974-01-29

A field-emission cathode having a multitude of field emission points for emitting a copious stream of electrons when subjected to a high field is described. The cathode is constructed by compressing a multitude of tungsten strips alternately arranged with molybdenum strips and copper ribbons or compressing alternately arranged copper plated tungsten and molybdenum strips, heating the arrangement to braze the tungsten and molybdenum strips together with the copper, machining and grinding the exposed strip edges of one side of the brazed arrangement to obtain a precisely planar surface, etching a portion of the molybdenum and copper to leave the edges of the tungsten strips protruding for electron emission, and subjecting the protruding edges of the tungsten strips to a high electric field to degas and roughen the surface to pnovide a large number of emitting points. The resulting structure is particularly useful as a cathode in a transversely excited gaseous laser where the cathode is mounted in a vacuum chamber for emitting electrons under the influence of a high electric field between the cathode and an extractor grid. The electrons pass through the extractor grid, a thin window in the wall of the laser chamber and into the laser chamber which is filled with a gaseous mixture of helium, nitrogen, and carbon dioxide. A second grid is mounted on the gaseous side of the window. The electrons pass into the laser chamber under the influence of a second electric field between the second grid and an anode in the laser chamber to raise selected gas atoms of the gaseous mixture to appropriately excited states so that a subsequent coherent light beam passing through the mixture transversely to the electron stream through windows in opposite ends of the laser chamber stimulates the excited atoms to amplify the beam. (Official Gazette)

Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration.

PubMed

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J; Vassallo, David A; Vega, Irving E; Arold, Stefan T; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP domains for increasing the yield of fatty acids in bacterial cultures.

Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

PubMed Central

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J.; Vassallo, David A.; Vega, Irving E.; Arold, Stefan T.; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP domains for increasing the yield of fatty acids in bacterial cultures. PMID:23469090

Atomic layer deposition of nanoporous biomaterials.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Narayan, R. J.; Adiga, S. P.; Pellin, M. J.

2010-03-01

Due to its chemical stability, uniform pore size, and high pore density, nanoporous alumina is being investigated for use in biosensing, drug delivery, hemodialysis, and other medical applications. In recent work, we have examined the use of atomic layer deposition for coating the surfaces of nanoporous alumina membranes. Zinc oxide coatings were deposited on nanoporous alumina membranes using atomic layer deposition. The zinc oxide-coated nanoporous alumina membranes demonstrated antimicrobial activity against Escherichia coli and Staphylococcus aureus bacteria. These results suggest that atomic layer deposition is an attractive technique for modifying the surfaces of nanoporous alumina membranes and other nanostructured biomaterials.more » Nanoporous alumina, also known as anodic aluminum oxide (AAO), is a nanomaterial that exhibits several unusual properties, including high pore densities, straight pores, small pore sizes, and uniform pore sizes. In 1953, Keller et al. showed that anodizing aluminum in acid electrolytes results in a thick layer of nearly cylindrical pores, which are arranged in a close-packed hexagonal cell structure. More recently, Matsuda & Fukuda demonstrated preparation of highly ordered platinum and gold nanohole arrays using a replication process. In this study, a negative structure of nanoporous alumina was initially fabricated and a positive structure of a nanoporous metal was subsequently fabricated. Over the past fifteen years, nanoporous alumina membranes have been used as templates for growth of a variety of nanostructured materials, including nanotubes, nanowires, nanorods, and nanoporous membranes.« less

Structural morphology of cotunnite, PbCl 2, laurionite, Pb(OH)Cl, and SbSI

NASA Astrophysics Data System (ADS)

Woensdregt, C. F.; Hartman, P.

1988-03-01

The structural morphology of compounds having the PbCl 2 and the closely related SbSI structures has been determined. Based upon the nine-coordination of the Pb atoms the F forms of the PbCl 2 structure are {110}, {020}, {120}, {011}, {200}, {111} , {201}, {121} and {211}. These forms are arranged in an order of increasing attachment energies, that were calculated using a broken bond model. In the SbSI structure type the Sb atom has a seven-coordination with the consequence that {020} becomes a different surface structure and that {120} is an S face. The theoretical habit of PbCl 2 and Pb(OH)Cl is short prismatic, elongated along the c axis, with {011} as terminal form. The appearance of {211} as main form on PbCl 2 when growth takes place from pure aqueous solution is ascribed to the preferential adsorption of OH - ions on that face. The predominance of {020} and {121} on PbCl 2 from solutions containing HCl is explained by adsorption of H 3O + on these faces. The theoretical habit of the SbSI structure type is slender prismatic {110} with {011} as terminal form.

Conformational analysis of cellobiose by electronic structure theories.

PubMed

French, Alfred D; Johnson, Glenn P; Cramer, Christopher J; Csonka, Gábor I

2012-03-01

Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory. Published by Elsevier Ltd.

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perilla, Juan R.; Schulten, Klaus

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

DOE PAGES

Perilla, Juan R.; Schulten, Klaus

2017-07-19

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

A Hybrid Density Functional Study of Atomic Hydrogen and Oxygen Adsorptions on the (0001) Surface of Non-Magnetic DHCP Americium

NASA Astrophysics Data System (ADS)

Amdani-Moten, Shafaq; Atta-Fynn, Raymond; Ray, Asok

2010-03-01

As our group have recently shown^+, hybrid density functional theory (HDFT) which replaces a fraction (40%) of approximate DFT exchange with exact Hartree-Fock exchange yield structural, magnetic, and electronic properties for Americium-I that are in excellent agreement with experimental data. As a natural progression, ab initio calculations for atomic adsorptions on the (0001) surface of non-magnetic americium have been performed using HDFT. The americium surface is modeled by a seven-layer slab using inversion symmetry consisting of one atom per layer and non-magnetic ABAC stacking arrangement of these layers. Top, bridge, hcp and fcc chemisorption sites have been investigated with energies optimized with respect to the adatom distance from the surface. Details of the chemisorptions processes as well as comparisons of different sites will be presented. ^+ R. Atta-Fynn and A. K. Ray, Chemical Physics Letters, 482, 223-227 (2009).

The mechanics of tessellations - bioinspired strategies for fracture resistance.

PubMed

Fratzl, Peter; Kolednik, Otmar; Fischer, F Dieter; Dean, Mason N

2016-01-21

Faced with a comparatively limited palette of minerals and organic polymers as building materials, evolution has arrived repeatedly on structural solutions that rely on clever geometric arrangements to avoid mechanical trade-offs in stiffness, strength and flexibility. In this tutorial review, we highlight the concept of tessellation, a structural motif that involves periodic soft and hard elements arranged in series and that appears in a vast array of invertebrate and vertebrate animal biomaterials. We start from basic mechanics principles on the effects of material heterogeneities in hypothetical structures, to derive common concepts from a diversity of natural examples of one-, two- and three-dimensional tilings/layerings. We show that the tessellation of a hard, continuous surface - its atomization into discrete elements connected by a softer phase - can theoretically result in maximization of material toughness, with little expense to stiffness or strength. Moreover, the arrangement of soft/flexible and hard/stiff elements into particular geometries can permit surprising functions, such as signal filtering or 'stretch and catch' responses, where the constrained flexibility of systems allows a built-in safety mechanism for ensuring that both compressive and tensile loads are managed well. Our analysis unites examples ranging from exoskeletal materials (fish scales, arthropod cuticle, turtle shell) to endoskeletal materials (bone, shark cartilage, sponge spicules) to attachment devices (mussel byssal threads), from both invertebrate and vertebrate animals, while spotlighting success and potential for bio-inspired manmade applications.

A Bibliography of Basic Books on Atomic Energy. Update.

ERIC Educational Resources Information Center

Atomic Energy Commission, Washington, DC. Office of Information Services.

This booklet, part of the United States Atomic Energy Commission's series of information booklets, lists selected commerically published books for the general public on atomic energy and closely related subjects. It includes annotated bibliographies for children (grade level indicated) and adults. The books are arranged by subject, alphabetized by…

Exploring symmetry as an avenue to the computational design of large protein domains.

PubMed

Fortenberry, Carie; Bowman, Elizabeth Anne; Proffitt, Will; Dorr, Brent; Combs, Steven; Harp, Joel; Mizoue, Laura; Meiler, Jens

2011-11-16

It has been demonstrated previously that symmetric, homodimeric proteins are energetically favored, which explains their abundance in nature. It has been proposed that such symmetric homodimers underwent gene duplication and fusion to evolve into protein topologies that have a symmetric arrangement of secondary structure elements--"symmetric superfolds". Here, the ROSETTA protein design software was used to computationally engineer a perfectly symmetric variant of imidazole glycerol phosphate synthase and its corresponding symmetric homodimer. The new protein, termed FLR, adopts the symmetric (βα)(8) TIM-barrel superfold. The protein is soluble and monomeric and exhibits two-fold symmetry not only in the arrangement of secondary structure elements but also in sequence and at atomic detail, as verified by crystallography. When cut in half, FLR dimerizes readily to form the symmetric homodimer. The successful computational design of FLR demonstrates progress in our understanding of the underlying principles of protein stability and presents an attractive strategy for the in silico construction of larger protein domains from smaller pieces.

Anti-site disorder and improved functionality of Mn₂NiX (X = Al, Ga, In, Sn) inverse Heusler alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paul, Souvik; Kundu, Ashis; Ghosh, Subhradip, E-mail: subhra@iitg.ernet.in

2014-10-07

Recent first-principles calculations have predicted Mn₂NiX (X = Al, Ga, In, Sn) alloys to be magnetic shape memory alloys. Moreover, experiments on Mn₂NiGa and Mn₂NiSn suggest that the alloys deviate from the perfect inverse Heusler arrangement and that there is chemical disorder at the sublattices with tetrahedral symmetry. In this work, we investigate the effects of such chemical disorder on phase stabilities and magnetic properties using first-principles electronic structure methods. We find that except Mn₂NiAl, all other alloys show signatures of martensitic transformations in presence of anti-site disorder at the sublattices with tetrahedral symmetry. This improves the possibilities of realizingmore » martensitic transformations at relatively low fields and the possibilities of obtaining significantly large inverse magneto-caloric effects, in comparison to perfect inverse Heusler arrangement of atoms. We analyze the origin of such improvements in functional properties by investigating electronic structures and magnetic exchange interactions.« less

Structural phase transitions of (Bi 1$-$xSb x ) 2(Te 1$-$y Se y) 3 compounds under high pressure and the influence of the atomic radius on the compression processes of tetradymites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Jinggeng; Yu, Zhenhai; Hu, Qingyang

Recently, A 2B 3-type tetradymites have developed into a hot topic in physical and material research fields, where the A and B atoms represent V and VI group elements, respectively. In this study, in situ angle-dispersive X-ray diffraction measurements were performed on Bi 2Te 2Se, BiSbTeSe 2, and Sb 2Te 2Se tetradymites under high pressure. Bi 2Te 2Se transforms from a layered rhombohedral structure (phase I) into 7-fold monoclinic (phase II) and body-centered tetragonal (phase IV) structures at about 8.0 and 14.3 GPa, respectively, without an 8-fold monoclinic structure (phase III) similar to that in Bi 2Te 3. Thus, themore » compression behavior of Bi 2Te 2Se is the same as that of Bi 2Se 3, which could also be obtained from first-principles calculations and in situ high-pressure electrical resistance measurements. Under high pressure, BiSbTeSe 2 and Sb 2Te 2Se undergo similar structural phase transitions to Bi 2Te 2Se, which indicates that the compression process of tellurides can be modulated by doping Se in Te sites. According to these high-pressure investigations of A 2B 3-type tetradymites, the decrease of the B-site atomic radius shrinks the stable pressure range of phase III and expands that of phase II, whereas the decrease of the A-site atomic radius induces a different effect, i.e. expanding the stable pressure range of phase III and shrinking that of phase II. Lastly, the influence of the atomic radius on the compression process of tetradymites is closely related to the chemical composition and the atom arrangement in the quintuple layer.« less

Structural phase transitions of (Bi 1$-$xSb x ) 2(Te 1$-$y Se y) 3 compounds under high pressure and the influence of the atomic radius on the compression processes of tetradymites

DOE PAGES

Zhao, Jinggeng; Yu, Zhenhai; Hu, Qingyang; ...

2016-12-14

Recently, A 2B 3-type tetradymites have developed into a hot topic in physical and material research fields, where the A and B atoms represent V and VI group elements, respectively. In this study, in situ angle-dispersive X-ray diffraction measurements were performed on Bi 2Te 2Se, BiSbTeSe 2, and Sb 2Te 2Se tetradymites under high pressure. Bi 2Te 2Se transforms from a layered rhombohedral structure (phase I) into 7-fold monoclinic (phase II) and body-centered tetragonal (phase IV) structures at about 8.0 and 14.3 GPa, respectively, without an 8-fold monoclinic structure (phase III) similar to that in Bi 2Te 3. Thus, themore » compression behavior of Bi 2Te 2Se is the same as that of Bi 2Se 3, which could also be obtained from first-principles calculations and in situ high-pressure electrical resistance measurements. Under high pressure, BiSbTeSe 2 and Sb 2Te 2Se undergo similar structural phase transitions to Bi 2Te 2Se, which indicates that the compression process of tellurides can be modulated by doping Se in Te sites. According to these high-pressure investigations of A 2B 3-type tetradymites, the decrease of the B-site atomic radius shrinks the stable pressure range of phase III and expands that of phase II, whereas the decrease of the A-site atomic radius induces a different effect, i.e. expanding the stable pressure range of phase III and shrinking that of phase II. Lastly, the influence of the atomic radius on the compression process of tetradymites is closely related to the chemical composition and the atom arrangement in the quintuple layer.« less

Dipole-dipole interactions in a hot atomic vapor and in an ultracold gas of Rydberg atoms

NASA Astrophysics Data System (ADS)

Sautenkov, V. A.; Saakyan, S. A.; Bronin, S. Ya; Klyarfeld, A. B.; Zelener, B. B.; Zelener, B. V.

2018-01-01

In our paper ideal and non-ideal gas media of neutral atoms are analyzed. The first we discuss a dipole broadening of atomic transitions in excited dilute and dense metal vapors. Then the theoretical studies of the dipole-dipole interactions in dense ultracold gas of Rydberg atoms are considered. Possible future experiments on a base of our experimental arrangement are suggested.

76 FR 37343 - Proposed Subsequent Arrangement

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-27

... International Security, National Nuclear Security Administration, Department of Energy. ACTION: Proposed... arrangement under the Agreement for Cooperation Concerning Civil Uses of Nuclear Energy Between the Government... Peaceful Uses of Nuclear Energy Between the United States of America and the European Atomic Energy...

Tris-(hydroxyamino)triazines: high-affinity chelating tridentate O,N,O-hydroxylamine ligand for the cis-V(V)O2(+) cation.

PubMed

Nikolakis, Vladimiros A; Exarchou, Vassiliki; Jakusch, Tamás; Woolins, J Derek; Slawin, Alexandra M Z; Kiss, Tamás; Kabanos, Themistoklis A

2010-10-14

The treatment of the trichloro-1,3,5-triazine with N-methylhydroxylamine hydrochloride results in the replacement of the three chlorine atoms of the triazine ring with the function -N(OH)CH(3) yielding the symmetrical tris-(hydroxyamino)triazine ligand H(3)trihyat. Reaction of the ligand H(3)trihyat with NaV(V)O(3) in aqueous solution followed by addition of Ph(4)PCl gave the mononuclear vanadium(V) compound Ph(4)P[V(V)O(2)(Htrihyat)] (1). The structure of compound 1 was determined by X-ray crystallography and indicates that this compound has a distorted square-pyramidal arrangement around vanadium. The ligand Htrihyat(2-) is bonded to vanadium atom in a tridentate fashion at the triazine ring nitrogen atom and the two deprotonated hydroxylamido oxygen atoms. The high electron density of the triazine ring nitrogen atoms, which results from the resonative contribution of electrons of exocyclic nitrogen atoms, leads to a very strong V-N bond. The cis-[V(V)O(2)(Htrihyat)](-) species exhibits high hydrolytic stability in aqueous solution over a wide pH range, 2.5-11.5, as was evidenced by potentiometry.

Deciphering chemical order/disorder and material properties at the single-atom level

DOE PAGES

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.; ...

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

A Novel Method for Sampling Alpha-Helical Protein Backbones

DOE R&D Accomplishments Database

Fain, Boris; Levitt, Michael

2001-01-01

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.

Structural and dynamical characterization of water on the Au (100) and graphene surfaces: A molecular dynamics simulation approach

NASA Astrophysics Data System (ADS)

Foroutan, Masumeh; Darvishi, Mehdi; Fatemi, S. Mahmood

2017-09-01

The positioning, adsorption, and movement of water on substrates is dependent upon the chemical nature and arrangement of the atoms of the surface. Therefore the behavior of water molecules on a substrate is a reflection of properties of the surface. Based on this premise, graphene and gold substrates were chosen to study this subject from a molecular perspective. In this work, the structural and dynamical behaviors of a water nanodroplet on Au (100) and the graphene interfaces have been studied by molecular dynamics simulation. The results have shown how the structural and dynamical behaviors of water molecules at the interface reflect the characteristics of these surfaces. The results have demonstrated that residence time and hydrogen bonds' lifetime at the water-Au (100) interface are bigger than at the water-graphene interface. Energy contour map analysis indicates a more uniform surface energy on graphene than on the gold surface. The obtained results illustrate that water clusters on gold and graphene form tetramer and hexamer structures, respectively. Furthermore, the water molecules are more ordered on the gold surface than on graphene. The study of hydrogen bonds showed that the order, stability, and the number of hydrogen bonds is higher on the gold surface. The positioning pattern of water molecules is also similar to the arrangement of gold atoms while no regularity was observed on graphene. The study of dynamical behavior of water molecules revealed that the movement of water on gold is much less than on graphene which is in agreement with the strong water-gold interaction in comparison to the water-graphene interaction.

Synthesis, Structure and Electrochemistry of Tetranuclear Oxygen-Centered Copper(II) Clusters with Acetylacetone and Benz-pyrazole Hydrolyzed Derivatives as Ligand.

PubMed

Vafazadeh, Rasoul; Willis, Anthony C

2016-01-01

Two copper(II) clusters Cu(4)OCl(6)(pyrazole)4, 1, and Cu(4)OBr(6)(Br-pyrazole)4, 2, have been synthesized by reacting acetylacetone and benzohydrazide (1:1 ratio) with CuX(2) (X = Cl for 1 and X= Br for 2) in methanol solutions. The structures of both clusters have been established by X-ray crystallography. The clusters contain four Cu, one O, six μ(2)-X atoms, and four pyrazole ligands. The pyrazoles was prepared in situ by the reaction of acetylacetone with benzohydrazide in methanol under reflux. In 2, the methine hydrogens of the pyrazole ligands have been replaced by bromine atoms. The four copper atoms encapsulate the central O atom in a tetrahedral arrangement. All copper atoms are five-coordinate and have similar coordination environments with slightly distorted trigonal bipyramidal geometry. The cyclic voltammogram of the clusters 1 and 2 show a one-electron quasi-reversible reduction wave in the region 0.485 to 0.731 V, and a one-electron quasi-reversible oxidation wave in the region 0.767 to 0.898 V. In 1, one irreversible oxidative response is observed on the positive of side of the voltammogram at 1.512 V and this can be assigned to Cu(II) to Cu(III) oxidation.

The spatial distributions of large gap-like structure on Fe(Se,Te) single crystals observed by STM/STS

NASA Astrophysics Data System (ADS)

Sugimoto, Akira; Sakai, Yuta; Nagasaka, Kouhei; Ekino, Toshikazu

2015-11-01

The nanoscale spatial distributions of large gap-like structure on superconducting FeSe1-xTex were investigated by scanning tunneling microscopy/spectroscopy (STM/STS). The STM topography shows regular atomic lattice arrangements with the lattice spacing ∼0.38 nm, together with the randomly distributed large spots due to the excess Fe atoms. From the STS measurements, the small gap structures of Δ ∼ 7 meV were partly observed. On the other hand, the high-bias dI/dV curves exhibit the broad peak structures at the negative biases of VPG = -200 to -400 mV in the measured whole surface area. The average of these large gaps is |VPGave| ∼ 305 mV with the standard deviation of σ ∼ 48 mV. The spatial distributions of the VPG exhibit the domain structures consisting of the relatively smaller gaps (<250 meV), which correspond to the excess Fe positions. The small gap Δ ∼ 7 meV is also observed at those positions, suggesting that the excess Fe affects the electronic structures of FeSe1-xTex.

Designing and building a permanent magnet Zeeman slower for calcium atoms using a 3D printer

NASA Astrophysics Data System (ADS)

Parsagian, Alexandria; Kleinert, Michaela

2015-10-01

We present the design of a Zeeman slower for calcium atoms using permanent magnets instead of more traditional electromagnets and the novel technique of 3D printing to create a very robust and flexible structure for these magnets. Zeeman slowers are ideal tools to slow atoms from several hundreds of meters per second to just a few tens of meters per second. These slower atoms can then easily be trapped in a magneto-optical trap, making Zeeman slowers a very valuable tool in many cold atom labs. The use of permanent magnets and 3D printing results in a highly stable and robust slower that is suitable for undergraduate laboratories. In our design, we arranged 28 magnet pairs, 2.0 cm apart along the axis of the slower and at varying radial distances from the axis. We determined the radial position of the magnets by simulating the combined field of all magnet pairs using Mathematica and comparing it to the ideal theoretical field for a Zeeman slower. Finally, we designed a stable, robust, compact, and easy-to-align mounting structure for the magnets in Google Sketchup, which we then printed using a commercially available 3D printer by Solidoodle. The resulting magnetic field is well suited to slow calcium atoms from the 770 m/s rms velocity at a temperature of 950 K, down to the capture velocity of the magneto-optical trap.

Detailed intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules with C(3v) symmetry: chloroform, bromoform, and methyl-iodide.

PubMed

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2011-01-28

Analyses of the intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules of the CXY(3)-type are described. The process is composed of the determination of several different distance-dependent orientational correlation functions, including ones that are introduced here. As a result, a complete structure classification could be provided for CXY(3) molecular liquids, namely for liquid chloroform, bromoform, and methyl-iodide. In the present work, the calculations have been conducted on particle configurations resulting from reverse Monte Carlo computer modeling: these particle arrangements have the advantage that they are fully consistent with structure factors from neutron and x-ray diffraction measurements. It has been established that as the separation between neighboring molecules increases, the dominant mutual orientations change from face-to-face to edge-to-edge, via the edge-to-face arrangements. Depending on the actual liquid, these geometrical elements (edges and faces of the distorted tetrahedra) were found to contain different atoms. From the set of liquids studied here, the structure of methyl-iodide was found to be easiest to describe on the basis of pure steric effects (molecular shape, size, and density) and the structure of liquid chloroform seems to be the furthest away from the corresponding "flexible fused hard spheres" like reference system.

A Structure-Function Study of RecA: The Structural Basis for ATP Specificity in the Strand Exchange Reaction

NASA Astrophysics Data System (ADS)

Gegner, Julie; Spruill, Natalie; Plesniak, Leigh A.

1999-11-01

The terms "structure" and "function" can assume a variety of meanings. In biochemistry, the "structure" of a protein can refer to its sequence of amino acids, the three-dimensional arrangement of atoms within a subunit, or the arrangement of subunits into a larger oligomeric or filamentous state. Likewise, the function of biological macromolecules can be examined at many levels. The function of a protein can be described by its role in an organism's survival or by a chemical reaction that it promotes. We have designed a three-part biochemical laboratory experiment that characterizes the structure and function of the Escherichia coli RecA protein. The first part examines the importance of RecA in the survival of bacteria that have been exposed to UV light. This is the broadest view of function of the enzyme. Second, the students use an in vitro assay of RecA whereby the protein promotes homologous recombination. Because RecA functions not catalytically, but rather stoichiometrically, in this recombination reaction, the oligomeric state of RecA in complex with DNA must also be discussed. Finally, through molecular modeling of X-ray crystallographic structures, students identify functionally important features of the ATP cofactor binding site of RecA.

A phase width for CaGaSn. Crystal structure of mixed intermetallic Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} and SmGa{sub x}Sn{sub 3−x}, stability, geometry and electronic structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tillard, Monique, E-mail: mtillard@univ-montp2.fr

X-ray single-crystal structure has been established for new compositions in intermetallic systems of tin and gallium. Crystals were successfully obtained in alloys prepared from elements. The structure of SmGaSn{sub 2} (cubic Pm3̄m, a=4.5778(8) Å, Z=1, R1=0.012) is described with atomic disorder at all Sn/Ga positions and the structure of Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} (hexagonal, P6{sub 3}/mmc, a=4.2233(9), c=17.601(7) Å, Z=1, R1=0.062) raises an interesting question about existence of a composition domain for CaGaSn. Finally, Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} should be considered as a particular composition of Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}, a compound assumed to exist in the range x ~more » 0−1. Partial atomic ordering characterizes the Sn/Ga puckered layers of hexagons whose geometries are analyzed and discussed comparatively with analogous arrangements in AlB{sub 2} related hexagonal compounds. The study is supported by rigid band model and DFT calculations performed for different experimental and hypothetic arrangements. - Graphical abstract: A phase width for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} belonging to the hexagonal YPtAs structure-type. - Highlights: • Single crystals of mixed tin gallium ternary intermetallics were obtained. • Partial ordering at metal sites and phase width are evidenced for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}. • Layer deviation to flatness is studied comparatively with related structures. • Geometry and stability analyses based on DFT calculations are provided.« less

Dielectric Response at THz Frequencies of Fe Water Complexes and Their Interaction with O3 Calculated by Density Functional Theory

DTIC Science & Technology

2012-10-24

geometric arrangement of the atoms in a chemical system , at the maximal peak of the energy surface separating reactants from products . In the...Sonnenberg, M. Hada, M. Ehara, K. Toyota , R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda , O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery... using DFT. The calculation of ground state resonance structure is for the construction of parameterized dielectric response functions for excitation

Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: A systematic and unbiased approach to structures of mixed-metallic clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weigend, Florian, E-mail: florian.weigend@kit.edu

2014-10-07

Energy surfaces of metal clusters usually show a large variety of local minima. For homo-metallic species the energetically lowest can be found reliably with genetic algorithms, in combination with density functional theory without system-specific parameters. For mixed-metallic clusters this is much more difficult, as for a given arrangement of nuclei one has to find additionally the best of many possibilities of assigning different metal types to the individual positions. In the framework of electronic structure methods this second issue is treatable at comparably low cost at least for elements with similar atomic number by means of first-order perturbation theory, asmore » shown previously [F. Weigend, C. Schrodt, and R. Ahlrichs, J. Chem. Phys. 121, 10380 (2004)]. In the present contribution the extension of a genetic algorithm with the re-assignment of atom types to atom sites is proposed and tested for the search of the global minima of PtHf{sub 12} and [LaPb{sub 7}Bi{sub 7}]{sup 4−}. For both cases the (putative) global minimum is reliably found with the extended technique, which is not the case for the “pure” genetic algorithm.« less

Crystal structure and Hirshfeld surface analysis of aqua-bis-(nicotinamide-κN)bis-(4-sulfamoylbenzoato-κO1)copper(II).

PubMed

Hökelek, Tuncer; Yavuz, Vijdan; Dal, Hakan; Necefoğlu, Hacali

2018-01-01

In the crystal of the title complex, [Cu(C 7 H 6 NO 4 S) 2 (C 6 H 6 N 2 O) 2 (H 2 O)], the Cu II cation and the O atom of the coordinated water mol-ecule reside on a twofold rotation axis. The Cu II ion is coordinated by two carboxyl-ate O atoms of the two symmetry-related 4-sulfamoylbenzoate (SB) anions and by two N atoms of the two symmetry-related nicotinamide (NA) mol-ecules at distances of 1.978 (2) and 2.025 (3) Å, respectively, forming a slightly distorted square-planar arrangement. The distorted square-pyramidal coordination environment is completed by the water O atom in the axial position at a distance of 2.147 (4) Å. In the crystal, the mol-ecules are linked via O-H⋯O and N-H⋯O hydrogen bonds with R 2 2 (8) and R 2 2 (18) ring motifs, forming a three-dimensional architecture. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯O/O⋯H (42.2%), H⋯H (25.7%) and H⋯C/C⋯H (20.0%) inter-actions.

Crown ethers in graphene

DOE PAGES

Guo, Junjie; Lee, Jaekwang; Contescu, Cristian I.; ...

2014-11-13

Crown ethers, introduced by Pedersen1, are at their most basic level neutral rings constructed of oxygen atoms linked by two- or three-carbon chains. They have attracted special attention for their ability to selectively incorporate various atoms2 or molecules within the cavity formed by the ring3-6. This property has led to the use of crown ethers and their compounds in a wide range of chemical and biological applications7,8. However, crown ethers are typically highly flexible, frustrating efforts to rigidify them for many uses that demand higher binding affinity and selectivity9,10. In this Letter, we report atomic-resolution images of the same basicmore » structures of the original crown ethers embedded in graphene. This arrangement constrains the crown ethers to be rigid and planar and thus uniquely suited for the many applications that crown ethers are known for. First-principles calculations show that the close similarity of the structures seen in graphene with those of crown ether molecules also extends to their selectivity towards specific metal cations depending on the ring size. Atoms (or molecules) incorporated within the crown ethers in graphene offer a simple environment that can be easily and systematically probed and modeled. Thus, we expect that this discovery will introduce a new wave of investigations and applications of chemically functionalized graphene.« less

The Periodic Pyramid

ERIC Educational Resources Information Center

Hennigan, Jennifer N.; Grubbs, W. Tandy

2013-01-01

The chemical elements present in the modern periodic table are arranged in terms of atomic numbers and chemical periodicity. Periodicity arises from quantum mechanical limitations on how many electrons can occupy various shells and subshells of an atom. The shell model of the atom predicts that a maximum of 2, 8, 18, and 32 electrons can occupy…

STRUCTURAL UNITS OF STARCH DETERMINED BY X-RAY CRYSTAL STRUCTURE METHOD.

PubMed

Sponsler, O L

1923-07-20

A few brief statements summarizing the foregoing conclusions may make a picture of the structure of the starch grain somewhat clearer. 1. The presence of lines on the negatives indicates a regular arrangement of the planes of atoms. 2. The lines are in close agreement with lines which would be produced by a lattice of the tetragonal system, the elementary cell of which is a square prism with the dimensions 5.94 x 5.94 x 5.05 A.u. 3. The unit of the lattice occupies a space equal to the volume of the starch group, C(6)H(10)O(5). 4. The large number of atoms in the unit makes it highly probable that principal planes and secondary planes of atoms occur for every reflecting position. 5. The effect of the secondary upon the principal planes may readily account for the differences in the density of the lines produced on the negatives. 6. From theoretical considerations, reflections, such as those obtained, would occur if starch grains were built up of concentric layers of units. 7. Two other factors which might affect the density of the lines are thermal agitation and the curvature of the concentric layers. 8. A model of the starch group was constructed to scale based on the accepted sizes of the atoms involved and upon rather meager chemical evidence. The model apparently fulfills the requirements necessary to produce reflections such as were obtained. 9. The model fits the elementary cell loosely enough to suggest a low density and to allow for considerable thermal movement. At the same time, parts of it approach the faces of the cell closely enough to make cohesion seem possible. 10. The model makes clearer the basis for the assumption that reflection from certain positions would be stronger than from others. If the interpretation of the data is correct and if the assumptions made are sound, then the starch grain is built up of units arranged in concentric layers, and the units are groups of atoms, each containing 6 carbon, 10 hydrogen, and 5 oxygen atoms. Such a structure is certainly not an amorphous structure, and on the other hand it is not crystalline in the common sense of the term. Parts of the grain, it is true, act as crystals in that for certain distances the layers of units are in planes, but taken as a whole the layers are curved. As to the validity of the conclusions, those pertaining to the type of lattice and to the size of the unit may be accepted as sound in our present knowledge of x-rays and crystal structure; those, however, pertaining to the nature and the spherical arrangement of the units, while they seem convincing, need the support of further investigation into the various structures deposited by living protoplasm. In conclusion, the assumption that the units form a sort of spherical space lattice, gives a picture of the starch grain which leads us to ponder over the nature of the activity in protoplasm when it is depositing solid substances. Starch, cellulose, and pectic bodies are about the only solid deposits made directly by the living substance of plants, and all three have the same proportional formula, C(6)H(10)O(5). Investigations, as yet incomplete, indicate that cellulose also consists of a regular arrangement of C(6)H(10)O(5) groups, each acting as a unit, but the spacing (6.14 x 6.14 x 5.55) is slightly different from that of starch. Pectin has not been studied. Protoplasm may be thought of as being composed of molecules of many different sizes, polypeptides, or even proteins forming the larger, and amino-acids the smaller, if water and electrolytes are ignored. The smaller molecules, such as those of the amino-acid, leucine, are approximately equal in size to the C(6)H(10)O(5) group of starch. That being the case, what can be the state of affairs at the interface when the starch particles are being deposited? Is it probable that protoplasm is homogeneous to the extent of being able to deposit these particles at 6 A.u. intervals? From quite another view-point a clear picture of the units of structure and their arrangement in cellulose should give a new point of attack on the many problems connected with osmosis. And from still a different view-point, it might lead perhaps, to a solution of problems connected with swelling. Another line of thought is suggested by the uniformity of the groups in the starch grain. Since the C(6)H(10)O(5) group occurs as an individual unit, one is inclined to suspect that it is really the molecule. Generally the starch molecule is considered to be very large, to be composed of several dozens of such groups, and to have a molecular weight of 7,000 or much more. No one figure, however, seems satisfactory to the different authorities. There is already at hand considerable evidence which will be assembled in a later paper favoring the single group, C(6)H(10)O(5), as the molecule. Finally, problems in polarized light may receive more satisfactory explanations through a clearer notion of the molecular structure of the carbohydrates.

Controlled coordination in vanadium(V) dimethylhydrazido compounds.

PubMed

Sakuramoto, Takashi; Moriuchi, Toshiyuki; Hirao, Toshikazu

2016-11-01

The vanadium(V) dimethylhydrazido compounds were structurally characterized to elucidate the effect of the alkoxide ligands in the coordination environment of vanadium(V) hydrazido center. The single-crystal X-ray structure determination of the vanadium(V) dimethylhydrazido compound with isopropoxide ligands revealed a dimeric structure with the V(1)-N(1) distance of 1.680(5)Å, in which each vanadium atom is coordinated in a distorted trigonal-bipyramidal geometry (τ 5 =0.81) with the hydrazido and bridging isopropoxide ligands in the apical positions. On the contrary, nearly tetrahedral arrangement around the vanadium metal center (τ 4 =0.06) with the V(1)-N(1) distance of 1.660(2)Å was observed in the vanadium(V) dimethylhydrazido compound with tert-butoxide ligands. The introduction of the 2,2',2″-nitrilotriethoxide ligand led to a pseudo-trigonal-bipyramidal geometry (τ 5 =0.92) at the vanadium center with the V(1)-N(1) distance of 1.691(5)Å, wherein vanadium atom is pulled out of the plane formed by the nitrilotriethoxide oxygen atoms in the direction of the hydrazido nitrogen. The coordination from the apical ligand in the vanadium(V) dimethylhydrazido compound was found to result in the longer V(1)-N(1) distance. Copyright © 2016 Elsevier Inc. All rights reserved.

Computer simulation of backscattering spectra from paint

NASA Astrophysics Data System (ADS)

Mayer, M.; Silva, T. F.

2017-09-01

To study the role of lateral non-homogeneity on backscattering analysis of paintings, a simplified model of paint consisting of randomly distributed spherical pigment particles embedded in oil/binder has been developed. Backscattering spectra for lead white pigment particles in linseed oil have been calculated for 3 MeV H+ at a scattering angle of 165° for pigment volume concentrations ranging from 30 vol.% to 70 vol.% using the program STRUCTNRA. For identical pigment volume concentrations the heights and shapes of the backscattering spectra depend on the diameter of the pigment particles: This is a structural ambiguity for identical mean atomic concentrations but different lateral arrangement of materials. Only for very small pigment particles the resulting spectra are close to spectra calculated supposing atomic mixing and assuming identical concentrations of all elements. Generally, a good fit can be achieved when evaluating spectra from structured materials assuming atomic mixing of all elements and laterally homogeneous depth distributions. However, the derived depth profiles are inaccurate by a factor of up to 3. The depth range affected by this structural ambiguity ranges from the surface to a depth of roughly 0.5-1 pigment particle diameters. Accurate quantitative evaluation of backscattering spectra from paintings therefore requires taking the correct microstructure of the paint layer into account.

