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Sample records for 1d chain structure

  1. Magnetic properties driven by local structure in quasi-1D Ising chain system cobaltate system

    NASA Astrophysics Data System (ADS)

    Kim, Bongjae; Kim, Beom Hyun; Kim, Kyoo; Choi, Hong Chul; Park, Sang-Yeon; Jeong, Y.-H.; Min, B. I.

    2012-02-01

    Using ab-initio band structure method and the microscopic model calculation, the origins of the large orbital magnetic moment and unique magnetic anisotropy in the quasi-1D magnetic cobaltate, α-CoV2O6, is investigated. Unique crystal electric field effect in α-CoV2O6 is combined with the strong spin-orbit coupling, results in intriguing magnetic properties of the system. Based on the estimated strengths of the intra- and the inter-chain exchange interaction, experimentally found 1/3 magnetization plateau in the MH curve can be attributed to spin-flop mechanism. Origin of the reduced magnetic entropy behavior is found to be the strong uniaxial magnetic anisotropy in the quasi-1D Ising chain system.

  2. Structural variation from heterometallic cluster-based 1D chain to heterometallic tetranuclear cluster: Syntheses, structures and magnetic properties

    SciTech Connect

    Zhang, Shu-Hua; Zhao, Ru-Xia; Li, He-Ping; Ge, Cheng-Min; Li, Gui; Huang, Qiu-Ping; Zou, Hua-Hong

    2014-08-15

    Using the solvothermal method, we present the comparative preparation of ([Co{sub 3}Na(dmaep){sub 3}(ehbd)(N{sub 3}){sub 3}]·DMF){sub n} (1) and [Co{sub 2}Na{sub 2}(hmbd){sub 4}(N{sub 3}){sub 2}(DMF){sub 2}] (2), where Hehbd is 3-ethoxy-2-hydroxy-benzaldehyde, Hhmbd is 3-methoxy-2-hydroxy-benzaldehyde, and Hdmaep is 2-dimethylaminomethyl-6-ethoxy-phenol, which was synthesized by an in-situ reaction. Complexes 1 and 2 were characterized by elemental analysis, IR spectroscopy, and X-ray single-crystal diffraction. Complex 1 is a novel heterometallic cluster-based 1-D chain and 2 is a heterometallic tetranuclear cluster. The (Co{sub 3}{sup II}Na) and (Co{sub 2}{sup II}Na{sub 2}) cores display dominant ferromagnetic interaction from the nature of the binding modes through μ{sub 1,1,1}-N{sub 3}{sup –} (end-on, EO). - Graphical abstract: Two novel cobalt complexes have been prepared. Compound 1 consists of tetranuclear (Co{sub 3}{sup II}Na) units, which further formed a 1-D chain. Compound 2 is heterometallic tetranuclear cluster. Two complexes display dominant ferromagnetic interaction. - Highlights: • Two new heterometallic complexes have been synthesized by solvothermal method. • The stereospecific blockade of the ligands in the synthesis system seems to be the most important synthetic parameter. • The magnetism studies show that 1 and 2 exhibit ferromagnetic interactions. • Complex 1 shows slowing down of magnetization and not blocking of magnetization.

  3. Crystal structures of bovine CD1d reveal altered αGalCer presentation and a restricted A' pocket unable to bind long-chain glycolipids.

    PubMed

    Wang, Jing; Guillaume, Joren; Pauwels, Nora; Van Calenbergh, Serge; Van Rhijn, Ildiko; Zajonc, Dirk M

    2012-01-01

    NKT cells play important roles in immune surveillance. They rapidly respond to pathogens by detecting microbial glycolipids when presented by the non-classical MHC I homolog CD1d. Previously, ruminants were considered to lack NKT cells due to the lack of a functional CD1D gene. However, recent data suggest that cattle express CD1d with unknown function. In an attempt to characterize the function of bovine CD1d, we assessed the lipid binding properties of recombinant Bos taurus CD1d (boCD1d) in vitro. BoCD1d is able to bind glycosphingolipids (GSLs) with fatty acid chain lengths of C₁₈, while GSLs with fatty acids of C₂₄ do not bind. Crystal structures of boCD1d bound to a short-chain C₁₂-di-sulfatide antigen, as well as short-chain C₁₆-αGalCer revealed that the Á pocket of boCD1d is restricted in size compared to that of both mouse and human CD1d, explaining the inability of long chain GSL's to bind to boCD1d. Moreover, while di-sulfatide is presented similarly compared to the presentation of sulfatide by mouse CD1d, αGalCer is presented differently at the cell surface, due to an amino acid Asp151Asn substitution that results in loss of intimate contacts between the αGalCer headgroup and CD1d. The altered αGalCer presentation by boCD1d also explains its lack of cross-activation of mouse iNKT cells and raises the interesting question of the nature and function of bovine lipid-reactive T cells.

  4. Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A’ Pocket Unable to Bind Long-Chain Glycolipids

    PubMed Central

    Wang, Jing; Guillaume, Joren; Pauwels, Nora; Van Calenbergh, Serge; Van Rhijn, Ildiko; Zajonc, Dirk M.

    2012-01-01

    NKT cells play important roles in immune surveillance. They rapidly respond to pathogens by detecting microbial glycolipids when presented by the non-classical MHC I homolog CD1d. Previously, ruminants were considered to lack NKT cells due to the lack of a functional CD1D gene. However, recent data suggest that cattle express CD1d with unknown function. In an attempt to characterize the function of bovine CD1d, we assessed the lipid binding properties of recombinant Bos taurus CD1d (boCD1d) in vitro. BoCD1d is able to bind glycosphingolipids (GSLs) with fatty acid chain lengths of C18, while GSLs with fatty acids of C24 do not bind. Crystal structures of boCD1d bound to a short-chain C12-di-sulfatide antigen, as well as short-chain C16-αGalCer revealed that the Á pocket of boCD1d is restricted in size compared to that of both mouse and human CD1d, explaining the inability of long chain GSL’s to bind to boCD1d. Moreover, while di-sulfatide is presented similarly compared to the presentation of sulfatide by mouse CD1d, αGalCer is presented differently at the cell surface, due to an amino acid Asp151Asn substitution that results in loss of intimate contacts between the αGalCer headgroup and CD1d. The altered αGalCer presentation by boCD1d also explains its lack of cross-activation of mouse iNKT cells and raises the interesting question of the nature and function of bovine lipid-reactive T cells. PMID:23110152

  5. Heat Capacity of 1D Molecular Chains

    NASA Astrophysics Data System (ADS)

    Bagatskii, M. I.; Barabashko, M. S.; Sumarokov, V. V.; Jeżowski, A.; Stachowiak, P.

    2017-04-01

    The heat capacity of 1D chains of nitrogen and methane molecules (adsorbed in the outer grooves of bundles of closed-cap single-walled carbon nanotubes) has been studied in the temperature ranges 2-40 and 2-60 K, respectively. The temperature dependence of the heat capacity of 1D chains of nitrogen molecules below 3 K is close to a linear. It was found that the rotational heat capacity of methane molecules is a significant part of the total heat capacity of the chains throughout the whole investigated temperature range, whereas in the case of nitrogen, the librations are significant only above 15 K. The dependence of the heat capacity for methane below 10 K indicates the presence of a Schottky anomaly caused by the tunneling between the lowest energy levels of the CH4 molecule rotational spectra. Characteristic features observed in the temperature dependence of the heat capacity of 1D methane crystals are also discussed.

  6. Structural and Magnetic Behavior of a Quasi-1D Antiferromagnetic Chain Compound Cu(NCS)(2)(PYZ)

    SciTech Connect

    Bordallo, H. N.; Chapon, L. C.; Manson, Jamie L; Qualls, J. S.; Hall, D.; Argyriou, D. N.

    2003-01-01

    Synchrotron X-ray diffraction (XRD) and neutron powder diffraction (NPD) were used to determine the structure of Cu(NCS){sub 2}(pyz) (pyz=pyrazine=C{sub 4}N{sub 2}H{sub 4}), which consists of a stacking of Cu-pyz-Cu chains. While NPD measurements showed no evidence of long-range magnetic ordering, the temperature dependence of the magnetic susceptibility and magnetization suggests that the system can be adequately described on the local scale as a spin-1/2 antiferromagnet (AFM) chain with an intrachain exchange interaction J/k{sub B} = -8 K ({approx}0.7 meV). Comparison of isothermal magnetization data acquired up to 30 T at 1.6 K to a linear chain model shows excellent agreement, making this material a nearly ideal example of an isotropic Heisenberg AFM chain.

  7. Two novel 1-D helical chains Zn(II)/Cd(II) polymers based on tetrazolate-1-acetic acid: Crystal structures, solid state fluorescence and thermal behaviors

    NASA Astrophysics Data System (ADS)

    Lu, Ying-Bing; Jin, Shuang; Jian, Fang-Mei; Xie, Yong-Rong; Luo, Guo-Tian

    2014-03-01

    Two new d10 metal complexes with tetrazolate-1-acetic acid, [Zn(1-tza)(Cl)(H2O)] (1) and [Cd(1-tza)(phen)(NO3)] (2) (1-Htza = tetrazole-1-acetic acid, phen = 1,10-phenanthroline), have been prepared, and their structures have been characterized by single-crystal X-ray diffraction. The flexibilities of 1-tza ligands result in 1-D helical chained structures of the two obtained complexes, in which the 1-tza ligands adopt different coordination mode: 1 with μ2-kO1: kN4 and 2 with μ2-kO1, O2: kN3. Compounds 1 exhibits a nonracemic enantiopure topology while compound 2 reveals to be mesomeric structures. The crystal packing in 1 and 2 is controlled mainly by hydrogen bonds and face-to-face π-π stacking interactions, respectively. Photoluminescence studies show that 1 and 2 exhibit strong luminescence. Moreover, compound 1 exhibits a second-order nonlinear optical coefficient equal to that of potassium dihydrogen phosphate (KDP). The thermal stability of the two complexes has also been investigated.

  8. The molecular spin filter constructed from 1D organic chain

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Xu, Ning; Wang, Baolin; Bian, Baoan

    2014-06-01

    We proposed a molecular spin filter, which is constructed from the 1D metallic organic chain (Fen+1(C6H4)n). The spin-polarized transport properties of the molecular spin filter are explored by combining density functional theory with nonequilibrium Green's function formalism. Theoretical results reveal that Fen+1(C6H4)n molecular chain exhibits robust spin filtering effect, and only the spin-down electrons can transmit through the molecular chain. At the given bias voltage window [-1 eV,1 eV], the calculated spin filter efficiency is close to 100% in the case of n≥3. We find that the effect of spin polarization origin from both Fen+1 and (C6H4)n. In addition, negative difference resistance behavior appears in Fen+1(C6H4)n molecular chain. The results can help us understand the spin transport properties of organic molecular chain.

  9. Three new 2-D metal-organic frameworks containing 1-D metal chains bridged by N-benzesulfonyl-glutamic acid: Syntheses, crystal structures and properties

    NASA Astrophysics Data System (ADS)

    Ma, Lu-Fang; Huo, Xian-Kuan; Wang, Li-Ya; Wang, Jian-Ge; Fan, Yao-Ting

    2007-05-01

    To explore the possibility of obtaining the metal-organic frameworks (MOFs) bearing the bsgluH 2 ligand, two new Cd(II) and one Cu(II) coordination polymers, [Cd(bsglu)(bipy)] n ( 1), [Cd(bsglu)·(H 2O)] n ( 2) and {[Cu 2(bsglu) 2(bipy) 2]·4H 2O} n ( 3) (bsglu= N-benzesulfonyl-glutamic acid bianion, bipy=2,2'-bipyridine) were synthesized and characterized by IR, elemental analysis and X-ray diffraction analysis. Compounds 1 and 3 exhibit one-dimensional coordination chains, which are further connected to form two-dimensional supramolecular networks through π-π aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. To the best of our knowledge, 2 is the first two-dimensional complex formed from transition metal and bsgluH 2 ligand. Interestingly, the bsglu anion exhibits remarkable versatile coordination modes in these complexes. Fluorescent analyses show that 1 exhibits photoluminescence in the solid state. Magnetic measurements for 3 revealed that the Cu(II) chain exhibit a weak antiferromagnetic behavior with a J value of -0.606 cm -1.

  10. Structural Modulation from 1D Chain to 3D Framework: Improved Thermostability, Insensitivity, and Energies of Two Nitrogen-Rich Energetic Coordination Polymers.

    PubMed

    Guo, Zhaoqi; Wu, Yunlong; Deng, Chongqing; Yang, Guoping; Zhang, Jiangong; Sun, Zhihua; Ma, Haixia; Gao, Chao; An, Zhongwei

    2016-11-07

    Two new energetic coordination polymers (CPs) [Pb(BT)(H2O)3]n (1) and [Pb3(DOBT)3(H2O)2]n·(4H2O)n (2) with 1D and 3D structures were synthesized by employing two rational designed ligands, 1H,1'H-5,5'-bitetrazole (H2BT) and 1H,1'H-[5,5'-bitetrazole]-1,1'-diol ligands (DHBT), respectively. Thermal analyses and sensitivity tests show that the 3D architecture reinforces the network of 2 which has higher thermal stability and lower sensitivity than that of 1. Through oxygen-bomb combustion calorimetry the molar enthalpy of formation of 2 is derived to be much higher than that of 1 as well as the reported CPs. Herein, more importantly, the heats of detonation (ΔHdet) were calculated according to the decomposition products of TG-DSC-MS-FTIR simultaneous analyses for the first time. The calculated results show that ΔHdet of 2 is 23% higher than that of 1. This research demonstrates that 3D energetic CP with outstanding energetic properties can be obtained through efficient and reasonable design.