The new barium zinc mercurides Ba3ZnHg10 and BaZn0.6Hg3.4 - Synthesis, crystal and electronic structure

NASA Astrophysics Data System (ADS)

Schwarz, Michael; Wendorff, Marco; Röhr, Caroline

2012-12-01

The title compounds Ba3ZnHg10 and BaZn0.6Hg3.4 were synthesized from stoichiometric ratios of the elements in Ta crucibles. Their crystal structures, which both represent new structure types, have been determined using single crystal X-ray data. The structure of Ba3ZnHg10 (orthorhombic, oP28, space group Pmmn, a=701.2(3), b=1706.9(8), c=627.3(3)pm, Z=2, R1=0.0657) contains folded 44 Hg nets, where the meshes form the bases of flat rectangular pyramids resembling the structure of BaAl4. The flat pyramids are connected via Hg-Zn/Hg bonds, leaving large channels at the folds, in which Ba(1) and Hg(2) atoms alternate. Whereas the remaining Hg/Zn atoms form a covalent 3D network of three- to five-bonded atoms with short M-M distances (273-301 pm; CN 9-11), the Hg(2) atoms in the channels adopt a comparatively large coordination number of 12 and increased distances (317-348 pm) to their Zn/Hg neighbours. In the structure of BaZn0.6Hg3.4 (cubic, cI320, space group I4bar3d, a=2025.50(7) pm, Z=64, R1=0.0440), with a chemical composition not much different from that of Ba3ZnHg10, the Zn/Hg atoms of the mixed positions M(1/2) are arranged in an slightly distorted primitive cubic lattice with a 4×4×4 subcell relation to the unit cell. The 24 of the originating 64 cubes contain planar cis tetramers Hg(5,6)4 with Hg in a nearly trigonal planar or tetrahedral coordination. In another 24 of the small cubes, two opposing faces are decorated by Hg(3,4)2 dumbbells, two by Ba(2) atoms respectively. The third type of small cubes are centered by Ba(1) atoms only. The complex 3D polyanionic Hg/Zn network thus formed is compared with the Hg partial structure in Rb3Hg20 applying a group-subgroup relation. Despite their different overall structures, the connectivity of the negatively charged Hg atoms, the rather metallic Zn bonding characteristic (as obtained from FP-LAPW band structure calculations) and the coordination number of 16 for all Ba cations relate the two title compounds.

Faradaurate-940: Synthesis, Mass Spectrometry, STEM, PDF, and SAXS Study of Au~940(SR)~160 Nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumara, Chanaka; Zuo, Xiaobing; Cullen, David A

2014-01-01

Obtaining monodisperse nanocrystals, and determining its composition to the atomic level and its atomic structure is highly desirable, but is generally lacking. Here, we report the discovery and comprehensive characterization of a 3-nm plasmonic nanocrystal with a composition of Au940 20(SCH2CH2Ph)160 4, which is, the largest mass spectrometrically characterized gold thiolate nanoparticle produced to date. The compositional assignment has been made using electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS). The MS results show an unprecedented size monodispersity, where the number of Au atoms vary by only 40 atoms (940 20). The mass spectrometrically-determined sizemore » and composition are supported by aberration-corrected scanning transmission electron microscopy (STEM) and synchrotron-based methods such as atomic pair distribution function (PDF) and small angle X-ray scattering (SAXS). Lower resolution STEM images show an ensemble of particles 1000 s per frame visually demonstrating monodispersity. Modelling of SAXS on statistically significant nanoparticle population approximately 1012 individual nanoparticles - shows that the diameter is 3.0 0.2nm, supporting mass spectrometry and electron microscopy results on monodispersity. Atomic PDF based on high energy X-ray diffraction experiments show decent match with either a Marks decahedral or truncated octrahedral structure. Atomic resolution STEM images of single particles and its FFT suggest face-centered cubic (fcc) arrangement. UV-visible spectroscopy data shows that the 940-atom size supports a surface plasmon resonance peak at 505 nm. These monodisperse plasmonic nanoparticles minimize averaging effects and has potential application in solar cells, nano-optical devices, catalysis and drug delivery.« less

Atomistic Model of Physical Ageing in Se-rich As-Se Glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golovchak,R.; Shpotyuk, O.; Kozdras, A.

2007-01-01

Thermal, optical, X-ray excited and magnetic methods were used to develop a microstructural model of physical ageing in Se-rich glasses. The glass composition As10Se90, possessing a typical cross-linked chain structure, was chosen as a model object for the investigations. The effect of physical ageing in this glass was revealed by differential scanning calorimetry, whereas the corresponding changes in its atomic arrangement were studied by extended X-ray absorption fine structure, Raman and solid-state 77Se nuclear magnetic resonance spectroscopy. Straightening-shrinkage processes are shown to be responsible for the physical ageing in this Se-rich As-Se glass.

The characterization of organic monolayers at gold surfaces using scanning tunneling microscopy and atomic force microscopy correlation with macrostructural properties

NASA Astrophysics Data System (ADS)

Alves, C. A.

1992-09-01

Monolayer films formed by self-assembly of organothiols at epitaxially grown Au(111) films at mica were examined in air using scanning tunneling (STM) and atomic force microscopies (AFM). n-Alkanethiolate monolayers exhibit a hexagonal packing arrangement with nearest-neighbor and next-nearest-neighbor spacings of 0.50 and 0.87 nm. This arrangement is consistent with (the square root of 3 x the square root of 3)R30 deg adlayer structure at Au(111). STM reveals the structure of the Au-bound sulfur, while AFM details the structure at the monolayer/air interface, revealing that the order at the Au-S interface is retained up to the monolayer/air interface. The investigation of the self-assembled (CF3CF2)7(CH2)2SH monolayer at Au(111) by AFM reveals a (2 x 2) adlayer structure, with nearest-neighbor and next-nearest-neighbor spacings of 0.58 plus or minus 0.02 nm and 1.0 plus or minus 0.02 nm, respectively. This is consistent with the larger van der Waals diameter of the fluorinated chain. Coverage of this fluorinated thiolate monolayer is (6.3 plus or minus 0.8) x 10(exp -10) mol/cm(sup 2), consistent with the expected 0.25 monolayer coverage of the (2 x 2) adlayer structure at Au(111). Infrared reflection spectroscopy also confirmed this. Upon prolonged exposure to air, the thiolate species is oxidized to elemental sulfur in the forms of cyclooctasulfur (cyclo-S8) and other allotropes. STM reveals square structures on aged thiolate monolayers. Dimensions of these squares (0.40-0.50 nm per side) are close to those of cyclo-S8. Electrochemical reductive desorption experiments also reveal a change in the surface species with time, with a second desorption wave.

Disentangling neighbors and extended range density oscillations in monatomic amorphous semiconductors.

PubMed

Roorda, S; Martin, C; Droui, M; Chicoine, M; Kazimirov, A; Kycia, S

2012-06-22

High energy x-ray diffraction measurements of pure amorphous Ge were made and its radial distribution function (RDF) was determined at high resolution, revealing new information on the atomic structure of amorphous semiconductors. Fine structure in the second peak in the RDF provides evidence that a fraction of third neighbors are closer than some second neighbors; taking this into account leads to a narrow distribution of tetrahedral bond angles, (8.5 ± 0.1)°. A small peak which appears near 5 Å upon thermal annealing shows that some ordering in the dihedral bond-angle distribution takes place during structural relaxation. Extended range order is detected (in both a-Ge and a-Si) which persists to beyond 20 Å, and both the periodicity and its decay length increase upon thermal annealing. Previously, the effect of structural relaxation was only detected at intermediate range, involving reduced tetrahedral bond-angle distortions. These results enhance our understanding of the atomic order in continuous random networks and place significantly more stringent requirements on computer models intending to describe these networks, or their alternatives which attempt to describe the structure in terms of an arrangement of paracrystals.

75 FR 62121 - Proposed Subsequent Arrangement

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-07

... Cooperation in the Peaceful Uses of Nuclear Energy Between the Government of the United States and the... Japan Concerning Peaceful Uses of Nuclear Energy. This subsequent arrangement concerns the retransfer of... segments, from Studsvik Nuclear AB, Nyk[ouml]ping, Sweden, to the Japan Atomic Energy Agency (JAEA), Tokai...

Effects of wettability and interfacial nanobubbles on flow through structured nanochannels: an investigation of molecular dynamics

NASA Astrophysics Data System (ADS)

Yen, Tsu-Hsu

2015-12-01

Solid-fluid boundary conditions are strongly influenced by a number of factors, including the intrinsic properties of the solid/fluid materials, surface roughness, wettability, and the presence of interfacial nanobubbles (INBs). The interconnected nature of these factors means that they should be considered jointly. This paper employs molecular dynamics (MD) simulation in a series of studies aimed at elucidating the influence of wettability in boundary behaviour and the accumulation of interfacial gas. Specifically, we examined the relationship between effective slip length, the morphology of nanobubbles, and wettability. Two methods were employed for the promotion of hydrophobicity between two structured substrates with similar intrinsic contact angles. We also compared anisotropic and isotropic atomic arrangements in the form of graphite and Si(100), respectively. A physical method was employed to deal with variations in surface roughness, whereas a chemical method was used to adjust the wall-fluid interaction energy (ɛwf). We first compared the characteristic properties of wettability, including contact angle and fluid density within the cavity. We then investigated the means by which variations in solid-fluid interfacial wettability affect interfacial gas molecules. Our results reveal that the morphology of INB on a patterned substrate is determined by wettability as well as the methods employed for the promotion of hydrophobicity. The present study also illustrates the means by which the multiple effects of the atomic arrangement of solids, surface roughness, wettability and INB influence effective slip length.

A controllable molecular sieve for Na+ and K+ ions.

PubMed

Gong, Xiaojing; Li, Jichen; Xu, Ke; Wang, Jianfeng; Yang, Hui

2010-02-17

The selective rate of specific ion transport across nanoporous material is critical to biological and nanofluidic systems. Molecular sieves for ions can be achieved by steric and electrical effects. However, the radii of Na(+) and K(+) are quite similar; they both carry a positive charge, making them difficult to separate. Biological ionic channels contain precisely arranged arrays of amino acids that can efficiently recognize and guide the passage of K(+) or Na(+) across the cell membrane. However, the design of inorganic channels with novel recognition mechanisms that control the ionic selectivity remains a challenge. We present here a design for a controllable ion-selective nanopore (molecular sieve) based on a single-walled carbon nanotube with specially arranged carbonyl oxygen atoms modified inside the nanopore, which was inspired by the structure of potassium channels in membrane spanning proteins (e.g., KcsA). Our molecular dynamics simulations show that the remarkable selectivity is attributed to the hydration structure of Na(+) or K(+) confined in the nanochannels, which can be precisely tuned by different patterns of the carbonyl oxygen atoms. The results also suggest that a confined environment plays a dominant role in the selectivity process. These studies provide a better understanding of the mechanism of ionic selectivity in the KcsA channel and possible technical applications in nanotechnology and biotechnology, including serving as a laboratory-in-nanotube for special chemical interactions and as a high-efficiency nanodevice for purification or desalination of sea and brackish water.

Crystal structure of aqua-1κO-{μ-2-[(2-hydroxy-ethyl)methylamino]ethanolato-2:1κ(4) O (1),N,O (2):O (1)}[μ-2,2'-(methylimino)diethanolato-1:2κ(4) O,N,O':O]dithiocyanato-1κN,2κN-chromium(III)copper(II).

PubMed

Rusanova, Julia A; Semenaka, Valentina V; Dyakonenko, Viktoriya V; Shishkin, Oleg V

2015-09-01

The title compound, [CrCu(C5H11NO2)(C5H12NO2)(NCS)2(H2O)] or [Cr(μ-mdea)Cu(μ-Hmdea)(NCS)2H2O], (where mdeaH2 is N-methylethanolamine, C5H13NO2) is formed as a neutral heterometal Cu(II)/Cr(III) complex. The mol-ecular structure of the complex is based on a binuclear {CuCr(μ-O)2} core. The coordination environment of each metal atom involves the N,O,O atoms of the tridentate ligand, one bridging O atom of the ligand and the N atom of the thio-cyanato ligands. The Cu(II) ion adopts a distorted square-pyramidal coordination while the Cr(III) ion has a distorted octa-hedral coordination geometry completed by the aqua ligand. In the crystal, the binuclear complexes are linked via two pairs of O-H⋯O hydrogen bonds to form inversion dimers, which are arranged in columns parallel to the a axis. In the μ-mdea ligand two -CH2 groups and the methyl group were refined as disordered over two sets of sites with equal occupancies. The structure was refined as a two-component twin with a twin scale factor of 0.242 (1).

On the Functionality of Complex Intermetallics: Frustration, Chemical Pressure Relief, and Potential Rattling Atoms in Y11Ni60C6.

PubMed

Guo, Yiming; Fredrickson, Daniel C

2016-10-17

Intermetallic carbides provide excellent model systems for exploring how frustration can shape the structures and properties of inorganic materials. Combinations of several metals with carbon can be designed in which the formation of tetrahedrally close-packed (TCP) intermetallics conflicts with the C atoms' requirement of trigonal prismatic or octahedral coordination environments, as offered by the simple close-packings (SCP) of equally sized spheres. In this Article, we explore the driving forces that lead to the coexistence of these incompatible arrangements in the Yb 11 Ni 60 C 6 -type compound Y 11 Ni 60 C 6 (cI154), as well as potential consequences of this intergrowth for the phase's physical properties. Our focus begins on the structure's SCP regions, which appear as C-stuffed versions of a AuCu 3 -type YNi 3 phase that is not observed on its own in the Y-Ni system. DFT-Chemical Pressure (DFT-CP) calculations on this hypothetical YNi 3 phase reveal large negative pressures within the Ni sublattice, as it is stretched to accommodate the size requirements of the Y atoms. In the Y 11 Ni 60 C 6 structure, two structural mechanisms for addressing these CP issues appear: the incorporation of interstitial C atoms, and the presence of interfaces with CaCu 5 -type domains. The relative roles of these two mechanisms are investigated with the CP analysis on a hypothetical YNi 3 C x series of C-stuffed AuCu 3 -type phases, the Y-Ni sublattice of Y 11 Ni 60 C 6 , and finally the full Y 11 Ni 60 C 6 structure. Through these calculations, the C atoms appear to play the roles of relieving positive Y CPs and supporting relaxation at the AuCu 3 -type/CaCu 5 -type interfaces, where the cancellation occurs between opposite CPs experienced by the Y atoms in the two parent structures (following the epitaxial stabilization mechanism). The CP analysis of Y 11 Ni 60 C 6 also highlights a sublattice of Y and Ni atoms with large negative CPs (and thus the potential for soft vibrational modes), illustrating how frustrated structures could lead to the full realization of the phonon glass-electron crystal concept.

Atomic-scale compositional mapping reveals Mg-rich amorphous calcium phosphate in human dental enamel

PubMed Central

La Fontaine, Alexandre; Zavgorodniy, Alexander; Liu, Howgwei; Zheng, Rongkun; Swain, Michael; Cairney, Julie

2016-01-01

Human dental enamel, the hardest tissue in the body, plays a vital role in protecting teeth from wear as a result of daily grinding and chewing as well as from chemical attack. It is well established that the mechanical strength and fatigue resistance of dental enamel are derived from its hierarchical structure, which consists of periodically arranged bundles of hydroxyapatite (HAP) nanowires. However, we do not yet have a full understanding of the in vivo HAP crystallization process that leads to this structure. Mg2+ ions, which are present in many biological systems, regulate HAP crystallization by stabilizing its precursor, amorphous calcium phosphate (ACP), but their atomic-scale distribution within HAP is unknown. We use atom probe tomography to provide the first direct observations of an intergranular Mg-rich ACP phase between the HAP nanowires in mature human dental enamel. We also observe Mg-rich elongated precipitates and pockets of organic material among the HAP nanowires. These observations support the postclassical theory of amelogenesis (that is, enamel formation) and suggest that decay occurs via dissolution of the intergranular phase. This information is also useful for the development of more accurate models to describe the mechanical behavior of teeth. PMID:27617291

Atomic-scale compositional mapping reveals Mg-rich amorphous calcium phosphate in human dental enamel.

PubMed

La Fontaine, Alexandre; Zavgorodniy, Alexander; Liu, Howgwei; Zheng, Rongkun; Swain, Michael; Cairney, Julie

2016-09-01

Human dental enamel, the hardest tissue in the body, plays a vital role in protecting teeth from wear as a result of daily grinding and chewing as well as from chemical attack. It is well established that the mechanical strength and fatigue resistance of dental enamel are derived from its hierarchical structure, which consists of periodically arranged bundles of hydroxyapatite (HAP) nanowires. However, we do not yet have a full understanding of the in vivo HAP crystallization process that leads to this structure. Mg(2+) ions, which are present in many biological systems, regulate HAP crystallization by stabilizing its precursor, amorphous calcium phosphate (ACP), but their atomic-scale distribution within HAP is unknown. We use atom probe tomography to provide the first direct observations of an intergranular Mg-rich ACP phase between the HAP nanowires in mature human dental enamel. We also observe Mg-rich elongated precipitates and pockets of organic material among the HAP nanowires. These observations support the postclassical theory of amelogenesis (that is, enamel formation) and suggest that decay occurs via dissolution of the intergranular phase. This information is also useful for the development of more accurate models to describe the mechanical behavior of teeth.

An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase

NASA Astrophysics Data System (ADS)

Golden, Emily; Yu, Li-Juan; Meilleur, Flora; Blakeley, Matthew P.; Duff, Anthony P.; Karton, Amir; Vrielink, Alice

2017-01-01

The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.

Synthesis, structure, and magnetic characterization of Cr{sub 4}US{sub 8}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, Matthew D.; Chan, Ian Y.; Malliakas, Christos D.

The compound Cr{sub 4}US{sub 8} has been synthesized at 1073 K and its crystal structure has been determined at 100 K. The structure is modulated with a two-fold commensurate supercell. The subcell may be indexed in an orthorhombic cell but weak supercell reflections lead to the monoclinic superspace group P2{sub 1}/c(α0γ)0s with two Cr sites, one U site, and four S sites. The structure comprises a three-dimensional framework of CrS{sub 6} octahedra with channels that are partially occupied by U atoms. Each U atom in these channels is coordinated by eight S atoms in a bicapped trigonal-prismatic arrangement. The magneticmore » behavior of Cr{sub 4}US{sub 8} is complex. At temperatures above ~120 K at all measured fields, there is little difference between field-cooled and zero field-cooled data and χ(T) decreases monotonously with temperature, which is reminiscent of the Curie–Weiss law. At lower temperatures, the temperature dependence of χ(T) is complex and strongly dependent on the magnetic field strength. - Graphical abstract: Structure of Cr{sub 4}US{sub 8} viewed down the a axis. - Highlights: • At 1073 K Cr{sub 4}US{sub 8} was synthesized and at 100 K its crystal structure was determined. • The 3D structure comprises CrS{sub 6} octahedra with channels partially occupied by U. • The magnetic behavior of Cr{sub 4}US{sub 8} is complex.« less

Spontaneous formation of suboxidic coordination around Co in ferromagnetic rutile Ti 0.95Co 0.5O 2 film

DOE PAGES

Hu, Wen; Hayaski, Kouichi; Fukumura, Tomoteru; ...

2015-06-02

To evaluate local atomic structures around Co in high temperature diluted ferromagnetic semiconductor Co-doped TiO 2, x-ray fluorescence holography and x-ray absorption fine structure experiments were carried out on rutile paramagnetic Ti 0.99Co 0.01O 2 and ferromagnetic Ti 0.95Co 0.05O 2 films. The Co atoms in the Ti 0.99Co 0.01O 2 simply substituted for Ti sites in the rutile structure, whereas a suboxidic arrangement of CoO 2Ti 4 formed around Co in the Ti 0.95Co 0.05O 2 films. A theoretical investigation based on a series of first-principles calculations indicated the stability of the aggregated suboxidic clusters in the rutile TiOmore » 2, supporting our hypothesis for the formation of suboxidic coordination in the highly Co-doped sample. As a result, the suboxidic coordination may be the source of strong exchange interaction, resulting in the high Curie temperature in Co-doped TiO 2.« less

Sublattice reversal in GaAs/Ge/GaAs (113)B heterostructures and its application to THz emitting devices based on a coupled multilayer cavity

NASA Astrophysics Data System (ADS)

Lu, Xiangmeng; Kumagai, Naoto; Minami, Yasuo; Kitada, Takahiro

2018-04-01

We fabricated a coupled multilayer cavity with a GaAs/Ge/GaAs sublattice reversal structure for terahertz emission application. Sublattice reversal in GaAs/Ge/GaAs was confirmed by comparing the anisotropic etching profile of an epitaxial sample with those of reference (113)A and (113)B GaAs substrates. The interfaces of GaAs/Ge/GaAs were evaluated at the atomic level by scanning transmission electron microscopy (STEM) and energy-dispersive X-ray spectroscopy (EDX) mapping. Defect-free GaAs/Ge/GaAs heterostructures were observed in STEM images and the sublattice lattice was directly seen through atomic arrangements in EDX mapping. A GaAs/AlAs coupled multilayer cavity with a sublattice reversal structure was grown on the (113)B GaAs substrate after the confirmation of sublattice reversal. Smooth GaAs/AlAs interfaces were formed over the entire region of the coupled multilayer cavity structure both below and above the Ge layer. Two cavity modes with a frequency difference of 2.9 THz were clearly observed.

Revealing molecular-level surface structure of amyloid fibrils in liquid by means of frequency modulation atomic force microscopy

NASA Astrophysics Data System (ADS)

Fukuma, Takeshi; Mostaert, Anika S.; Serpell, Louise C.; Jarvis, Suzanne P.

2008-09-01

We have investigated the surface structure of islet amyloid polypeptide (IAPP) fibrils and α-synuclein protofibrils in liquid by means of frequency modulation atomic force microscopy (FM-AFM). Ångström-resolution FM-AFM imaging of isolated macromolecules in liquid is demonstrated for the first time. Individual β-strands aligned perpendicular to the fibril axis with a spacing of 0.5 nm are resolved in FM-AFM images, which confirms cross-β structure of IAPP fibrils in real space. FM-AFM images also reveal the existence of 4 nm periodic domains along the axis of IAPP fibrils. Stripe features with 0.5 nm spacing are also found in images of α-synuclein protofibrils. However, in contrast to the case for IAPP fibrils, the stripes are oriented 30° from the axis, suggesting the possibility of β-strand alignment in protofibrils different from that in mature fibrils or the regular arrangement of thioflavin T molecules present during the fibril preparation aligned at the surface of the protofibrils.

Intramolecular structural model for photoinduced plasticity in chalcogenide glasses

NASA Astrophysics Data System (ADS)

Yannopoulos, S. N.

2003-08-01

Selected spectral features of Raman spectra of glassy As2S3 subjected to elongation stress and sub-band-gap light illumination are analyzed and compared with polarization-dependent information obtained from the bulk glass at room temperature and near the glass transition temperature. The data are suggestive of specific structural changes which involve the transformation of atomic arrangements from realgarlike As4S4 molecules, originally present in virgin (untreated) fibers, into planar orpimentlike clusters. Implications of these atomic rearrangements to the incipient photoinduced fluidity—the onset of plastic deformation—in As2S3 glass are discussed. Kinetics of photoinduced plastic changes is compared to that of Raman spectra changes, revealing a qualitative similar behavior. An approximate estimation of the relative contribution of intermolecular rearrangements and the intramolecular structural mechanism proposed in this paper has revealed that the latter is responsible for almost 30% of the photoinduced elongation of the fiber’s length at room temperature. The proposed mechanism can as well serve as rationale for understanding the photoinduced volume expansion observed in chalcogenide glasses.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu Qiang; Zeng Xierong; Shenzhen Key Laboratory of Special Functional Materials, Shenzhen 518060

This paper reports the observation of the clear Invar effects of (Fe{sub 71.2}B{sub 24}Y{sub 4.8}){sub 96}Nb{sub 4} bulk metallic glass. The Invar effects of (Fe{sub 71.2}B{sub 24}Y{sub 4.8}){sub 96}Nb{sub 4} alloys in different structural states are also investigated in situ through cyclic thermal dilation tests at different cyclic temperatures. The results show that these Invar effects are strengthened in the relaxation amorphous state, weakened in the nanocrystalline state, and absent in the complete crystalline state. X-ray diffraction and Moessbauer spectroscopy demonstrate that the structural influences on Invar effects can be explained by the different local atomic arrangements around Fe atomsmore » in different structural states.« less

Ordered and layered structure of liquid nitromethane within a graphene bilayer: toward stabilization of energetic materials through nanoscale confinement.

PubMed

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Kang, Ying; Ge, Zhongxue

2015-03-01

The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and layered structures are formed at the confinement of the GRA bilayer induced by the van der Waals attractions of NM with GRA and the dipole-dipole interactions of NM, which is strongly dependent on the confinement size, i.e., the GRA bilayer distance. These unique intermolecular arrangements and preferred orientations of confined NM lead to higher stabilities than bulk NM revealed by bond dissociation energy calculations.

Equations of state of anhydrous AlF3 and AlI3: Modeling of extreme condition halide chemistry

NASA Astrophysics Data System (ADS)

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; Crowhurst, Jonathan C.; Goncharov, Alexander F.; Radousky, Harry B.; Armstrong, Michael R.; Roberts, Sarah K.; Plaue, Jonathan W.

2015-06-01

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF3) and separately, aluminum triiodide (AlI3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF3 and AlI3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: applied stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. Results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.

Effect of Base Sequence "Defects" on the Electrostatic Potential of Dissolved DNA

NASA Astrophysics Data System (ADS)

Adams, Scott V.; Wagner, Katrina; Kephart, Thomas S.; Edwards, Glenn

1997-11-01

An analytical model of the electrostatic potential surrounding dissolved DNA has been developed. The model consists of an all-atom, mathematically helical structure for DNA, in which the atoms are arranged in infinite lines of discrete point charges on concentric cylindrical surfaces. The surrounding solvent and counterions are treated with the Debye-Huckel approximation (Wagner et al., Biophysical Journal 73, 21-30, 1997). Variation in the electrostatic potential due to structural differences between A, B, and Z conformations and homopolymer base sequence is apparent. The most recent modification to the model exploits the principle of superposition to calculate the potential of DNA with a base sequence containing `defects.' That is, the base sequence is no longer uniform along the polymer. Differences between the potential of homopolymer DNA and the potential of DNA containing base `defects' are immediately obvious. These results may aid in understanding the role of electrostatics in base-sequence specificity exhibited by DNA-binding proteins.

Micromorphology of cactus-pear (Opuntia ficus-indica (L.) Mill) cladodes based on scanning microscopies.

PubMed

Ben Salem-Fnayou, Asma; Zemni, Hassène; Nefzaoui, Ali; Ghorbel, Abdelwahed

2014-01-01

Cladode ultrastructural features of two prickly and two spineless Opuntia ficus-indica cultivars were examined using environmental scanning electron and atomic force microscopies. Observations focused on cladode as well as spine and glochid surface micromorphologies. Prickly cultivars were characterized by abundant cracked epicuticular wax deposits covering the cladode surface, with an amorphous structure as observed by AFM, while less abundant waxy plates were observed by ESEM on spineless cultivar cladodes. Further AFM observations allowed a rough granular and crystalloid epicuticular wax structure to be distinguished in spineless cultivars. Regarding spine micromorphology, prickly cultivars had strong persistent spines, observed by ESEM as a compact arrangement of oblong epidermal cells with a rough granular structure. However, deciduous spines in spineless cultivars had a broken transversely fissured epidermis covering a parallel arrangement of fibres. Through AFM, the deciduous spine surface presented an irregular hilly and smooth microrelief while persistent spines exhibited rough helical filamentous prints. ESEM and AFM studies of cladode surfaces from prickly and spineless cactus pear cultivars revealed valuable micro-morphological details that ought to be extended to a large number of O. ficus-indica cultivars. Copyright © 2013 Elsevier Ltd. All rights reserved.

Antiparallel Triple-strand Architecture for Prefibrillar Aβ42 Oligomers*

PubMed Central

Gu, Lei; Liu, Cong; Stroud, James C.; Ngo, Sam; Jiang, Lin; Guo, Zhefeng

2014-01-01

Aβ42 oligomers play key roles in the pathogenesis of Alzheimer disease, but their structures remain elusive partly due to their transient nature. Here, we show that Aβ42 in a fusion construct can be trapped in a stable oligomer state, which recapitulates characteristics of prefibrillar Aβ42 oligomers and enables us to establish their detailed structures. Site-directed spin labeling and electron paramagnetic resonance studies provide structural restraints in terms of side chain mobility and intermolecular distances at all 42 residue positions. Using these restraints and other biophysical data, we present a novel atomic-level oligomer model. In our model, each Aβ42 protein forms a single β-sheet with three β-strands in an antiparallel arrangement. Each β-sheet consists of four Aβ42 molecules in a head-to-tail arrangement. Four β-sheets are packed together in a face-to-back fashion. The stacking of identical segments between different β-sheets within an oligomer suggests that prefibrillar oligomers may interconvert with fibrils via strand rotation, wherein β-strands undergo an ∼90° rotation along the strand direction. This work provides insights into rational design of therapeutics targeting the process of interconversion between toxic oligomers and non-toxic fibrils. PMID:25118290

SABER: A computational method for identifying active sites for new reactions

PubMed Central

Nosrati, Geoffrey R; Houk, K N

2012-01-01

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

X-Ray diffraction and mu-Raman investigation of the monoclinic-orthorhombic phase transition in Th(1-x)U(x)(C(2)O(4))(2).2H(2)O solid solutions.

PubMed

Clavier, Nicolas; Hingant, Nina; Rivenet, Murielle; Obbade, Saïd; Dacheux, Nicolas; Barré, Nicole; Abraham, Francis

2010-02-15

A complete Th(1-x)U(x)(C(2)O(4))(2).2H(2)O solid solution was prepared by mild hydrothermal synthesis from a mixture of hydrochloric solutions containing cations and oxalic acid. The crystal structure has been solved from twinned single crystals for x = 0, 0.5, and 1 with monoclinic symmetry, space group C2/c, leading to unit cell parameters of a approximately 10.5 A, b approximately 8.5 A, and c approximately 9.6 A. The crystal structure consists of a two-dimensional arrangement of actinide centers connected through bis-bidentate oxalate ions forming squares. The actinide metal is coordinated by eight oxygen atoms from four oxalate entities and two water oxygen atoms forming a bicapped square antiprism. The connection between the layers is assumed by hydrogen bonds between the water molecules and the oxygen of oxalate of an adjacent layer. Under these conditions, the unit cell contains two independent oxalate ions. From high-temperature mu-Raman and X-ray diffraction studies, the compounds were found to undergo a transition to an orthorhombic form (space group Ccca). The major differences in the structural arrangement concern the symmetry of uranium, which decreases from C2 to D2, leading to a unique oxalate group. Consequently, the nu(s)(C-O) double band observed in the Raman spectra recorded at room temperature turned into a singlet. This transformation was then used to make the phase transition temperature more precise as a function of the uranium content of the sample.

Atomic substitutions in synthetic apatite; Insights from solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Vaughn, John S.

Apatite, Ca5(PO4)3X (where X = F, Cl, or OH), is a unique mineral group capable of atomic substitutions for cations and anions of varied size and charge. Accommodation of differing substituents requires some kind of structural adaptation, e.g. new atomic positions, vacancies, or coupled substitutions. These structural adaptations often give rise to important physicochemical properties relevant to a range of scientific disciplines. Examples include volatile trapping during apatite crystallization, substitution for large radionuclides for long-term storage of nuclear fission waste, substitution for fluoride to improve acid resistivity in dental enamel composed dominantly of hydroxylapatite, and the development of novel biomaterials with enhanced biocompatibility. Despite the importance and ubiquity of atomic substitutions in apatite materials, many of the mechanisms by which these reactions occur are poorly understood. Presence of substituents at dilute concentration and occupancy of disordered atomic positions hinder detection by bulk characterization methods such as X-ray diffraction (XRD) and infrared (IR) spectroscopy. Solid-state nuclear magnetic resonance (NMR) spectroscopy is an isotope-specific structural characterization technique that does not require ordered atomic arrangements, and is therefore well suited to investigate atomic substitutions and structural adaptations in apatite. In the present work, solid-state NMR is utilized to investigate structural adaptations in three different types of apatite materials; a series of near-binary F, Cl apatite, carbonate-hydroxylapatite compositions prepared under various synthesis conditions, and a heat-treated hydroxylapatite enriched in 17O. The results indicate that hydroxyl groups in low-H, near binary F,Cl apatite facilitate solid-solution between F and Cl via column reversals, which result in average hexagonal symmetry despite very dilute OH concentration ( 2 mol percent). In addition, 19F NMR spectra indicate that fluorine occupies a complex distribution of atomic positions, which give rise to complex 19F peak shapes owing to varied F-Ca distance. 13C NMR analysis of carbonate-hydroxylapatite indicates that AB-type carbonate hydroxylapatite can be prepared without the presence of sodium or heat treatment. Isotopic 17O enrichment of hydroxylapatite and 17O NMR analysis reveals distinct signals corresponding to phosphate and hydroxyl oxygens, and heat treatment under vacuum results in loss of hydroxyl signal due to decomposition to tricalcium phosphate, which was observed by powder X-Ray diffraction (PXRD).

Superposition of two tRNA{sup Ser} acceptor stem crystal structures: Comparison of structure, ligands and hydration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eichert, Andre; Fuerste, Jens P.; Ulrich, Alexander

2010-05-07

We solved the X-ray structures of two Escherichia coli tRNA{sup Ser} acceptor stem microhelices. As both tRNAs are aminoacylated by the same seryl-tRNA-synthetase, we performed a comparative structure analysis of both duplexes to investigate the helical conformation, the hydration patterns and magnesium binding sites. It is well accepted, that the hydration of RNA plays an important role in RNA-protein interactions and that the extensive solvent content of the minor groove has a special function in RNA. The detailed comparison of both tRNA{sup Ser} microhelices provides insights into the structural arrangement of the isoacceptor tRNA aminoacyl stems with respect to themore » surrounding water molecules and may eventually help us to understand their biological function at atomic resolution.« less

Metal complexes of alkyl-aryl dithiocarbamates: Structural studies, anticancer potentials and applications as precursors for semiconductor nanocrystals

NASA Astrophysics Data System (ADS)

Andrew, Fartisincha P.; Ajibade, Peter A.

2018-03-01

Dithiocarbamates are versatile ligands able to stabilize wide range of metal ions in their various oxidation states with the partial double bond character of Csbnd N and Csbnd S of thioureide moiety. Variation of the substituents attached to the nitrogen atom of dithiocarbamate moiety generates various intermolecular interactions, which lead to different structural arrangement in the solid state. The presence of bulky substituents on the N atom obviates the supramolecular aggregation via secondary Msbnd S interactions whereas smaller substituents encourage such aggregation that results in their wide properties and applications. Over the past decades, the synthesis and structural studies of metal complexes of dithiocarbamates have received considerable attention as potential anticancer agents with various degree of DNA binding affinity and cytotoxicity and as single molecule precursors for the preparation of semiconductor nanocrystals. In this paper, we review the synthesis, structural studies, anticancer potency and the use of alkyl-phenyl dithiocarbamate complexes as precursors for the preparation of semiconductor nanocrystals. The properties of these compounds and activities are ascribed to be due to either the dithiocarbamate moieties, the nature or type of the substituents around the dithiocarbamate backbone and the central metal ions or combination of these factors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Hao; Lee, H. S.; Sarahan, M. C.

Grain boundaries (GBs) in complex oxides such as perovskites have been shown to readily accommodate nonstoichiometry changing the electrostatic potential at the boundary plane and effectively controlling material properties such as capacitance, magnetoresistance and superconductivity. Understanding and quantifying exactly how variations in atomic scale nonstoichiometry at the boundary plane extend to the practical mesoscale operating length of the system is therefore critical for improving the overall properties. Bicrystals of SrTiO 3 were fabricated to provide the model GB model structures that are analysed in this paper. We show that statistical analysis of aberration-corrected scanning transmission electron microscope images acquired frommore » a large area of GB is an effective routine to understanding the variation in boundary structure that occurs to accommodate nonstoichiometry. In the case of the SrTiO 3 22.6° Σ13 (510)/[100] GB analysed here, the symmetric atomic structures observed from a micron-long GB can be categorized as two different competing structural arrangements, with and without a rigid-body translation along the boundary plane. How this quantified experimental approach can provide direct insights into the GB energetics is further confirmed from the first principles density functional theory, and the effect of nonstoichiometry in determining the GB energies is quantified.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shipra, Fnu; Idrobo Tapia, Juan Carlos; Sefat, Athena Safa

This study provides an account of the bulk preparation of TlBa 2Ca 2Cu 3O 9-δ (Tl-1223) superconductor at ambient pressure, and the Tc features under thermal-annealing conditions. The ‘as-prepared’ Tl-1223 (Tc =106 K) presents a significantly higher T c = 125 K after annealing the polycrystalline material in either flowing Ar+4% H 2, or N 2 gases. In order to understand the fundamental reasons for a particular Tc, we refined the average bulk structures using powder X-ray diffraction data. Although Ar+4%H2 annealed Tl- 1223 shows an increased ‘c’ lattice parameter, it shrinks by 0.03% (approximately unchanged) upon N2 anneal. Duemore » to such indeterminate conclusions on the average structural changes, local structures were investigated at using aberration-corrected scanning-transmission electron microscopy technique. Similar compositional changes in the atomic arrangements of both annealed-samples of Tl-1223 were detected in which the plane containing Ca atomic layer gives a non-uniform contrast, due to substitution of some heavier Tl. In this report, extensive bulk properties are summarized through temperature-dependent resistivity, and shielding and Meissner fractions of magnetic susceptibility results; the bulk and local structures are investigated to correlate to properties.« less

Geometrically frustrated magnetic structures of the heavy-fermion compound CePdAl studied by powder neutron diffraction

NASA Astrophysics Data System (ADS)

Dönni, A.; Ehlers, G.; Maletta, H.; Fischer, P.; Kitazawa, H.; Zolliker, M.