  11. The synthesis and structure of a chiral 1D aluminophosphate chain compound: d-Co(en) 3[AlP 2O 8]·6.5H 2O

    NASA Astrophysics Data System (ADS)

    Chen, Peng; Li, Jiyang; Yu, Jihong; Wang, Yu; Pan, Qinhe; Xu, Ruren

    2005-06-01

    A new chiral one-dimensional (1D) aluminophosphate chain compound [ d-Co(en) 3][AlP 2O 8]·6.5H 2O (designated AlPO-CJ22) has been hydrothermally synthesized by using the optically pure d-Co(en) 3I 3 complex as the template. Single-crystal structural analysis reveals that its structure is built up from alternating connection of AlO 4 and PO 2(=O 2) tetrahedra to form corner-shared Al 2P 2 four-membered ring (4-MR) chains. The d-Co(en) 33+ complex cations extended along the 2 1 screw axis interact with the inorganic chains through hydrogen-bonds of N⋯O atoms in a helical fashion. Optical rotation measurement shows that AlPO-CJ22 is chiral as with d-Co(en) 33+ complex cations. Crystal data: orthorhombic, I2 12 12 1, a=8.5573(8) Å, b=22.613(2) Å, c=22.605(2) Å, Z=8, R1=0.067, wR2=0.1291, and Flack parameter: -0.02(3). CCDC number: 254179.

  12. Self-assembled 1D magnetic Ising chains: epitaxial islands of Co/Ru(0001)

    NASA Astrophysics Data System (ADS)

    Li, Dongqi; Yu, Chengtao; Pearson, John; Bader, Samuel

    2002-03-01

    We have self-assembled magnetic Co dot chains via epitaxial island decoration of grooved Ru(0001) to create a model 1D system. Co wedge-like structures of 0-60 nm thick were deposited onto flat and grooved Ru(0001) substrates via molecular beam epitaxy at 350¢ªC and characterized ex-situ with atomic force and the magnetic force microscopy (MFM), and magneto-optic Kerr effect. The grooved substrate has a saw-tooth profile with spacing of order of 1 um, due to residual polishing scratches / step bunching. Co forms strain-induced, quasi-hexagonal dots of 70-500 nm in diameter and 1-20 nm high, depending on nominal dosage. On grooved substrate, the dots self align into chains along the groove near the top and bottom of the saw-tooth structure.[1] The dots are ferromagnetically coupled along the chain and exhibit magnetic single-domains with in-plane uniaxial anisotropy along the grooves. The inter-dot magnetic pair correlation was deduced from the MFM images of the dot-chains, and can be understood in terms of the classic 1D Ising model. * Work supported by DOE BES-MS under #W-31-109-ENG-38. 1. Chengtao Yu, Dongqi Li, J. Pearson, and S.D. Bader, Appl. Phys. Lett. 78, 1228 (2001); ibid. 79, 3848 (2001).

  13. Formation of Water Chains on CaO(001): What Drives the 1D Growth?

    PubMed

    Zhao, Xunhua; Shao, Xiang; Fujimori, Yuichi; Bhattacharya, Saswata; Ghiringhelli, Luca M; Freund, Hans-Joachim; Sterrer, Martin; Nilius, Niklas; Levchenko, Sergey V

    2015-04-02

    Formation of partly dissociated water chains is observed on CaO(001) films upon water exposure at 300 K. While morphology and orientation of the 1D assemblies are revealed from scanning tunneling microscopy, their atomic structure is identified with infrared absorption spectroscopy combined with density functional theory calculations. The latter exploit an ab initio genetic algorithm linked to atomistic thermodynamics to determine low-energy H2O configurations on the oxide surface. The development of 1D structures on the C4v symmetric CaO(001) is triggered by symmetry-broken water tetramers and a favorable balance between adsorbate-adsorbate versus adsorbate-surface interactions at the constraint of the CaO lattice parameter.

  14. Nanojet-induced modes in 1D chains of microspheres

    NASA Astrophysics Data System (ADS)

    Kapitonov, A. M.; Astratov, V. N.

    2007-02-01

    We report on the light transport phenomena in linear chains composed of several tens of touching spherical microcavities. A new optical mode type, namely nanojet-induced modes (NIMs) is observed. These modes result from the optical coupling of microspheres acting as a series of micro-lenses, which periodically focus propagating wave into photonic nanojets. Theoretically, formation of periodic nanojets has been predicted in Z. Chen et al., Opt. Lett. 31, 389 (2006). The chains were produced by means of the self-assembly directed by micro-flows of water suspension of polystyrene microspheres. The mean size of spheres was varied in the 2-10 micron range. To couple light to NIMs we used built-in emission sources formed by several locally excited dye-doped microcavities from the same chain. Conversion of modes emitted by the light source into the NIMs results in losses of several dB per sphere in the vicinity (first few tens of spheres) of such sources. At longer distances we found an attenuation rate as small as 0.5 dB per sphere that reveals low intrinsic propagation loss for NIMs. The NIMs have potential applications for coupling and guiding of light in compact arrays of spherical cavities with extremely high quality (Q) whispering gallery modes.

  15. 1D cerium(III) coordination polymer with pivalate bridges: Synthesis, structure and magnetic properties

    NASA Astrophysics Data System (ADS)

    Akhtar, Muhammad Nadeem; Mateen, Muhammad; Sadakiyo, Masaaki; Warsi, Muhammad Farooq; AlDamen, Murad A.; Song, You

    2017-08-01

    In the present work, synthesis, characterization, and properties of a new 1D-polymeric chain of [Ce(piv)3(MeOH)2]n (1D-Ce) are described. This polymeric structure was synthesized via reaction of Ce(NO3)3·6H2O with pivalic acid in presence of triethylamine. Crystal structure consists of cerium coordinated to eight oxygen atoms from five pivalate and two methanol moieties. Magnetic studies on the complex revealed a strong antiferromagnetic interaction between CeIII ions in the 1D chain.

  16. Bi3+/M2+ oxyphosphate: a continuous series of polycationic species from the 1D single chain to the 2D planes. Part 2: Crystal structure of three original structural types showing a combination of new ribbonlike polycations.