1996-12-01

The heavy-fermion compound CePdAl with ZrNiAl-type crystal structure (hexagonal space group 0953-8984/8/50/043/img8) was investigated by powder neutron diffraction. The triangular coordination symmetry of magnetic Ce atoms on site 3f gives rise to geometrical frustration. CePdAl orders below 0953-8984/8/50/043/img9 with an incommensurate antiferromagnetic propagation vector 0953-8984/8/50/043/img10, and a longitudinal sine-wave (LSW) modulated spin arrangement. Magnetically ordered moments at Ce(1) and Ce(3) coexist with frustrated disordered moments at Ce(2). The experimentally determined magnetic structure is in agreement with group theoretical symmetry analysis considerations, calculated by the program MODY, which confirm that for Ce(2) an ordered magnetic moment parallel to the magnetically easy c-axis is forbidden by symmetry. Further low-temperature experiments give evidence for a second magnetic phase transition in CePdAl between 0.6 and 1.3 K. Magnetic structures of CePdAl are compared with those of the isostructural compound TbNiAl, where a non-zero ordered magnetic moment for the geometrically frustrated Tb(2) atoms is allowed by symmetry.

Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements

PubMed Central

Anada, Masato; Nakanishi-Ohno, Yoshinori; Okada, Masato; Kimura, Tsuyoshi; Wakabayashi, Yusuke

2017-01-01

Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes’ theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3 film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites. PMID:29217989

Surface study of irradiated sapphires from Phrae Province, Thailand using AFM

NASA Astrophysics Data System (ADS)

Monarumit, N.; Jivanantaka, P.; Mogmued, J.; Lhuaamporn, T.; Satitkune, S.

2017-09-01

The irradiation is one of the gemstone enhancements for improving the gem quality. Typically, there are many varieties of irradiated gemstones in the gem market such as diamond, topaz, and sapphire. However, it is hard to identify the gemstones before and after irradiation. The aim of this study is to analyze the surface morphology for classifying the pristine and irradiated sapphires using atomic force microscope (AFM). In this study, the sapphire samples were collected from Phrae Province, Thailand. The samples were irradiated by high energy electron beam for a dose of ionizing radiation at 40,000 kGy. As the results, the surface morphology of pristine sapphires shows regular atomic arrangement, whereas, the surface morphology of irradiated sapphires shows the nano-channel observed by the 2D and 3D AFM images. The atomic step height and root mean square roughness have changed after irradiation due to the micro-structural defect on the sapphire surface. Therefore, this study is a frontier application for sapphire identification before and after irradiation.

An epistemology on the nature of polymers.

PubMed

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity.

An Epistemology on the Nature of Polymers

PubMed Central

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity. PMID:25329440

Crystallographic features of the approximant H (Mn7Si2V) phase in the Mn-Si-V alloy system

NASA Astrophysics Data System (ADS)

Nakayama, Kei; Komatsuzaki, Takumi; Koyama, Yasumasa

2018-07-01

The intermetallic compound H (Mn7Si2V) phase in the Mn-Si-V alloy system can be regarded as an approximant phase of the dodecagonal quasicrystal as one of the two-dimensional quasicrystals. To understand the features of the approximant H phase, in this study, the crystallographic features of both the H phase and the (σ → H) reaction in Mn-Si-V alloy samples were investigated, mainly by transmission electron microscopy. It was found that, in the H phase, there were characteristic structural disorders with respect to an array of a dodecagonal structural unit consisting of 19 dodecagonal atomic columns. Concretely, penetrated structural units consisting of two dodecagonal structural units were presumed to be typical of such disorders. An interesting feature of the (σ → H) reaction was that regions with a rectangular arrangement of penetrated structural units (RAPU) first appeared in the σ matrix as the initial state, and H regions were then nucleated in contact with RAPU regions. The subsequent conversion of RAPU regions into H regions eventually resulted in the formation of the approximant H state as the final state. Furthermore, atomic positions in both the H structure and the dodecagonal quasicrystal were examined using a simple plane-wave model with 12 plane waves.

catena-Poly[[triphenyl-tin(IV)]-μ-phenyl-phosphinato-κO:O'].

PubMed

Diop, Tidiane; Diop, Libasse; Kociok-Köhn, Gabriele; Molloy, Kieran C; Stoeckli-Evans, Helen

2011-12-01

In the structure of the title coordination polymer, [Sn(C(6)H(5))(3)(C(6)H(6)O(2)P)](n) or [PhP(H)O(2)Sn(IV)(Ph)(3)](n), the Sn(IV) atom is five-coordinate, with the SnC(3)O(2) framework in a trans trigonal-bipyramidal arrangement having the PhP(H)O(2) (-) anions in apical positions. In the crystal, neighbouring polymer chains are linked via C-H⋯π inter-actions, forming a two-dimensional network lying parallel to (001).

Diazido­bis(5,5′-dimethyl-2,2′-bipyridyl-κ2 N,N′)nickel(II) monohydrate

PubMed Central

Phatchimkun, Jaturong; Kongsaeree, Palangpon; Suchaichit, Nattawut; Chaichit, Narongsak

2009-01-01

In the crystal structure of the title compound, [Ni(N3)2(C12H12N2)2]·H2O, the NiII atom is situated on a twofold axis and adopts a distorted octa­hedral geometry with the two 5,5′-dimethyl-2,2′-bipyridyl (dmbpy) and the two azide ligands in a cis arrangement. The water solvent mol­ecule is disordered over two positions in a 1:1 ratio. PMID:21577389

On the Tetragonal Forms of KMo 4O 6

NASA Astrophysics Data System (ADS)

McCarroll, W. H.; Ramanujachary, K. V.; Greenblatt, M.; Marsh, Richard E.

1995-06-01

A reexamination of the X-ray diffraction data for the tetragonal form of KMo4O6 prepared by fused salt electrolysis leads to the conclusion that the crystal structure is better described by using space group P 4/mbm and not P4¯ as previously reported. However, refinement in the new space group does not result in any significant changes in the atomic arrangement. Possible reasons for the significant difference between the c lattice parameter of this form of KMo4O6 and that prepared at high pressures are also discussed.

Atomistic insight into the adsorption site selectivity of stepped Au(111) surfaces

NASA Astrophysics Data System (ADS)

Gaspari, Roberto; Pignedoli, Carlo A.; Fasel, Roman; Treier, Matthias; Passerone, Daniele

2010-07-01

Using classical and ab initio simulations, we study the interplay between the Au(111) surface reconstruction and monoatomic steps on a vicinal face. The experimentally observed discommensuration line patterns on a specific vicinal are reproduced and explained, and a complete description of the structure is given. An unusual atomic arrangement is shown to be responsible for the lower reactivity of hcp segments of step edges compared to the one of fcc segments. Our results provide an unprecedented understanding of the electronic and geometric properties of the complex Au(111) surface.

Boroxol rings from diffraction data on vitreous boron trioxide.

PubMed

Soper, Alan K

2011-09-14

There has been a considerable debate about the nature of the short range atomic order in vitreous B(2)O(3). Some authorities state that it is not possible to build a model of glassy boron oxide of the correct density containing a large number of six-membered rings which also fits experimental diffraction data, but recent computer simulations appear to overrule that view. To discover which view is correct I use empirical potential structure refinement (EPSR) on existing neutron and x-ray diffraction data to build two models of vitreous B(2)O(3). One of these consists only of single boron and oxygen atoms arranged in a network to reproduce the diffraction data as closely as possible. This model has less than 10% of boron atoms in boroxol rings. The second model is made up of an equimolar mixture of B(3)O(3) hexagonal ring 'molecules' and BO(3) triangular molecules, with no free boron or oxygen atoms. This second model therefore has 75% of the boron atoms in boroxol rings. It is found that both models give closely similar diffraction patterns, suggesting that the diffraction data in this case are not sensitive to the number of boroxol rings present in the structure. This reinforces recent Raman, ab initio, and NMR claims that the percentage of boroxol rings in this material may be as high as 75%. The findings of this study probably explain why some interpretations based on different simulation techniques only find a small fraction of boroxol rings. The results also highlight the power of EPSR for the extraction of accurate atomistic representations of amorphous structures, provided adequate additional, non-scattering data (such as Raman and NMR in this case) are available.

Sr{sub 7}Ge{sub 6}, Ba{sub 7}Ge{sub 6} and Ba{sub 3}Sn{sub 2} -Three new binary compounds containing dumbbells and four-membered chains of tetrel atoms with considerable Ge-Ge {pi}-bonding character

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siggelkow, Lisa; Hlukhyy, Viktor; Faessler, Thomas F., E-mail: thomas.faessler@lrz.tum.de

2012-07-15

The germanides Sr{sub 7}Ge{sub 6} and Ba{sub 7}Ge{sub 6} as well as the stannide Ba{sub 3}Sn{sub 2} were prepared by arc melting and annealing in welded tantalum ampoules using induction as well as resistance furnaces. The compounds were investigated by powder and single crystal X-ray diffraction. Sr{sub 7}Ge{sub 6} and Ba{sub 7}Ge{sub 6} crystallize in the Ca{sub 7}Sn{sub 6} structure type (space group Pmna, Z=4: a=7.777(2) A, b=23.595(4) A, c=8.563(2) A, wR{sub 2}=0.081 (all data), 2175 independent reflections, 64 variable parameters for Sr{sub 7}Ge{sub 6} and a=8.0853(6) A, b=24.545(2) A, c=8.9782(8) A, wR{sub 2}=0.085 (all data), 2307 independent reflections, 64more » variable parameters for Ba{sub 7}Ge{sub 6}). Ba{sub 3}Sn{sub 2} crystallizes in an own structure type with the space group P4{sub 3}2{sub 1}2, Z=4, a=6.6854(2) A, c=17.842(2) A, wR{sub 2}=0.037 (all data), 1163 independent reflections, 25 variable parameters. In Sr{sub 7}Ge{sub 6} and Ba{sub 7}Ge{sub 6} the Ge atoms are arranged as Ge{sub 2} dumbbells and Ge{sub 4} four-membered atom chains. Their crystal structures cannot be rationalized according to the (8-N) rule. In contrast, Ba{sub 3}Sn{sub 2} presents Sn{sub 2} dumbbells as a main structural motif and thereby can be described as an electron precise Zintl phase. The chemical bonding situation in these structures is discussed on the basis of partial and total Density Of States (DOS) curves, band structures including fatbands, topological analysis of the Electron Localization Function (ELF) as well as Bader analysis of the bond critical points using the programs TB-LMTO-ASA and WIEN2K. While Ba{sub 3}Sn{sub 2} reveals semiconducting behaviour, all germanides Ae{sub 7}Ge{sub 6} (Ae=Ca, Sr, and Ba) show metallic properties and a considerable {pi}-bonding character between the Ge atoms of the four-membered chains and the dumbbells. The {pi}-bonding character of the germanides is best reflected by the resonance hybrid structures {l_brace}[Ge-Ge]{sup 6-}/[Ge-{sup ....}Ge-{sup ....}Ge-{sup ....}Ge]{sup 8-}{r_brace}{r_reversible}{l_brace}[Ge=Ge]{sup 4-}/[Ge-Ge-Ge-Ge]{sup 10-}{r_brace}. - Graphical abstract: The structure of Ba{sub 3}Sn{sub 2} contains Sn{sub 2} dumbbells as a main structural motif and thereby can be described as an electron precise Zintl phase. Ge{sub 2} dumbbells and Ge{sub 4} four-membered atom chains are the predominant features in Sr{sub 7}Ge{sub 6} and Ba{sub 7}Ge{sub 6}. Their crystal structures cannot be rationalized according to the (8-N) rule. While Ba{sub 3}Sn{sub 2} reveals semiconducting behaviour, the germanides Ae{sub 7}Ge{sub 6} (Ae=Ca, Sr, and Ba) show metallic properties and a considerable {pi}-bonding character between the Ge atoms of the four-membered chains and the dumbbells. Highlights: Black-Right-Pointing-Pointer The germanides Sr{sub 7}Ge{sub 6} and Ba{sub 7}Ge{sub 6} as well as the stannide Ba{sub 3}Sn{sub 2} have been synthesized. Black-Right-Pointing-Pointer In Sr{sub 7}Ge{sub 6} and Ba{sub 7}Ge{sub 6} the Ge atoms are arranged as dumbbells and four-membered atom chains. Black-Right-Pointing-Pointer Ba{sub 3}Sn{sub 2} presents Sn{sub 2} dumbbells as a main structural motif. Black-Right-Pointing-Pointer The chemical bonding situation within these structures is discussed.« less

Synthesizing new, high-temperature superconductors

NASA Astrophysics Data System (ADS)

Weaver, Claire; Aronson, Meigan

2015-03-01

Currently, there is no accepted theory behind type-II, high-temperature superconductors, but there is a distinct relationship between anti-ferromagnetism and superconductivity. Our research focuses on synthesizing new superconducting materials by observing the link between atomic structure and magnetic moments of anti-ferromagnetic compounds and attempting to reproduce the molecular physics of these known materials in new compounds. Consider the square-planar arrangement of the transition metal Fe in the Fe-pnictide superconductors of the ZrCuSiAs ``11 11'' and the ThCr2Si2 ``122'' structure types. We believe that the physics behind this superconductor, where Fe has d6 valence electrons, contributes to the superconducting state, not the presence of Fe itself. For this reason, we are synthesizing materials containing neighboring transition metals, like Mn and Co, combined with other elements in similar crystal lattice arrangements, having ionization properties that hopefully impose d6 valence electrons on the transition metals. This project was supported in part by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internships Program (SULI).

Bacterial actin MreB forms antiparallel double filaments

PubMed Central

van den Ent, Fusinita; Izoré, Thierry; Bharat, Tanmay AM; Johnson, Christopher M; Löwe, Jan

2014-01-01

Filaments of all actin-like proteins known to date are assembled from pairs of protofilaments that are arranged in a parallel fashion, generating polarity. In this study, we show that the prokaryotic actin homologue MreB forms pairs of protofilaments that adopt an antiparallel arrangement in vitro and in vivo. We provide an atomic view of antiparallel protofilaments of Caulobacter MreB as apparent from crystal structures. We show that a protofilament doublet is essential for MreB's function in cell shape maintenance and demonstrate by in vivo site-specific cross-linking the antiparallel orientation of MreB protofilaments in E. coli. 3D cryo-EM shows that pairs of protofilaments of Caulobacter MreB tightly bind to membranes. Crystal structures of different nucleotide and polymerisation states of Caulobacter MreB reveal conserved conformational changes accompanying antiparallel filament formation. Finally, the antimicrobial agents A22/MP265 are shown to bind close to the bound nucleotide of MreB, presumably preventing nucleotide hydrolysis and destabilising double protofilaments. DOI: http://dx.doi.org/10.7554/eLife.02634.001 PMID:24843005

Bacterial actin MreB forms antiparallel double filaments.

PubMed

van den Ent, Fusinita; Izoré, Thierry; Bharat, Tanmay Am; Johnson, Christopher M; Löwe, Jan

2014-05-02

Filaments of all actin-like proteins known to date are assembled from pairs of protofilaments that are arranged in a parallel fashion, generating polarity. In this study, we show that the prokaryotic actin homologue MreB forms pairs of protofilaments that adopt an antiparallel arrangement in vitro and in vivo. We provide an atomic view of antiparallel protofilaments of Caulobacter MreB as apparent from crystal structures. We show that a protofilament doublet is essential for MreB's function in cell shape maintenance and demonstrate by in vivo site-specific cross-linking the antiparallel orientation of MreB protofilaments in E. coli. 3D cryo-EM shows that pairs of protofilaments of Caulobacter MreB tightly bind to membranes. Crystal structures of different nucleotide and polymerisation states of Caulobacter MreB reveal conserved conformational changes accompanying antiparallel filament formation. Finally, the antimicrobial agents A22/MP265 are shown to bind close to the bound nucleotide of MreB, presumably preventing nucleotide hydrolysis and destabilising double protofilaments.DOI: http://dx.doi.org/10.7554/eLife.02634.001. Copyright © 2014, van den Ent et al.

Crystal structure and Hirshfeld surface analysis of aqua­bis­(nicotinamide-κN)bis­(4-sulfamoylbenzoato-κO 1)copper(II)

PubMed Central

Hökelek, Tuncer; Yavuz, Vijdan; Dal, Hakan; Necefoğlu, Hacali

2018-01-01

In the crystal of the title complex, [Cu(C7H6NO4S)2(C6H6N2O)2(H2O)], the CuII cation and the O atom of the coordinated water mol­ecule reside on a twofold rotation axis. The CuII ion is coordinated by two carboxyl­ate O atoms of the two symmetry-related 4-sulfamoylbenzoate (SB) anions and by two N atoms of the two symmetry-related nicotinamide (NA) mol­ecules at distances of 1.978 (2) and 2.025 (3) Å, respectively, forming a slightly distorted square-planar arrangement. The distorted square-pyramidal coordination environment is completed by the water O atom in the axial position at a distance of 2.147 (4) Å. In the crystal, the mol­ecules are linked via O—H⋯O and N—H⋯O hydrogen bonds with R 2 2(8) and R 2 2(18) ring motifs, forming a three-dimensional architecture. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯O/O⋯H (42.2%), H⋯H (25.7%) and H⋯C/C⋯H (20.0%) inter­actions. PMID:29416889

Evidence of benzenoid domains in nanographenes.

PubMed

Baldoni, Matteo; Mercuri, Francesco

2015-01-21

Calculations based on density functional theory demonstrate the occurrence of local deformations of the perfect honeycomb lattice in nanographenes to form arrangements, with triangular symmetry, composed of six-membered ring patterns. The formation of these locally regular superstructures, which can be considered as benzenoid-like domains on the 2D graphene lattice, is ascribed to the gain in resonance energy deriving from aromaticity. The relationship between the atomic morphology of nanographenes and details of the relaxed structure is rationalized in terms of Clar's theory of the aromatic sextet and by extending concepts borrowed from valence bond theory to 2D carbon nanostructures. Namely, two regular arrangements can be evidenced, defined as Clar (fully benzenoid) and Kekulé domains, which correspond to two different regular bond patterns in sets of adjacent six-membered rings. Our findings are compatible with recent experiments and have potentially relevant consequences in the development of novel electronic devices based on graphene materials.

Ordered Structure Formed by Biologically Related Molecules

NASA Astrophysics Data System (ADS)

Hatta, Ichiro; Nishino, Junichiro; Sumi, Akinori; Hibino, Masahiro

1995-07-01

The two-dimensional arrangement of biologically related molecules was studied by means of scanning probe microscopy. For monolayers of fatty acid molecules with a saturated hydrocarbon chain adsorbed on a graphite substrate, in the scanning tunneling microscope image, the position associated with the carbon atoms was clearly distinguished. In addition, based on the image for fatty acid molecules with an unsaturated hydrocarbon chain, at the position of a double bond, local electrical conductance was found to increase. Based on the images, it was pointed out that not the position of each carbon but the interaction between a graphite substrate and an alkyl chain plays an important role in imaging. On the other hand, for the surface of Langmuir-Blodgett films composed of phosphatidic acids with cations, the scanning force microscope image shows, for the first time, evidence of the methyl ends in the arrangement of phospholipid molecules.

Configuration of twins in glass-embedded silver nanoparticles of various origin

NASA Astrophysics Data System (ADS)

Hofmeister, H.; Dubiel, M.; Tan, G. L.; Schicke, K.-D.

2005-09-01

Structural characterization using high resolution electron microscopy and diffractogram analysis of silver nanoparticles embedded in glass by various routes of fabrication was aimed at revealing the characteristic features of twin faults occuring in such particles. Nearly spherical silver nanoparticles well below 10 nm size embedded in commercial soda-lime silicate float glass have been fabricated either by silver/sodium ion exchange or by Ag+ ion implantation. Twinned nanoparticles, besides single crystalline species, have frequently been observed for both fabrication routes, mainly at sizes above 5 nm, but also at smaller sizes, even around 1 nm. The variety of particle forms comprises single crystalline particles of nearly cuboctahedron shape, particles containing single twin faults, and multiply twinned particles containing parallel twin lamellae, or cyclic twinned segments arranged around axes of fivefold symmetry. Parallel twinning is distinctly favoured by ion implantation whereas cyclic twinning preferably occurs upon ion exchange processing. Regardless of single or repeated twinning, parallel or cyclic twin arrangement, one may classify simple twin faults of regular atomic configuration and compound twin faults whose irregular configuration consists of additional planar defects like associated stacking faults or secondary twin faults. Besides, a particular superstructure composed of parallel twin lamellae of only three atomic layers thickness is observed.

DNA-nanostructure-assembly by sequential spotting

PubMed Central

2011-01-01

Background The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions. Results For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures. Conclusions The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element. PMID:22099392

Tests of Si(111)-7 × 7 structural models by comparison with transmission electron diffraction patterns

NASA Astrophysics Data System (ADS)

McRae, E. G.; Petroff, P. M.

1984-11-01

Several structural models of the Si(111)-7 × 7 surface are tested by comparing calculated and observed transmission electron diffraction (TED) patterns. The models comprise "adatom" models where the unit mesh contains 12 adatoms or atom clusters in a locally (2 × 2) arrangement, and "triangle-dimer" models where the unit mesh contains 9 dimers or pairs of dimers bordering a triangular subunit of the unit mesh. The distribution of diffraction intensity among fractional-order spots is calculated kinematically and compared with TED patterns observed by Petroff and Wilson and others. No agreement is found for adatom models. Good but not perfect agreement is found for one triangle-dimer model.

Incoherent Diffractive Imaging via Intensity Correlations of Hard X Rays

NASA Astrophysics Data System (ADS)

Classen, Anton; Ayyer, Kartik; Chapman, Henry N.; Röhlsberger, Ralf; von Zanthier, Joachim

2017-08-01

Established x-ray diffraction methods allow for high-resolution structure determination of crystals, crystallized protein structures, or even single molecules. While these techniques rely on coherent scattering, incoherent processes like fluorescence emission—often the predominant scattering mechanism—are generally considered detrimental for imaging applications. Here, we show that intensity correlations of incoherently scattered x-ray radiation can be used to image the full 3D arrangement of the scattering atoms with significantly higher resolution compared to conventional coherent diffraction imaging and crystallography, including additional three-dimensional information in Fourier space for a single sample orientation. We present a number of properties of incoherent diffractive imaging that are conceptually superior to those of coherent methods.

Time-resolved atomic inner-shell spectroscopy

NASA Astrophysics Data System (ADS)

Drescher, M.; Hentschel, M.; Kienberger, R.; Uiberacker, M.; Yakovlev, V.; Scrinzi, A.; Westerwalbesloh, Th.; Kleineberg, U.; Heinzmann, U.; Krausz, F.

2002-10-01

The characteristic time constants of the relaxation dynamics of core-excited atoms have hitherto been inferred from the linewidths of electronic transitions measured by continuous-wave extreme ultraviolet or X-ray spectroscopy. Here we demonstrate that a laser-based sampling system, consisting of a few-femtosecond visible light pulse and a synchronized sub-femtosecond soft X-ray pulse, allows us to trace these dynamics directly in the time domain with attosecond resolution. We have measured a lifetime of 7.9-0.9^{+1.0fs of M-shell vacancies of krypton in such a pump-probe experiment.}

Chemical Makeup and Hydrophilic Behavior of Graphene Oxide Nanoribbons after Low-Temperature Fluorination.

PubMed

Romero Aburto, Rebeca; Alemany, Lawrence B; Weldeghiorghis, Thomas K; Ozden, Sehmus; Peng, Zhiwei; Lherbier, Aurélien; Botello Méndez, Andrés Rafael; Tiwary, Chandra Sekhar; Taha-Tijerina, Jaime; Yan, Zheng; Tabata, Mika; Charlier, Jean-Christophe; Tour, James M; Ajayan, Pulickel M

2015-07-28

Here we investigated the fluorination of graphene oxide nanoribbons (GONRs) using H2 and F2 gases at low temperature, below 200 °C, with the purpose of elucidating their structure and predicting a fluorination mechanism. The importance of this study is the understanding of how fluorine functional groups are incorporated in complex structures, such as GONRs, as a function of temperature. The insight provided herein can potentially help engineer application-oriented materials for several research and industrial sectors. Direct (13)C pulse magic angle spinning (MAS) nuclear magnetic resonance (NMR) confirmed the presence of epoxy, hydroxyl, ester and ketone carbonyl, tertiary alkyl fluorides, as well as graphitic sp(2)-hybridized carbon. Moreover, (19)F-(13)C cross-polarization MAS NMR with (1)H and (19)F decoupling confirmed the presence of secondary alkyl fluoride (CF2) groups in the fluorinated graphene oxide nanoribbon (FGONR) structures fluorinated above 50 °C. First-principles density functional theory calculations gained insight into the atomic arrangement of the most dominant chemical groups. The fluorinated GONRs present atomic fluorine percentages in the range of 6-35. Interestingly, the FGONRs synthesized up to 100 °C, with 6-19% of atomic fluorine, exhibit colloidal similar stability in aqueous environments when compared to GONRs. This colloidal stability is important because it is not common for materials with up to 19% fluorine to have a high degree of hydrophilicity.

Crystal structure of trans-bis­(ethane-1,2-diamine-κ2 N,N′)bis­(thio­cyanato-κN)chromium(III) perchlorate from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2015-01-01

The structure of the title compound, [Cr(NCS)2(C2H8N2)2]ClO4, has been determined from synchroton data. The asymmetric unit consists of one half of a centrosymmetric CrIII complex cation and half of a perchlorate anion with the Cl atom on a twofold rotation axis. The CrIII ion is coordinated by the four N atoms of two ethane-1,2-di­amine (en) ligands in the equatorial plane and two N-bound thio­cyanate (NCS−) anions in a trans-axial arrangement, displaying a slightly distorted octa­hedral geometry with crystallographic inversion symmetry. The Cr—N(en) bond lengths are in the range 2.053 (16)–2.09 (2) Å, while the Cr—N(thio­cyanate) bond length is 1.983 (2) Å. The five-membered en rings are disordered over two sites, with occupancy ratios of 0.522 (16):0.478 (16). Each ClO4 − anion is disordered over two sites with equal occupancy. The crystal structure is stabilized by inter­molecular hydrogen bonds involving the en NH2 groups as donors and perchlorate O and thio­cyanate S atoms as acceptors. PMID:26090142

Crystal structure of bis­[trans-(ethane-1,2-di­amine-κ2 N,N′)bis­(thio­cyanato-κN)chromium(III)] tetra­chlorido­zincate from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2015-01-01

The structure of the title compound, [Cr(NCS)2(C2H8N2)2]2[ZnCl4], has been determined from synchrotron data. In the asymmetric unit, there are four independent halves of the CrIII complex cations, each of which lies on an inversion centre, and one tetra­chlorido­zincate anion in a general position. The CrIII atoms are coordinated by the four N atoms of two ethane-1,2-di­amine (en) ligands in the equatorial plane and two N-bound NCS− anions in a trans arrangement, displaying a slightly distorted octa­hedral geometry with crystallographic inversion symmetry. The Cr—N(en) and Cr—N(NCS) bond lengths range from 2.0653 (10) to 2.0837 (10) Å and from 1.9811 (10) to 1.9890 (10) Å, respectively. The five-membered metalla-rings are in stable gauche conformations. The [ZnCl4]2− anion has a distorted tetra­hedral geometry. The crystal structure is stabilized by inter­molecular hydrogen bonds involving the en NH2 or CH2 groups as donors and chloride ligands of the anion and S atoms of NCS− ligands as acceptors. PMID:25705463

Electronic structure of ruthenium-doped iron chalcogenides

NASA Astrophysics Data System (ADS)

Winiarski, M. J.; Samsel-Czekała, M.; Ciechan, A.

2014-12-01

The structural and electronic properties of hypothetical RuxFe1-xSe and RuxFe1-xTe systems have been investigated from first principles within the density functional theory (DFT). Reasonable values of lattice parameters and chalcogen atomic positions in the tetragonal unit cell of iron chalcogenides have been obtained with the use of norm-conserving pseudopotentials. The well known discrepancies between experimental data and DFT-calculated results for structural parameters of iron chalcogenides are related to the semicore atomic states which were frozen in the used here approach. Such an approach yields valid results of the electronic structures of the investigated compounds. The Ru-based chalcogenides exhibit the same topology of the Fermi surface (FS) as that of FeSe, differing only in subtle FS nesting features. Our calculations predict that the ground states of RuSe and RuTe are nonmagnetic, whereas those of the solid solutions RuxFe1-xSe and RuxFe1-xTe become the single- and double-stripe antiferromagnetic, respectively. However, the calculated stabilization energy values are comparable for each system. The phase transitions between these magnetic arrangements may be induced by slight changes of the chalcogen atom positions and the lattice parameters a in the unit cell of iron selenides and tellurides. Since the superconductivity in iron chalcogenides is believed to be mediated by the spin fluctuations in single-stripe magnetic phase, the RuxFe1-xSe and RuxFe1-xTe systems are good candidates for new superconducting iron-based materials.

76 FR 17406 - Proposed Subsequent Arrangement

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-29

... the Peaceful Uses of Nuclear Energy Between the European Atomic Energy Community (EURATOM) and the... America and the Government of Norway Concerning Peaceful Uses of Nuclear Energy. DATES: This subsequent... Peaceful Uses of Nuclear Energy. In accordance with section 131a. of the Atomic Energy Act of 1954, as...

Investigation of Local Ordering in Amorphous Materials.

NASA Astrophysics Data System (ADS)

Fan, Gary Guoyou

The intent of the research described in this dissertation, as indicated by the title, is to provide a better understanding of the structure of amorphous material. The possibility of using electron microscopy to study the amorphous structure is investigated. Chapter 1 gives a brief introduction to the understanding and modeling of the amorphous structure, electron microscopy and the image analysis in general. The difficulty of using 2-D images to infer 3-D structures information is illustrated in Chapter 2, where it is shown that some high resolution images are not qualitatively different from images of white -noises weak-phase objects or those of random atomic arrangements. The means of obtaining statistical information from these images is given in Chapters 3 and 5, where the quantitative differences between experimental images and simulated white-noise or simulated images corresponding to random arrangements are revealed. The use of image processing techniques in electron microscopy and the possible artifacts are presented in Chapter 4. The pattern recognition technique outlined in Chapter 6 demonstrates a feasible mode of scanning transition electron microscope operation. Statistical analysis can be effectively performed on a large number of nano-diffraction patterns from, for example, locally ordered samples. Some recent developments in physics as well as in electron microscopy are briefly reviewed, and their possible applications in the study of amorphous structures are discussed in Chapter 7.

Crystal structure of aqua-1κO-{μ-2-[(2-hydroxy­ethyl)methylamino]ethanolato-2:1κ4 O 1,N,O 2:O 1}[μ-2,2′-(methylimino)diethanolato-1:2κ4 O,N,O′:O]dithiocyanato-1κN,2κN-chromium(III)copper(II)

PubMed Central

Rusanova, Julia A.; Semenaka, Valentina V.; Dyakonenko, Viktoriya V.; Shishkin, Oleg V.

2015-01-01

The title compound, [CrCu(C5H11NO2)(C5H12NO2)(NCS)2(H2O)] or [Cr(μ-mdea)Cu(μ-Hmdea)(NCS)2H2O], (where mdeaH2 is N-methylethanolamine, C5H13NO2) is formed as a neutral heterometal CuII/CrIII complex. The mol­ecular structure of the complex is based on a binuclear {CuCr(μ-O)2} core. The coordination environment of each metal atom involves the N,O,O atoms of the tridentate ligand, one bridging O atom of the ligand and the N atom of the thio­cyanato ligands. The CuII ion adopts a distorted square-pyramidal coordination while the CrIII ion has a distorted octa­hedral coordination geometry completed by the aqua ligand. In the crystal, the binuclear complexes are linked via two pairs of O—H⋯O hydrogen bonds to form inversion dimers, which are arranged in columns parallel to the a axis. In the μ-mdea ligand two –CH2 groups and the methyl group were refined as disordered over two sets of sites with equal occupancies. The structure was refined as a two-component twin with a twin scale factor of 0.242 (1). PMID:26396853

Structural and superconducting features of Tl-1223 prepared at ambient pressure

DOE PAGES

Shipra, Fnu; Idrobo Tapia, Juan Carlos; Sefat, Athena Safa

2015-09-25

This study provides an account of the bulk preparation of TlBa 2Ca 2Cu 3O 9-δ (Tl-1223) superconductor at ambient pressure, and the Tc features under thermal-annealing conditions. The ‘as-prepared’ Tl-1223 (Tc =106 K) presents a significantly higher T c = 125 K after annealing the polycrystalline material in either flowing Ar+4% H 2, or N 2 gases. In order to understand the fundamental reasons for a particular Tc, we refined the average bulk structures using powder X-ray diffraction data. Although Ar+4%H2 annealed Tl- 1223 shows an increased ‘c’ lattice parameter, it shrinks by 0.03% (approximately unchanged) upon N2 anneal. Duemore » to such indeterminate conclusions on the average structural changes, local structures were investigated at using aberration-corrected scanning-transmission electron microscopy technique. Similar compositional changes in the atomic arrangements of both annealed-samples of Tl-1223 were detected in which the plane containing Ca atomic layer gives a non-uniform contrast, due to substitution of some heavier Tl. In this report, extensive bulk properties are summarized through temperature-dependent resistivity, and shielding and Meissner fractions of magnetic susceptibility results; the bulk and local structures are investigated to correlate to properties.« less

Ultracold few fermionic atoms in needle-shaped double wells: spin chains and resonating spin clusters from microscopic Hamiltonians emulated via antiferromagnetic Heisenberg and t-J models

NASA Astrophysics Data System (ADS)

Yannouleas, Constantine; Brandt, Benedikt B.; Landman, Uzi

2016-07-01

Advances with trapped ultracold atoms intensified interest in simulating complex physical phenomena, including quantum magnetism and transitions from itinerant to non-itinerant behavior. Here we show formation of antiferromagnetic ground states of few ultracold fermionic atoms in single and double well (DW) traps, through microscopic Hamiltonian exact diagonalization for two DW arrangements: (i) two linearly oriented one-dimensional, 1D, wells, and (ii) two coupled parallel wells, forming a trap of two-dimensional, 2D, nature. The spectra and spin-resolved conditional probabilities reveal for both cases, under strong repulsion, atomic spatial localization at extemporaneously created sites, forming quantum molecular magnetic structures with non-itinerant character. These findings usher future theoretical and experimental explorations into the highly correlated behavior of ultracold strongly repelling fermionic atoms in higher dimensions, beyond the fermionization physics that is strictly applicable only in the 1D case. The results for four atoms are well described with finite Heisenberg spin-chain and cluster models. The numerical simulations of three fermionic atoms in symmetric DWs reveal the emergent appearance of coupled resonating 2D Heisenberg clusters, whose emulation requires the use of a t-J-like model, akin to that used in investigations of high T c superconductivity. The highly entangled states discovered in the microscopic and model calculations of controllably detuned, asymmetric, DWs suggest three-cold-atom DW quantum computing qubits.

Roughness-Induced Magnetic Domain in Fe Thin Films on Land-and-Groove Structures Studied by Spin-Polarized Secondary Electron Microscopy

NASA Astrophysics Data System (ADS)

Ueda, Shigenori; Iwasaki, Yoh; Ushioda, Sukekatsu

2003-10-01

The magnetic domain structures of Fe thin films on two-dimensionally arranged land-and-groove structures have been studied by spin-polarized secondary electron microscopy (SP-SEM) under an applied dc field. The coercive force on the land area was found to be higher than that on the groove area under magnetization reversal. The surface roughness measured by atomic force microscopy (AFM) was greater on the land area than on the groove area. The roughness-induced high-coercivity on the land prevented the reversed magnetic domain on the groove from spreading over the land in the initial magnetization reversal. This result indicates that surface roughness is an important factor in domain size control of thin magnetic films.

On the coordination of Zn2+ ion in Tf2N- based ionic liquids: structural and dynamic properties depending on the nature of the organic cation.

PubMed

Sessa, Francesco; Migliorati, Valentina; Serva, Alessandra; Lapi, Andrea; Aquilanti, Giuliana; Mancini, Giordano; D'Angelo, Paola

2018-01-24

A synergic approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy has been used to investigate diluted solutions of zinc bis(trifluoromethanesulfonyl)imide (Zn(Tf 2 N) 2 ) in Tf 2 N - based ionic liquids (ILs) having different organic cations, namely the 1-butyl-3-methylimidazolium ([C 4 (mim)] + ), 1,8-bis(3-methylimidazolium-1-yl)octane ([C 8 (mim) 2 ] 2+ ), N,N,N-trimethyl-N-(2-hydroxyethyl)ammonium ([Choline] + ) and butyltrimethylammonium ([BTMA] + ) ions. All of the ILs tend to dissolve the Zn(Tf 2 N) 2 species giving rise to a different structural arrangement around the Zn 2+ as compared to that of the salt crystallographic structure. A quantitative analysis of the Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra of the solutions has been carried out based on the microscopic description of the systems derived from the MD simulations. A very good agreement between theoretical and experimental EXAFS signals has been obtained, allowing us to assess the reliability of the MD structural results for all the investigated solutions. The Zn 2+ ion has been shown to be coordinated by six oxygen atoms of the Tf 2 N - anions arranged in an octahedral geometry in all the Tf 2 N - based ILs, regardless of the organic cation of the IL solvent. However, the nature of the organic cation has a small influence on the overall spatial arrangement of the Tf 2 N - anions in the Zn 2+ first solvation shell: two different Zn-Tf 2 N complexes are found in solution, a 5-fold one, with one bidentate and four monodentate Tf 2 N - anions, and a 6-fold one with only monodentate ligands, with the ratio between the two species being slightly dependent on the IL cation. The IL ion three-dimensional arrangements in the different IL solutions were also investigated by carrying out a thorough analysis of the MD simulations, highlighting similarities and differences between imidazolium and ammonium based IL systems.