    PubMed

    Colmont, Marie; Huvé, Marielle; Mentré, Olivier

    2006-08-21

    With the assistance of structural models deduced from the high-resolution electron microscope (HREM) investigation presented in Part 1 of this work, three new structural types were pointed out in Bi2O3-MO-P2O5 ternary systems. Their crystal structures are built on the arrangement of 2D polycationic ribbons formed of edge-sharing O(Bi,M)4 tetrahedra and isolated by PO4 groups. Prior to this study, materials with ribbons up to n = 3 tetrahedra wide have been discovered. The original structures presented here display longer n = 4-6 cases, which suggests a possible continuous series of polycationic entities that range from the single chain (one tetrahedron wide) to the infinite [Bi2O2]2+ Aurivillius layer. The ribbons with n > 3 show strong structural modifications that are able to bring a good ribbon-phosphate cohesion. In addition to these fascinating structural results, this work fully confirms the validity of the decoding established from HREM images of a single crystallite in inhomogeneous mixtures.

  17. A novel cryogenic magnetic refrigerant metal-organic framework based on 1D gadolinium(III) chain

    NASA Astrophysics Data System (ADS)

    Tang, Qun; Li, Peng-Fei; Zou, Zhi-Ming; Liu, Zheng; Liu, Shu-Xia

    2017-02-01

    A metal-organic framework (MOF) based on gadolinium ion (Gd3+) and tricarboxylate ligand, [Gd(BTPCA)(H2O)]·2DMF·3H2O (Gd-BTPCA) (H3BTPCA =1,1‧,1‧-(benzene-1,3,5-triyl)tripiperidine-4-carboxylic acid; DMF=dimethylformamide), was synthesized and structurally characterized. The adjacent Gd3+ ions are intraconnected by the carboxylate groups of the BTPCA3- ligands to form a 1D Gd3+ ion chain. The 1D Gd3+ ion chains are interconnected by the BTPCA3- ligands, giving rise to a 3D framework with 1D open channel. The magnetic studies indicate that Gd-BTPCA exhibits weak ferromagnetic interactions, and acts as a cryogenic magnetic refrigerant having the magnetic entropy change (-ΔSm) of 20.40 J kg-1 K-1 for ΔH =7 T at 3 K.

  18. From 1D chain to 3D network: a new family of inorganic-organic hybrid semiconductors MO3(L)(x) (M = Mo, W; L = organic linker) built on perovskite-like structure modules.

    PubMed

    Zhang, Xiao; Hejazi, Mehdi; Thiagarajan, Suraj J; Woerner, William R; Banerjee, Debasis; Emge, Thomas J; Xu, Wenqian; Teat, Simon J; Gong, Qihan; Safari, Ahmad; Yang, Ronggui; Parise, John B; Li, Jing

    2013-11-20

    MO3 (M = Mo, W) or VI-VI binary compounds are important semiconducting oxides that show great promise for a variety of applications. In an effort to tune and enhance their properties in a systematic manner we have applied a designing strategy to deliberately introduce organic linker molecules in these perovskite-like crystal lattices. This approach has led to a wealth of new hybrid structures built on one-dimensional (1D) and two-dimensional (2D) VI-VI modules. The hybrid semiconductors exhibit a number of greatly improved properties and new functionality, including broad band gap tunability, negative thermal expansion, largely reduced thermal conductivity, and significantly enhanced dielectric constant compared to their MO3 parent phases.

  19. A novel coordination polymer containing both interdigitated 1D chains and interpenetrated 2D grids.

    PubMed

    Ayyappan, Ponnaiyan; Evans, Owen R; Lin, Wenbin

    2002-07-01

    A hydro(solvo)thermal reaction between zinc perchlorate and ethyl ester of a new pyridinecarboxylate bridging ligand of approximately 17.6 A in length yields a unique coordination polymer which contains both interdigitated infinite 1D chains and interpenetrated 2D rhombohedral grids [Zn(2.5)(L)(4)(mu(3)-OH)] x (H(2)O)(5), 1, where L is 3-[[4-(4-pyridylethenyl)phenyl]ethenyl]benzoate. The 1D chains contain mu(3)-bridged hydroxy groups and have a [Zn(4)(mu(3)-OH)(2)(L)(6)] stoichiometry, while the 2D grids have a Zn(L)(2) formula and diagonal distances of 31.7 and 25.2 A. Crystal data for 1: monoclinic space group P2/c, a = 15.686(2) A, b = 12.6103(16) A, c = 38.999(5) A, beta = 98.397(2) degrees, and Z = 4.

  20. Analysis of the rotational structure in the high-resolution infrared spectra of trans-hexatriene-1,1-d2 and -cis-1-d1

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.

    2012-09-01

    Mixtures of trans-hexatriene-1,1-d2, -cis-1-d1, and -trans-1-d1 have been synthesized. Anharmonic frequencies and harmonic intensities were predicted with the B3LYP/cc-pVTZ model for the out-of-plane (a″) modes of the three isotopologues. Assignments are proposed for most of the a″ vibrational modes above 500 cm-1. Ground state (GS) rotational constants have been determined for the 1,1-d2 and cis-1-d1 species from the analysis of rotational structure of C-type bands in the high-resolution (0.0015 cm-1) infrared spectra in a mixture of the three isotopologues. The GS constants for the 1,1-d2 species are A0 = 0.8018850(6), B0 = 0.0418540(6), and C0 = 0.0397997(4) cm-1. The GS constants for the cis-1-d1 species are A0 = 0.809388(1), B0 = 0.043532(2), and C0 = 0.041320(1) cm-1. Small inertial defects confirm planarity for both species. These ground state rotational constants are intended for use in determining a semiexperimental equilibrium structure and evaluating the influence of chain length on π-electron delocalization in polyenes.

  1. Propagation of excitation in long 1D chains: Transition from regular quantum dynamics to stochastic dynamics

    SciTech Connect

    Benderskii, V. A.; Kats, E. I.

    2013-01-15

    The quantum dynamics problem for a 1D chain consisting of 2N + 1 sites (N Much-Greater-Than 1) with the interaction of nearest neighbors and an impurity site at the middle differing in energy and in coupling constant from the sites of the remaining chain is solved analytically. The initial excitation of the impurity is accompanied by the propagation of excitation over the chain sites and with the emergence of Loschmidt echo (partial restoration of the impurity site population) in the recurrence cycles with a period proportional to N. The echo consists of the main (most intense) component modulated by damped oscillations. The intensity of oscillations increases with increasing cycle number and matrix element C of the interaction of the impurity site n = 0 with sites n = {+-}1 (0 < C {<=} 1; for the remaining neighboring sites, the matrix element is equal to unity). Mixing of the components of echo from neighboring cycles induces a transition from the regular to stochastic evolution. In the regular evolution region, the wave packet propagates over the chain at a nearly constant group velocity, embracing a number of sites varying periodically with time. In the stochastic regime, the excitation is distributed over a number of sites close to 2N, with the populations varying irregularly with time. The model explains qualitatively the experimental data on ballistic propagation of the vibrational energy in linear chains of CH{sub 2} fragments and predicts the possibility of a nondissipative energy transfer between reaction centers associated with such chains.