Crystal structure of [NaZn(BTC)(H2O)4]·1.5H2O (BTC = benzene-1,3,5-tri-carb-oxy-l-ate): a heterometallic coordination compound.

PubMed

Ni, Min; Li, Quanle; Chen, Hao; Li, Shengqing

2015-07-01

The title coordination polymer, poly[[μ-aqua-tri-aqua-(μ3-benzene-1,3,5-tri-carboxyl-ato)sodiumzinc] sesquihydrate], {[NaZn(C9H3O6)(H2O)4]·1.5H2O} n , was obtained in ionic liquid microemulsion at room temperture by the reaction of benzene-1,3,5-tri-carb-oxy-lic acid (H3BTC) with Zn(NO3)2·6H2O in the presence of NaOH. The asymmetric unit comprises two Na(+) ions (each located on an inversion centre), one Zn(2+) ion, one BTC ligand, four coordinating water mol-ecules and two solvent water molecules, one of which is disordered about an inversion centre and shows half-occupation. The Zn(2+) cation is five-coordinated by two carboxyl-ate O atoms from two different BTC ligands and three coordinating H2O mol-ecules; the Zn-O bond lengths are in the range 1.975 (2)-2.058 (3) Å. The Na(+) cations are six-coordinated but have different arrangements of the ligands: one is bound to two carboxyl-ate O atoms of two BTC ligands and four O atoms from four coordinating H2O mol-ecules while the other is bound by four carboxyl-ate O atoms from four BTC linkers and two O atoms of coordinating H2O mol-ecules. The completely deprotonated BTC ligand acts as a bridging ligand binding the Zn(2+) atom and Na(+) ions, forming a layered structure extending parallel to (100). An intricate network of O-H⋯O hydrogen bonds is present within and between the layers.

Stability of surface and subsurface hydrogen on and in Au/Ni near-surface alloys

DOE PAGES

Celik, Fuat E.; Mavrikakis, Manos

2015-01-12

Periodic, self-consistent DFT-GGA (PW91) calculations were used to study the interaction of hydrogen atoms with the (111) surfaces of substitutional near-surface alloys (NSAs) of Au and Ni with different surface layer compositions and different arrangements of Au atoms in the surface layer. The effect of hydrogen adsorption on the surface and in the first and second subsurface layers of the NSAs was studied. Increasing the Au content in the surface layer weakens hydrogen binding on the surface, but strengthens subsurface binding, suggesting that the distribution of surface and subsurface hydrogen will be different than that on pure Ni(111). While themore » metal composition of the surface layer has an effect on the binding energy of hydrogen on NSA surfaces, the local composition of the binding site has a stronger effect. For example, fcc hollow sites consisting of three Ni atoms bind H nearly as strongly as on Ni(111), and fcc sites consisting of three Au atoms bind H nearly as weakly as on Au(111). Sites with one or two Au atoms show intermediate binding energies. The preference of hydrogen for three-fold Ni hollow sites alters the relative stabilities of different surface metal atom arrangements, and may provide a driving force for adsorbate-induced surface rearrangement.« less

Stability of Surface and Subsurface Hydrogen on and in Au/Ni Near-Surface Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Celik, Fuat E.; Mavrikakis, Manos

2015-10-01

Periodic, self-consistent DFT-GGA (PW91) calculations were used to study the interaction of hydrogen atoms with the (111) surfaces of substitutional near-surface alloys (NSAs) of Au and Ni with different surface layer compositions and different arrangements of Au atoms in the surface layer. The effect of hydrogen adsorption on the surface and in the first and second subsurface layers of the NSAs was studied. Increasing the Au content in the surface layer weakens hydrogen binding on the surface, but strengthens subsurface binding, suggesting that the distribution of surface and subsurface hydrogen will be different than that on pure Ni(111). While themore » metal composition of the surface layer has an effect on the binding energy of hydrogen on NSA surfaces, the local composition of the binding site has a stronger effect. For example, fcc hollow sites consisting of three Ni atoms bind H nearly as strongly as on Ni(111), and fcc sites consisting of three Au atoms bind H nearly as weakly as on Au(111). Sites with one or two Au atoms show intermediate binding energies. The preference of hydrogen for three-fold Ni hollow sites alters the relative stabilities of different surface metal atom arrangements, and may provide a driving force for adsorbate-induced surface rearrangement.« less

Stability of surface and subsurface hydrogen on and in Au/Ni near-surface alloys

NASA Astrophysics Data System (ADS)

Celik, Fuat E.; Mavrikakis, Manos

2015-10-01

Periodic, self-consistent DFT-GGA (PW91) calculations were used to study the interaction of hydrogen atoms with the (111) surfaces of substitutional near-surface alloys (NSAs) of Au and Ni with different surface layer compositions and different arrangements of Au atoms in the surface layer. The effect of hydrogen adsorption on the surface and in the first and second subsurface layers of the NSAs was studied. Increasing the Au content in the surface layer weakens hydrogen binding on the surface, but strengthens subsurface binding, suggesting that the distribution of surface and subsurface hydrogen will be different than that on pure Ni(111). While the metal composition of the surface layer has an effect on the binding energy of hydrogen on NSA surfaces, the local composition of the binding site has a stronger effect. For example, fcc hollow sites consisting of three Ni atoms bind H nearly as strongly as on Ni(111), and fcc sites consisting of three Au atoms bind H nearly as weakly as on Au(111). Sites with one or two Au atoms show intermediate binding energies. The preference of hydrogen for three-fold Ni hollow sites alters the relative stabilities of different surface metal atom arrangements, and may provide a driving force for adsorbate-induced surface rearrangement.

SABER: a computational method for identifying active sites for new reactions.

PubMed

Nosrati, Geoffrey R; Houk, K N

2012-05-01

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. Copyright © 2012 The Protein Society.

Ternary lithium stannides Li xT 3Sn 7-x ( T=Rh, Ir)

NASA Astrophysics Data System (ADS)

Sreeraj, Puravankara; Kurowski, Daniel; Hoffmann, Rolf-Dieter; Wu, Zhiyun; Pöttgen, Rainer

2005-11-01

The ternary stannides Li xRh 3Sn 7-x ( x=0.45, 0.64, 0.80) and Li xIr 3Sn 7-x ( x=0.62 and 0.66) were synthesized from the elements in sealed tantalum tubes in a water-cooled sample chamber of an induction furnace. The samples were characterized by X-ray diffraction on powders and single crystals. The stannides adopt the cubic Ir 3Ge 7-type structure (space group Im3¯m, Z=4). In this structure type the tin atoms occupy the Wyckoff positions 12 d and 16 f and form two interpenetrating frameworks consisting of cubes and square antiprisms. The rhodium and iridium atoms center the square antiprisms and are arranged in pairs. With increasing lithium substitution the lattice parameter of Ir 3Sn 7 (936.7) decreases via 932.2 pm ( x=0.62) to 931.2 pm ( x=0.66), while the Ir-Ir distance remains almost the same (290 pm). A similar trend is observed for the rhodium compounds. The lithium atoms substitute Sn on both framework sites. However, the 16 f site shows a substantially larger preference for Li occupation. This is in contrast to the isotypic magnesium based compounds.

Walking Down the Chalcogenic Group of the Periodic Table: From Singlet to Triplet Organic Emitters.

PubMed

Kremer, Adrian; Aurisicchio, Claudia; De Leo, Federica; Ventura, Barbara; Wouters, Johan; Armaroli, Nicola; Barbieri, Andrea; Bonifazi, Davide

2015-10-19

The synthesis, X-ray crystal structures, ground- and excited-state UV/Vis absorption spectra, and luminescence properties of chalcogen-doped organic emitters equipped on both extremities with benzoxa-, benzothia-, benzoselena- and benzotellurazole (1X and 2X ) moieties have been reported for the first time. The insertion of the four different chalcogen atoms within the same molecular skeleton enables the investigation of only the chalcogenic effect on the organisation and photophysical properties of the material. Detailed crystal-structure analyses provide evidence of similar packing for 2O -2Se , in which the benzoazoles are engaged in π-π stacking and, for the heavier atoms, in secondary X⋅⋅⋅X and X⋅⋅⋅N bonding interactions. Detailed computational analysis shows that the arrangement is essentially governed by the interplay of van der Waals and secondary bonding interactions. Progressive quenching of the fluorescence and concomitant onset of phosphorescence features with gradually shorter lifetimes are detected as the atomic weight of the chalcogen heteroatom increases, with the tellurium-doped derivatives exhibiting only emission from the lowest triplet excited state. Notably, the phosphorescence spectra of the selenium and tellurium derivatives can be recorded even at room temperature; this is a very rare finding for fully organic emitters. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of a dimeric β-diketiminate magnesium complex

PubMed Central

MacNeil, Connor S.; Johnson, Kevin R. D.; Hayes, Paul G.; Boeré, René T.

2016-01-01

The solid-state structure of a dimeric β-diketiminate magnesium(II) complex is discussed. The compound, di-μ-iodido-bis­[(­{4-amino-1,5-bis­[2,6-bis­(propan-2-yl)phen­yl]pent-3-en-2-yl­idene}aza­nido-κ2 N,N′)magnesium(II)] toluene sesquisolvate, [Mg2(C29H41N2)2I2]·1.5C7H8, crystallizes as two independent mol­ecules, each with 2/m crystallographic site symmetry, located at Wyckoff sites 2c and 2d. These have symmetry-equivalent magnesium atoms bridged by μ-iodide ligands with very similar Mg—I distances. The two Mg atoms are located slightly below (∼0.5 Å) the least-squares plane defined by N–C—C–N atoms in the ligand scaffold, and are approximately tetra­hedrally coordinated. One and one-half toluene solvent mol­ecules are disordered with respect to mirror-site symmetry at Wyckoff sites 4i and 2a, respectively. In the former case, two toluene mol­ecules inter­act in an off-center parallel stacking arrangement; the shortest C to C′ (π–π) distance of 3.72 (1) Å was measured for this inter­action. PMID:27980823

An intermetallic Au24Ag20 superatom nanocluster stabilized by labile ligands.

PubMed

Wang, Yu; Su, Haifeng; Xu, Chaofa; Li, Gang; Gell, Lars; Lin, Shuichao; Tang, Zichao; Häkkinen, Hannu; Zheng, Nanfeng

2015-04-08

An intermetallic nanocluster containing 44 metal atoms, Au24Ag20(2-SPy)4(PhC≡C)20Cl2, was successfully synthesized and structurally characterized by single-crystal analysis and density funtional theory computations. The 44 metal atoms in the cluster are arranged as a concentric three-shell Au12@Ag20@Au12 Keplerate structure having a high symmetry. For the first time, the co-presence of three different types of anionic ligands (i.e., phenylalkynyl, 2-pyridylthiolate, and chloride) was revealed on the surface of metal nanoclusters. Similar to thiolates, alkynyls bind linearly to surface Au atoms using their σ-bonds, leading to the formation of two types of surface staple units (PhC≡C-Au-L, L = PhC≡C(-) or 2-pyridylthiolate) on the cluster. The co-presence of three different surface ligands allows the site-specific surface and functional modification of the cluster. The lability of PhC≡C(-) ligands on the cluster was demonstrated, making it possible to keep the metal core intact while removing partial surface capping. Moreover, it was found that ligand exchange on the cluster occurs easily to offer various derivatives with the same metal core but different surface functionality and thus different solubility.

Fast Atom Ionization in Strong Electromagnetic Radiation

NASA Astrophysics Data System (ADS)

Apostol, M.

2018-05-01

The Goeppert-Mayer and Kramers-Henneberger transformations are examined for bound charges placed in electromagnetic radiation in the non-relativistic approximation. The consistent inclusion of the interaction with the radiation field provides the time evolution of the wavefunction with both structural interaction (which ensures the bound state) and electromagnetic interaction. It is shown that in a short time after switching on the high-intensity radiation the bound charges are set free. In these conditions, a statistical criterion is used to estimate the rate of atom ionization. The results correspond to a sudden application of the electromagnetic interaction, in contrast with the well-known ionization probability obtained by quasi-classical tunneling through classically unavailable non-stationary states, or other equivalent methods, where the interaction is introduced adiabatically. For low-intensity radiation the charges oscillate and emit higher-order harmonics, the charge configuration is re-arranged and the process is resumed. Tunneling ionization may appear in these circumstances. Extension of the approach to other applications involving radiation-induced charge emission from bound states is discussed, like ionization of molecules, atomic clusters or proton emission from atomic nuclei. Also, results for a static electric field are included.

Electrodeposited Ni-Based Magnetic Mesoporous Films as Smart Surfaces for Atomic Layer Deposition: An "All-Chemical" Deposition Approach toward 3D Nanoengineered Composite Layers.

PubMed

Zhang, Jin; Quintana, Alberto; Menéndez, Enric; Coll, Mariona; Pellicer, Eva; Sort, Jordi

2018-05-02

Mesoporous Ni and Cu-Ni (Cu 20 Ni 80 and Cu 45 Ni 55 in at. %) films, showing a three-dimensional (3D) porous structure and tunable magnetic properties, are prepared by electrodeposition from aqueous surfactant solutions using micelles of P-123 triblock copolymer as structure-directing entities. Pores between 5 and 30 nm and dissimilar space arrangements (continuous interconnected networks, circular pores, corrugated mesophases) are obtained depending on the synthetic conditions. X-ray diffraction studies reveal that the Cu-Ni films have crystallized in the face-centered cubic structure, are textured, and exhibit certain degree of phase separation, particularly those with a higher Cu content. Atomic layer deposition (ALD) is used to conformally coat the mesopores of Cu 20 Ni 80 film with amorphous Al 2 O 3 , rendering multiphase "nano-in-meso" metal-ceramic composites without compromising the ferromagnetic response of the metallic scaffold. From a technological viewpoint, these 3D nanoengineered composite films could be appealing for applications like magnetically actuated micro/nanoelectromechanical systems (MEMS/NEMS), voltage-driven magneto-electric devices, capacitors, or as protective coatings with superior strength and tribological performance.

Crystal structure of cis-aqua­chlorido­bis­(1,10-phenanthroline-κ2 N,N′)chromium(III) tetra­chlorido­zincate monohydrate from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2015-01-01

The structure of the title compound, [CrCl(C12H8N2)2(H2O)][ZnCl4]·H2O, has been determined from synchrotron data. The CrIII ion is bonded to four N atoms from two 1,10-phenanthroline (phen) ligands, one water mol­ecule and a Cl atom in a cis arrangement, displaying an overall distorted octa­hedral coordination environment. The Cr—N(phen) bond lengths are in the range of 2.0495 (18) to 2.0831 (18) Å, while the Cr—Cl and Cr—(OH2) bond lengths are 2.2734 (7) and 1.9986 (17) Å, respectively. The tetra­hedral [ZnCl4]2− anion is slightly distorted owing to its involvement in O—H⋯Cl hydrogen bonding with coordinating and non-coordinating water mol­ecules. The two types of water mol­ecules also inter­act through O—H⋯O hydrogen bonds. The observed hydrogen-bonding pattern leads to the formation of a three-dimensional network structure. PMID:25844190

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Chen, Tao; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-03-01

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.

Using Latex Balls and Acrylic Resin Plates to Investigate the Stacking Arrangement and Packing Efficiency of Metal Crystals

ERIC Educational Resources Information Center

Ohashi, Atsushi

2015-01-01

A high-school third-year or undergraduate first-semester general chemistry laboratory experiment introducing simple-cubic, face-centered cubic, body-centered cubic, and hexagonal closest packing unit cells is presented. Latex balls and acrylic resin plates are employed to make each atomic arrangement. The volume of the vacant space in each cell is…

Tetra-butyl-ammonium tetra-kis-(trimethyl-silanolato-κO)ferrate(III).

PubMed

Hay, Michael; Staples, Richard; Lee, Andre

2012-09-01

In the title salt, (C(16)H(36)N)[Fe(C(3)H(9)OSi)(4)], the cation contains a central N atom bonded to four n-butyl alkyl groups in a tetra-hedral arrangement, while the anion contains a central Fe(III) atom tetra-hedrally coordinated by four trimethyl-silanolate ligands.

Influence of the local structure in phase-change materials on their dielectric permittivity.

PubMed

Shportko, Kostiantyn V; Venger, Eugen F

2015-01-01

Ge-Sb-Te alloys, which belong to the phase-change materials, are promising materials for data storage and display and data visualization applications due to their unique properties. This includes a remarkable difference of their electrical and optical properties in the amorphous and crystalline state. Pronounced change of optical properties for Ge-Sb-Te alloys is linked to the different bonding types and different atomic arrangements in amorphous and crystalline states. The dielectric function of phase-change materials has been investigated in the far infrared (FIR) range. Phonons have been detected by FTIR spectroscopy. Difference of the dispersion of the dielectric permittivity of amorphous and crystalline samples is caused by different structures in different states which contribute to the dielectric permittivity.

Self-organized patterns along sidewalls of iron silicide nanowires on Si(110) and their origin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Debolina; Mahato, J. C.; Bisi, Bhaskar

Iron silicide (cubic FeSi{sub 2}) nanowires have been grown on Si(110) by reactive deposition epitaxy and investigated by scanning tunneling microscopy and scanning/transmission electron microscopy. On an otherwise uniform nanowire, a semi-periodic pattern along the edges of FeSi{sub 2} nanowires has been discovered. The origin of such growth patterns has been traced to initial growth of silicide nanodots with a pyramidal Si base at the chevron-like atomic arrangement of a clean reconstructed Si(110) surface. The pyramidal base evolves into a comb-like structure along the edges of the nanowires. This causes the semi-periodic structure of the iron silicide nanowires along theirmore » edges.« less

Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments.

PubMed

Potapov, V; Reichmann, D; Abramovich, R; Filchtinski, D; Zohar, N; Ben Halevy, D; Edelman, M; Sobolev, V; Schreiber, G

2008-12-05

A new method is presented for the redesign of protein-protein interfaces, resulting in specificity of the designed pair while maintaining high affinity. The design is based on modular interface architecture and was carried out on the interaction between TEM1 beta-lactamase and its inhibitor protein, beta-lactamase inhibitor protein. The interface between these two proteins is composed of several mostly independent modules. We previously showed that it is possible to delete a complete module without affecting the overall structure of the interface. Here, we replace a complete module with structure fragments taken from nonrelated proteins. Nature-optimized fragments were chosen from 10(7) starting templates found in the Protein Data Bank. A procedure was then developed to identify sets of interacting template residues with a backbone arrangement mimicking the original module. This generated a final list of 361 putative replacement modules that were ranked using a novel scoring function based on grouped atom-atom contact surface areas. The top-ranked designed complex exhibited an affinity of at least the wild-type level and a mode of binding that was remarkably specific despite the absence of negative design in the procedure. In retrospect, the combined application of three factors led to the success of the design approach: utilizing the modular construction of the interface, capitalizing on native rather than artificial templates, and ranking with an accurate atom-atom contact surface scoring function.

The structure of PX3 (X = Cl, Br, I) molecular liquids from X-ray diffraction, molecular dynamics simulations, and reverse Monte Carlo modeling.

PubMed

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2014-02-07

Synchrotron X-ray diffraction measurements have been conducted on liquid phosphorus trichloride, tribromide, and triiodide. Molecular Dynamics simulations for these molecular liquids were performed with a dual purpose: (1) to establish whether existing intermolecular potential functions can provide a picture that is consistent with diffraction data and (2) to generate reliable starting configurations for subsequent Reverse Monte Carlo modelling. Structural models (i.e., sets of coordinates of thousands of atoms) that were fully consistent with experimental diffraction information, within errors, have been prepared by means of the Reverse Monte Carlo method. Comparison with reference systems, generated by hard sphere-like Monte Carlo simulations, was also carried out to demonstrate the extent to which simple space filling effects determine the structure of the liquids (and thus, also estimating the information content of measured data). Total scattering structure factors, partial radial distribution functions and orientational correlations as a function of distances between the molecular centres have been calculated from the models. In general, more or less antiparallel arrangements of the primary molecular axes that are found to be the most favourable orientation of two neighbouring molecules. In liquid PBr3 electrostatic interactions seem to play a more important role in determining intermolecular correlations than in the other two liquids; molecular arrangements in both PCl3 and PI3 are largely driven by steric effects.

Interfacial B-site atomic configuration in polar (111) and non-polar (001) SrIrO3/SrTiO3 heterostructures

NASA Astrophysics Data System (ADS)

Anderson, T. J.; Zhou, H.; Xie, L.; Podkaminer, J. P.; Patzner, J. J.; Ryu, S.; Pan, X. Q.; Eom, C. B.

2017-09-01

The precise control of interfacial atomic arrangement in ABO3 perovskite heterostructures is paramount, particularly in cases where the subsequent electronic properties of the material exhibit geometrical preferences along polar crystallographic directions that feature inevitably complex surface reconstructions. Here, we present the B-site interfacial structure in polar (111) and non-polar (001) SrIrO3/SrTiO3 interfaces. The heterostructures were examined using scanning transmission electron microscopy and synchrotron-based coherent Bragg rod analysis. Our results reveal the preference of B-site intermixing across the (111) interface due to the polarity-compensated SrTiO3 substrate surface prior to growth. By comparison, the intermixing at the non-polar (001) interface is negligible. This finding suggests that the intermixing may be necessary to mitigate epitaxy along heavily reconstructed and non-stoichiometric (111) perovskite surfaces. Furthermore, this preferential B-site configuration could allow the geometric design of the interfacial perovskite structure and chemistry to selectively engineer the correlated electronic states of the B-site d-orbital.

Crystal structure of cis-aqua­bis­(2,2′-bi­pyridine-κ2 N,N′)chlorido­chromium(III) tetra­chlorido­zincate determined from synchrotron data

PubMed Central

Moon, Dohyun; Ryoo, Keon Sang; Choi, Jong-Ha

2016-01-01

The structure of the title salt, [CrCl(C10H8N2)2(H2O)][ZnCl4], has been determined from synchrotron data. The CrIII ion is coordinated by four N atoms from two 2,2′-bi­pyridine (bipy) ligands, one O atom from a water mol­ecule and a chloride anion in a cis arrangement, displaying a distorted octa­hedral geometry. The tetra­hedral [ZnCl4]2− anion is slightly distorted owing to its involvement in O—H⋯Cl hydrogen bonding with the coordinating water mol­ecule. The Cr—N(bipy) bond lengths are in the range 2.0485 (13)–2.0632 (12) Å, while the Cr—Cl and Cr—(OH2) bond lengths are 2.2732 (6) and 1.9876 (12) Å, respectively. In the crystal, mol­ecules are stacked along the a axis. PMID:27006786

Equations of state of anhydrous AlF 3 and AlI 3 : Modeling of extreme condition halide chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF 3) and separately, aluminum triiodide (AlI 3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF 3 and AlI 3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. In conclusion, results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Equations of state of anhydrous AlF{sub 3} and AlI{sub 3}: Modeling of extreme condition halide chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stavrou, Elissaios, E-mail: stavrou1@llnl.gov; Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, P.O. Box 808 L-350, Livermore, California 94550; Zaug, Joseph M., E-mail: zaug1@llnl.gov

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF{sub 3}) and separately, aluminum triiodide (AlI{sub 3}) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF{sub 3} and AlI{sub 3} were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. Results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Equations of state of anhydrous AlF 3 and AlI 3 : Modeling of extreme condition halide chemistry

DOE PAGES

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; ...

2015-06-04

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF 3) and separately, aluminum triiodide (AlI 3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF 3 and AlI 3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. In conclusion, results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

A quasi-atomic model of human adenovirus type 5 capsid

PubMed Central

Fabry, Céline M S; Rosa-Calatrava, Manuel; Conway, James F; Zubieta, Chloé; Cusack, Stephen; Ruigrok, Rob W H; Schoehn, Guy

2005-01-01

Adenoviruses infect a wide range of vertebrates including humans. Their icosahedral capsids are composed of three major proteins: the trimeric hexon forms the facets and the penton, a noncovalent complex of the pentameric penton base and trimeric fibre proteins, is located at the 12 capsid vertices. Several proteins (IIIa, VI, VIII and IX) stabilise the capsid. We have obtained a 10 Å resolution map of the human adenovirus 5 by image analysis from cryo-electron micrographs (cryoEMs). This map, in combination with the X-ray structures of the penton base and hexon, was used to build a quasi-atomic model of the arrangement of the two major capsid components and to analyse the hexon–hexon and hexon–penton interactions. The secondary proteins, notably VIII, were located by comparing cryoEM maps of native and pIX deletion mutant virions. Minor proteins IX and IIIa are located on the outside of the capsid, whereas protein VIII is organised with a T=2 lattice on the inner face of the capsid. The capsid organisation is compared with the known X-ray structure of bacteriophage PRD1. PMID:15861131

Glide dislocation nucleation from dislocation nodes at semi-coherent {111} Cu–Ni interfaces

DOE PAGES

Shao, Shuai; Wang, Jian; Beyerlein, Irene J.; ...

2015-07-23

Using atomistic simulations and dislocation theory on a model system of semi-coherent {1 1 1} interfaces, we show that misfit dislocation nodes adopt multiple atomic arrangements corresponding to the creation and redistribution of excess volume at the nodes. We identified four distinctive node structures: volume-smeared nodes with (i) spiral or (ii) straight dislocation patterns, and volume-condensed nodes with (iii) triangular or (iv) hexagonal dislocation patterns. Volume-smeared nodes contain interfacial dislocations lying in the Cu–Ni interface but volume-condensed nodes contain two sets of interfacial dislocations in the two adjacent interfaces and jogs across the atomic layer between the two adjacent interfaces.more » Finally, under biaxial tension/compression applied parallel to the interface, we show that the nucleation of lattice dislocations is preferred at the nodes and is correlated with the reduction of excess volume at the nodes.« less

Combining atomic force and fluorescence microscopy for analysis of quantum-dot labeled protein–DNA complexes

PubMed Central

Ebenstein, Yuval; Gassman, Natalie; Kim, Soohong; Weiss, Shimon

2011-01-01

Atomic force microscopy (AFM) and fluorescence microscopy are widely used for the study of protein-DNA interactions. While AFM excels in its ability to elucidate structural detail and spatial arrangement, it lacks the ability to distinguish between similarly sized objects in a complex system. This information is readily accessible to optical imaging techniques via site-specific fluorescent labels, which enable the direct detection and identification of multiple components simultaneously. Here, we show how the utilization of semiconductor quantum dots (QDs), serving as contrast agents for both AFM topography and fluorescence imaging, facilitates the combination of both imaging techniques, and with the addition of a flow based DNA extension method for sample deposition, results in a powerful tool for the study of protein-DNA complexes. We demonstrate the inherent advantages of this novel combination of techniques by imaging individual RNA polymerases (RNAP) on T7 genomic DNA. PMID:19452448

Heptagraphene: Tunable dirac cones in a graphitic structure

DOE PAGES

Lopez-Bezanilla, Alejandro; Martin, Ivar; Littlewood, Peter B.

2016-09-13

Here, we predict the existence and dynamical stability of heptagraphene, a new graphitic structure formed of rings of 10 carbon atoms bridged by carbene groups yielding seven-membered rings. Despite the rectangular unit cell, the band structure is topologically equivalent to that of strongly distorted graphene. Density-functional-theory calculations demonstrate that heptagraphene has Dirac cones on symmetry lines that are robust against biaxial strain but which open a gap under shear. At high deformation values bond reconstructions lead to different electronic band arrangements in dynamically stable configurations. Within a tight-binding framework this richness of the electronic behavior is identified as a directmore » consequence of the symmetry breaking within the cell which, unlike other graphitic structures, leads to band gap opening. A combined approach of chemical and physical modification of graphene unit cell unfurls the opportunity to design carbon-based systems in which one aims to tune an electronic band gap.« less

Control of terahertz nonlinear transmission with electrically gated graphene metadevices.

PubMed

Choi, Hyun Joo; Baek, In Hyung; Kang, Bong Joo; Kim, Hyeon-Don; Oh, Sang Soon; Hamm, Joachim M; Pusch, Andreas; Park, Jagang; Lee, Kanghee; Son, Jaehyeon; Jeong, Young U K; Hess, Ortwin; Rotermund, Fabian; Min, Bumki

2017-02-20

Graphene, which is a two-dimensional crystal of carbon atoms arranged in a hexagonal lattice, has attracted a great amount of attention due to its outstanding mechanical, thermal and electronic properties. Moreover, graphene shows an exceptionally strong tunable light-matter interaction that depends on the Fermi level - a function of chemical doping and external gate voltage - and the electromagnetic resonance provided by intentionally engineered structures. In the optical regime, the nonlinearities of graphene originated from the Pauli blocking have already been exploited for mode-locking device applications in ultrafast laser technology, whereas nonlinearities in the terahertz regime, which arise from a reduction in conductivity due to carrier heating, have only recently been confirmed experimentally. Here, we investigated two key factors for controlling nonlinear interactions of graphene with an intense terahertz field. The induced transparencies of graphene can be controlled effectively by engineering meta-atoms and/or changing the number of charge carriers through electrical gating. Additionally, nonlinear phase changes of the transmitted terahertz field can be observed by introducing the resonances of the meta-atoms.

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.

PubMed

Li, Jinghui; Nagamochi, Hiroshi; Akutsu, Tatsuya

2018-01-01

Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph with no other cycles than benzene rings is called tree-like, and becomes a tree possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation are called the substituted benzene isomers of . When we replace each virtual atom in with a benzene ring to obtain a substituted benzene isomer, distinct isomers of are caused by the difference in arrangements of atom groups around a benzene ring. In this paper, we propose an efficient algorithm that enumerates all substituted benzene isomers of a given tree representation . Our algorithm first counts the number of all the isomers of the tree representation by a dynamic programming method. To enumerate all the isomers, for each , our algorithm then generates the th isomer by backtracking the counting phase of the dynamic programming. We also implemented our algorithm for computational experiments.

Ternary arsenides ATt{sub 3}As{sub 3} (A=K, Rb; Tt=Ge, Sn) with layered structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khatun, Mansura; Stoyko, Stanislav S.; Mar, Arthur, E-mail: arthur.mar@ualberta.ca

2016-06-15

The four ternary arsenides ATt{sub 3}As{sub 3} (A=K, Rb; Tt=Ge, Sn) were obtained by reaction of the elements at 600–650 °C. They adopt an orthorhombic structure (space group Pnma, Z=4, with cell parameters ranging from a=9.9931(11) Å, b=3.7664(4) Å, c=18.607(2) Å for KGe{sub 3}As{sub 3} to a=10.3211(11) Å, b=4.0917(4) Å, c=19.570(2) Å for RbSn{sub 3}As{sub 3}) containing corrugated [Tt{sub 3}As{sub 3}] layers built from Tt-centred trigonal pyramids and tetrahedra forming five-membered rings decorated with As handles. They can be considered to be Zintl phases with Tt atoms in +4, +3, and +1 oxidation states. Band structure calculations predict that thesemore » compounds are semiconductors with narrow band gaps (0.71 eV in KGe{sub 3}As{sub 3}, 0.50 eV in KSn{sub 3}As{sub 3}). - Graphical abstract: Ternary arsenides ATt{sub 3}As{sub 3} (A=K, Rb; Tt=Ge, Sn) contain corrugated layers with Tt atoms in three different oxidation states and are narrow band gap semiconductors. Display Omitted - Highlights: • ATt{sub 3}As{sub 3} (A=K, Rb; Tt=Ge, Sn) contains Tt atoms in three oxidation states. • The structure differs from NaGe{sub 3}P{sub 3} in terms of layer stacking arrangement. • The compounds are predicted to be narrow band gap semiconductors.« less

Ab Initio Studies of Metal Hexaboride Materials

NASA Astrophysics Data System (ADS)

Schmidt, Kevin M.

Metal hexaborides are refractory ceramics with several qualities relevant to materials design, such as low work functions, high hardness, low thermal expansion coefficients, and high melting points, among many other properties of interest for industrial applications. Thermal and mechanical stability is a common feature provided by the covalently-bonded network boron atoms, and electronic properties can vary significantly with the resident metal. While these materials are currently employed as electron emitters and abrasives, promising uses of these materials also include catalytic applications for chemical dissociation reactions of various molecules such as hydrogen, water and carbon monoxide, for example. However, these extensions require a thorough understanding of particular mechanical and electronic properties. This dissertation is a collection of studies focused on understanding the behavior of metal hexaboride materials using computational modeling methods to investigate materials properties of these from both classical and quantum mechanical points of view. Classical modeling is performed using molecular dynamics methods with interatomic potentials obtained from density functional theory (DFT) calculations. Atomic mean-square displacements from the quasi-harmonic approximation and lattice energetic data are produced with DFT for developing the potentials. A generalized method was also developed for the inversion of cohesive energy curves of crystalline materials; pairwise interatomic potentials are extracted using detailed geometrical descriptions of the atomic interactions and a list of atomic displacements and degeneracies. The surface structure of metal hexaborides is studied with DFT using several model geometries to describe the terminal cation layouts, and these provide a basis for further studies on metal hexaboride interactions with hydrogen. The surface electronic structure calculations show that segregated regions of metal and boron-terminations produce the lowest energies for di-cations of CaB6, SrB6 and BaB6, while tri-valent LaB6 minimizes its surface energy by arranging the metal ions in parallel rows on the surface. Studies involving hydrogen suggest that a single molecule per surface unit-cell is possible, and evidence is given for a dissociative adsorption pathway. Ternary mixtures of metal hexaborides containing two alkaline-earth cations in each crystal are also investigated with electronic structure methods. Multiple geometries are used to understand how spatial arrangements of cations within the mixture can affect properties related to stability. Bond-lengths within the boron framework are found to be heavily dependent upon the local cation environment, and energies taken at absolute zero suggest certain stoichiometries naturally lead to phase splitting.

The fourth crystallographic closest packing unveiled in the gold nanocluster crystal

NASA Astrophysics Data System (ADS)

Gan, Zibao; Chen, Jishi; Wang, Juan; Wang, Chengming; Li, Man-Bo; Yao, Chuanhao; Zhuang, Shengli; Xu, An; Li, Lingling; Wu, Zhikun

2017-03-01

Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au-S interface. Importantly, the fourth crystallographic closest-packed pattern, termed 6H left-handed helical (6HLH) arrangement, which results in the distinct loss of solid photoluminescence of amorphous Au60S6(SCH2Ph)36, is found in the crystals of Au60S6(SCH2Ph)36. The solvent-polarity-dependent solution photoluminescence is also demonstrated. Overall, this work provides important insights about the structure, Au-S bonding and solid photoluminescence of gold nanoclusters.

Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

PubMed

Sahakyan, Aleksandr B; Vendruscolo, Michele

2013-02-21

Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.

Crystal structure of bis­[cis-(1,4,8,11-tetra­aza­cyclo­tetra­deca­ne-κ4 N)bis(thio­cyanato-κN)chrom­ium(III)] dichromate monohydrate from synchrotron X-ray diffraction data

PubMed Central

Moon, Dohyun; Takase, Masahiro; Akitsu, Takashiro; Choi, Jong-Ha

2017-01-01

The structure of the complex salt, cis-[Cr(NCS)2(cyclam)]2[Cr2O7]·H2O (cyclam = 1,4,8,11-tetra­aza­cyclo­tetra­decane, C10H24N4), has been determined from synchrotron data. The asymmetric unit comprises of one [Cr(NCS)2(cyclam)]+ cation, one half of a Cr2O7 2− anion (completed by inversion symmetry) and one half of a water mol­ecule (completed by twofold rotation symmetry). The CrIII ion is coordinated by the four cyclam N atoms and by two N atoms of cis-arranged thio­cyanate anions, displaying a distorted octa­hedral coordination sphere. The Cr—N(cyclam) bond lengths are in the range 2.080 (2) to 2.097 (2) Å while the average Cr—N(NCS) bond length is 1.985 (4) Å. The macrocyclic cyclam moiety adopts the cis-V conformation. The bridging O atom of the dichromate anion is disordered around an inversion centre, leading to a bending of the Cr—O—Cr bridging angle [157.7 (3)°]; the anion has a staggered conformation. The crystal structure is stabilized by inter­molecular hydrogen bonds involving the cyclam N—H groups and water O—H groups as donor groups, and the O atoms of the Cr2O7 2− anion and water mol­ecules as acceptor groups, giving rise to a three-dimensional network. PMID:28083140

Crystal structure of Cr-bearing Mg3BeAl8O16, a new polytype of magnesiotaaffeite-2N'2S.

PubMed

Malcherek, Thomas; Schlüter, Jochen

2016-07-01

The crystal structure of a new polytype of magnesiotaaffeite-2N'2S, ideally Mg3BeAl8O16 (trimagnesium beryllium octa-aluminium hexa-deca-oxide), is described in space-group symmetry P-3m1. It has been identified in a fragment of a mineral sample from Burma (Myanmar). The new polytype is composed of two Mg2Al4O8 (S)- and two BeMgAl4O8 (N')-modules in a stacking sequence N'SSN'' which differs from the N'SN'S-stacking sequence of the known magnesiotaaffeite-2N'2S polytype. The crystal structure can be derived from a close-packed arrangement of O atoms and is discussed with regard to its polytypism and its Cr(3+) chromophore content.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3.

PubMed

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J L; Zhong, Ruidan; Schneeloch, John A; Liu, Tiansheng; Valla, Tonica; Tranquada, John M; Gu, Genda; Davis, J C Séamus

2015-02-03

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a "Dirac-mass gap" in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship [Formula: see text] is confirmed throughout and exhibits an electron-dopant interaction energy J* = 145 meV·nm(2). These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3

PubMed Central

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J. L.; Zhong, Ruidan; Schneeloch, John A.; Liu, Tiansheng; Valla, Tonica; Tranquada, John M.; Gu, Genda; Davis, J. C. Séamus

2015-01-01

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a “Dirac-mass gap” in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship Δ(r)∝n(r) is confirmed throughout and exhibits an electron–dopant interaction energy J* = 145 meV·nm2. These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential. PMID:25605947

New Coarse-Grained Model and Its Implementation in Simulations of Graphene Assemblies.