  2. Constitutive modeling and control of 1D smart composite structures

    NASA Astrophysics Data System (ADS)

    Briggs, Jonathan P.; Ostrowski, James P.; Ponte-Castaneda, Pedro

    1998-07-01

    Homogenization techniques for determining effective properties of composite materials may provide advantages for control of stiffness and strain in systems using hysteretic smart actuators embedded in a soft matrix. In this paper, a homogenized model of a 1D composite structure comprised of shape memory alloys and a rubber-like matrix is presented. With proportional and proportional/integral feedback, using current as the input state and global strain as an error state, implementation scenarios include the use of tractions on the boundaries and a nonlinear constitutive law for the matrix. The result is a simple model which captures the nonlinear behavior of the smart composite material system and is amenable to experiments with various control paradigms. The success of this approach in the context of the 1D model suggests that the homogenization method may prove useful in investigating control of more general smart structures. Applications of such materials could include active rehabilitation aids, e.g. wrist braces, as well as swimming/undulating robots, or adaptive molds for manufacturing processes.

  3. Analysis of Rotational Structure in the High-Resolution Infrared Spectra of the TRANS-HEXATRIENE-1,1-D2 and -CIS-1-D1 Species

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.

    2011-06-01

    Hexatriene-1,1-D2 with some admixture of the cis-1-D1 and trans-1-D1 species was synthesized by reaction of 2,4-pentadienal and (methyl-D3)-triphenylphosphonium iodide (Wittig reagent). The trans isomer was isolated by preparative gas chromatography, and the high-resolution (0.0015 Cm-1) infrared spectrum was recorded on a Bruker IFS 125HR instrument. The rotational structure in two C-type bands for the 1,1-D2 species was analyzed. For this species the bands at 902.043 and 721.864 Cm-1 yielded composite ground state rotational constants of A0 = 0.801882(1), B0 = 0.041850(2), and C0 = 0.039804(1) Cm-1. For the cis-1-D1 species the C-type band at 803.018 Cm-1 gave A0 = 0.809384(2), B0 = 0.043530(3), and C0 = 0.041321(2) Cm-1. By iodine-catalyzed isomerization, we have obtained some of the much less favored cis isomer and hope to obtain microwave spectra for its three deuterium-substituted species. The rotational constants reported here contribute to data needed for determining a semi-experimental structure for trans-hexatriene, which should show that the structural consequences of pi-electron delocalization increase with the chain length of polyenes.

  4. Formation of Gd coordination polymer with 1D chains mediated by Bronsted acidic ionic liquids

    NASA Astrophysics Data System (ADS)

    Luo, Qianqian; Han, Ying; Lin, Hechun; Zhang, Yuanyuan; Duan, Chungang; Peng, Hui

    2017-03-01

    One dimensional coordination polymer Gd[(SO4)(NO3)(C2H6SO)2] (1) is prepared through the mediation of Bronsted acid ionic liquid, which crystallized in the monoclinic space of C2/c. In this polymer, adjacent Gd atoms are linked by two SO42- ions to generate a 1-D chain, and all oxygen atoms in SO42- groups are connected to three nearest Gd atoms in μ3:η1:η1:η2 fashion. Gd, S and N from SO42- and NO3- are precisely coplanar. The planar is coordinated by a pair of DMSO molecules, which is parallel and linked by hydrogen bonding to form a three-dimensional supramolecular network. Magnetic susceptibility measurement of 1 reveals weak antiferromagnetic interactions between the Gd (III) ions. It exhibits relatively large magneto-caloric effect with -ΔSm=28.8 J Kg-1 K-1 for ΔH=7 T.

  5. Bi3+/M2+ oxyphosphate: a continuous series of polycationic species from the 1D single chain to the 2D planes. Part 1: From HREM images to crystal-structure deduction.

    PubMed

    Huvé, M; Colmont, M; Mentré, O

    2006-08-21

    This work deals with the crystal-structure deduction of new structural types of Bi3+-M2+ oxyphosphates (M is a transition element) from HREM images. Previous studies showed the unequivocal attribution of particular HREM contrasts to the corresponding Bi/M/O-based polycationic species in similar materials. On this basis, the examination of isolated crystallites of polyphased samples led to new HREM contrasts assigned to new polycationic species in three new structural types. This helped us to solve one crystal structure, and the two other forms have been deduced through HREM image decoding. It helped to model the investigated materials from the structural point of view as well as the chemical one. The three assumed crystal structures are formed by polycationic ribbons, n tetrahedra wide, surrounded by PO4 groups, as already encountered in these series of oxyphosphates. However, here we deal with the original n= 4-6 cases, whereas, up to this work, only the n= 1-3 ribbons have been reported. The greater size of ribbons is associated with particular structural modifications responsible for complex HREM contrasts. The validity of the proposed models is verified in Part 2 of this work.

  6. Assembling carbon fiber-graphene-carbon fiber hetero-structures into 1D-2D-1D junction fillers and patterned structures for improved microwave absorption

    NASA Astrophysics Data System (ADS)

    Li, Huimin; Liu, Lin; Li, Hai-Bing; Song, Wei-Li; Bian, Xing-Ming; Zhao, Quan-Liang; Chen, Mingji; Yuan, Xujin; Chen, Haosen; Fang, Daining

    2017-04-01

    Since carbon-based structures of various dimensions, including one-dimensional (1D) carbon nanotubes, two-dimensional (2D) graphene and three-dimensional (3D) carbon foams, have attracted significant attention as microwave absorption fillers, we present an exceptional hetero-junction filler with a 1D-2D-1D feature, achieved by manipulating 2D graphene into 1D carbon fibers in the fiber-extruding process under the electric field. The as-fabricated 1D-2D-1D structural fillers exhibited much-improved dielectric properties and promoted microwave absorption performance in their composites, which is linked to the establishment of enhanced polarization capability, the generation of increased electric loss pathway and the creation of more favorable electromagnetic energy consumption conditions. The results suggest that employing 2D graphene in the 1D-2D-1D nanostructures played the critical role in tuning the electromagnetic response ability, because of its intrinsic electric advantages and dimensional features. To broaden the effective absorption bandwidth, periodic pattern-absorbing structures were designed, which showed combined absorption advantages for various thicknesses. Our strategy for fabricating 1D-2D-1D structural fillers illuminates a universal approach for manipulating dimensions and structures in the nanotechnology.