PubMed

Shang, Jun-Jun; Yang, Qing-Sheng; Liu, Xia

2017-08-08

Graphene is a one-atom thick layer of carbon atoms arranged in a hexagonal pattern, which makes it the strongest material in the world. The Tersoff potential is a suitable potential for simulating the mechanical behavior of the complex covalently bonded system of graphene. In this paper, we describe a new coarse-grained (CG) potential, TersoffCG, which is based on the function form of the Tersoff potential. The TersoffCG applies to a CG model of graphene that uses the same hexagonal pattern as the atomistic model. The parameters of the TersoffCG potential are determined using structural feature and potential-energy fitting between the CG model and the atomic model. The modeling process of graphene is highly simplified using the present CG model as it avoids the necessity to define bonds/angles/dihedrals connectivity. What is more, the present CG model provides a new perspective of coarse-graining scheme for crystal structures of nanomaterials. The structural changes and mechanical properties of multilayer graphene were calculated using the new potential. Furthermore, a CG model of a graphene aerogel was built in a specific form of assembly. The chemical bonding in the joints of graphene-aerogel forms automatically during the energy relaxation process. The compressive and recover test of the graphene aerogel was reproduced to study its high elasticity. Our computational examples show that the TersoffCG potential can be used for simulations of graphene and its assemblies, which have many applications in areas of environmental protection, aerospace engineering, and others.

Characterization and formation of σ/γ interface in Ni-based single crystal superalloys

NASA Astrophysics Data System (ADS)

Ma, Shiyu; Zhang, Jianxin; Li, Xueqiao; Mao, Shengcheng

2017-11-01

High-resolution transmission electron microscopy was used to study interfacial characteristics between the plate-shaped σ phase and the γ phase in a Ni-based single crystal superalloy. The atomic structure of the σ/γ interface constituted by steps was presented. However, the HRTEM micrograph of σ phase is not almost identical with the veritable atomic arrangement of σ phase on the same zone axis. The image formation of HRTEM relies on phase contrast, instead of the amplification of the atomic arrangement. From the simulated HRTEM images, the approximate defocus and thickness of the sample can be got as  -3 nm and 6 nm. σ phase has the following crystallographic orientations relations with γ matrix: [0 0 1] γ //[1 1 2] σ , (1 1 0) γ //(1   -1 0) σ , (-1 1 0) γ //(1 1   -1) σ , which can be proved by the stereographic projection. The interfacial steps are made up by (1 1 0) γ and (-1 1 0) γ or (1   -1 0) σ and (1 1   -1) σ . In the interface steps, the length of (-1 1 0) γ //(1 1   -1) σ is longer than (1 1 0) γ //(1   -1 0) σ , which is caused by that distortion factor of (-1 1 0) γ //(1 1   -1)σ is much smaller than that of (1 1 0) γ //(1   -1 0) σ .

Crystal Initiation Structures in Developing Enamel: Possible Implications for Caries Dissolution of Enamel Crystals

PubMed Central

Robinson, Colin; Connell, Simon D.

2017-01-01

Investigations of developing enamel crystals using Atomic and Chemical Force Microscopy (AFM, CFM) have revealed a subunit structure. Subunits were seen in height images as collinear swellings about 30 nM in diameter on crystal surfaces. In friction mode they were visible as positive regions. These were similar in size (30–50 nM) to collinear spherical structures, presumably mineral matrix complexes, seen in developing enamel using a freeze fracturing/freeze etching procedure. More detailed AFM studies on mature enamel suggested that the 30–50 nM structures were composed of smaller units, ~10–15 nM in diameter. These were clustered in hexagonal or perhaps a spiral arrangement. It was suggested that these could be the imprints of initiation sites for mineral precipitation. The investigation aimed at examining original freeze etched images at high resolution to see if the smaller subunits observed using AFM in mature enamel were also present in developing enamel i.e., before loss of the organic matrix. The method used was freeze etching. Briefly samples of developing rat enamel were rapidly frozen, fractured under vacuum, and ice sublimed from the fractured surface. The fractured surface was shadowed with platinum or gold and the metal replica subjected to high resolution TEM. For AFM studies high-resolution tapping mode imaging of human mature enamel sections was performed in air under ambient conditions at a point midway between the cusp and the cervical margin. Both AFM and freeze etch studies showed structures 30–50 nM in diameter. AFM indicated that these may be clusters of somewhat smaller structures ~10–15 nM maybe hexagonally or spirally arranged. High resolution freeze etching images of very early enamel showed ~30–50 nM spherical structures in a disordered arrangement. No smaller units at 10–15 nM were clearly seen. However, when linear arrangements of 30–50 nM units were visible the picture was more complex but also smaller units including ~10–15 nM units could be observed. Conclusions: Structures ~10–15 nM in diameter were detected in developing enamel. While the appearance was complex, these were most evident when the 30–5 nM structures were in linear arrays. Formation of linear arrays of subunits may be associated with the development of mineral initiation sites and attendant processing of matrix proteins. PMID:28670283

Crystal Structure of Faradaurate-279: Au279(SPh-tBu)84 Plasmonic Nanocrystal Molecules.

PubMed

Sakthivel, Naga Arjun; Theivendran, Shevanuja; Ganeshraj, Vigneshraja; Oliver, Allen G; Dass, Amala

2017-11-01

We report the discovery of an unprecedentedly large, 2.2 nm diameter, thiolate protected gold nanocrystal characterized by single crystal X-ray crystallography (sc-XRD), Au 279 (SPh-tBu) 84 named Faradaurate-279 (F-279) in honor of Michael Faraday's (1857) pioneering work on nanoparticles. F-279 nanocrystal has a core-shell structure containing a truncated octahedral core with bulk face-centered cubic-like arrangement, yet a nanomolecule with a precise number of metal atoms and thiolate ligands. The Au 279 S 84 geometry was established from a low-temperature 120 K sc-XRD study at 0.90 Å resolution. The atom counts in core-shell structure of Au 279 follows the mathematical formula for magic number shells: Au@Au 12 @Au 42 @Au 92 @Au 54 , which is further protected by a final shell of Au 48 . Au 249 core is protected by three types of staple motifs, namely: 30 bridging, 18 monomeric, and 6 dimeric staple motifs. Despite the presence of such diverse staple motifs, Au 279 S 84 structure has a chiral pseudo-D 3 symmetry. The core-shell structure can be viewed as nested, concentric polyhedra, containing a total of five forms of Archimedean solids. A comparison between the Au 279 and Au 309 cuboctahedral superatom model in shell-wise growth is illustrated. F-279 can be synthesized and isolated in high purity in milligram quantities using size exclusion chromatography, as evidenced by mass spectrometry. Electrospray ionization-mass spectrometry independently verifies the X-ray diffraction study based heavy atoms formula, Au 279 S 84 , and establishes the molecular formula with the complete ligands, namely, Au 279 (SPh-tBu) 84 . It is also the smallest gold nanocrystal to exhibit metallic behavior, with a surface plasmon resonance band around 510 nm.

X-ray absorption spectroscopy to watch catalysis by metalloenzymes: status and perspectives discussed for the water-splitting manganese complex of photosynthesis.

PubMed

Dau, Holger; Haumann, Michael

2003-01-01

Understanding structure-function relations is one of the main interests in the molecular biosciences. X-ray absorption spectroscopy of biological samples (BioXAS) has gained the status of a useful tool for characterization of the structure of protein-bound metal centers with respect to the electronic structure (oxidation states, orbital occupancies) and atomic structure (arrangement of ligand atoms). Owing to progress in the performance characteristics of synchrotron radiation sources and of experimental stations dedicated to the study of (ultra-dilute) biological samples, it is now possible to carry out new types of BioXAS experiments, which have been impracticable in the past. Of particular interest are approaches to follow biological catalysis at metal sites by characterization of functionally relevant structural changes. In this Article, the first steps towards the use of BioXAS to 'watch' biological catalysis are reviewed for the water-splitting reactions occurring at the manganese complex of photosynthesis. The following aspects are considered: the role of BioXAS in life sciences; methodological aspects of BioXAS; catalysis at the Mn complex of photosynthesis; combination of EXAFS and crystallographic information; the freeze-quench technique to capture semi-stable states; time-resolved BioXAS using a freeze-quench approach; room-temperature experiments and 'real-time' BioXAS; tasks and perspectives.

Two-dimensional silica opens new perspectives

NASA Astrophysics Data System (ADS)

Büchner, Christin; Heyde, Markus

2017-12-01

In recent years, silica films have emerged as a novel class of two-dimensional (2D) materials. Several groups succeeded in epitaxial growth of ultrathin SiO2 layers using different growth methods and various substrates. The structures consist of tetrahedral [SiO4] building blocks in two mirror symmetrical planes, connected via oxygen bridges. This arrangement is called a silica bilayer as it is the thinnest 2D arrangement with the stoichiometry SiO2 known today. With all bonds saturated within the nano-sheet, the interaction with the substrate is based on van der Waals forces. Complex ring networks are observed, including hexagonal honeycomb lattices, point defects and domain boundaries, as well as amorphous domains. The network structures are highly tuneable through variation of the substrate, deposition parameters, cooling procedure, introducing dopants or intercalating small species. The amorphous networks and structural defects were resolved with atomic resolution microscopy and modeled with density functional theory and molecular dynamics. Such data contribute to our understanding of the formation and characteristic motifs of glassy systems. Growth studies and doping with other chemical elements reveal ways to tune ring sizes and defects as well as chemical reactivities. The pristine films have been utilized as molecular sieves and for confining molecules in nanocatalysis. Post growth hydroxylation can be used to tweak the reactivity as well. The electronic properties of silica bilayers are favourable for using silica as insulators in 2D material stacks. Due to the fully saturated atomic structure, the bilayer interacts weakly with the substrate and can be described as quasi-freestanding. Recently, a mm-scale film transfer under structure retention has been demonstrated. The chemical and mechanical stability of silica bilayers is very promising for technological applications in 2D heterostacks. Due to the impact of this bilayer system for glass science, catalysis and the field of 2D materials, a large number of theoretical and experimental studies on silica bilayers have been reported in the last years. This review aims to provide an overview on the insights gained on this material and to point out opportunities for further discovery in various fields.

Geometry dependent suppression of collective quantum jumps in Rydberg atoms

NASA Astrophysics Data System (ADS)

Lees, Eitan; Clemens, James

2015-05-01

We consider N driven, damped Rydberg atoms in different spatial arrangements. Treating the atoms as two-level systems we model the coupling to the environment via the Lehmberg-Agarwal master equation which interpolates between fully independent and fully collective spontaneous emission depending on the specific locations of the atoms. We also include a collective dipole-dipole energy shift in the excited Rydberg state which leads to collective quantum jumps in the atomic excitation when the system is driven off resonance. We show that the quantum jumps are suppressed as the system makes a transition from independent to collective emission as the spacing of a linear array of atoms is decreased below the emission wavelength.

Chirality specific and spatially uniform synthesis of single-walled carbon nanotubes from a sputtered Co-W bimetallic catalyst

NASA Astrophysics Data System (ADS)

An, Hua; Kumamoto, Akihito; Takezaki, Hiroki; Ohyama, Shinnosuke; Qian, Yang; Inoue, Taiki; Ikuhara, Yuichi; Chiashi, Shohei; Xiang, Rong; Maruyama, Shigeo

2016-07-01

Synthesis of single-walled carbon nanotubes (SWNTs) with well-defined atomic arrangements has been widely recognized in the past few decades as the biggest challenge in the SWNT community, and has become a bottleneck for the application of SWNTs in nano-electronics. Here, we report a selective synthesis of (12, 6) SWNTs with an enrichment of 50%-70% by chemical vapor deposition (CVD) using sputtered Co-W as a catalyst. This is achieved under much milder reduction and growth conditions than those in the previous report using transition-metal molecule clusters as catalyst precursors (Nature, 2014, 510, 522). Meanwhile, in-plane transmission electron microscopy unambiguously identified an intermediate structure of Co6W6C, which is strongly associated with selective growth. However, most of the W atoms disappear after a 5 min CVD growth, which implies that anchoring W may be important in this puzzling Co-W system.Synthesis of single-walled carbon nanotubes (SWNTs) with well-defined atomic arrangements has been widely recognized in the past few decades as the biggest challenge in the SWNT community, and has become a bottleneck for the application of SWNTs in nano-electronics. Here, we report a selective synthesis of (12, 6) SWNTs with an enrichment of 50%-70% by chemical vapor deposition (CVD) using sputtered Co-W as a catalyst. This is achieved under much milder reduction and growth conditions than those in the previous report using transition-metal molecule clusters as catalyst precursors (Nature, 2014, 510, 522). Meanwhile, in-plane transmission electron microscopy unambiguously identified an intermediate structure of Co6W6C, which is strongly associated with selective growth. However, most of the W atoms disappear after a 5 min CVD growth, which implies that anchoring W may be important in this puzzling Co-W system. Electronic supplementary information (ESI) available: Raman spectroscopy (G-band) of SWNTs grown from Co and Co-W catalyst; Kataura plot for chirality assignment; Raman spectra (RBM region) of SWNTs grown from low temperature reduced monometallic Co; relative intensities of the 197 cm-1 peak with respect to the total sum intensity; TEM image of Co-W catalyst reduced at six different temperatures (600, 650, 700, 750, 800, and 850 °C) TEM images of SWNTs grown from Co monometallic catalyst. See DOI: 10.1039/c6nr02749k

SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups.

PubMed

Singh, J; Thornton, J M

1990-02-05

Automated methods have been developed to determine the preferred packing arrangement between interacting protein groups. A suite of FORTRAN programs, SIRIUS, is described for calculating and analysing the geometries of interacting protein groups using crystallographically derived atomic co-ordinates. The programs involved in calculating the geometries search for interacting pairs of protein groups using a distance criterion, and then calculate the spatial disposition and orientation of the pair. The second set of programs is devoted to analysis. This involves calculating the observed and expected distributions of the angles and assessing the statistical significance of the difference between the two. A database of the geometries of the 400 combinations of side-chain to side-chain interaction has been created. The approach used in analysing the geometrical information is illustrated here with specific examples of interactions between side-chains, peptide groups and particular types of atom. At the side-chain level, an analysis of aromatic-amino interactions, and the interactions of peptide carbonyl groups with arginine residues is presented. At the atomic level the analyses include the spatial disposition of oxygen atoms around tyrosine residues, and the frequency and type of contact between carbon, nitrogen and oxygen atoms. This information is currently being applied to the modelling of protein interactions.

Resolving the Structure of a Well-Ordered Hydroxyl Overlayer on In 2O 3 (111): Nanomanipulation and Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, Margareta; Lackner, Peter; Seiler, Steffen

Changes in chemical and physical properties resulting from water adsorption play an important role in the characterization and performance of device-relevant materials. Studies of model oxides with well-characterized surfaces can provide detailed information that is vital for a general understanding of water–oxide interactions. In this work, we study single crystals of indium oxide, the prototypical transparent contact material that is heavily used in a wide range of applications and most prominently in optoelectronic technologies. Water adsorbs dissociatively already at temperatures as low as 100 K, as confirmed by scanning tunneling microscopy (STM), photoelectron spectroscopy, and density functional theory. This dissociationmore » takes place on lattice sites of the defect-free surface. While the In 2O 3(111)-(1 × 1) surface offers four types of surface oxygen atoms (12 atoms per unit cell in total), water dissociation happens exclusively at one of them together with a neighboring pair of 5-fold coordinated In atoms. These O–In groups are symmetrically arranged around the 6-fold coordinated In atoms at the surface. At room temperature, the In 2O 3(111) surface thus saturates at three dissociated water molecules per unit cell, leading to a well-ordered hydroxylated surface with (1 × 1) symmetry, where the three water OWH groups plus the surface OSH groups are imaged together as one bright triangle in STM. Manipulations with the STM tip by means of voltage pulses preferentially remove the H atom of one surface OSH group per triangle. The change in contrast due to strong local band bending provides insights into the internal structure of these bright triangles. The experimental results are further confirmed by quantitative simulations of the STM image corrugation.« less

Resolving the Structure of a Well-Ordered Hydroxyl Overlayer on In 2O 3 (111): Nanomanipulation and Theory

DOE PAGES

Wagner, Margareta; Lackner, Peter; Seiler, Steffen; ...

2017-11-01

Changes in chemical and physical properties resulting from water adsorption play an important role in the characterization and performance of device-relevant materials. Studies of model oxides with well-characterized surfaces can provide detailed information that is vital for a general understanding of water–oxide interactions. In this work, we study single crystals of indium oxide, the prototypical transparent contact material that is heavily used in a wide range of applications and most prominently in optoelectronic technologies. Water adsorbs dissociatively already at temperatures as low as 100 K, as confirmed by scanning tunneling microscopy (STM), photoelectron spectroscopy, and density functional theory. This dissociationmore » takes place on lattice sites of the defect-free surface. While the In 2O 3(111)-(1 × 1) surface offers four types of surface oxygen atoms (12 atoms per unit cell in total), water dissociation happens exclusively at one of them together with a neighboring pair of 5-fold coordinated In atoms. These O–In groups are symmetrically arranged around the 6-fold coordinated In atoms at the surface. At room temperature, the In 2O 3(111) surface thus saturates at three dissociated water molecules per unit cell, leading to a well-ordered hydroxylated surface with (1 × 1) symmetry, where the three water OWH groups plus the surface OSH groups are imaged together as one bright triangle in STM. Manipulations with the STM tip by means of voltage pulses preferentially remove the H atom of one surface OSH group per triangle. The change in contrast due to strong local band bending provides insights into the internal structure of these bright triangles. The experimental results are further confirmed by quantitative simulations of the STM image corrugation.« less

A theoretical study of the omega-phase transformation in metals

NASA Astrophysics Data System (ADS)

Sanati, Mahdi

I have studied the formation of o-phase from electronic and mesoscopic (domain wall) points of view. To study the formation of domain walls, I have extended the Landau model of Cook for the o-phase transition by including a spatial gradient (Ginzburg) term of the scalar order parameter. In general, the Landau free energy is an asymmetric double-well potential. From the variational derivative of the total free energy I obtained a static equilibrium condition. By solving this equation for different physical parameters and boundary conditions, I obtained different quasi-one-dimensional soliton-like solutions. These solutions correspond to three different types of domain walls between the o-phase and the beta-matrix. These results are used to model the formation of the o-phase in bcc Ti. Canonical band model and first principles calculations confirmed the instability of the bcc-phase of group III and IV transition metals with respect to the o-phase transformation. I showed that the d-electron density is the controlling parameter for this type of the transformation. Also the possibility of formation of the o-phase for rare earth metals is discussed. First-principles full-potential linear muffin-tin orbital method (FPLMTO) calculations are performed for o-type displacement of the atoms to study the formation of the o-phase in TiAl and Ti 3Al2Nb alloys. The results of my calculations showed an instability in ordered B2 TiAl structure with respect to the o-phase when one third of the Al atoms are replaced by Nb atoms. These phenomena are explained, first by symmetry arguments; then a pair potential model is used to illustrate this instability based on interactions between different pair of atoms derived from the electronic structure. In addition, importance of the atomic arrangements on the structural stability of the Ti3Al2 Nb system is discussed.

Control of electronic properties of 2D carbides (MXenes) by manipulating their transition metal layers

DOE PAGES

Anasori, Babak; Shi, Chenyang; Moon, Eun Ju; ...

2016-02-24

In this paper, a transition from metallic to semiconducting-like behavior has been demonstrated in two-dimensional (2D) transition metal carbides by replacing titanium with molybdenum in the outer transition metal (M) layers of M 3C 2 and M 4C 3 MXenes. The MXene structure consists of n + 1 layers of near-close packed M layers with C or N occupying the octahedral site between them in an [MX] nM arrangement. Recently, two new families of ordered 2D double transition metal carbides MXenes were discovered, M' 2M"C 2 and M' 2M" 2C 3 – where M' and M" are two different earlymore » transition metals, such as Mo, Cr, Ta, Nb, V, and Ti. The M' atoms only occupy the outer layers and the M" atoms fill the middle layers. In other words, M' atomic layers sandwich the middle M"–C layers. Using X-ray atomic pair distribution function (PDF) analysis on Mo 2TiC 2 and Mo 2Ti 2C 3 MXenes, we present the first quantitative analysis of structures of these novel materials and experimentally confirm that Mo atoms are in the outer layers of the [MC] nM structures. The electronic properties of these Mo-containing MXenes are compared with their Ti 3C 2 counterparts, and are found to be no longer metallic-like conductors; instead the resistance increases mildly with decreasing temperatures. Density functional theory (DFT) calculations suggest that OH terminated Mo–Ti MXenes are semiconductors with narrow band gaps. Measurements of the temperature dependencies of conductivities and magnetoresistances have confirmed that Mo 2TiC 2T x exhibits semiconductor-like transport behavior, while Ti 3C 2T x is a metal. Finally, this finding opens new avenues for the control of the electronic and optical applications of MXenes and for exploring new applications, in which semiconducting properties are required.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anasori, Babak; Shi, Chenyang; Moon, Eun Ju

In this paper, a transition from metallic to semiconducting-like behavior has been demonstrated in two-dimensional (2D) transition metal carbides by replacing titanium with molybdenum in the outer transition metal (M) layers of M 3C 2 and M 4C 3 MXenes. The MXene structure consists of n + 1 layers of near-close packed M layers with C or N occupying the octahedral site between them in an [MX] nM arrangement. Recently, two new families of ordered 2D double transition metal carbides MXenes were discovered, M' 2M"C 2 and M' 2M" 2C 3 – where M' and M" are two different earlymore » transition metals, such as Mo, Cr, Ta, Nb, V, and Ti. The M' atoms only occupy the outer layers and the M" atoms fill the middle layers. In other words, M' atomic layers sandwich the middle M"–C layers. Using X-ray atomic pair distribution function (PDF) analysis on Mo 2TiC 2 and Mo 2Ti 2C 3 MXenes, we present the first quantitative analysis of structures of these novel materials and experimentally confirm that Mo atoms are in the outer layers of the [MC] nM structures. The electronic properties of these Mo-containing MXenes are compared with their Ti 3C 2 counterparts, and are found to be no longer metallic-like conductors; instead the resistance increases mildly with decreasing temperatures. Density functional theory (DFT) calculations suggest that OH terminated Mo–Ti MXenes are semiconductors with narrow band gaps. Measurements of the temperature dependencies of conductivities and magnetoresistances have confirmed that Mo 2TiC 2T x exhibits semiconductor-like transport behavior, while Ti 3C 2T x is a metal. Finally, this finding opens new avenues for the control of the electronic and optical applications of MXenes and for exploring new applications, in which semiconducting properties are required.« less

RaptorX server: a resource for template-based protein structure modeling.

PubMed

Källberg, Morten; Margaryan, Gohar; Wang, Sheng; Ma, Jianzhu; Xu, Jinbo

2014-01-01

Assigning functional properties to a newly discovered protein is a key challenge in modern biology. To this end, computational modeling of the three-dimensional atomic arrangement of the amino acid chain is often crucial in determining the role of the protein in biological processes. We present a community-wide web-based protocol, RaptorX server ( http://raptorx.uchicago.edu ), for automated protein secondary structure prediction, template-based tertiary structure modeling, and probabilistic alignment sampling.Given a target sequence, RaptorX server is able to detect even remotely related template sequences by means of a novel nonlinear context-specific alignment potential and probabilistic consistency algorithm. Using the protocol presented here it is thus possible to obtain high-quality structural models for many target protein sequences when only distantly related protein domains have experimentally solved structures. At present, RaptorX server can perform secondary and tertiary structure prediction of a 200 amino acid target sequence in approximately 30 min.

μ-Carbonato-bis­(bis­{2-[(diethyl­amino)­meth­yl]phen­yl}bis­muth(III))

PubMed Central

Soran, Albert P.; Nema, Mihai G.; Breunig, Hans J.; Silvestru, Cristian

2011-01-01

The mol­ecular structure of the title compound, [Bi2(C11H16N)4(CO3)], consists of a symmetrically bridging carbonato group which binds two [2-Et2NCH2C6H4]2Bi units that are crystallographically related via a twofold rotation axis bis­ecting the carbonate group. The two Bi atoms and two of the C atoms directly bonded to bis­muth are quasi-planar [deviations of 0.323 (1) and 0.330 (9)Å for the Bi and C atoms, respectively] with the carbonate group. The remaining two ligands are in a trans arrangement relative to the quasi-planar (CBi)2CO3 system. The metal atom is strongly coordinated by the N atom of one pendant arm [Bi—N = 2.739 (6) Å], almost trans to the O atom, while the N atom of the other pendant arm exhibits a weaker intra­molecular inter­action [Bi⋯N = 3.659 (7) Å] almost trans to a C atom. If both these intra­molecular N→Bi inter­actions per metal atom are considered, the overall coordination geometry at bis­muth becomes distorted square-pyramidal [(C,N)2BiO cores] and the compound can be described as a hypervalent 12-Bi-5 species. Additional quite short intra­molecular Bi⋯O inter­actions are also present [3.796 (8)–4.020 (9) Å]. Inter­molecular associations through weak η6⋯Bi inter­actions [Bi⋯centroid of benzene ring = 3.659 (1) Å] lead to a ribbon-like supra­molecular association. PMID:21522836

High-temperature site preference and atomic short-range ordering characteristics of ternary alloying elements in γ'-Ni3Al intermetallics

NASA Astrophysics Data System (ADS)

Eriş, Rasim; Mekhrabov, Amdulla O.; Akdeniz, M. Vedat

2017-10-01

Remarkable high-temperature mechanical properties of nickel-based superalloys are correlated with the arrangement of ternary alloying elements in L12-type-ordered γ‧-Ni3Al intermetallics. In the current study, therefore, high-temperature site occupancy preference and energetic-structural characteristics of atomic short-range ordering (SRO) of ternary alloying X elements (X = Mo, W, Ta, Hf, Re, Ru, Pt or Co) in Ni75Al21.875X3.125 alloy systems have been studied by combining the statistico-thermodynamical theory of ordering and electronic theory of alloys in the pseudopotential approximation. Temperature dependence of site occupancy tendencies of alloying X element atoms has been predicted by calculating partial ordering energies and SRO parameters of Ni-Al, Ni-X and Al-X atomic pairs. It is shown that, all ternary alloying element atoms (except Pt) tend to occupy Al, whereas Pt atoms prefer to substitute for Ni sub-lattice sites of Ni3Al intermetallics. However, in contrast to other X elements, sub-lattice site occupancy characteristics of Re atoms appear to be both temperature- and composition-dependent. Theoretical calculations reveal that site occupancy preference of Re atoms switches from Al to both Ni and Al sites at critical temperatures, Tc, for Re > 2.35 at%. Distribution of Re atoms at both Ni and Al sub-lattice sites above Tc may lead to localised supersaturation of the parent Ni3Al phase and makes possible the formation of topologically close-packed (TCP) phases. The results of the current theoretical and simulation study are consistent with other theoretical and experimental investigations published in the literature.

Effect of magnetism and atomic order on static atomic displacements in the Invar alloy Fe-27 at.% Pt

NASA Astrophysics Data System (ADS)

Sax, C. R.; Schönfeld, B.; Ruban, A. V.

2015-08-01

Fe-27 at.% Pt was aged at 1123 K and quenched to room temperature (RT) to set up a state of thermal equilibrium. The local atomic arrangement was studied by diffuse x-ray scattering above (at 427 K) and below (at RT) the Curie temperature as well as at RT under a saturating magnetic field. The separated short-range order scattering remained unchanged for all three states, with maxima at 100 positions. Effective pair interaction parameters determined by the inverse Monte Carlo method gave an order-disorder transition temperature of about 1088 K, close to direct experimental findings. The species-dependent static atomic displacements for the first two shells show large differences, with a strong increase in magnitude from the state at 427 K over RT to the state under saturating magnetic field. This outcome is in agreement with an increase in atomic volume of Fe with increasing local magnetic moment. Electronic-structure calculations closely reproduce the values for the static atomic displacements in the ferromagnetic state, and predict their dependence on the atomic configuration. They also reveal a strong dependence of the magnetic exchange interactions in Fe-Pt on the atomic configuration state and lattice parameter. In particular, the increase of the Curie temperature in a random state relative to that in the ordered one is demonstrated to be related to the corresponding change of the magnetic exchange interactions due to the different local atomic chemical environment. There exists a similar strong concentration dependence of the chemical interactions as in the case of magnetic exchange interactions. Theoretical effective interactions for Fe-27 at.% Pt alloy are in good agreement with experimental results, and they also reproduce well the L1 2-A1 transition temperature.

μ-Carbonato-bis-(bis-{2-[(diethyl-amino)-meth-yl]phen-yl}bis-muth(III)).

PubMed

Soran, Albert P; Nema, Mihai G; Breunig, Hans J; Silvestru, Cristian

2011-01-12

The mol-ecular structure of the title compound, [Bi(2)(C(11)H(16)N)(4)(CO(3))], consists of a symmetrically bridging carbonato group which binds two [2-Et(2)NCH(2)C(6)H(4)](2)Bi units that are crystallographically related via a twofold rotation axis bis-ecting the carbonate group. The two Bi atoms and two of the C atoms directly bonded to bis-muth are quasi-planar [deviations of 0.323 (1) and 0.330 (9)Å for the Bi and C atoms, respectively] with the carbonate group. The remaining two ligands are in a trans arrangement relative to the quasi-planar (CBi)(2)CO(3) system. The metal atom is strongly coordinated by the N atom of one pendant arm [Bi-N = 2.739 (6) Å], almost trans to the O atom, while the N atom of the other pendant arm exhibits a weaker intra-molecular inter-action [Bi⋯N = 3.659 (7) Å] almost trans to a C atom. If both these intra-molecular N→Bi inter-actions per metal atom are considered, the overall coordination geometry at bis-muth becomes distorted square-pyramidal [(C,N)(2)BiO cores] and the compound can be described as a hypervalent 12-Bi-5 species. Additional quite short intra-molecular Bi⋯O inter-actions are also present [3.796 (8)-4.020 (9) Å]. Inter-molecular associations through weak η(6)⋯Bi inter-actions [Bi⋯centroid of benzene ring = 3.659 (1) Å] lead to a ribbon-like supra-molecular association.

Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties.

PubMed

Zhang, Z; Fenter, P; Cheng, L; Sturchio, N C; Bedzyk, M J; Predota, M; Bandura, A; Kubicki, J D; Lvov, S N; Cummings, P T; Chialvo, A A; Ridley, M K; Bénézeth, P; Anovitz, L; Palmer, D A; Machesky, M L; Wesolowski, D J

2004-06-08

A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affinities calculated using ab initio bond lengths and partial charges. These results allow a direct correlation of the three-dimensional, crystallographically controlled arrangements of various species (H2O, Na+, Rb+, Ca2+, Sr2+, Zn2+, Y3+, Nd3+) with macroscopic observables (H+ release, metal uptake, zeta potential) and thermodynamic/electrostatic constraints. All cations are found to be adsorbed as "inner sphere" species bonded directly to surface oxygen atoms, while the specific binding geometries and reaction stoichiometries are dependent on ionic radius. Ternary surface complexes of sorbed cations with electrolyte anions are not observed. Finally, surface oxygen proton affinities computed using the MUSIC model are improved by incorporation of ab initio bond lengths and hydrogen bonding information derived from MD simulations. This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties (structure, diffusivity, dielectric constant), surface protonation and hydrolysis, and the effect of solution ionic strength.

Bose–Einstein condensation versus Dicke–Hepp–Lieb transition in an optical cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piazza, Francesco, E-mail: francesco.piazza@ph.tum.de; Strack, Philipp; Zwerger, Wilhelm

We provide an exact solution for the interplay between Bose–Einstein condensation and the Dicke–Hepp–Lieb self-organization transition of an ideal Bose gas trapped inside a single-mode optical cavity and subject to a transverse laser drive. Based on an effective action approach, we determine the full phase diagram at arbitrary temperature, which features a bi-critical point where the transitions cross. We calculate the dynamically generated band structure of the atoms and the associated suppression of the critical temperature for Bose–Einstein condensation in the phase with a spontaneous periodic density modulation. Moreover, we determine the evolution of the polariton spectrum due to themore » coupling of the cavity photons and the atomic field near the self-organization transition, which is quite different above or below the Bose–Einstein condensation temperature. At low temperatures, the critical value of the Dicke–Hepp–Lieb transition decreases with temperature and thus thermal fluctuations can enhance the tendency to a periodic arrangement of the atoms. -- Highlights: •Atoms inside a driven cavity can undergo two transitions: self-organization and BEC. •The phase diagram has four phases which coexist at a bi-critical point. •Atom–cavity coupling creates a dynamical lattice for the atoms. •Finite temperature can enhance the tendency towards self-organization. •We calculate the detailed spectrum of the polaritonic excitations.« less

Entropic Comparison of Atomic-Resolution Electron Tomography of Crystals and Amorphous Materials.

PubMed

Collins, S M; Leary, R K; Midgley, P A; Tovey, R; Benning, M; Schönlieb, C-B; Rez, P; Treacy, M M J

2017-10-20

Electron tomography bears promise for widespread determination of the three-dimensional arrangement of atoms in solids. However, it remains unclear whether methods successful for crystals are optimal for amorphous solids. Here, we explore the relative difficulty encountered in atomic-resolution tomography of crystalline and amorphous nanoparticles. We define an informational entropy to reveal the inherent importance of low-entropy zone-axis projections in the reconstruction of crystals. In turn, we propose considerations for optimal sampling for tomography of ordered and disordered materials.

Highly thermally conductive and mechanically strong graphene fibers.

PubMed

Xin, Guoqing; Yao, Tiankai; Sun, Hongtao; Scott, Spencer Michael; Shao, Dali; Wang, Gongkai; Lian, Jie

2015-09-04

Graphene, a single layer of carbon atoms bonded in a hexagonal lattice, is the thinnest, strongest, and stiffest known material and an excellent conductor of heat and electricity. However, these superior properties have yet to be realized for graphene-derived macroscopic structures such as graphene fibers. We report the fabrication of graphene fibers with high thermal and electrical conductivity and enhanced mechanical strength. The inner fiber structure consists of large-sized graphene sheets forming a highly ordered arrangement intercalated with small-sized graphene sheets filling the space and microvoids. The graphene fibers exhibit a submicrometer crystallite domain size through high-temperature treatment, achieving an enhanced thermal conductivity up to 1290 watts per meter per kelvin. The tensile strength of the graphene fiber reaches 1080 megapascals. Copyright © 2015, American Association for the Advancement of Science.

A new five-coordinated copper compound for efficient degradation of methyl orange and Congo red in the absence of UV-visible radiation.

PubMed

Han, Li-Juan; Kong, Ya-Jie; Yan, Ting-Jiang; Fan, Lu-Tong; Zhang, Qi; Zhao, Hua-Jun; Zheng, He-Gen

2016-11-22

A new copper-based coordination compound Cu 2 (2,2'-bipy) 2 (pfbz) 4 (1) (where 2,2'-bipy = 2,2'-bipyridine; pfbz = pentafluorobenzoate), was hydrothermally synthesized and structurally characterized. Compound 1 having a binuclear structure consists of two copper cations and two oxygen atoms alternately in a plane square arrangement. In the presence of very small amounts of H 2 O 2 , the catalytic properties of compound 1 for the degradation of methyl orange (MO) are excellent in the absence of UV-visible radiation. Moreover, compound 1 presents suitable properties for degradation of Congo red (CR). Our results indicated that the five-coordinated copper compound, 1, will be a promising candidate for efficient degradation of organic dyes.

Crystal structure of tetra­aqua­[2-(pyridin-2-yl)-1H-imidazole-κ2 N 2,N 3]iron(II) sulfate

PubMed Central

Setifi, Zouaoui; Setifi, Fatima; Francuski, Bojana M.; Novaković, Sladjana B.; Merazig, Hocine

2015-01-01

In the title compound, [Fe(C8H7N3)(H2O)4]SO4, the central FeII ion is octa­hedrally coordinated by two N atoms from the bidentate 2-(pyridin-2-yl)-1H-imidazole ligand and by four O atoms of the aqua ligands. The largest deviation from the ideal octa­hedral geometry is reflected by the small N—Fe—N bite angle of 76.0 (1)°. The Fe—N coordination bonds have markedly different lengths [2.1361 (17) and 2.243 (2) Å], with the shorter one to the pyrimidine N atom. The four Fe—O coordination bond lengths vary from 2.1191 (18) to 2.1340 (17) Å. In the crystal, the cations and anions are arranged by means of medium-strength O—H⋯O hydrogen bonds into layers parallel to the ab plane. Neighbouring layers further inter­connect by N—H⋯O hydrogen bonds involving the imidazole fragment as donor group to one sulfate O atom as an acceptor. The resulting three-dimensional network is consolidated by C—H⋯O, C—H⋯π and π–π inter­actions. PMID:26029386

The Use of Contact Mode Atomic Force Microscopy in Aqueous Medium for Structural Analysis of Spinach Photosynthetic Complexes

DOE PAGES

Phuthong, Witchukorn; Huang, Zubin; Wittkopp, Tyler M.; ...