  7. New Mononuclear Cu(II) Complexes and 1D Chains with 4-Amino-4H-1,2,4-triazole

    PubMed Central

    Dîrtu, Marinela M.; Boland, Yves; Gillard, Damien; Tinant, Bernard; Robeyns, Koen; Safin, Damir A.; Devlin, Eamonn; Sanakis, Yiannis; Garcia, Yann

    2013-01-01

    The crystal structures of two mononuclear Cu(II) NH2trz complexes [Cu(NH2trz)4(H2O)](AsF6)2 (I) and [Cu(NH2trz)4(H2O)](PF6)2 (II) as well as two coordination polymers [Cu(μ2-NH2trz)2Cl]Cl·H2O (III) and [Cu(μ2-NH2trz)2Cl] (SiF6)0.5·1.5H2O (IV) are presented. Cationic 1D chains with bridging bis-monodentate μ2-coordinated NH2trz and bridging μ2-coordinated chloride ligands are present in III and IV. In these coordination polymers, the Cu(II) ions are strongly antiferromagnetically coupled with J = −128.4 cm−1 for III and J = −143 cm−1 for IV (H = −J∑SiSi+1), due to the nature of the bridges between spin centers. Inter-chain interactions present in the crystal structures were taken into consideration, as well as g factors, which were determined experimentally, for the quantitative modeling of their magnetic properties. PMID:24300095

  8. 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.

  9. Controlling Structural Anisotropy of Anisotropic 2D Layers in Pseudo-1D/2D Material Heterojunctions.

    PubMed

    Chen, Bin; Wu, Kedi; Suslu, Aslihan; Yang, Sijie; Cai, Hui; Yano, Aliya; Soignard, Emmanuel; Aoki, Toshihiro; March, Katia; Shen, Yuxia; Tongay, Sefaattin

    2017-07-10

    Chemical vapor deposition and growth dynamics of highly anisotropic 2D lateral heterojunctions between pseudo-1D ReS2 and isotropic WS2 monolayers are reported for the first time. Constituent ReS2 and WS2 layers have vastly different atomic structure, crystallizing in anisotropic 1T' and isotropic 2H phases, respectively. Through high-resolution scanning transmission electron microscopy, electron energy loss spectroscopy, and angle-resolved Raman spectroscopy, this study is able to provide the very first atomic look at intimate interfaces between these dissimilar 2D materials. Surprisingly, the results reveal that ReS2 lateral heterojunctions to WS2 produce well-oriented (highly anisotropic) Re-chains perpendicular to WS2 edges. When vertically stacked, Re-chains orient themselves along the WS2 zigzag direction, and consequently, Re-chains exhibit six-fold rotation, resulting in loss of macroscopic scale anisotropy. The degree of anisotropy of ReS2 on WS2 largely depends on the domain size, and decreases for increasing domain size due to randomization of Re-chains and formation of ReS2 subdomains. Present work establishes the growth dynamics of atomic junctions between novel anisotropic/isotropic 2D materials, and overall results mark the very first demonstration of control over anisotropy direction, which is a significant leap forward for large-scale nanomanufacturing of anisotropic systems. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. The role of solitons in charge and energy transfer in 1D molecular chains

    NASA Astrophysics Data System (ADS)

    Ivić , Zoran

    1998-03-01

    The idea that polarons and solitons could play the crucial role in the transport processes in biological structures, has been critically reexamined on the basis of the general theory of self-trapping phenomena. The criteria which enable one to determine conditions for the existence and stability of polarons and solitons and to determine their character, in dependence of the values of the basic physical parameters of the system, were formulated. Validity of the so-called Davydov's soliton model was discussed on the basis of these criteria. It was found that the original Davydov's proposal, based upon the idea of the soliton creation due to the single excitation (particle, vibron, etc.) self-trapping, cannot explain the intramolecular energy transfer in α-helix and acetanilide. However, Davydov theory is flexible enough to describe the single electron transfer in some systems (α-helix and acetanilide for example). In the many-particle systems, dressing effect, due to the quantum nature of phonons, may cause the creation of the bound states of the several excitons in the molecular chain. The possibility of creation of the soliton states of this type is discussed for the simple Fröhlich's one-dimensional model. The regions of the system parameter space where different mechanisms dominate the behaviour of such entities are characterized.

  11. Topological defect formation in 1D and 2D spin chains realized by network of optical parametric oscillators

    NASA Astrophysics Data System (ADS)

    Hamerly, Ryan; Inaba, Kensuke; Inagaki, Takahiro; Takesue, Hiroki; Yamamoto, Yoshihisa; Mabuchi, Hideo

    2016-09-01

    A network of optical parametric oscillators (OPOs) is used to simulate classical Ising and XY spin chains. The collective nonlinear dynamics of this network, driven by quantum noise rather than thermal fluctuations, seeks out the Ising/XY ground state as the system transitions from below to above the lasing threshold. We study the behavior of this “Ising machine” for three canonical problems: a 1D ferromagnetic spin chain, a 2D square lattice and problems where next-nearest-neighbor couplings give rise to frustration. If the pump turn-on time is finite, topological defects form (domain walls for the Ising model, winding number and vortices for XY) and their density can be predicted from a numerical model involving a linear “growth stage” and a nonlinear “saturation stage”. These predictions are compared against recent data for a 10,000-spin 1D Ising machine.

  12. The 1D Ising model and the topological phase of the Kitaev chain

    SciTech Connect

    Greiter, Martin Schnells, Vera Thomale, Ronny

    2014-12-15

    It has been noted that the Kitaev chain, a p-wave superconductor with nearest-neighbor pairing amplitude equal to the hopping term Δ=t, and chemical potential μ=0, can be mapped into a nearest neighbor Ising model via a Jordan–Wigner transformation. Starting from the explicit eigenstates of the open Kitaev chain in terms of the original fermion operators, we elaborate that despite this formal equivalence the models are physically inequivalent, and show how the topological phase in the Kitaev chain maps into conventional order in the Ising model.

  13. Tunable Design of Structural Colors Produced by Pseudo-1D Photonic Crystals of Graphene Oxide.

    PubMed

    Tong, Liping; Qi, Wei; Wang, Mengfan; Huang, Renliang; Su, Rongxin; He, Zhimin

    2016-07-01

    It is broadly observed that graphene oxide (GO) films appear transparent with a thickness of about several nanometers, whereas they appear dark brown or almost black with thickness of more than 1 μm. The basic color mechanism of GO film on a sub-micrometer scale, however, is not well understood. This study reports on GO pseudo-1D photonic crystals (p1D-PhCs) exhibiting tunable structural colors in the visible wavelength range owing to its 1D Bragg nanostructures. Striking structural colors of GO p1D-PhCs could be tuned by simply changing either the volume or concentration of the aqueous GO dispersion during vacuum filtration. Moreover, the quantitative relationship between thickness and reflection wavelength of GO p1D-PhCs has been revealed, thereby providing a theoretical basis to rationally design structural colors of GO p1D-PhCs. The spectral response of GO p1D-PhCs to humidity is also obtained clearly showing the wavelength shift of GO p1D-PhCs at differently relative humidity values and thus encouraging the integration of structural color printing and the humidity-responsive property of GO p1D-PhCs to develop a visible and fast-responsive anti-counterfeiting label. The results pave the way for a variety of potential applications of GO in optics, structural color printing, sensing, and anti-counterfeiting.