2015-07-28

To investigate the dynamics of photosynthetic pigment-protein complexes in vascular plants at high resolution in an aqueous environment, membrane-protruding oxygen-evolving complexes (OECs) associated with photosystem II (PSII) on spinach ( Spinacia oleracea) grana membranes were examined using contact mode atomic force microscopy. This study represents, to our knowledge, the first use of atomic force microscopy to distinguish the putative large extrinsic loop of Photosystem II CP47 reaction center protein (CP47) from the putative oxygen-evolving enhancer proteins 1, 2, and 3 (PsbO, PsbP, and PsbQ) and large extrinsic loop of Photosystem II CP43 reaction center protein (CP43) in the PSII-OEC extrinsicmore » domains of grana membranes under conditions resulting in the disordered arrangement of PSII-OEC particles. Moreover, we observed uncharacterized membrane particles that, based on their physical characteristics and electrophoretic analysis of the polypeptides associated with the grana samples, are hypothesized to be a domain of photosystem I that protrudes from the stromal face of single thylakoid bilayers. Furthermore, our results are interpreted in the context of the results of others that were obtained using cryo-electron microscopy (and single particle analysis), negative staining and freeze-fracture electron microscopy, as well as previous atomic force microscopy studies.« less

First-principles study of Ti intercalation between graphene and Au surface

NASA Astrophysics Data System (ADS)

Kaneko, T.; Imamura, H.

2011-06-01

We investigate the effects of Ti intercalation between graphene and Au surface on binding energy and charge doping by using the first-principles calculations. We show that the largest binding energy is realized by the intercalation of single mono-layer of Ti. We also show that electronic structure is very sensitive to the arrangement of metal atoms at the interface. If the composition of the interface layer is Ti0.33Au0.67 and the Ti is located at the top site, the Fermi level lies closely at the Dirac point, i.e., the Dirac cone of the ideal free-standing graphene is recovered.

Method and apparatus for atomization and spraying of molten metals

DOEpatents

Hobson, David O.; Alexeff, Igor; Sikka, Vinod K.

1990-01-01

A method and device for dispersing molten metal into fine particulate spray, the method comprises applying an electric current through the molten metal and simultaneously applying a magnetic field to the molten metal in a plane perpendicular to the electric current, whereby the molten metal is caused to form into droplets at an angle perpendicular to both the electric current and the magnetic field. The device comprises a structure for providing a molten metal, appropriately arranged electrodes for applying an electric current through the molten metal, and a magnet for providing a magnetic field in a plane perpendicular to the electric current.

Method and apparatus for atomization and spraying of molten metals

DOEpatents

Hobson, D.O.; Alexeff, I.; Sikka, V.K.

1988-07-19

A method and device for dispersing molten metal into fine particulate spray, the method comprises applying an electric current through the molten metal and simultaneously applying a magnetic field to the molten metal in a plane perpendicular to the electric current, whereby the molten metal is caused to form into droplets at an angle perpendicular to both the electric current and the magnetic field. The device comprises a structure for providing a molten metal, appropriately arranged electrodes for applying an electric current through the molten metal, and a magnet for providing a magnetic field in a plane perpendicular to the electric current. 11 figs.

Characterization of conductive nanobiomaterials derived from viral assemblies by low-voltage STEM imaging and Raman scattering

NASA Astrophysics Data System (ADS)

Plascencia-Villa, Germán; Carreño-Fuentes, Liliana; Bahena, Daniel; José-Yacamán, Miguel; Palomares, Laura A.; Ramírez, Octavio T.

2014-09-01

New technologies require the development of novel nanomaterials that need to be fully characterized to achieve their potential. High-resolution low-voltage scanning transmission electron microscopy (STEM) has proven to be a very powerful technique in nanotechnology, but its use for the characterization of nanobiomaterials has been limited. Rotavirus VP6 self-assembles into nanotubular assemblies that possess an intrinsic affinity for Au ions. This property was exploited to produce hybrid nanobiomaterials by the in situ functionalization of recombinant VP6 nanotubes with gold nanoparticles. In this work, Raman spectroscopy and advanced analytical electron microscopy imaging with spherical aberration-corrected (Cs) STEM and nanodiffraction at low-voltage doses were employed to characterize nanobiomaterials. STEM imaging revealed the precise structure and arrangement of the protein templates, as well as the nanostructure and atomic arrangement of gold nanoparticles with high spatial sub-Angstrom resolution and avoided radiation damage. The imaging was coupled with backscattered electron imaging, ultra-high resolution scanning electron microscopy and x-ray spectroscopy. The hybrid nanobiomaterials that were obtained showed unique properties as bioelectronic conductive devices and showed enhanced Raman scattering by their precise arrangement into superlattices, displaying the utility of viral assemblies as functional integrative self-assembled nanomaterials for novel applications.

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

2015-11-02

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.

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

DOE PAGES

Smetana, Volodymyr; Steinberg, Simon; Mudryk, Yaroslav; ...

2015-10-19

Four complex intermetallic compounds BaAu 6±xGa 6±y (x = 1, y = 0.9) (I), BaAu 6±xAl 6±y (x = 0.9, y = 0.6) (II), EuAu 6.2Ga 5.8 (III), and EuAu 6.1Al 5.9 (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 NaZn 13-type structure (cF104–112, Fm3C), III (tP52, P4/nbm) is derived from the tetragonal Ce 2Ni 17Si 9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupationmore » 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 “EuAu 6Tr 6” 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 “EuAu 6Tr 6” models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu 6.2Ga 5.8 (III) and EuAu 6.1Al 5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at T C = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. As a result, 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.« less

Atom-by-atom assembly of defect-free one-dimensional cold atom arrays.

PubMed

Endres, Manuel; Bernien, Hannes; Keesling, Alexander; Levine, Harry; Anschuetz, Eric R; Krajenbrink, Alexandre; Senko, Crystal; Vuletic, Vladan; Greiner, Markus; Lukin, Mikhail D

2016-11-25

The realization of large-scale fully controllable quantum systems is an exciting frontier in modern physical science. We use atom-by-atom assembly to implement a platform for the deterministic preparation of regular one-dimensional arrays of individually controlled cold atoms. In our approach, a measurement and feedback procedure eliminates the entropy associated with probabilistic trap occupation and results in defect-free arrays of more than 50 atoms in less than 400 milliseconds. The technique is based on fast, real-time control of 100 optical tweezers, which we use to arrange atoms in desired geometric patterns and to maintain these configurations by replacing lost atoms with surplus atoms from a reservoir. This bottom-up approach may enable controlled engineering of scalable many-body systems for quantum information processing, quantum simulations, and precision measurements. Copyright © 2016, American Association for the Advancement of Science.

Interpenetration of a 3D Icosahedral M@Ni12 (M=Al, Ga) Framework with Porphyrin-Reminiscent Boron Layers in MNi9 B8.

PubMed

Zheng, Qiang; Wagner, Frank R; Ormeci, Alim; Prots, Yurii; Burkhardt, Ulrich; Schmidt, Marcus; Schnelle, Walter; Grin, Yuri; Leithe-Jasper, Andreas

2015-11-09

Two ternary borides MNi9 B8 (M=Al, Ga) were synthesized by thermal treatment of mixtures of the elements. Single-crystal X-ray diffraction data reveal AlNi9 B8 and GaNi9 B8 crystallizing in a new type of structure within the space group Cmcm and the lattice parameters a=7.0896(3) Å, b=8.1181(3) Å, c=10.6497(4) Å and a=7.0897(5) Å, b=8.1579(4) Å, c=10.6648(7) Å, respectively. The boron atoms build up two-dimensional layers, which consist of puckered [B16 ] rings with two tailing B atoms, whereas the M atoms reside in distorted vertices-condensed [Ni12 ] icosahedra, which form a three-dimensional framework interpenetrated by boron porphyrin-reminiscent layers. An unusual local arrangement resembling a giant metallo-porphyrin entity is formed by the [B16 ] rings, which, due to their large annular size of approximately 8 Å, chelate four of the twelve icosahedral Ni atoms. An analysis of the chemical bonding by means of the electron localizability approach reveals strong covalent B-B interactions and weak Ni-Ni interactions. Multi-center dative B-Ni interaction occurs between the Al-Ni framework and the boron layers. In agreement with the chemical bonding analysis and band structure calculations, AlNi9 B8 is a Pauli-paramagnetic metal. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First-principles theoretical investigation of monoatomic and dimer Mn adsorption on noble metal (111) surfaces

NASA Astrophysics Data System (ADS)

Muñoz, Francisco; Romero, Aldo H.; Mejía-López, Jose; Morán-López, J. L.

2012-03-01

A theoretical investigation of the adsorption of Mn single atoms and dimers on the (111) surface of Cu, Ag, and Au, within the framework of the density functional theory, is presented. First, the bulk and the clean (111) surface electronic structures are calculated, with results that agree well with previous reports. To understand the adatom-substrate interaction, also the electronic characteristics of the free Mn dimer are determined. Then, the electronic structure of the Mn adatom, chemisorbed on four different surface geometries, is analyzed for the three noble metals. It is found that the most stable geometry, in all three cases, Cu, Ag, and Au, occurs when the Mn atom is chemisorbed on threefold coordinated sites. For the dimer, the lowest-energy configuration corresponds to the molecule lying parallel to the surface. In the three noble metals, the geometry corresponds to both atoms chemisorbed in threefold coordinated sites, but with different local symmetry. It is also found that the magnetic configuration with the lowest energy corresponds to the antiferromagnetic arrangement of Mn atoms, with individual magnetic moments close to 5μB. The ferromagnetic and antiferromagnetic solutions, in the case of a Ag substrate, are close in energy. It is also found that in this case the Mn2 molecule is chemisorbed with very similar energy on various geometries. To study the dynamical motion of the dimer components, we calculated the potential energy barriers for the Mn motion in the various surfaces. In contrast to Cu and Au, this leads to the conclusion that on Ag the Mn dimer moves relatively freely.

The antitumour drug 7-ethyl-10-hydroxycamptothecin monohydrate and its solid-state hydrolysis mechanism on heating.

PubMed

Ali, Md Ashraf; Noguchi, Shuji; Watanabe, Miteki; Iwao, Yasunori; Itai, Shigeru

2016-10-01

7-Ethyl-10-hydroxycamptothecin [systematic name: (4S)-4,11-diethyl-4,9-dihydroxy-1H-pyrano[3',4':6,7]indolizino[1,2-b]quinoline-3,14(4H,12H)-dione, SN-38] is an antitumour drug which exerts activity through the inhibition of topoisomerase I. The crystal structure of SN-38 as the monohydrate, C 22 H 20 N 2 O 5 ·H 2 O, reveals that it is a monoclinic crystal, with one SN-38 molecule and one water molecule in the asymmetric unit. When the crystal is heated to 473 K, approximately 30% of SN-38 is hydrolyzed at its lactone ring, resulting in the formation of the inactive carboxylate form. The molecular arrangement around the water molecule and the lactone ring of SN-38 in the crystal structure suggests that SN-38 is hydrolyzed by the water molecule at (x, y, z) nucleophilically attacking the carbonyl C atom of the lactone ring at (x - 1, y, z - 1). Hydrogen bonding around the water molecules and the lactone ring appears to promote this hydrolysis reaction: two carbonyl O atoms, which are hydrogen bonded as hydrogen-bond acceptors to the water molecule at (x, y, z), might enhance the nucleophilicity of this water molecule, while the water molecule at (-x, y + 1/2, -z), which is hydrogen bonded as a hydrogen-bond donor to the carbonyl O atom at (x - 1, y, z - 1), might enhance the electrophilicity of the carbonyl C atom.

Rigor-like structures from muscle myosins reveal key mechanical elements in the transduction pathways of this allosteric motor.

PubMed

Yang, Yuting; Gourinath, S; Kovács, Mihály; Nyitray, László; Reutzel, Robbie; Himmel, Daniel M; O'Neall-Hennessey, Elizabeth; Reshetnikova, Ludmilla; Szent-Györgyi, Andrew G; Brown, Jerry H; Cohen, Carolyn

2007-05-01

Unlike processive cellular motors such as myosin V, whose structure has recently been determined in a "rigor-like" conformation, myosin II from contracting muscle filaments necessarily spends most of its time detached from actin. By using squid and sea scallop sources, however, we have now obtained similar rigor-like atomic structures for muscle myosin heads (S1). The significance of the hallmark closed actin-binding cleft in these crystal structures is supported here by actin/S1-binding studies. These structures reveal how different duty ratios, and hence cellular functions, of the myosin isoforms may be accounted for, in part, on the basis of detailed differences in interdomain contacts. Moreover, the rigor-like position of switch II turns out to be unique for myosin V. The overall arrangements of subdomains in the motor are relatively conserved in each of the known contractile states, and we explore qualitatively the energetics of these states.

First-principles studies of the v7×v7R19.1° structure of sulfur on the Pd(1 1 1) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alfonso, D.R.

2007-11-01

Density functional theory is used to investigate the v7×v7R19.1° structure of sulfur on the Pd(111) surface. Among the different models that were considered, the densely packed mixed sulfur-metal overlayer structure proposed by Liu et al. [W. Liu, K.A.R. Mitchell, W. Berndt, Surf. Sci. 393 (1997) L119] was found to be the most energetically favorable. This model consists of arrangement of Pd triangles and pentagons on top of Pd(111) with the sulfur atoms at 3/7 monolayer coverage. The dominant mechanism for sulfur interaction with Pd in the overlayer region is the rehybridization of sulfur 3p and metal 4d bands. Simulated scanningmore » tunneling microscopy image for this structure shows some similarity with that obtained from experiment. Our study confirms that surface sulfide with no structural resemblance to its bulk counterparts can form on Pd(111).« less

Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy

NASA Astrophysics Data System (ADS)

Malkin, A. J.; Kuznetsov, Yu. G.; McPherson, A.

2001-11-01

In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.

Crystal structures and atomic model of NADPH oxidase.

PubMed

Magnani, Francesca; Nenci, Simone; Millana Fananas, Elisa; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W; Mattevi, Andrea

2017-06-27

NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.

Dynamic Stabilization of Metal Oxide–Water Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

McBriarty, Martin E.; von Rudorff, Guido Falk; Stubbs, Joanne E.

2017-02-08

The interaction of water with metal oxide surfaces plays a crucial role in the catalytic and geochemical behavior of metal oxides. In a vast majority of studies, the interfacial structure is assumed to arise from a relatively static lowest energy configuration of atoms, even at room temperature. Using hematite (α-Fe2O3) as a model oxide, we show through a direct comparison of in situ synchrotron X-ray scattering with density functional theory-based molecular dynamics simulations that the structure of the (1102) termination is dynamically stabilized by picosecond water exchange. Simulations show frequent exchanges between terminal aquo groups and adsorbed water in locationsmore » and with partial residence times consistent with experimentally determined atomic sites and fractional occupancies. Frequent water exchange occurs even for an ultrathin adsorbed water film persisting on the surface under a dry atmosphere. The resulting time-averaged interfacial structure consists of a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Surface pKa prediction based on bond valence analysis suggests that water exchange will influence the proton-transfer reactions underlying the acid/base reactivity at the interface. Our findings provide important new insights for understanding complex interfacial chemical processes at metal oxide–water interfaces.« less

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane.

PubMed

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-15

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Deep Eutectic Solvents as Convenient Media for Synthesis of Novel Coumarinyl Schiff Bases and Their QSAR Studies.

PubMed

Molnar, Maja; Komar, Mario; Brahmbhatt, Harshad; Babić, Jurislav; Jokić, Stela; Rastija, Vesna

2017-09-05

Deep eutectic solvents, as green and environmentally friendly media, were utilized in the synthesis of novel coumarinyl Schiff bases. Novel derivatives were synthesized from 2-((4-methyl-2-oxo-2 H -chromen-7-yl)oxy)acetohydrazide and corresponding aldehyde in choline chloride:malonic acid (1:1) based deep eutectic solvent. In these reactions, deep eutectic solvent acted as a solvent and catalyst as well. Novel Schiff bases were synthesized in high yields (65-75%) with no need for further purification, and their structures were confirmed by mass spectra, ¹H and 13 C NMR. Furthermore, their antioxidant activity was determined and compared to antioxidant activity of previously synthesized derivatives, thus investigating their structure-activity relationship utilizing quantitative structure-activity relationship QSAR studies. Calculation of molecular descriptors has been performed by DRAGON software. The best QSAR model ( R tr = 0.636; R ext = 0.709) obtained with three descriptors ( MATS3m , Mor22u , Hy ) implies that the pairs of atoms higher mass at the path length 3, three-dimensional arrangement of atoms at scattering parameter s = 21 Å - ¹, and higher number of hydrophilic groups (-OH, -NH) enhanced antioxidant activity. Electrostatic potential surface of the most active compounds showed possible regions for donation of electrons to 1,1-diphenyl-2-picryhydrazyl (DPPH) radicals.

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

NASA Astrophysics Data System (ADS)

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-01

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Ab initio structure determination of n-diamond.

PubMed

Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian

2015-08-24

A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon.

Single crystal synthesis and magnetism of the Ba Ln 2O 4 family ( Ln = lanthanide)

DOE PAGES

Besara, Tiglet; Lundberg, Matthew S.; Sun, Jifeng; ...

2014-05-27

The series of compounds in the Ba Ln 2O 4 family (Ln = La–Lu, Y) has been synthesized for the first time in single crystalline form, using a molten metal flux. The series crystallizes in the CaV 2O 4 structure type with primitive orthorhombic symmetry (space group Pnma, #62), and a complete structural study of atomic positions, bonds, angles, and distortions across the lanthanide series is presented. With the exception of the Y, La, Eu, and Lu members, magnetic susceptibility measurements were performed between 2 K and 300 K. BaCe 2O 4 and BaYb 2O 4 display large crystal fieldsmore » effects and suppression of magnetic ordering. As a result, all compounds show signs of magnetic frustration due to the trigonal arrangements of the trivalent lanthanide cations in the structure.« less

Molecular association via halogen bonding and other weak interactions in the crystal structures of 11-bromo-12-oxo-5β-cholan derivatives

NASA Astrophysics Data System (ADS)

Salunke, Deepak B.; Hazra, Braja G.; Gonnade, Rajesh G.; Pore, Vandana S.; Bhadbhade, Mohan M.

2008-12-01

Methyl 3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 2, methyl 11α-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 3, methyl 11β-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 4 and methyl 11,11-dibromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 5 were synthesized. The crystal structures of these molecules were resolved to study the effect of bulky bromine atom in the steroid skeleton of cholic acid with different stereo-chemical orientations at C-11 on the two-dimensional arrangement of molecules and solid-state properties. All the molecules associate only via weak intermolecular interactions in their crystal structures, notable one being the Halogen Bonded assembly (C-Br…O) in 5.

3-Methyl-5-methyl­sulfanyl-1,3,4-thia­diazole-2(3H)-thione

PubMed Central

Suarez, Sebastian A.; Hazari, Saroj K. S.; Ganguly, Biplab; Doctorovich, Fabio; G. Roy, Tapashi; Baggio, Ricardo

2012-01-01

The title compound, C4H6N2S3, has two very similar mol­ecules per asymmetric unit. The nine non-H atoms in each mol­ecule are coplanar, both having comparable r.m.s. deviations of 0.002 Å. The main inter­est in the rather simple structure resides in a survey of very weak (in some cases, borderline) non-bonding inter­actions of various kinds, viz. S⋯S, C—H⋯π, π–π [centroid–centroid distance = 3.8958 (13) Å] and C—S⋯π [3.7271 (11) Å], which act as the major driving force for the arrangement of mol­ecules in the structure. The role of long, though highly directional, S⋯S contacts (d > 3.60 Å), and their relevance to the stability of the structure is discussed. PMID:23125808

Extending the high-order-harmonic spectrum using surface plasmon polaritons

NASA Astrophysics Data System (ADS)

Ebadian, H.; Mohebbi, M.

2017-08-01

Nanoparticle assisted high-order-harmonic generation by low-intensity ultrashort laser pulses in hydrogen atomic gas is studied. This work is based on surface plasmon-polariton coupling in metal-insulator-metal structures. The necessary laser intensity is provided by enhancement of the incident laser power in the vicinity of bowtie nanoparticles installed on an insulator-metal structure. The inhomogeneous electric field distribution in the Au nanobowtie gap region is investigated. Simulations show that the insulator layer installed on the Au metal film that supports the plasmon-polariton interactions has a dramatic effect on the field enhancement factor. High-order-harmonic generation cutoffs for different arrangements are calculated and results show that the metal-insulator-metal structure is an excellent device for high-order-harmonic generation purposes. Also, the harmonic cutoff order is extended to more than 170, which is a considerable value and will be an efficient source for extreme ultraviolet radiation.

Molecular dynamics study about the effect of substrate temperature on a-Si:H structure

NASA Astrophysics Data System (ADS)

Luo, Yaorong; Gong, Hongyong; Zhou, Naigen; Huang, Haibin; Zhou, Lang

2018-01-01

Molecular dynamics simulation of the microstructure of hydrogenated amorphous silicon (a-Si:H) thin film with different substrate temperatures has been performed based on the Tersoff potential. The results showed that: the silicon thin film maintained amorphous structure in the substrate temperature range from 200 to 1000 K; high substrate temperature could smooth the surface. The first neighbour Voronoi polyhedron was dominated by the tetrahedron. When the substrate temperature increased, the content of tetrahedrons increased due to the transition from pentahedrons and hexahedrons to tetrahedrons. The change of the second neighbour Voronoi polyhedron could be classified into two cases: one case with low medium coordination number decreased as temperature increased, while the other one with high medium coordination number showed an opposite change tendency. It indicated that the local paracrystalline structure arrangement of the second neighbour atoms had been enhanced as substrate temperature rose.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamdani, Hazrina Yusof, E-mail: hazrina@mfrlab.org; Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas; Artymiuk, Peter J., E-mail: p.artymiuk@sheffield.ac.uk

A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graphmore » theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.« less

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Cr x(Bi 0.1Sb 0.9) 2-xTe 3

DOE PAGES

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; ...

2015-01-20

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a “Dirac-mass gap” in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in themore » ferromagnetic TI Cr₀.₀₈(Bi₀.₁Sb₀.₉)₁.₉₂Te₃. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship Δ(r)∝n(r) is confirmed throughout and exhibits an electron–dopant interaction energy J* = 145 meV·nm². In addition, these observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential.« less

Packing in protein cores

NASA Astrophysics Data System (ADS)

Gaines, J. C.; Clark, A. H.; Regan, L.; O'Hern, C. S.

2017-07-01

Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and predicting protein structure and stability. It is well-established that a large contribution to protein stability originates from the sequestration from solvent of hydrophobic residues in the protein core. How are such hydrophobic residues arranged in the core; how can one best model the packing of these residues, and are residues loosely packed with multiple allowed side chain conformations or densely packed with a single allowed side chain conformation? Here we show that to properly model the packing of residues in protein cores it is essential that amino acids are represented by appropriately calibrated atom sizes, and that hydrogen atoms are explicitly included. We show that protein cores possess a packing fraction of φ ≈ 0.56 , which is significantly less than the typically quoted value of 0.74 obtained using the extended atom representation. We also compare the results for the packing of amino acids in protein cores to results obtained for jammed packings from discrete element simulations of spheres, elongated particles, and composite particles with bumpy surfaces. We show that amino acids in protein cores pack as densely as disordered jammed packings of particles with similar values for the aspect ratio and bumpiness as found for amino acids. Knowing the structural properties of protein cores is of both fundamental and practical importance. Practically, it enables the assessment of changes in the structure and stability of proteins arising from amino acid mutations (such as those identified as a result of the massive human genome sequencing efforts) and the design of new folded, stable proteins and protein-protein interactions with tunable specificity and affinity.

The role of OH…O and CH…O hydrogen bonds and H…H interactions in ethanol/methanol-water heterohexamers.

PubMed

Mejía, Sol M; Espinal, Juan F; Mills, Matthew J L; Mondragón, Fanor

2016-08-01

Bioethanol is one of the world's most extensively produced biofuels. However, it is difficult to purify due to the formation of the ethanol-water azeotrope. Knowledge of the azeotrope structure at the molecular level can help to improve existing purification methods. In order to achieve a better understanding of this azeotrope structure, the characterization of (ethanol)5-water heterohexamers was carried out by analyzing the results of electronic structure calculations performed at the B3LYP/6-31+G(d) level. Hexamerization energies were found to range between -36.8 and -25.8 kcal/mol. Topological analysis of the electron density confirmed the existence of primary (OH…O) hydrogen bonds (HBs), secondary (CH…O) HBs, and H…H interactions in these clusters. Comparison with three different solvated alcohol systems featuring the same types of atom-atom interactions permitted the following order of stability to be determined: (methanol)5-water > (methanol)6 > (ethanol)5-water > (ethanol)6. These findings, together with accompanying geometric and spectroscopic analyses, show that similar cooperative effects exist among the primary HBs for structures with the same arrangement of primary HBs, regardless of the nature of the molecules involved. This result provides an indication that the molecular ratio can be considered to determine the unusual behavior of the ethanol-water system. The investigation also highlights the presence of several types of weak interaction in addition to primary HBs. Graphical Abstract Water-ethanol clusters exhibit a variety of interaction types between their atoms, such as primary OH...O (blue), secondary CH...O (green) and H...H (yellow) interactions as revealed by Quantum Chemical Topology.

In situ growth, structure, and real-time chemical reactivity of well-defined CeO x-Ru(0001) model surfaces

DOE PAGES

Grinter, David C.; Senanayake, Sanjaya D.; Flege, Jan Ingo

2016-11-15

Ceria is an important material for chemical conversion processes in catalysis. Its intrinsic properties as a reducible oxide can be exploited to achieve catalytic selectivity and activity. However, numerous phenomenological characteristics of ceria remain unknown and its active nature is ever slowly being unraveled. Well defined models of ceria (111) are an important way to systematically study these properties and take advantage of new in situ methods that require pristine materials that allow for the interrogation of the most fundamental traits of this material. The ceria-Ru(0001) model is now the most well studied model surface with numerous aspects of itsmore » preparation, atomic structure and reactivity studied by several groups. The preparation of CeO x structures oriented with a (111) surface termination can be achieved through molecular beam deposition, facilitating the growth of well-defined nanostructures, microparticles, and films on the Ru(0001) surface. The growth mechanism exploits the epitaxial relationship between CeOx and Ru to form a carpet mode of well oriented layers of Osingle bondCesingle bondO. These models can be studied to unravel the atomic structure and the oxidation state (Ce 4+ and Ce 3+), as prepared and under redox conditions (reduction/oxidation) or with reaction using reactants (e.g., H 2, methanol). Here, we present a discussion of these most recent observations pertaining to the growth mode, arrangement of atoms on the surface, characteristic chemical state, and redox chemistry of the CeO x-Ru surface. As a result, with insights from these studies we propose new strategies to further unravel the chemistry of ceria.« less

A family of rare earth molybdenum bronzes: Oxides consisting of periodic arrays of interacting magnetic units

DOE PAGES

Schneemeyer, L. F.; Siegrist, T.; Besara, T.; ...

2015-04-06

The family of rare earth molybdenum bronzes, reduced ternary molybdates of composition LnMo 16O 44, was synthesized and a detailed structural study carried out. Bond valence sum (BVS) calculations clearly show that the molybdenum ions in tetrahedral coordination are hexavalent while the electron count in the primitive unit cell is odd. Yet, measurements show that the phases are semiconductors. The temperature dependence of the magnetic susceptibility of samples containing several different rare earth elements was measured. These measurements verified the presence of a 6.5 K magnetic phase transition not arising from the rare earth constituent, but likely associated with themore » unique isolated ReO 3-type Mo 8O 36 structural subunits in this phase. To better understand the behavior of these materials, electronic structure calculations were performed within density functional theory. Results suggest a magnetic state in which these structural moieties have an internal ferromagnetic arrangement, with small ~1/8 μ B moments on each Mo. We suggest that the Mo 8O 36 units behave like pseudoatoms with spin ½ derived from a single hole distributed over the eight Mo atoms that are strongly hybridized with the O atoms of the subunit. As a result, while the compound is antiferromagnetic, our calculations suggest that a field-stabilized ferromagnetic state, if achievable, will be a narrow band half-metal.« less

Surface morphology and grain analysis of successively industrially grown amorphous hydrogenated carbon films (a-C:H) on silicon

NASA Astrophysics Data System (ADS)

Catena, Alberto; McJunkin, Thomas; Agnello, Simonpietro; Gelardi, Franco M.; Wehner, Stefan; Fischer, Christian B.

2015-08-01

Silicon (1 0 0) has been gradually covered by amorphous hydrogenated carbon (a-C:H) films via an industrial process. Two types of these diamond-like carbon (DLC) coatings, one more flexible (f-DLC) and one more robust (r-DLC), have been investigated. Both types have been grown by a radio frequency plasma-enhanced chemical vapor deposition (RF-PECVD) technique with acetylene plasma. Surface morphologies have been studied in detail by atomic force microscopy (AFM) and Raman spectroscopy has been used to investigate the DLC structure. Both types appeared to have very similar morphology and sp2 carbon arrangement. The average height and area for single grains have been analyzed for all depositions. A random distribution of grain heights was found for both types. The individual grain structures between the f- and r-type revealed differences: the shape for the f-DLC grains is steeper than for the r-DLC grains. By correlating the average grain heights to the average grain areas for all depositions a limited region is identified, suggesting a certain regularity during the DLC deposition mechanisms that confines both values. A growth of the sp2 carbon entities for high r-DLC depositions is revealed and connected to a structural rearrangement of carbon atom hybridizations and hydrogen content in the DLC structure.

Poly[[sesqui[mu2-1,4-bis(imidazol-1-ylmethyl)benzene-kappa(2)N:N'](carbonato-kappa(2)O,O')copper(II)] 1,4-bis(imidazol-1-ylmethyl)benzene hemisolvate pentahydrate].

PubMed

Dai, Yu-Mei; Tang, En; Huang, Jin-Feng; Yang, Qiu-Yan

2008-10-01

The asymmetric unit of the title compound, {[Cu(CO(3))(C(14)H(14)N(4))(1.5)] x 0.5 C(14)H(14)N(4) x 5 H(2)O}(n), contains one Cu(II) cation in a slightly distorted square-pyramidal coordination environment, one CO(3)(2-) anion, one full and two half 1,4-bis(imidazol-1-ylmethyl)benzene (bix) ligands, one half-molecule of which is uncoordinated, and five uncoordinated water molecules. One of the coordinated bix ligands and the uncoordinated bix molecule are situated about centers of symmetry, located at the centers of the benzene rings. The coordinated bix ligands link the copper(II) ions into a [Cu(bix)(1.5)](n) molecular ladder. These molecular ladders do not form interpenetrated ladders but are arranged in an ABAB parallel terrace, i.e. with the ladders arranged one above another, with sequence A translated with respect to B by 8 A. To best of our knowledge, this arrangement has not been observed in any of the molecular ladder frameworks synthesized to date. The coordination environment of the Cu(II) atom is completed by two O atoms of the CO(3)(2-) anion. The framework is further strengthened by extensive O-H...O and O-H...N hydrogen bonds involving the water molecules, the O atoms of the CO(3)(2-) anion and the N atoms of the bix ligands. This study describes the first example of a molecular ladder coordination polymer based on bix and therefore demonstrates further the usefulness of bix as a versatile multidentate ligand for constructing coordination polymers with interesting architectures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grinter, David C.; Senanayake, Sanjaya D.; Flege, Jan Ingo

Ceria is an important material for chemical conversion processes in catalysis. Its intrinsic properties as a reducible oxide can be exploited to achieve catalytic selectivity and activity. However, numerous phenomenological characteristics of ceria remain unknown and its active nature is ever slowly being unraveled. Well defined models of ceria (111) are an important way to systematically study these properties and take advantage of new in situ methods that require pristine materials that allow for the interrogation of the most fundamental traits of this material. The ceria-Ru(0001) model is now the most well studied model surface with numerous aspects of itsmore » preparation, atomic structure and reactivity studied by several groups. The preparation of CeO x structures oriented with a (111) surface termination can be achieved through molecular beam deposition, facilitating the growth of well-defined nanostructures, microparticles, and films on the Ru(0001) surface. The growth mechanism exploits the epitaxial relationship between CeOx and Ru to form a carpet mode of well oriented layers of Osingle bondCesingle bondO. These models can be studied to unravel the atomic structure and the oxidation state (Ce 4+ and Ce 3+), as prepared and under redox conditions (reduction/oxidation) or with reaction using reactants (e.g., H 2, methanol). Here, we present a discussion of these most recent observations pertaining to the growth mode, arrangement of atoms on the surface, characteristic chemical state, and redox chemistry of the CeO x-Ru surface. As a result, with insights from these studies we propose new strategies to further unravel the chemistry of ceria.« less

Engineering Plasmonic Nanocrystal Coupling through Template-Assisted Self-Assembly

NASA Astrophysics Data System (ADS)

Greybush, Nicholas J.

The construction of materials from nanocrystal building blocks represents a powerful new paradigm for materials design. Just as nature's materials orchestrate intricate combinations of atoms from the library of the periodic table, nanocrystal "metamaterials" integrate individual nanocrystals into larger architectures with emergent collective properties. The individual nanocrystal "meta-atoms" that make up these materials are themselves each a nanoscale atomic system with tailorable size, shape, and elemental composition, enabling the creation of hierarchical materials with predesigned structure at multiple length scales. However, an improved fundamental understanding of the interactions among individual nanocrystals is needed in order to translate this structural control into enhanced functionality. The ability to form precise arrangements of nanocrystals and measure their collective properties is therefore essential for the continued development of nanocrystal metamaterials. In this dissertation, we utilize template-assisted self-assembly and spatially-resolved spectroscopy to form and characterize individual nanocrystal oligomers. At the intersection of "top-down" and "bottom-up" nanoscale patterning schemes, template-assisted self-assembly combines the design freedom of lithography with the chemical control of colloidal synthesis to achieve unique nanocrystal configurations. Here, we employ shape-selective templates to assemble new plasmonic structures, including heterodimers of Au nanorods and upconversion phosphors, a series of hexagonally-packed Au nanocrystal oligomers, and triangular formations of Au nanorods. Through experimental analysis and numerical simulation, we elucidate the means through which inter-nanocrystal coupling imparts collective optical properties to the plasmonic assemblies. Our self-assembly and measurement strategy offers a versatile platform for exploring optical interactions in a wide range of material systems and application areas.

Fabricating Large-Area Sheets of Single-Layer Graphene by CVD

NASA Technical Reports Server (NTRS)

Bronikowski, Michael; Manohara, Harish

2008-01-01

This innovation consists of a set of methodologies for preparing large area (greater than 1 cm(exp 2)) domains of single-atomic-layer graphite, also called graphene, in single (two-dimensional) crystal form. To fabricate a single graphene layer using chemical vapor deposition (CVD), the process begins with an atomically flat surface of an appropriate substrate and an appropriate precursor molecule containing carbon atoms attached to substituent atoms or groups. These molecules will be brought into contact with the substrate surface by being flowed over, or sprayed onto, the substrate, under CVD conditions of low pressure and elevated temperature. Upon contact with the surface, the precursor molecules will decompose. The substituent groups detach from the carbon atoms and form gas-phase species, leaving the unfunctionalized carbon atoms attached to the substrate surface. These carbon atoms will diffuse upon this surface and encounter and bond to other carbon atoms. If conditions are chosen carefully, the surface carbon atoms will arrange to form the lowest energy single-layer structure available, which is the graphene lattice that is sought. Another method for creating the graphene lattice includes metal-catalyzed CVD, in which the decomposition of the precursor molecules is initiated by the catalytic action of a catalytic metal upon the substrate surface. Another type of metal-catalyzed CVD has the entire substrate composed of catalytic metal, or other material, either as a bulk crystal or as a think layer of catalyst deposited upon another surface. In this case, the precursor molecules decompose directly upon contact with the substrate, releasing their atoms and forming the graphene sheet. Atomic layer deposition (ALD) can also be used. In this method, a substrate surface at low temperature is covered with exactly one monolayer of precursor molecules (which may be of more than one type). This is heated up so that the precursor molecules decompose and form one monolayer of the target material.

AUTOMATIC AIR BURST DIRECTION FINDER

DOEpatents

Allard, G.A.

1952-01-31

This patent application describes an atomic explosion direction indicator comprising a geometric heat-scorchable indicating surface symmetrical about an axis, elevation and azimuth markings on the heat scorchable surface, and an indicating rod at the axis of said surface arranged to cast a shadow hereon, whereby heat from an atomic explosion will scorch a pattern on said surface indicative of the azimuth and elevation of said explosion.

Tetra­butyl­ammonium tetra­kis­(trimethyl­silanolato-κO)ferrate(III)

PubMed Central

Hay, Michael; Staples, Richard; Lee, Andre

2012-01-01

In the title salt, (C16H36N)[Fe(C3H9OSi)4], the cation contains a central N atom bonded to four n-butyl alkyl groups in a tetra­hedral arrangement, while the anion contains a central FeIII atom tetra­hedrally coordinated by four trimethyl­silanolate ligands. PMID:22969479

How a Spatial Arrangement of Secondary Structure Elements Is Dispersed in the Universe of Protein Folds

PubMed Central

Minami, Shintaro; Sawada, Kengo; Chikenji, George

2014-01-01

It has been known that topologically different proteins of the same class sometimes share the same spatial arrangement of secondary structure elements (SSEs). However, the frequency by which topologically different structures share the same spatial arrangement of SSEs is unclear. It is important to estimate this frequency because it provides both a deeper understanding of the geometry of protein folds and a valuable suggestion for predicting protein structures with novel folds. Here we clarified the frequency with which protein folds share the same SSE packing arrangement with other folds, the types of spatial arrangement of SSEs that are frequently observed across different folds, and the diversity of protein folds that share the same spatial arrangement of SSEs with a given fold, using a protein structure alignment program MICAN, which we have been developing. By performing comprehensive structural comparison of SCOP fold representatives, we found that approximately 80% of protein folds share the same spatial arrangement of SSEs with other folds. We also observed that many protein pairs that share the same spatial arrangement of SSEs belong to the different classes, often with an opposing N- to C-terminal direction of the polypeptide chain. The most frequently observed spatial arrangement of SSEs was the 2-layer α/β packing arrangement and it was dispersed among as many as 27% of SCOP fold representatives. These results suggest that the same spatial arrangements of SSEs are adopted by a wide variety of different folds and that the spatial arrangement of SSEs is highly robust against the N- to C-terminal direction of the polypeptide chain. PMID:25243952

Structural Evolution of Iron Antimonides from Amorphous Precursors to Crystalline Products Studied by Total Scattering Techniques.

PubMed

Bauers, Sage R; Wood, Suzannah R; Jensen, Kirsten M Ø; Blichfeld, Anders B; Iversen, Bo B; Billinge, Simon J L; Johnson, David C

2015-08-05

Homogeneous reaction precursors may be used to form several solid-state compounds inaccessible by traditional synthetic routes, but there has been little development of techniques that allow for a priori prediction of what may crystallize in a given material system. Here, the local structures of FeSbx designed precursors are determined and compared with the structural motifs of their crystalline products. X-ray total scattering and atomic pair distribution function (PDF) analysis are used to show that precursors that first nucleate a metastable FeSb3 compound share similar local structure to the product. Interestingly, precursors that directly crystallize to thermodynamically stable FeSb2 products also contain local structural motifs of the metastable phase, despite their compositional disagreement. While both crystalline phases consist of distorted FeSb6 octahedra with Sb shared between either two or three octahedra as required for stoichiometry, a corner-sharing arrangement indicative of AX3-type structures is the only motif apparent in the PDF of either precursor. Prior speculation was that local composition controlled which compounds nucleate from amorphous intermediates, with different compositions favoring different local arrangements and hence different products. This data suggests that local environments in these amorphous intermediates may not be very sensitive to overall composition. This can provide insight into potential metastable phases which may form in a material system, even with a precursor that does not crystallize to the kinetically stabilized product. Determination of local structure in homogeneous amorphous reaction intermediates from techniques such as PDF can be a valuable asset in the development of systematic methods to prepare targeted solid-state compounds from designed precursors.

Local structure controls the nonaffine shear and bulk moduli of disordered solids

NASA Astrophysics Data System (ADS)

Schlegel, M.; Brujic, J.; Terentjev, E. M.; Zaccone, A.

2016-01-01

Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices; all of these models assume central-force interactions between particles/atoms. Each of these models differs in the spatial arrangement and the correlations among particles. In turn, this is reflected in the widely different behaviours of the shear (G) and compression (K) elastic moduli. The relation between the macroscopic elasticity as encoded in G, K and their ratio, and the microscopic lattice structure/order, is not understood. We provide a quantitative analytical connection between the local orientational order and the elasticity in model amorphous solids with different internal microstructure, focusing on the two opposite limits of packings (strong excluded-volume) and networks (no excluded-volume). The theory predicts that, in packings, the local orientational order due to excluded-volume causes less nonaffinity (less softness or larger stiffness) under compression than under shear. This leads to lower values of G/K, a well-documented phenomenon which was lacking a microscopic explanation. The theory also provides an excellent one-parameter description of the elasticity of compressed emulsions in comparison with experimental data over a broad range of packing fractions.

Crystal structure, Hirshfeld surface analysis, quantum mechanical study and spectroscopic characterization of the non-centrosymmetric coordination compound bis(4-fluoroaniline)dichloridozincate

NASA Astrophysics Data System (ADS)

Ben Nasr, M.; Soudani, S.; Lefebvre, F.; Jelsch, C.; Ben Nasr, C.

2017-06-01

The Zn(II) complex with the monodentate ligand 4-fluoroaniline, ZnCl2(C6H4FNH2)2, has been prepared and characterized by single crystal X-ray diffraction, solid state nuclear magnetic resonance, infrared spectroscopy and differential scanning calorimetry. The Zn(II) ion is tetracoordinated by two nitrogen atoms of two monodentate 4-fluoroaniline ligands and two chlorine atoms. In the molecular arrangement, the ZnCl2(C6H4FNH2)2 entities are interconnected via Nsbnd H⋯Cl hydrogen bonds to form layers parallel to the (a, b) plane. The nature and proportion of contacts in the crystal packing were investigated through the Hirshfeld surfaces. The crystal is mainly maintained by electrostatic attractions Cl- … Hsbnd N and by extensive hydrophobic contacts as revealed by the Hirshfeld 2D fingerprint plots and statistical analysis. The13C and 19F CP-MAS NMR spectra are in agreement with the X-ray structure and confirm the phase purity of the crystalline sample. The vibrational absorption bands were identified by infrared spectroscopy. A calorimetric study shows that the title compound is stable until 262.5 °C.

Interfaces in Heterogeneous Catalysts: Advancing Mechanistic Understanding through Atomic-Scale Measurements.

PubMed

Gao, Wenpei; Hood, Zachary D; Chi, Miaofang

2017-04-18

Developing novel catalysts with high efficiency and selectivity is critical for enabling future clean energy conversion technologies. Interfaces in catalyst systems have long been considered the most critical factor in controlling catalytic reaction mechanisms. Interfaces include not only the catalyst surface but also interfaces within catalyst particles and those formed by constructing heterogeneous catalysts. The atomic and electronic structures of catalytic surfaces govern the kinetics of binding and release of reactant molecules from surface atoms. Interfaces within catalysts are introduced to enhance the intrinsic activity and stability of the catalyst by tuning the surface atomic and chemical structures. Examples include interfaces between the core and shell, twin or domain boundaries, or phase boundaries within single catalyst particles. In supported catalyst nanoparticles (NPs), the interface between the metallic NP and support serves as a critical tuning factor for enhancing catalytic activity. Surface electronic structure can be indirectly tuned and catalytically active sites can be increased through the use of supporting oxides. Tuning interfaces in catalyst systems has been identified as an important strategy in the design of novel catalysts. However, the governing principle of how interfaces contribute to catalyst behavior, especially in terms of interactions with intermediates and their stability during electrochemical operation, are largely unknown. This is mainly due to the evolving nature of such interfaces. Small changes in the structural and chemical configuration of these interfaces may result in altering the catalytic performance. These interfacial arrangements evolve continuously during synthesis, processing, use, and even static operation. A technique that can probe the local atomic and electronic interfacial structures with high precision while monitoring the dynamic interfacial behavior in situ is essential for elucidating the role of interfaces and providing deeper insight for fine-tuning and optimizing catalyst properties. Scanning transmission electron microscopy (STEM) has long been a primary characterization technique used for studying nanomaterials because of its exceptional imaging resolution and simultaneous chemical analysis. Over the past decade, advances in STEM, that is, the commercialization of both aberration correctors and monochromators, have significantly improved the spatial and energy resolution. Imaging atomic structures with subangstrom resolution and identifying chemical species with single-atom sensitivity are now routine for STEM. These advancements have greatly benefitted catalytic research. For example, the roles of lattice strain and surface elemental distribution and their effect on catalytic stability and reactivity have been well documented in bimetallic catalysts. In addition, three-dimensional atomic structures revealed by STEM tomography have been integrated in theoretical modeling for predictive catalyst NP design. Recent developments in stable electronic and mechanical devices have opened opportunities to monitor the evolution of catalysts in operando under synthesis and reaction conditions; high-speed direct electron detectors have achieved sub-millisecond time resolutions and allow for rapid structural and chemical changes to be captured. Investigations of catalysts using these latest microscopy techniques have provided new insights into atomic-level catalytic mechanisms. Further integration of new microscopy methods is expected to provide multidimensional descriptions of interfaces under relevant synthesis and reaction conditions. In this Account, we discuss recent insights on understanding catalyst activity, selectivity, and stability using advanced STEM techniques, with an emphasis on how critical interfaces dictate the performance of precious metal-based heterogeneous catalysts. The role of extended interfacial structures, including those between core and shell, between separate phases and twinned grains, between the catalyst surface and gas, and between metal and support are discussed. We also provide an outlook on how emerging electron microscopy techniques, such as vibrational spectroscopy and electron ptychography, will impact future catalysis research.

Efficient Procedure for the Numerical Calculation of Harmonic Vibrational Frequencies Based on Internal Coordinates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miliordos, Evangelos; Xantheas, Sotiris S.

We propose a general procedure for the numerical calculation of the harmonic vibrational frequencies that is based on internal coordinates and Wilson’s GF methodology via double differentiation of the energy. The internal coordinates are defined as the geometrical parameters of a Z-matrix structure, thus avoiding issues related to their redundancy. Linear arrangements of atoms are described using a dummy atom of infinite mass. The procedure has been automated in FORTRAN90 and its main advantage lies in the nontrivial reduction of the number of single-point energy calculations needed for the construction of the Hessian matrix when compared to the corresponding numbermore » using double differentiation in Cartesian coordinates. For molecules of C 1 symmetry the computational savings in the energy calculations amount to 36N – 30, where N is the number of atoms, with additional savings when symmetry is present. Typical applications for small and medium size molecules in their minimum and transition state geometries as well as hydrogen bonded clusters (water dimer and trimer) are presented. Finally, in all cases the frequencies based on internal coordinates differ on average by <1 cm –1 from those obtained from Cartesian coordinates.« less

First-order ferromagnetic to helimagnetic transition in MgMn6Ge6

NASA Astrophysics Data System (ADS)

Mazet, T.; Ihou-Mouko, H.; Malaman, B.

2008-02-01

The magnetic and magnetocaloric properties of the new HfFe6Ge6-type (P6/mmm) MgMn6Ge6 compound have been studied by magnetic measurements and powder neutron diffraction experiments. MgMn6Ge6 magnetically orders at TC˜345 K in a ferromagnetic easy-plane arrangement. At TAF˜235 K, it undergoes a first-order transition to a helical structure, characterized by a temperature dependent propagation vector k =⟨0,0,qz⟩ (qz˜0.116 reciprocal lattice units at 1.4 K), without structural modification. The Mn atoms carry a magnetic moment of about 2 μB. A metamagnetic transition with a low critical field (Hcr<1 T) is observed below TAF. At low temperature, both magnetic and magnetocaloric data strongly suggest that some kinds of intermediate noncollinear ferromagnetic arrangements are stabilized above the critical field while the pure ferromagnetic state is obtained for significantly higher magnetic fields (H >5 T). The magnitude of the magnetic entropy change at TC (-ΔSM˜20.5 mJ cm-3 K-1 for ΔH =5 T) is about 25% that of Gd metal. The magnetocaloric effect at the order-order transition is of opposite sign and of lower magnitude.

A heated vapor cell unit for dichroic atomic vapor laser lock in atomic rubidium.

PubMed

McCarron, Daniel J; Hughes, Ifan G; Tierney, Patrick; Cornish, Simon L

2007-09-01

The design and performance of a compact heated vapor cell unit for realizing a dichroic atomic vapor laser lock (DAVLL) for the D(2) transitions in atomic rubidium is described. A 5 cm long vapor cell is placed in a double-solenoid arrangement to produce the required magnetic field; the heat from the solenoid is used to increase the vapor pressure and correspondingly the DAVLL signal. We have characterized experimentally the dependence of important features of the DAVLL signal on magnetic field and cell temperature. For the weaker transitions both the amplitude and gradient of the signal are increased by an order of magnitude.

Physics with Trapped Antihydrogen

NASA Astrophysics Data System (ADS)

Charlton, Michael

2017-04-01

For more than a decade antihydrogen atoms have been formed by mixing antiprotons and positrons held in arrangements of charged particle (Penning) traps. More recently, magnetic minimum neutral atom traps have been superimposed upon the anti-atom production region, promoting the trapping of a small quantity of the antihydrogen yield. We will review these advances, and describe some of the first physics experiments performed on anrtihydrogen including the observation of the two-photon 1S-2S transition, invesigation of the charge neutrailty of the anti-atom and studies of the ground state hyperfine splitting. We will discuss the physics motivations for undertaking these experiments and describe some near-future initiatives.

Thermal Entanglement Between Atoms in the Four-Cavity Linear Chain Coupled by Single-Mode Fibers

NASA Astrophysics Data System (ADS)

Wang, Jun-Biao; Zhang, Guo-Feng

2018-05-01

Natural thermal entanglement between atoms of a linear arranged four coupled cavities system is studied. The results show that there is no thermal pairwise entanglement between atoms if atom-field interaction strength f or fiber-cavity coupling constant J equals to zero, both f and J can induce thermal pairwise entanglement in a certain range. Numerical simulations show that the nearest neighbor concurrence C A B is always greater than alternate concurrence C A C in the same condition. In addition, the effect of temperature T on the entanglement of alternate qubits is much stronger than the nearest neighbor qubits.

Static and Dynamic Electron Microscopy Investigations at the Atomic and Ultrafast Scales

NASA Astrophysics Data System (ADS)

Suri, Pranav Kumar

Advancements in the electron microscopy capabilities - aberration-corrected imaging, monochromatic spectroscopy, direct-electron detectors - have enabled routine visualization of atomic-scale processes with millisecond temporal resolutions in this decade. This, combined with progress in the transmission electron microscopy (TEM) specimen holder technology and nanofabrication techniques, allows comprehensive experiments on a wide range of materials in various phases via in situ methods. The development of ultrafast (sub-nanosecond) time-resolved TEM with ultrafast electron microscopy (UEM) has further pushed the envelope of in situ TEM to sub-nanosecond temporal resolution while maintaining sub-nanometer spatial resolution. A plethora of materials phenomena - including electron-phonon coupling, phonon transport, first-order phase transitions, bond rotation, plasmon dynamics, melting, and dopant atoms arrangement - are not yet clearly understood and could be benefitted with the current in situ TEM capabilities having atomic-level and ultrafast precision. Better understanding of these phenomena and intrinsic material dynamics (e.g. how phonons propagate in a material, what time-scales are involved in a first-order phase transition, how fast a material melts, where dopant atoms sit in a crystal) in new-generation and technologically important materials (e.g. two-dimensional layered materials, semiconductor and magnetic devices, rare-earth-element-free permanent magnets, unconventional superconductors) could bring a paradigm shift in their electronic, structural, magnetic, thermal and optical applications. Present research efforts, employing cutting-edge static and dynamic in situ electron microscopy resources at the University of Minnesota, are directed towards understanding the atomic-scale crystallographic structural transition and phonon transport in an iron-pnictide parent compound LaFeAsO, studying the mechanical stability of fast moving hard-drive heads in heat-assisted magnetic recording (HAMR) technology, exploring the possibility of ductile ceramics in magnesium oxide (MgO) nanomaterials, and revealing the atomic-structure of newly discovered rare-earth-element-free iron nitride (FeN) magnetic materials. Via atomic-resolution imaging and electron diffraction coupled with in situ TEM cooling on LaFeAsO, it was found that additional effects not related to the structural transition, namely dynamical scattering and electron channeling, can give signatures reminiscent of those typically associated with the symmetry change. UEM studies on LaFeAsO revealed direct, real-space imaging of the emergence and evolution of acoustic phonons and resolved dispersion behavior during propagation and scattering. Via UEM bright-field imaging, megahertz vibrational frequencies were observed upon laser-illumination in TEM specimens made out of HAMR devices which could be detrimental to their long-term thermal and structural reliability. Compression testing of 100-350 nm single-crystal MgO nanocubes shows size-dependent stresses and engineering strains of 4-13.8 GPa and 0.046-0.221 respectively at the first signs of yield accompanied by an absence of brittle fracture, which is a significant increase in plasticity of a brittle ceramic material. Atomic-scale characterization of FeN phases show that it is possible to detect interstitial locations of low atomic-number nitrogen atoms in iron crystal and hints at a development of novel routes (without involving rare-earth elements) for bulk permanent magnet synthesis.

Atomic configurations at InAs partial dislocation cores associated with Z-shape faulted dipoles.

PubMed

Li, Luying; Gan, Zhaofeng; McCartney, Martha R; Liang, Hanshuang; Yu, Hongbin; Gao, Yihua; Wang, Jianbo; Smith, David J

2013-11-15

The atomic arrangements of two types of InAs dislocation cores associated by a Z-shape faulted dipole are observed directly by aberration-corrected high-angle annular-dark-field imaging. Single unpaired columns of different atoms in a matrix of dumbbells are clearly resolved, with observable variations of bonding lengths due to excess Coulomb force from bare ions at the dislocation core. The corresponding geometric phase analysis provides confirmation that the dislocation cores serve as origins of strain field inversion while stacking faults maintain the existing strain status.

Structure determination of Ba5AlF13 by coupling electron, synchrotron and neutron powder diffraction, solid-state NMR and ab initio calculations.

PubMed

Martineau, Charlotte; Allix, Mathieu; Suchomel, Matthew R; Porcher, Florence; Vivet, François; Legein, Christophe; Body, Monique; Massiot, Dominique; Taulelle, Francis; Fayon, Franck

2016-10-04

The room temperature structure of Ba 5 AlF 13 has been investigated by coupling electron, synchrotron and neutron powder diffraction, solid-state high-resolution NMR ( 19 F and 27 Al) and first principles calculations. An initial structural model has been obtained from electron and synchrotron powder diffraction data, and its main features have been confirmed by one- and two-dimensional NMR measurements. However, DFT GIPAW calculations of the 19 F isotropic shieldings revealed an inaccurate location of one fluorine site (F3, site 8a), which exhibited unusual long F-Ba distances. The atomic arrangement was reinvestigated using neutron powder diffraction data. Subsequent Fourier maps showed that this fluorine atom occupies a crystallographic site of lower symmetry (32e) with partial occupancy (25%). GIPAW computations of the NMR parameters validate the refined structural model, ruling out the presence of local static disorder and indicating that the partial occupancy of this F site reflects a local motional process. Visualisation of the dynamic process was then obtained from the Rietveld refinement of neutron diffraction data using an anharmonic description of the displacement parameters to account for the thermal motion of the mobile fluorine. The whole ensemble of powder diffraction and NMR data, coupled with first principles calculations, allowed drawing an accurate structural model of Ba 5 AlF 13 , including site-specific dynamical disorder in the fluorine sub-network.

Crystal structures of Ca(ClO4)2·4H2O and Ca(ClO4)2·6H2O

PubMed Central

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-01-01

The title compounds, calcium perchlorate tetra­hydrate and calcium perchlorate hexa­hydrate, were crystallized at low temperatures according to the solid–liquid phase diagram. The structure of the tetra­hydrate consists of one Ca2+ cation eightfold coordinated in a square-anti­prismatic fashion by four water mol­ecules and four O atoms of four perchlorate tetra­hedra, forming chains parallel to [01-1] by sharing corners of the ClO4 tetra­hedra. The structure of the hexa­hydrate contains two different Ca2+ cations, each coordinated by six water mol­ecules and two O atoms of two perchlorate tetra­hedra, forming [Ca(H2O)6(ClO4)]2 dimers by sharing two ClO4 tetra­hedra. The dimers are arranged in sheets parallel (001) and alternate with layers of non-coordinating ClO4 tetra­hedra. O—H⋯O hydrogen bonds between the water mol­ecules as donor and ClO4 tetra­hedra and water mol­ecules as acceptor groups lead to the formation of a three-dimensional network in the two structures. Ca(ClO4)2·6H2O was refined as a two-component inversion twin, with an approximate twin component ratio of 1:1 in each of the two structures. PMID:25552974

Rydberg blockade in three-atom systems

NASA Astrophysics Data System (ADS)

Barredo, Daniel; Ravets, Sylvain; Labuhn, Henning; Beguin, Lucas; Vernier, Aline; Chicireanu, Radu; Nogrette, Florence; Lahaye, Thierry; Browaeys, Antoine

2014-05-01

The control of individual neutral atoms in arrays of optical tweezers is a promising avenue for quantum science and technology. Here we demonstrate unprecedented control over a system of three Rydberg atoms arranged in linear and triangular configurations. The interaction between Rydberg atoms results in the observation of an almost perfect van der Waals blockade. When the single-atom Rabi frequency for excitation to the Rydberg state is comparable to the interaction energy, we directly observe the anisotropy of the interaction between nD-states. Using the independently measured two-body interaction energy shifts we fully reproduce the dynamics of the three-atom system with a model based on a master equation without any adjustable parameter. Combined with our ability to trap single atoms in arbitrary patterns of 2D arrays of up to 100 traps separated by a few microns, these results are very promising for a scalable implementation of quantum simulation of frustrated quantum magnetism with Rydberg atoms.

Programmable solid state atom sources for nanofabrication.

PubMed

Han, Han; Imboden, Matthias; Stark, Thomas; del Corro, Pablo G; Pardo, Flavio; Bolle, Cristian A; Lally, Richard W; Bishop, David J

2015-06-28

In this paper we discuss the development of a MEMS-based solid state atom source that can provide controllable atom deposition ranging over eight orders of magnitude, from ten atoms per square micron up to hundreds of atomic layers, on a target ∼1 mm away. Using a micron-scale silicon plate as a thermal evaporation source we demonstrate the deposition of indium, silver, gold, copper, iron, aluminum, lead and tin. Because of their small sizes and rapid thermal response times, pulse width modulation techniques are a powerful way to control the atomic flux. Pulsing the source with precise voltages and timing provides control in terms of when and how many atoms get deposited. By arranging many of these devices into an array, one has a multi-material, programmable solid state evaporation source. These micro atom sources are a complementary technology that can enhance the capability of a variety of nano-fabrication techniques.

Magnetic, electronic and optical properties of different graphene, BN and BC2N nanoribbons

NASA Astrophysics Data System (ADS)

Guerra, T.; Leite, L.; Azevedo, S.; de Lima Bernardo, B.

2017-04-01

Graphene nanoribbons are predicted to be essential components in future nanoelectronics. The size, edge type, form, arrangement of atoms and width of nanoribbons drastically change their properties. However, magnetic, electronic and optical properties of armchair, chevron and sawtooth of graphene, BN and BC2N nanoribbons are not fully understood so far. Here, we make use of first-principles calculations based on the density functional theory (DFT) to investigate the structural, magnetic, electronic and optical properties of nanoribbons of graphene, boron nitride and BC2N with armchair edge, chevron-type and sawtooth forms. The lowest formation energies were found for the armchair and chevron nanoribbons of graphene and boron nitride. We have shown that the imbalance of carbon atoms between different sublattices generates a net magnetic moment. Chevron-type nanoribbons of BC2N and graphene showed a band gap comparable with silicon, and a high light absorption in the visible spectrum when compared to the other configurations.

Properties at the interface of graphene and Ti2C MXene

NASA Astrophysics Data System (ADS)

Paul, Pallavi; Chakraborty, Poulami; Das, Tilak; Nafday, Dhani; Saha-Dasgupta, Tanusri

2017-07-01

Employing ab initio calculations, we characterize the interfaces formed between graphene, a much discussed two-dimensional material, and MXene, another two-dimensional material of recent interest. Our study considering the specific case of Ti2C , a member of the MXene family, shows the formation of chemical bonds between Ti atoms and C atoms of graphene. This results in reconstruction of the electronic structure at the interface, making the interface metallic, though graphene is a zero-gap semiconductor and Ti2C is an antiferromagnetic insulator in their respective native form. The optical and phonon properties of the interfaces are found to be strongly dependent on the stacking arrangement, driven by the nature of chemical-bond formation. Consideration of O-passivated Ti2C is found to weaken the interaction between graphene and Ti2C substantially, making it a physisorption process rather than chemisorption in the unpassivated situation. Our first-principles study is expected to motivate future experimental investigation.

σ–π-Band Inversion in a Novel Two-Dimensional Material

DOE PAGES

Lopez-Bezanilla, Alejandro; Littlewood, Peter B.

2015-07-24

In this paper, we present a theoretical study of a new type of two-dimensional material exhibiting a pentagonal arrangement of C and Si atoms. Pentagonal SiC 2 is investigated with density functional theory-based calculations to show that the buckled nanostructure is dynamically stable, and exhibits an indirect energy band gap and an enhanced electronic dispersion with respect to the all-carbon counterpart. Computed Born effective charges exhibit a significant anisotropy for C and Si atoms that deviates substantially from their static effective charges. We establish an accurate tunability of the vertical location of the p-p-σ and p-p-π bands and show thatmore » under compressive biaxial strain the density of states decreases, and conversely for tensile biaxial strain. Finally, this coupling between the tunability of strain-mediated density of states and semiconducting properties in a monolayered structure may allow for the development of applications in semiconducting stretchable electronics.« less

CO oxidation on Alsbnd Au nano-composite systems

NASA Astrophysics Data System (ADS)

Rajesh, C.; Majumder, C.

2018-03-01

Using first principles method we report the CO oxidation behaviour of Alsbnd Au nano-composites in three different size ranges: Al6Au8, Al13Au42 and a periodic slab of Alsbnd Au(1 1 1) surface. The clusters prefer enclosed structures with alternating arrangement of Al and Au atoms, maximising Auδ-sbnd Alδ+ bonds. Charge distribution analysis suggests the charge transfer from Al to Au atoms, corroborated by the red shift in the density of states spectrum. Further, CO oxidation on these nano-composite systems was investigated through both Eley - Rideal and Langmuir Hinshelwood mechanism. While, these clusters interact with O2 non-dissociatively with an elongation of the Osbnd O bond, further interaction with CO led to formation of CO2 spontaneously. On contrary, the CO2 evolution by co-adsorption of O2 and CO molecules has a transition state barrier. On the basis of the results it is inferred that nano-composite material of Alsbnd Au shows significant promise toward effective oxidative catalysis.

Atomically dispersed metal sites in MOF-based materials for electrocatalytic and photocatalytic energy conversion.

PubMed

Liang, Zibin; Qu, Chong; Xia, Dingguo; Zou, Ruqiang; Xu, Qiang

2018-02-19

Metal sites play an essential role for both electrocatalytic and photocatalytic energy conversion applications. The highly ordered arrangements of the organic linkers and metal nodes and the well-defined pore structures of metal-organic frameworks (MOFs) make them ideal substrates to support atomically dispersed metal sites (ADMSs) located in their metal nodes, linkers, and pores. Besides, porous carbon materials doped with ADMSs can be derived from these ADMS-incorporated MOF precursors through controlled treatments. These ADMSs incorporated in pristine MOFs and MOF-derived carbon materials possess unique merits over the molecular or the bulk metal-based catalysts, bridging the gap between homogeneous and heterogeneous catalysts for energy conversion applications. In this review, recent progress and perspective of design and incorporation of ADMSs in pristine MOFs and MOF-derived materials for energy conversion applications are highlighted, which will hopefully promote further developments of advanced MOF-based catalysts in foreseeable future. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding nanocellulose chirality and structure–properties relationship at the single fibril level

PubMed Central

Usov, Ivan; Nyström, Gustav; Adamcik, Jozef; Handschin, Stephan; Schütz, Christina; Fall, Andreas; Bergström, Lennart; Mezzenga, Raffaele

2015-01-01

Nanocellulose fibrils are ubiquitous in nature and nanotechnologies but their mesoscopic structural assembly is not yet fully understood. Here we study the structural features of rod-like cellulose nanoparticles on a single particle level, by applying statistical polymer physics concepts on electron and atomic force microscopy images, and we assess their physical properties via quantitative nanomechanical mapping. We show evidence of right-handed chirality, observed on both bundles and on single fibrils. Statistical analysis of contours from microscopy images shows a non-Gaussian kink angle distribution. This is inconsistent with a structure consisting of alternating amorphous and crystalline domains along the contour and supports process-induced kink formation. The intrinsic mechanical properties of nanocellulose are extracted from nanoindentation and persistence length method for transversal and longitudinal directions, respectively. The structural analysis is pushed to the level of single cellulose polymer chains, and their smallest associated unit with a proposed 2 × 2 chain-packing arrangement. PMID:26108282

Orientation relationship between the T structure and the icosahedral quasicrystal in the Zn-Mg-Al alloy system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakayama, Kei, E-mail: k.n@aoni.waseda.jp; Watanabe, Junya; Koyama, Yasumasa, E-mail: ykoyama@waseda.jp

2016-08-26

To understand the crystallographic relation between the Bergman-type icosahedral quasicrystal and its approximant-T structure, we have investigated the crystallographic features of prepared Zn-Mg-Al alloy samples, mainly by transmission electron microscopy. It was found that there existed three kinds of regions: that is, C14-Laves, approximant-T, and icosahedral-quasicrystal regions, in Zn-Mg-Al alloy samples with the composition of Zn-36at.%Mg-9at.%Al. Among these regions, in particular, we tried to determine an orientation relationship between neighboring icosahedral-quasicrystal and approximant-T regions. Based on the determined relationship, for instance, four threefold rotatory-inversion axes in the T structure were found to be parallel to four of ten threefold rotatory-inversionmore » axes in the icosahedral quasicrystal. It was thus understood that the atomic arrangements of the Bergman-type icosahedral quasicrystal and its approximant-T structure are likely to resemble each other.« less

Structural analysis and antimicrobial activity of 2[1H]-pyrimidinethione/selenone derivatives

NASA Astrophysics Data System (ADS)

Żesławska, Ewa; Korona-Głowniak, Izabela; Szczesio, Małgorzata; Olczak, Andrzej; Żylewska, Alicja; Tejchman, Waldemar; Malm, Anna

2017-08-01

Four new crystal structures of sulfur and selenium analogues of 2[1H]-pyrimidinone derivatives were determined with the use of X-ray diffraction method. The molecular geometry and intermolecular interactions of the investigated molecules were analyzed in order to find the structural features and geometrical parameters, which can be responsible for antimicrobial activities. The influence of chalcogen substituents (sulfur and selenium) on the crystal packing was also studied. The main differences in the molecular structures exist in mutual arrangement of two aromatic rings. The intermolecular interactions in all investigated compounds are similar. Furthermore, the in vitro antibacterial and antifungal activities for these compounds were evaluated. Preliminary investigations have identified two highly potent antibacterial compounds containing selenium atom, which display selectivity towards staphylococci and micrococci. This selectivity was not observed for a control compound used as a drug, namely vancomycin. These compounds possess also good antifungal activity. This is the first report of biological activities of 2[1H]-pyrimidineselenone derivatives.

Protein Innovations Advance Drug Treatments, Skin Care

NASA Technical Reports Server (NTRS)

2012-01-01

Dan Carter carefully layered the sheets of tracing paper on the light box. On each sheet were renderings of the atomic components of an essential human protein, one whose structure had long been a mystery. With each layer Carter laid down, a never-before-seen image became clearer. Carter joined NASA s Marshall Space Flight Center in 1985 and began exploring processes of protein crystal growth in space. By bouncing intense X-rays off the crystals, researchers can determine the electron densities around the thousands of atoms forming the protein molecules, unveiling their atomic structures. Cultivating crystals of sufficient quality on Earth was problematic; the microgravity conditions of space were far more accommodating. At the time, only a few hundred protein structures had been mapped, and the methods were time consuming and tedious. Carter hoped his work would help reveal the structure of human serum albumin, a major protein in the human circulatory system responsible for ferrying numerous small molecules in the blood. More was at stake than scientific curiosity. Albumin has a high affinity for most of the world s pharmaceuticals, Carter explains, and its interaction with drugs can change their safety and efficacy. When a medication enters the bloodstream a cancer chemotherapy drug, for example a majority of it can bind with albumin, leaving only a small percentage active for treatment. How a drug interacts with albumin can influence considerations like the necessary effective dosage, playing a significant role in the design and application of therapeutic measures. In spite of numerous difficulties, including having no access to microgravity following the 1986 Space Shuttle Challenger disaster, the image Carter had hoped to see was finally clarifying. In 1988, his lab had acquired specialized X-ray and detection equipment a tipping point. Carter and his colleagues began to piece together albumin s portrait, the formation of its electron densities coalescing on the sheets of tracing paper he arranged on the light box. While space-grown crystals were ultimately not involved in the achievement, a year later, Carter says, we were on the cover of Science magazine, having determined the atomic structure of albumin.

Synthesis and the crystal and molecular structures of (H{sub 3}L . Cl)[CoCl{sub 4}] and H{sub 2}L[CuBr{sub 4}] (L is 2,4,6-Tri(N,N-dimethylamino)methylphenol)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kovalchukova, O. V., E-mail: okovalchukova@mail.ru; Stash, A. I.; Strashnova, S. B.

2010-05-15

The complex compounds (H{sub 3}L . Cl)[CoCl{sub 4}] (I) and H{sub 2}L[CuBr{sub 4}] (II), where L is 2,4,6-tri(N,N-dimethylamino)methylphenol, were isolated in the crystalline state and studied by X-ray diffraction. The organic cations were found to be outer-sphere ligands. All three nitrogen atoms of the tertiary amino groups are protonated. In compound I, the H{sub 3}L{sup 3+} cation exists as the cis tautomer. In compound II, the H{sub 2}L{sup 2+} dication exists as the trans isomer. In the crystal structure, the dications are arranged in layers via hydrogen bonds.

From Glass Formation to Icosahedral Ordering by Curving Three-Dimensional Space.

PubMed

Turci, Francesco; Tarjus, Gilles; Royall, C Patrick

2017-05-26

Geometric frustration describes the inability of a local molecular arrangement, such as icosahedra found in metallic glasses and in model atomic glass formers, to tile space. Local icosahedral order, however, is strongly frustrated in Euclidean space, which obscures any causal relationship with the observed dynamical slowdown. Here we relieve frustration in a model glass-forming liquid by curving three-dimensional space onto the surface of a 4-dimensional hypersphere. For sufficient curvature, frustration vanishes and the liquid "freezes" in a fully icosahedral structure via a sharp "transition." Frustration increases upon reducing the curvature, and the transition to the icosahedral state smoothens while glassy dynamics emerge. Decreasing the curvature leads to decoupling between dynamical and structural length scales and the decrease of kinetic fragility. This sheds light on the observed glass-forming behavior in Euclidean space.

Polarity-driven oxygen vacancy formation in ultrathin LaNiO 3 films on SrTiO 3

DOE PAGES

Tung, I-Cheng; Luo, Guangfu; Lee, June Hyuk; ...

2017-10-18

Oxide heterostructures offer a pathway to control emergent phases in complex oxides, but their creation often leads to boundaries that have a polar discontinuity. In order to fabricate atomic-scale arrangements of dissimilar materials, we need a clear understanding of the pathways by which materials resolve polarity issues. By examining the real-time lattice structure in-situ during growth for the case of polar LaNiO 3 synthesized on non-polar SrTiO 3 (001), we demonstrate how films in ultra-thin limit form as LaNiO 2.5 and then evolve into LaNiO 3 as the thickness increases. Theory explains how the polar energetics drives the formation ofmore » oxygen vacancies and the stability of these phases with thickness and structure.« less

Cooling rate dependence of structural order in Al90Sm10 metallic glass

NASA Astrophysics Data System (ADS)

Sun, Yang; Zhang, Yue; Zhang, Feng; Ye, Zhuo; Ding, Zejun; Wang, Cai-Zhuang; Ho, Kai-Ming

2016-07-01

The atomic structure of Al90Sm10 metallic glass is studied using molecular dynamics simulations. By performing a long sub-Tg annealing, we developed a glass model closer to the experiments than the models prepared by continuous cooling. Using the cluster alignment method, we found that "3661" cluster is the dominating short-range order in the glass samples. The connection and arrangement of "3661" clusters, which define the medium-range order in the system, are enhanced significantly in the sub-Tg annealed sample as compared with the fast cooled glass samples. Unlike some strong binary glass formers such as Cu64.5Zr35.5, the clusters representing the short-range order do not form an interconnected interpenetrating network in Al90Sm10, which has only marginal glass formability.

Multiparametric AFM reveals turgor-responsive net-like peptidoglycan architecture in live streptococci

NASA Astrophysics Data System (ADS)

Saar Dover, Ron; Bitler, Arkady; Shimoni, Eyal; Trieu-Cuot, Patrick; Shai, Yechiel

2015-05-01

Cell-wall peptidoglycan (PG) of Gram-positive bacteria is a strong and elastic multi-layer designed to resist turgor pressure and determine the cell shape and growth. Despite its crucial role, its architecture remains largely unknown. Here using high-resolution multiparametric atomic force microscopy (AFM), we studied how the structure and elasticity of PG change when subjected to increasing turgor pressure in live Group B Streptococcus. We show a new net-like arrangement of PG, which stretches and stiffens following osmotic challenge. The same structure also exists in isogenic mutants lacking surface appendages. Cell aging does not alter the elasticity of the cell wall, yet destroys the net architecture and exposes single segmented strands with the same circumferential orientation as predicted for intact glycans. Together, we show a new functional PG architecture in live Gram-positive bacteria.

Iron-Rhodium and Iron-Iridium Mixed-Metal Nitrido-Carbonyl Clusters. Synthesis, Characterization, Redox Properties, and Solid-State Structure of the Octahedral Clusters [Fe(5)RhN(CO)(15)](2)(-), [Fe(5)IrN(CO)(15)](2)(-), and [Fe(4)Rh(2)N(CO)(15)](-). Infrared and Nuclear Magnetic Resonance Spectroscopic Studies on the Interstitial Nitride.