  14. Tandem repeats modify the structure of the canine CD1D gene.

    PubMed

    Looringh van Beeck, F A; Leegwater, P A J; Herrmann, T; Broere, F; Rutten, V P M G; Willemse, T; Van Rhijn, I

    2013-06-01

    Among the CD1 proteins that present lipid antigens to T cells, CD1d is the only one that stimulates a population of T cells with an invariant T-cell receptor known as NKT cells. Sequencing of a 722 nucleotide gap in the dog (Canis lupus familiaris) genome revealed that the canine CD1D gene lacks a sequence homologous to exon 2 of human CD1D, coding for the start codon and signal peptide. Also, the canine CD1D gene contains three different short tandem repeats that disrupt the expected gene structure. Because canine CD1D cDNA lacks sequences homologous to human exon 2 and 3, the functionality of canine CD1d protein may be affected, and this could have consequences for the development and activation of canine NKT cells.

  15. Multiple mobility edges in a 1D Aubry chain with Hubbard interaction in presence of electric field: Controlled electron transport

    NASA Astrophysics Data System (ADS)

    Saha, Srilekha; Maiti, Santanu K.; Karmakar, S. N.

    2016-09-01

    Electronic behavior of a 1D Aubry chain with Hubbard interaction is critically analyzed in presence of electric field. Multiple energy bands are generated as a result of Hubbard correlation and Aubry potential, and, within these bands localized states are developed under the application of electric field. Within a tight-binding framework we compute electronic transmission probability and average density of states using Green's function approach where the interaction parameter is treated under Hartree-Fock mean field scheme. From our analysis we find that selective transmission can be obtained by tuning injecting electron energy, and thus, the present model can be utilized as a controlled switching device.

  16. Characterizing gapped phases of a 1D spin chain with on-site and spatial symmetries

    NASA Astrophysics Data System (ADS)

    West, Colin; Prakash, Abhishodh; Wei, Tzu-Chieh

    We investigate the phase diagram of a spin-1 chain whose Hamiltonian is invariant under translation, lattice inversion and a global A4 symmetry in the spin degrees of freedom. The classification scheme by Chen, Gu, and Wen allows us to enumerate all possible phases under the given symmetry. Then, we determine which of these phases actually occur in the two-parameter Hamiltonian. Using numerical methods proposed by Pollmann and Turner (2012) we determine the characteristic projective parameters for the Symmetry Protected Topological (SPT) phases. In addition, we present a method for determining the projective commutation parameter in these phases. The resulting phase diagram is rich and contains at least nine different SPT phases. This work was supported in part by the National Science Foundation.

  17. Two unprecedented 1D coordination polymer chains based on tetranuclear copper(II) building blocks

    SciTech Connect

    Li Gaijuan; Xing Yan Song Shuyan; Xu Ning; Liu Xianchun; Su Zhongmin

    2008-09-15

    The reaction of copper(II) sulfate with pyridine in DMF or methanol yield two unprecedented Cu(II) coordination polymers {l_brace}[Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}][{mu}-Cu(py)(DMF){sub 2}]{r_brace}{sub n}(1) and {l_brace}[Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}][{mu}-Cu(py){sub 4}]{r_brace}{sub n}(2), respectively. Single-crystal X-ray diffraction indicated that compound 1 crystallizes in the monoclinic system, space group p2(1)/n, a=14.542(5) A, b=16.359(5) A, c=18.951(5) A, {beta}=92.047(5){sup o}, V=4505(2) A{sup 3}, Z=4 while 2 is monoclinic C2/c, a=23.078(5) A, b=10.214(5) A, c=23.142(5) A, {beta}=115.471(5){sup o}, V=4925(3) A{sup 3}, Z=4. Both of the two compounds consist of tetrahedral tetranuclear [Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}] clusters that are bridged by pentacoordinated Cu atom for 1 or hexacoordinated Cu atoms for 2 through the sulfate oxygen to form the infinite one-dimensional polymer chains. - Graphical abstract: Two unprecedented Cu(II) coordination polymers have been prepared by using solvothermal method; they consist of tetrahedral tetranuclear clusters that are bridged by unique Cu(II) atom through the sulfate oxygen to form the infinite one-dimensional polymer chains (a) for complex 1 and (b) for complex 2.

  18. Structure and Catalytic Mechanism of Human Steroid 5-Reductase (AKR1D1)

    SciTech Connect

    Costanzo, L.; Drury, J; Christianson, D; Penning, T

    2009-01-01

    Human steroid 5{beta}-reductase (aldo-keto reductase (AKR) 1D1) catalyzes reduction of {Delta}{sup 4}-ene double bonds in steroid hormones and bile acid precursors. We have reported the structures of an AKR1D1-NADP{sup +} binary complex, and AKR1D1-NADP{sup +}-cortisone, AKR1D1-NADP{sup +}-progesterone and AKR1D1-NADP{sup +}-testosterone ternary complexes at high resolutions. Recently, structures of AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone complexes showed that the product is bound unproductively. Two quite different mechanisms of steroid double bond reduction have since been proposed. However, site-directed mutagenesis supports only one mechanism. In this mechanism, the 4-pro-R hydride is transferred from the re-face of the nicotinamide ring to C5 of the steroid substrate. E120, a unique substitution in the AKR catalytic tetrad, permits a deeper penetration of the steroid substrate into the active site to promote optimal reactant positioning. It participates with Y58 to create a 'superacidic' oxyanion hole for polarization of the C3 ketone. A role for K87 in the proton relay proposed using the AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone structure is not supported.

  19. Synthesis, crystal structure, and properties of a 1-D terbium-substituted monolacunary Keggin-type polyoxotungstate.

    PubMed

    Ma, Pengtao; Si, Yanan; Wan, Rong; Zhang, Shaowei; Wang, Jingping; Niu, Jingyang

    2015-03-05

    A new 1-D linear chainlike terbium-substituted polyoxometalate [Tb(H2O)2(α-PW11O39)](4-) (1) has been synthesized in aqueous solution and characterized by elemental analysis, inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray powder diffraction (XRPD), IR spectrum, thermal analysis, electrospray ionization mass spectrometry (ESI-MS), and X-ray single-crystal diffraction. X-ray structural analysis reveals that 1 displays a 1-D linear chain containing [Tb(H2O)2(α-PW11O39)](4-) moieties. The Tb(III) cation incorporated into the monolacunary Keggin-type [α-PW11O39](7-) unit resides in a distorted monocapped triangular prismatic geometry and acts as a linker to join two adjacent [α-PW11O39](7-) units to form a 1-D chain structure. Solid-state photoluminescent property of 1 has been investigated at room temperature and the photoluminescent emission mainly results from the synergistic effect of the Tb(III) cation and the Na7[α-PW11O39] precursor. The ESI-MS spectrum of 1 confirms that the polyanion [Tb(H2O)(HPW11O39)](3-) is stable in aqueous solution.