PubMed

Della Pergola, Roberto; Cinquantini, Arnaldo; Diana, Eliano; Garlaschelli, Luigi; Laschi, Franco; Luzzini, Paola; Manassero, Mario; Repossi, Andrea; Sansoni, Mirella; Stanghellini, Pier Luigi; Zanello, Piero

1997-08-13

The cluster [Fe(5)RhN(CO)(15)](2)(-) was synthesized in 40% yield from [Fe(4)N(CO)(12)](-) and [Rh(CO)(4)](-) in refluxing tetrahydrofuran, whereas the analogous anion [Fe(5)IrN(CO)(15)](2)(-) was prepared in CH(3)CN at room temperature from [Fe(6)N(CO)(15)](3)(-) and [Ir(C(8)H(14))(2)Cl](2); the yields are higher than 60%. The monoanion [Fe(4)Rh(2)N(CO)(15)](-) was obtained in 70% yield from [Fe(5)RhN(CO)(15)](2)(-) and hydrated RhCl(3). The solid-state structures of the three anions were determined on their [PPh(4)](+) salts: the six metal atoms are arranged in octahedral cages and are coordinated to 3 edge-bridging and 12 terminal carbonyl ligands and to a &mgr;(6)-N ligand. The Rh and Ir atoms have less terminal COs than Fe, in order to equalize the excess electrons at the d(9) metal centers. The two rhodium atoms in [Fe(4)Rh(2)N(CO)(15)](-) are directly bound. The (15)N NMR spectra of the three compounds have been recorded; the signals of the nitride ligands were found at delta = 514 ppm for the dianions and 470 ppm for [Fe(4)Rh(2)N(CO)(15)](-); any group 9 atom shifts the resonance of nitrogen to higher fields. The coupling constants J((15)N-(103)Rh) are 8-9 Hz. The vibrational patterns of the metal cores have been interpreted on the basis of an idealized M(6) octahedral arrangement, subsequently modified by the perturbations given by different atomic masses and M-M stretching force constants. The motions of the nitrogen are related to the idealized symmetry of the cage; the M-N force constant values depend on the type of metal and on the charge of the anion. The dianions [Fe(5)MN(CO)(15)](2)(-) can be electrochemically oxidized at -20 degrees C to their short-lived monoanions, which can be characterized by EPR spectroscopy. In contrast, the cluster [Fe(4)Rh(2)N(CO)(15)](-) undergoes a single-step 2-electron reduction to the partially stable trianion [Fe(4)Rh(2)N(CO)(15)](3)(-), which was also characterized by EPR spectroscopy. The Fe-Rh nitride clusters are active catalysts for the hydroformylation of 1-pentene, but display low selectivity (35-65%) in n-hexanal and are demolished under catalytic conditions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Yiming; Fredrickson, Daniel C.

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternarymore » system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.« less

Phonon conductivity metrics for compact, linked-cage, layered, and filled-cage crystals, using ab initio, molecular dynamics and Boltzmann transport treatments

NASA Astrophysics Data System (ADS)

Huang, Baoling

Atomic-level thermal transport in compact, layered, linked-cage, and filled-cage crystals is investigated using a multiscale approach, combines the ab initio calculation, molecular dynamics (MD), Boltzman transport equations (BTE), and the kinetic theory. These materials are of great interests in energy storage, transport, and conversion. The structural metrics of phonon conductivity of these crystals are then explored. An atomic structure-based model is developed for the understanding the relationship between the atomic structure and phonon transport in compact crystals at high temperatures. The elemental electronegativity, element mass, and the arrangement of bonds are found to be the dominant factors to determine the phonon conductivity. As an example of linked-cage crystals, the phonon conductivity of MOF-5 is investigated over a wide temperature range using MD simulations and the Green-Kubo method. The temperature dependence of the thermal conductivity of MOF-5 is found to be weak at high temperatures, which results from the suppression of the long-range acoustic phonon transport by the special linked-cage structure. The mean free path of the majority of phonons in MOF-5 is limited by the cage size. The phonon and electron transport in layered Bi2Te3 structure are investigated using the first-principle calculations, MD, and BTE. Strong anisotropy has been found for both phonon and electron transport due to the special layered structure. The long-range acoustic phonons dominate the phonon transport with a strong temperature and direction dependence. Temperature dependence of the energy gap and appropriate modelling of relaxation times are found to be important for the prediction of the electrical transport in the intrinsic regime. The scattering by the acoustic, optical, and polar-optical phonons are found to dominate the electron transport. For filled skutterudite structure, strong coupling between the filler and the host is found, which contradicts the traditional "rattler" concept. The interatomic bonds of the host are significantly affected by the filler. It is shown that without changing the interatomic potentials for the host, the filler itself can not result in a lower phonon conductivity for the filled structure. It is also found that the behavior of partially-filled skutterudites can be better understood by treating the partially-filled structure as a solid solution of the empty structure and fully-filled structure. The combination of theoretical-analysis methods used in this work, provides for comparative insight into the role of atomic structure on the phonon transport in a variety of crystals used in energy storage, transport, and conversion.

Hydrogen bonding in water clusters and their ionized counterparts.

PubMed

Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

2010-12-30

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

{2-Hydr­oxy-3-[4-(2-methoxy­ethyl)­phen­oxy]prop­yl}isopropyl­ammonium hemisuccinate

PubMed Central

Bartolucci, Gianluca; Bruni, Bruno; Coran, Silvia A.; Di Vaira, Massimo

2009-01-01

Metoprolol, a widely used adrenoreceptor blocking drug, is commonly administered as the succinate or tartrate salt. The structure of metoprolol succinate, C15H26NO3 +·0.5C4H4O4 2−, is characterized by the presence of ribbons in which cations, generated by N-protonation of the metoprolol mol­ecules, are hydrogen bonded to succinate anions. The dicarboxylic acid transfers its H atoms to two metoprolol mol­ecules; the asymmetric unit contains one cation and half an anion, the latter possessing twofold rotational symmetry. There are localized nets of O—H⋯O and N—H⋯O hydrogen bonds along a ribbon, within centrosymmetric arrangements formed by pairs of metoprolol cations and pairs of anions, each of the latter contributing with one of its carboxyl groups to the localized net. This arrangement is repeated along the ribbon by the operation of the twofold axis bis­ecting the anion, as well as by the lattice translation. PMID:21583215

Self-rolling of an aluminosilicate sheet into a single walled imogolite nanotube: The role of the hydroxyl arrangement

DOE Office of Scientific and Technical Information (OSTI.GOV)

González, R. I.; Rogan, J.; Valdivia, J. A.

2015-12-31

Imogolite is an inorganic nanotube, that forms naturally in weathered volcanic ashes, and it can be synthesized in nearly monodisperse diameters. However, long after its successful synthesis, the details of the way it is achieved are not fully understood. Here we elaborate on a model of its synthesis, which starts with a planar aluminosilicate sheet that is allowed to evolve freely, by means of classical molecular dynamics, until it achieves its minimum energy configuration. The minimal structures that the system thus adopts are tubular, scrolled, and more complex conformations, depending mainly on temperature as a driving force. Here we focusmore » on the effect that the arrangement of the hydroxyl groups in the inner wall of the nanotube have on the minimal nanotubular configurations that we obtain are monodispersed in diameter, and quite similar to both from the those of weathered natural volcanic ashes, and to the ones that are synthesized in the laboratory. In this contribution we expand on the atomic mechanisms behind those behaviors.« less

Antiferromagnetic MnN layer on the MnGa(001) surface

NASA Astrophysics Data System (ADS)

Guerrero-Sánchez, J.; Takeuchi, Noboru

2016-12-01

Spin polarized first principles total energy calculations have been applied to study the stability and magnetic properties of the MnGa(001) surface and the formation of a topmost MnN layer with the deposit of nitrogen. Before nitrogen adsorption, surface formation energies show a stable gallium terminated ferromagnetic surface. After incorporation of nitrogen atoms, the antiferromagnetic manganese terminated surface becomes stable due to the formation of a MnN layer (Mn-N bonding at the surface). Spin density distribution shows a ferromagnetic/antiferromagnetic arrangement in the first surface layers. This thermodynamically stable structure may be exploited to growth MnGa/MnN magnetic heterostructures as well as to look for exchange biased systems.

Bis(diethylenetriamine-kappa3N)nickel(II) 5-amino-1,3,4-thiadiazole-2-sulfonamidate chloride monohydrate.

PubMed

Liu-Gonzalez, M; Sanz-Ruiz, F; Chufán, E E; Pedregosa, J C; Borras-Tortonda, J

2001-10-01

In the X-ray crystal structure of the title complex, [Ni(C(4)H(13)N(3))(2)](C(2)H(3)N(4)O(2)S(2))Cl.H(2)O, the coordination polyhedron is composed of non-centrosymmetric [Ni(diethylenetriamine)(2)](2+) cations in which the triamine ligands coordinate to the metal centre as tridentate ligands in a facial position. The Ni(II) ions are linked to six N atoms in an octahedral arrangement, slightly compressed in one extreme. The sulfonamide behaves as a counter-ion instead of as a ligand. Important information about the deprotonated sulfonamide group conformation has been obtained.

N-(2,3-Dimethyl-phen-yl)-4-hydr-oxy-2-methyl-2H-1,2-benzothia-zine-3-carboxamide 1,1-dioxide.

PubMed

Siddiqui, Waseeq Ahmad; Bukahari, Iftikhar Hussain; Zia-Ur-Rehman, Muhammad; Khan, Islam Ullah; Tizzard, Graham John

2009-02-28

In the crystal structure of the title compound, C(18)H(18)N(2)O(4)S, the thia-zine ring adopts a distorted half-chair conformation. 1,2-Benzothia-zines of this kind have a wide range of biological activities and are mainly used as medicines in the treatment of inflammation and rheumatoid arthritis. The enolic H atom is involved in an intra-molecular O-H⋯O hydrogen bond, forming a six-membered ring. The mol-ecules arrange themselves into centrosymmetric dimers by means of inter-molecular N-H⋯O hydrogen bonds. A weak inter-molcular C-H⋯O inter-action is also present.

Effect of scanning velocity on femtosecond laser-induced periodic surface structures on HgCdTe crystal

NASA Astrophysics Data System (ADS)

Gu, Hongan; Dai, Ye; Wang, Haodong; Yan, Xiaona; Ma, Guohong

2017-12-01

In this paper, a femtosecond laser line-scanning irradiation was used to induce the periodic surface microstructure on HgCdTe crystal. Low spatial frequency laser induced periodic surface structures of 650-770 nm and high spatial frequency laser induced periodic surface structures of 152-246 nm were respectively found with different scanning speeds. The evolution process from low spatial frequency laser induced periodic surface structures to high spatial frequency laser induced periodic surface structures is characterized by scanning electron microscope. Their spatial periods deduced by using a two-dimensional Fourier transformation partly agree with the predictions of the Sipe-Drude theory. Confocal micro-Raman spectral show that the atomic arrangement of induced low spatial frequency laser-induced structures are basically consistent with the crystal in the central area of laser-scanning line, however a new peak at 164 cm-1 for the CdTe-like mode becomes evident due to the Hg vaporization when strong laser ablation happens. The obtained surface periodic ripples may have applications in fabricating advanced infrared detector.

Local structural environments of Ge doped in eutectic Sb-Te film before and after crystallization

NASA Astrophysics Data System (ADS)

Shin, Sang Yeol; Cheong, Byung-ki; Choi, Yong Gyu

2018-06-01

Electrical phase change device using the Ge-doped eutectic Sb-Te (e.g., Ge1Sb8Te2) film is known to exhibit improved energy efficiency thanks to lowered threshold voltage as well as decreased power consumption for the reset operation, as compared with Ge2Sb2Te5 film. Ge K-edge EXAFS analysis is employed in this study in an effort to elucidate such merits of Ge1Sb8Te2 film in connection with its local atomic arrangements. It is then verified that a Ge atom is four-fold coordinated in its nearest-neighboring shell both in the as-deposited and in the annealed films. It needs to be highlighted that approximately two Sb atoms constitute the Ge tetrahedral units in its amorphous state; however, after being crystallized, heteropolar Ge-Sb bonds hardly exist in this Ge1Sb8Te2 film. It has been known that crystallization temperature and activation energy for crystallization of this Ge1Sb8Te2 composition are greater than those of Ge2Sb2Te5 composition. In addition, these two phase change materials exhibit distinctly different crystallization mechanisms, i.e., nucleation-dominant for Ge2Sb2Te5 film but growth-dominant for Ge1Sb8Te2 film. These discrepancies in the crystallization-related properties are delineated in terms of the local structural changes verified from the present EXAFS analysis.

Crystal structure of bis­[trans-(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4 N)bis­(thio­cyanato-κN)chromium(III)] tetra­chlorido­zincate from synchrotron data

PubMed Central

Moon, Dohyun; Ryoo, Keon Sang; Choi, Jong-Ha

2015-01-01

The structure of the title compound, [Cr(NCS)2(cyclam)]2[ZnCl4] (cyclam = 1,4,8,11-tetra­aza­cyclo­tetra­decane, C10H24N4), has been determined from synchrotron data. The asymmetric unit contains two independent halves of the CrIII complex cations and half of a tetra­chlorido­zincate anion. In each complex cation, the CrIII atom is coordinated by the four N atoms of the cyclam ligand in the equatorial plane and by two N-bound NCS− anions in a trans axial arrangement, displaying a distorted octa­hedral geometry with crystallographic inversion symmetry. The mean Cr—N(cyclam) and Cr—N(NCS) bond lengths are 2.065 (4) and 1.995 (6) Å, respectively. The macrocyclic cyclam moieties adopt centrosymmetric trans-III configurations with six- and five-membered chelate rings in chair and gauche configurations, respectively. The [ZnCl4]2− anion, which lies about a twofold rotation axis, has a slightly distorted tetra­hedral geometry. The crystal packing is stabilized by hydrogen-bonding inter­actions between the N—H groups of the cyclam ligands, the S atoms of the NCS− groups and the Cl− ligands of the anion. PMID:25995875

Crystal structure of bis­[(oxalato-κ2 O 1,O 2)(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4 N)chromium(III)] dichromate octa­hydrate from synchrotron X-ray data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2017-01-01

The asymmetric unit of the title compound, [Cr(C2O4)(C10H24N4)]2[Cr2O7]·8H2O (C10H24N4 = 1,4,8,11-tetra­aza­cyclo­tetra­decane, cyclam; C2O4 = oxalate, ox) contains one [Cr(ox)(cyclam)]+ cation, one half of a dichromate anion that lies about an inversion centre so that the bridging O atom is equally disordered over two positions, and four water mol­ecules. The terminal O atoms of the dichromate anion are also disordered over two positions with a refined occupancy ratio 0.586 (6):0.414 (6). The CrIII ion is coordinated by the four N atoms of the cyclam ligand and one bidentate oxalato ligand in a cis arrangement, resulting in a distorted octa­hedral geometry. The Cr—N(cyclam) bond lengths are in the range 2.069 (2)–2.086 (2) Å, while the average Cr—O(ox) bond length is 1.936 Å. The macrocyclic cyclam moiety adopts the cis-V conformation. The dichromate anion has a staggered conformation. The crystal structure is stabilized by inter­molecular hydrogen bonds involving the cyclam N—H groups and water O—H groups as donors, and the O atoms of oxalate ligand, water mol­ecules and the Cr2O7 2− anion as acceptors, giving rise to a three-dimensional network. PMID:28316819

Single Platinum Atoms Electrocatalysts: Oxygen Reduction and Hydrogen Oxidation Reactions

DOE PAGES

Vukmirovic, Miomir B.; Teeluck, Krishani M.; Liu, Ping; ...

2017-08-08

We prepared atomically dispersed catalyst consisting of Pt atoms arranged in a c(2 × 2) array on RuO2(110) substrate. A large interatomic distance of Pt atoms in a c(2 × 2) phase precludes the reactants to interact with more than one Pt atoms. A strong bond of Pt atoms with RuO2 prevents agglomeration of Pt atoms to form 2D-islands or 3D-clusters. The activities of single Pt atom catalyst for the oxygen reduction and hydrogen oxidation reactions were determined and compared with those of bulk Pt. It has lower catalytic activity for the oxygen reduction reaction and similar activity for hydrogenmore » oxidation reaction compared to Pt(111). This was explained by a large calculated up-shift of the dband center of Pt atoms and larger Pt-Pt interatomic distance than that of Pt(111). Our information is of considerable interest for further development of electrocatalysis.« less

A study of the native cell wall structures of the marine alga Ventricaria ventricosa (Siphonocladales, Chlorophyceae) using atomic force microscopy.

PubMed

Eslick, Enid M; Beilby, Mary J; Moon, Anthony R

2014-04-01

A substantial proportion of the architecture of the plant cell wall remains unknown with a few cell wall models being proposed. Moreover, even less is known about the green algal cell wall. Techniques that allow direct visualization of the cell wall in as near to its native state are of importance in unravelling the spatial arrangement of cell wall structures and hence in the development of cell wall models. Atomic force microscopy (AFM) was used to image the native cell wall of living cells of Ventricaria ventricosa (V. ventricosa) at high resolution under physiological conditions. The cell wall polymers were identified mainly qualitatively via their structural appearance. The cellulose microfibrils (CMFs) were easily recognizable and the imaging results indicate that the V. ventricosa cell wall has a cross-fibrillar structure throughout. We found the native wall to be abundant in matrix polysaccharides existing in different curing states. The soft phase matrix polysaccharides susceptible by the AFM scanning tip existed as a glutinous fibrillar meshwork, possibly incorporating both the pectic- and hemicellulosic-type substances. The hard phase matrix producing clearer images, revealed coiled fibrillar structures associated with CMFs, sometimes being resolved as globular structures by the AFM tip. The coiling fibrillar structures were also seen in the images of isolated cell wall fragments. The mucilaginous component of the wall was discernible from the gelatinous cell wall matrix as it formed microstructural domains over the surface. AFM has been successful in imaging the native cell wall and revealing novel findings such as the 'coiling fibrillar structures' and cell wall components which have previously not been seen, that is, the gelatinous matrix phase.

Conformational and NBO studies of serotonin as a radical scavenger. Changes induced by the OH group.

PubMed

Lobayan, Rosana M; Schmit, María Celia Pérez

2018-03-01

Serotonin (5-hydroxytryptamine, SER) is a neurotransmitter that affects many different processes within the human body. We studied the conformational space of SER, and explored in depth the significant stereoelectronic features for the structure stabilization and antioxidant activity. Forty-eight equilibrium structures were described at the B3LYP/6-311++G(d,p) level, characterizing four non-previously reported conformers. Electron distributions were analyzed by topological QTAIM (Quantum Theory of atoms in molecules) and natural bond orbital (NBO) studies. The study was supplemented by an exploration of molecular electrostatic potential (MEP). Intramolecular hydrogen interactions were also investigated; N10⋯HC4 or N10⋯HC2 hydrogen bondings were depicted in 5 conformers. The conformer stabilization and the corresponding energy arrangement were explained by hyperconjugation interactions obtained by NBO analysis. The present study is based on the effect of the 5-OH group on geometric and electronic behavior that we have previously reported on the similar structure tryptamine (TRA). Our interest also lies in SER's free radical scavenging capacity as a member of the indole family. The H-atom abstraction and single-electron transfer mechanisms were taken into account. Our results showed that donor-acceptor interactions play a major role in explaining the changes induced by the OH group, and free-radical scavenging capability of the indole compounds. Copyright © 2018 Elsevier Inc. All rights reserved.

Structural studies of a crystalline insulin analog complex with protamine by atomic force microscopy.

PubMed Central

Yip, C M; Brader, M L; Frank, B H; DeFelippis, M R; Ward, M D

2000-01-01

Crystallographic studies of insulin-protamine complexes, such as neutral protamine Hagedorn (NPH) insulin, have been hampered by high crystal solvent content, small crystal dimensions, and extensive disorder in the protamine molecules. We report herein in situ tapping mode atomic force microscopy (TMAFM) studies of crystalline neutral protamine Lys(B28)Pro(B29) (NPL), a complex of Lys(B28)Pro(B29) insulin, in which the C-terminal prolyl and lysyl residues of human insulin are inverted, and protamine that is used as an intermediate time-action therapy for treating insulin-dependent diabetes. Tapping mode AFM performed at 6 degrees C on bipyramidally tipped tetragonal rod-shaped NPL crystals revealed large micron-sized islands separated by 44-A tall steps. Lattice images obtained by in situ TMAFM phase and height imaging on these islands were consistent with the arrangement of individual insulin-protamine complexes on the P4(1)2(1)2 (110) crystal plane of NPH, based on a low-resolution x-ray diffraction structure of NPH, arguing that the NPH and NPL insulins are isostructural. Superposition of the height and phase images indicated that tip-sample adhesion was larger in the interstices between NPL complexes in the (110) crystal plane than over the individual complexes. These results demonstrate the utility of low-temperature TMAFM height and phase imaging for the structural characterization of biomolecular complexes. PMID:10620310

An XAS experimental approach to study low Pt content electrocatalysts operating in PEM fuel cells.

PubMed

Principi, Emiliano; Witkowska, Agnieszka; Dsoke, Sonia; Marassi, Roberto; Di Cicco, Andrea

2009-11-21

We present an X-ray absorption spectroscopy (XAS) study of a low Pt content catalyst layer (Pt loading 0.1 mg cm(-2)) operating at the cathode of a proton exchange membrane fuel cell (PEMFC). This catalyst is based on the use of a mesoporous inorganic matrix as a support for the catalyst Pt nanoparticles. Due to the high Pt dilution, in situ measurements of its structural properties by XAS are challenging and suitable experimental strategies must be devised for this purpose. In particular, we show that accurate XAS in situ fluorescence measurements can be obtained using an optimized fuel cell, suitable protocols for alignment of a focused X-ray beam and an appropriate filter for the background signal of the other atomic species contained in the electrodes. Details, advantages and limitations of the XAS technique for in situ measurements are discussed. Analysis of the near-edge XAS and EXAFS (extended X-ray absorption fine structure) data, corroborated by a HRTEM (high-resolution transmission electron microscopy) study, shows that the Pt particles have a local structure compatible with that of bulk Pt (fcc) and coordination numbers match those expected for particles with typical sizes in the 1.5-2.0 nm range. Substantial changes in the oxidation state and in local atomic arrangement of the Pt particles are found for different applied potentials. The catalyst support, containing W atoms, exhibits a partial reduction upon PEMFC activation, thus mimicking the catalyst behavior. This indicates a possible role of the mesoporous matrix in favouring the oxygen reduction reaction (ORR) and stimulates further research on active catalyst supports.

The solely motif-doped Au36-xAgx(SPh-tBu)24 (x = 1-8) nanoclusters: X-ray crystal structure and optical properties.

PubMed

Fan, Jiqiang; Song, Yongbo; Chai, Jinsong; Yang, Sha; Chen, Tao; Rao, Bo; Yu, Haizhu; Zhu, Manzhou

2016-08-18

We report the observation of new doping behavior in Au36-xAgx(SR)24 nanoclusters (NCs) with x = 1 to 8. The atomic arrangements of Au and Ag atoms are determined by X-ray crystallography. The new gold-silver bimetallic NCs share the same framework as that of the homogold counterpart, i.e. possessing an fcc-type Au28 kernel, four dimeric AuAg(SR)3 staple motifs and twelve simple bridging SR ligands. Interestingly, all the Ag dopants in the Au36-xAgx(SR)24 NCs are selectively incorporated into the surface motifs, which is in contrast to the previously reported Au-Ag alloy structures with the Ag dopants preferentially displacing the core gold atoms. This distinct doping behavior implies that the previous assignments of an fcc Au28 core with four dimers and 12 bridging thiolates for Au36(SR)24 are more justified than other assignments of core vs. surface motifs. The UV-Vis adsorption spectrum of Au36-xAgx(SR)24 is almost the same as that of Au36(SR)24, indicating that the Ag dopants in the motifs do not change the optical properties. The similar UV-Vis spectra are further confirmed by TD-DFT calculations. DFT also reveals that the energies of the HOMO and LUMO of the motif-doped AuAg alloy NC are comparable to those of the homogold Au36 NC, indicating that the electronic structure is not disturbed by the motif Ag dopants. Overall, this study reveals a new silver-doping mode in alloy NCs.

Structure analysis of Si(111)-7 × 7 reconstructed surface by transmission electron diffraction

NASA Astrophysics Data System (ADS)

Takayanagi, Kunio; Tanishiro, Yasumasa; Takahashi, Shigeki; Takahashi, Masaetsu

1985-12-01

The atomic structure of the 7 × 7 reconstructed Si(111) surface has been analysed by ultra-high vacuum (UHV) transmission electron diffraction (TED). A possible projected structure of the surface is deduced from the intensity distribution in TED patterns of normal electron incidence and from Patterson and Fourier syntheses of the intensities. A new three-dimensional structure model, the DAS model, is proposed: The model consists of 12 adatoms arranged locally in the 2 × 2 structure, a stacking fault layer and a layer with a vacancy at the corner and 9 dimers on the sides of each of the two triangular subcells of the 7 × 7 unit cell. The silicon layers in one subcell are stacked with the normal sequence, CcAaB + adatoms, while those in the other subcell are stacked with a faulted sequence, CcAa/C + adatoms. The model has only 19 dangling bonds, the smallest number among models so far proposed. Previously proposed models are tested quantitatively by the TED intensity. Advantages and limits of the TED analysis are discussed.

Superoxide reductase from the syphilis spirochete Treponema pallidum: crystallization and structure determination using soft X-rays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santos-Silva, Teresa; Trincão, José; Carvalho, Ana L.

2005-11-01

Superoxide reductase is a non-haem iron-containing protein involved in resistance to oxidative stress. The oxidized form of the protein has been crystallized and its three-dimensional structure solved. A highly redundant X-ray diffraction data set was collected on a rotating-anode generator using Cu Kα X-ray radiation. Four Fe atoms were located in the asymmetric unit corresponding to four protein molecules arranged as a dimer of homodimers. Superoxide reductase is a 14 kDa metalloprotein containing a catalytic non-haem iron centre [Fe(His){sub 4}Cys]. It is involved in defence mechanisms against oxygen toxicity, scavenging superoxide radicals from the cell. The oxidized form of Treponemamore » pallidum superoxide reductase was crystallized in the presence of polyethylene glycol and magnesium chloride. Two crystal forms were obtained depending on the oxidizing agents used after purification: crystals grown in the presence of K{sub 3}Fe(CN){sub 6} belonged to space group P2{sub 1} (unit-cell parameters a = 60.3, b = 59.9, c = 64.8 Å, β = 106.9°) and diffracted beyond 1.60 Å resolution, while crystals grown in the presence of Na{sub 2}IrCl{sub 6} belonged to space group C2 (a = 119.4, b = 60.1, c = 65.6 Å, β = 104.9°) and diffracted beyond 1.55 Å. A highly redundant X-ray diffraction data set from the C2 crystal form collected on a copper rotating-anode generator (λ = 1.542 Å) clearly defined the positions of the four Fe atoms present in the asymmetric unit by SAD methods. A MAD experiment at the iron absorption edge confirmed the positions of the previously determined iron sites and provided better phases for model building and refinement. Molecular replacement using the P2{sub 1} data set was successful using a preliminary trace as a search model. A similar arrangement of the four protein molecules could be observed.« less

Science Using an Electrostatic Levitation Furnace in the MUCAT Sector at the APS

NASA Technical Reports Server (NTRS)

Goldman, A.; Kelton, K. F.; Rogers, J. R.

2004-01-01

The original motivation for the construction of the BESL prototype was to obtain the first proof of a 50-year-old hypothesis regarding the solidification of liquid metals. Since the 1950s it has been known that under proper conditions liquid metals can be cooled below their melting temperature (undercooled) without crystallizing to the stable solid phase. In 1952 Frank proposed that this was because the atoms in the metallic liquid were arranged with the symmetry of an icosahedron, a Platonic solid consisting of 20 tetrahedra (4-sided pyramid-shaped polyhedra) arranged around a common center. Since this local atomic order is incompatible with the long-range translational periodicity of crystal phases, a barrier is formed to the formation of small regions of the crystal phase, the nucleation barrier. A proof of Frank's hypothesis required a direct correlation between measured icosahedral order in the undercooled liquid and the nucleation barrier. The tendency of sample containers to catalyze nucleation obscured this relation, requiring containerless techniques. Combining containerless processing techniques for electrostatically levitated droplets (ESL) with x-ray synchrotron methods, a team from Washington University, St. Louis, MO, NASA Marshall Space Flight Center, and MUCAT at the APS demonstrated an increasing icosahedral order in TiZrNi liquids with decreasing temperature below the melting temperature. The increased icosahedral order caused the transformation of the liquid to a metastable icosahedral quasicrystal phase, instead of the stable tetrahedrally-coordinated crystal intermetallic, giving the first clear demonstration of the connection between the nucleation barrier and the local structure of the liquid, verifying Frank's hypothesis for this alloy.

Zinc(II) complexes with potent cyclin-dependent kinase inhibitors derived from 6-benzylaminopurine: synthesis, characterization, X-ray structures and biological activity.

PubMed

Trávnícek, Zdenek; Krystof, Vladimír; Sipl, Michal

2006-02-01

The synthesis, characterization and biological activity of the first zinc(II) complexes with potent inhibitors of cyclin-dependent kinases (CDKs) derived from 6-benzylaminopurine are described. Based on the results following from elemental analyses, infrared, NMR and ES+MS (electrospray mass spectra in the positive ion mode) spectroscopies, conductivity data, thermal analysis and X-ray structures, the tetrahedral Zn(II) complexes of the compositions [Zn(Olo)Cl(2)](n) (1), [Zn(iprOlo)Cl(2)](n) (2), [Zn(BohH(+))Cl(3)] x H(2)O (3) and [Zn(iprOloH(+))Cl(3)] x H(2)O (4) have been prepared, where Olo=2-(2-hydroxyethylamino)-6-benzylamino-9-methylpurine (Olomoucine), iprOlo=2-(2-hydroxyethylamino)-6-benzylamino-9-isopropylpurine (i-propyl-Olomoucine), Boh=2-(3-hydroxypropylamino)-6-benzylamino-9-isopropylpurine (Bohemine). The 1D-polymeric chain structure for [Zn(Olo)Cl(2)](n) (1) as well as the monomeric one for [Zn(BohH(+))Cl(3)] x H(2)O (3) and [Zn(iprOloH(+))Cl(3)] x H(2)O (4) have been revealed unambiguously by single crystal X-ray analyses. The 1D-polymeric chain of 1 consists of Zn(Olo)Cl(2) monomeric units in which the Zn(II) ion is coordinated by two chlorine atoms and one oxygen atom of the 2-hydroxyethylamino group of Olomoucine. The next monomeric unit is bonded to Zn(II) through the N7 atom of a purine ring. Thus, each of Zn(II) ions is tetrahedrally coordinated and a ZnCl(2)NO chromophore occurs in the complex 1. The complexes 3 and 4 are mononuclear species with a distorted tetrahedral arrangement of donor atoms around the Zn(II) ion with a ZnCl(3)N chromophore. The corresponding CDK inhibitor, i.e., both Boh and iprOlo, is coordinated to Zn(II) via the N7 atom of the purine ring in 3 and 4. The cytotoxicity of the zinc(II) complexes against human melanoma, sarcoma, leukaemia and carcinoma cell lines has been determined as well as the inhibition of the CDK2/cyclin E kinase. A relationship between the structure and biological activity of the complexes is also discussed.

Phase transformation of Ca{sub 4}[Al{sub 6}O{sub 12}]SO{sub 4} and its disordered crystal structure at 1073 K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurokawa, Daisuke; R and D Center, Taiheiyo Cement Corporation, Chiba 285-8655; Takeda, Seiya

The phase transformation of Ca{sub 4}[Al{sub 6}O{sub 12}]SO{sub 4} and the crystal structure of its high-temperature phase were investigated by differential thermal analysis, temperature-dependent Raman spectroscopy and high-temperature X-ray powder diffraction (CuKα{sub 1}). We determined the starting temperature of the orthorhombic-to-cubic transformation during heating (=711 K) and that of the reverse transformation during cooling (=742 K). The thermal hysteresis was negative (=−31 K), suggesting the thermoelasticity of the transformation. The space group of the high temperature phase is I4{sup ¯}3m with the unit-cell dimensions of a=0.92426(2) nm and V=0.78955(2) nm{sup 3} (Z=2) at 1073 K. The initial structural model wasmore » derived by the direct methods and further refined by the Rietveld method. The final structural model showed the orientational disordering of SO{sub 4} tetrahedra. The maximum-entropy method-based pattern fitting method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. At around the transformation temperature during heating, the vibrational spectra, corresponding to the Raman-active SO{sub 4} internal stretching mode, showed the continuous and gradual change in the slope of full width at half maximum versus temperature curve. This strongly suggests that the orthorhombic-to-cubic phase transformation would be principally accompanied by the statistical disordering in orientation of the SO{sub 4} tetrahedra, without distinct dynamical reorientation. - Graphical abstract: (Left) Three-dimensional electron-density distributions of the SO{sub 4} tetrahedron with the split-atom model, and (right) a bird's eye view of electron densities on the plane parallel to (111). - Highlights: • Crystal structure of Ca{sub 4}[Al{sub 6}O{sub 12}]SO{sub 4} at 1073 K is determined by powder XRD. • The atom arrangements are represented by the split-atom model. • The MPF method is used to confirm the validity of the model. • The phase transition is accompanied by orientational disordering of SO{sub 4} tetrahedra.« less

A new nonlinear optical silicate carbonate K2Ca[Si2O5](CO3) with a hybrid structure of kalsilite and soda-like layered fragments

NASA Astrophysics Data System (ADS)

Belokoneva, Elena L.; Stefanovich, Sergey Yu.; Volkov, Anatoly S.; Dimitrova, Olga V.

2016-10-01

Single crystals of a new silicate carbonate, K2Ca[Si2O5](CO3), have been synthesized in a multi-components hydrothermal solution with a pH value close to neutral and a high concentration of a carbonate mineralizer. The new compound has an axial structure (s.g. P6322) with unit cell parameters a = 5.04789 (15), c = 17.8668 (6) Å. Pseudosymmetry of the structure corresponds to s.g. P63/mmc which is broken only by one oxygen position. The structure consists of two layered fragments: one of the type of the mineral kalsilite (KAlSiO4) and the other of the high-temperature soda-like α-Na2CO3, Ca substituting for Na. The electro-neutral layer K2[Si2O5] (denoted K) as well as the layer Ca(CO3) (denoted S) may separately correspond to individual structures. In K2Ca[Si2O5](CO3) the S-K layers are connected together via Ca-O interactions between Ca atoms from the carbonate layer and apical O atoms from the silicate one, and also via K-O interlayer interactions. A hypothetical acentric structure, sp.gr. P-62c, is predicted on the basis of the order-disorder theory. It presents another symmetrical option for the arrangement of K-layers relative to S-layers. The K,Ca-silicate-carbonate powder produces a moderate SHG signal that is two times larger that of the α-quartz powder standard and close to other silicates with acentric structures and low electronic polarizability.

Cooling rate dependence of structural order in Al 90Sm 10 metallic glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Yang; Zhang, Yue; Zhang, Feng

2016-07-07

Here, the atomic structure of Al 90Sm 10 metallic glass is studied using molecular dynamics simulations. By performing a long sub-T g annealing, we developed a glass model closer to the experiments than the models prepared by continuous cooling. Using the cluster alignment method, we found that “3661” cluster is the dominating short-range order in the glass samples. The connection and arrangement of “3661” clusters, which define the medium-range order in the system, are enhanced significantly in the sub-T g annealed sample as compared with the fast cooled glass samples. Unlike some strong binary glass formers such as Cu 64.5Zrmore » 35.5, the clusters representing the short-range order do not form an interconnected interpenetrating network in Al 90Sm 10, which has only marginal glass formability.« less

Cooling rate dependence of structural order in Al{sub 90}Sm{sub 10} metallic glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Yang; Ames Laboratory, US Department of Energy, Ames, Iowa 50011; Zhang, Yue

2016-07-07

The atomic structure of Al{sub 90}Sm{sub 10} metallic glass is studied using molecular dynamics simulations. By performing a long sub-T{sub g} annealing, we developed a glass model closer to the experiments than the models prepared by continuous cooling. Using the cluster alignment method, we found that “3661” cluster is the dominating short-range order in the glass samples. The connection and arrangement of “3661” clusters, which define the medium-range order in the system, are enhanced significantly in the sub-T{sub g} annealed sample as compared with the fast cooled glass samples. Unlike some strong binary glass formers such as Cu{sub 64.5}Zr{sub 35.5},more » the clusters representing the short-range order do not form an interconnected interpenetrating network in Al{sub 90}Sm{sub 10,} which has only marginal glass formability.« less

Trithiocyanurate complexes of iron, manganese and nickel and their anticholinesterase activity.

PubMed

Kopel, Pavel; Dolezal, Karel; Langer, Vratislav; Jun, Daniel; Adam, Vojtech; Kuca, Kamil; Kizek, Rene

2014-04-08

The complexes of Fe(II), Mn(II) and Ni(II) with a combination of a Schiff base, nitrogen-donor ligand or macrocyclic ligand and trithiocyanuric acid (ttcH3) were prepared and characterized by elemental analysis and spectroscopies. Crystal and molecular structures of the iron complex of composition [Fe(L1)](ttcH2)(ClO4)·EtOH·H2O (1), where L1 is Schiff base derived from tris(2-aminoethyl)amine and 2-pyridinecarboxaldehyde, were solved. It was found that the Schiff base is coordinated to the central iron atom by six nitrogens forming deformed octahedral arrangement, whereas trithiocyanurate(1-) anion, perchlorate and solvent molecules are not coordinated. The X-ray structure of the Schiff base sodium salt is also presented and compared with the iron complex. The anticholinesterase activity of the complexes was also studied.