  20. Synthesis, crystal structure, and properties of a 1-D terbium-substituted monolacunary Keggin-type polyoxotungstate

    NASA Astrophysics Data System (ADS)

    Ma, Pengtao; Si, Yanan; Wan, Rong; Zhang, Shaowei; Wang, Jingping; Niu, Jingyang

    2015-03-01

    A new 1-D linear chainlike terbium-substituted polyoxometalate [Tb(H2O)2(α-PW11O39)]4- (1) has been synthesized in aqueous solution and characterized by elemental analysis, inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray powder diffraction (XRPD), IR spectrum, thermal analysis, electrospray ionization mass spectrometry (ESI-MS), and X-ray single-crystal diffraction. X-ray structural analysis reveals that 1 displays a 1-D linear chain containing [Tb(H2O)2(α-PW11O39)]4- moieties. The Tb(III) cation incorporated into the monolacunary Keggin-type [α-PW11O39]7- unit resides in a distorted monocapped triangular prismatic geometry and acts as a linker to join two adjacent [α-PW11O39]7- units to form a 1-D chain structure. Solid-state photoluminescent property of 1 has been investigated at room temperature and the photoluminescent emission mainly results from the synergistic effect of the TbIII cation and the Na7[α-PW11O39] precursor. The ESI-MS spectrum of 1 confirms that the polyanion [Tb(H2O)(HPW11O39)]3- is stable in aqueous solution.

  1. Ultrasonic waves in biaxially stressed multi-layered and 1D phononic structures (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Demcenko, Andriejus; Volker, Arno W. F.; Cooper, Jonathan M.

    2017-04-01

    Elastic wave velocities as a function of applied stress are analysed in multilayered and 1-D phononic structures. The analysis is conducted by the means of the acoustoelasticity theory for isotropic elastic structures with application of this theory to stable formulation of stiffness and hybrid matrix methods for the eigenvalue analysis in the stressed elastic structures. The reformulated matrix methods are used for obtaining modal solutions, reflection and transmission coefficients for different multilayered media cases. Floquet wave analysis is presented for the stressed 1-D phononic structures. The analysis is supported by numerical examples.

  2. Hydrothermal synthesis and structural characterization of two 1-D and 2-D Dawson-based phosphotungstates

    SciTech Connect

    Zhao Junwei; Zheng Shoutian; Liu Wei; Yang Guoyu

    2008-03-15

    Two new Dawson-based phosphotungstates (H{sub 2}en){sub 0.5}H[Cu(en){sub 2}(H{sub 2}O)]{sub 2}{l_brace}[Cu(en){sub 2}]({alpha}{sub 1}-P{sub 2}W{sub 17}CuO{sub 61}){r_brace}.8H{sub 2}O (1) (en=ethylenediamine) and [4,4'-H{sub 2}bpy]{sub 2}{l_brace}[Cu(4,4'-bpy){sub 3}][Cu(4,4'-bpy){sub 4}(H{sub 2}O){sub 2}]{sub 2}[Cu(4,4'-bpy)][{alpha}-P{sub 2}W{sub 1=} 8O{sub 62}]{sub 2}{r_brace}.6H{sub 2}O (2) (4,4'-bpy=4,4'-bipyridine) have been hydrothermally synthesized and structurally characterized. 1 crystallizes in the triclinic space group P-1 with a=11.7626(17), b=13.246(2), c=29.350(5) A, {alpha}=87.355(5), {beta}=79.583(5), {gamma}=66.993(3){sup o}, V=4138.3(11) A{sup 3}, Z=2, GOF=1.089, R{sub 1}=0.0563 and wR{sub 2}=0.1505, whereas 2 belongs to the orthorhombic space group Iba2 with a=22.277(8), b=47.04(2), c=22.153(8) A, V=23215(17) A{sup 3}, Z=4, GOF=1.051, R{sub 1}=0.0627 and wR{sub 2}=0.1477. 1 consists of a 1-D linear chain structure constructed from monocopper{sup II}-substituted Dawson polyoxoanions, while 2 represents the first 2-D sheet-like structure with a (4,4)-connected topological net built up from plenary Dawson-type polyoxoanions and Cu{sup II}-4,4'-bpy complex cations in polyoxometalate chemistry. - Graphical abstract: Two Dawson-based phosphotungstates (H{sub 2}en){sub 0.5}H[Cu(en){sub 2}(H{sub 2}O)]{sub 2}{l_brace}[Cu(en){sub 2}]({alpha}{sub 1}-P{sub 2}W{sub 17}CuO{sub 61}){r_brace}.8H{sub 2}O (1) and [4,4'-H{sub 2}bpy]{sub 2}{l_brace}[Cu(4,4'-bpy){sub 3}][Cu(4,4'-bpy){sub 4}(H{sub 2}O){sub 2}]{sub 2}[Cu(4,4'-bpy)][{alpha}-P{sub 2}W{sub 1=} 8O{sub 62}]{sub 2}{r_brace}.6H{sub 2}O (2) have been hydrothermally synthesized and structurally characterized. 1 consists of a 1-D linear chain structure constructed from monocopper-substituted Dawson polyoxoanions, while 2 represents the first 2-D sheet-like structure with a (4,4)-connected topological net built up from saturated Dawson-type polyoxoanions and Cu{sup II}-4,4'-bpy complex cations in

  3. Two-step spin transition in a 1D Fe(II) 1,2,4-triazole chain compound.

    PubMed

    Dîrtu, Marinela M; Schmit, France; Naik, Anil D; Rusu, Ionela; Rotaru, Aurelian; Rackwitz, Sergej; Wolny, Juliusz A; Schünemann, Volker; Spinu, Leonard; Garcia, Yann

    2015-04-07

    A thermochromic 1D spin crossover coordination (SCO) polymer [Fe(βAlatrz)3](BF4)2⋅2 H2O (1⋅2 H2O), whose precursor βAlatrz, (1,2,4-triazol-4-yl-propionate) has been tailored from a β-amino acid ester is investigated in detail by a set of superconducting quantum interference device (SQUID), (57)Fe Mössbauer, differential scanning calorimetry, infrared, and Raman measurements. An hysteretic abrupt two-step spin crossover (T1/2(↓) = 230 K and T1/2(↑) = 235 K, and T1/2(↓) = 172 K and T1/2(↑) = 188 K, respectively) is registered for the first time for a 1,2,4-triazole-based Fe(II) 1D coordination polymer. The two-step SCO configuration is observed in a 1:2 ratio of low-spin/high-spin in the intermediate phase for a 1D chain. The origin of the stepwise transition was attributed to a distribution of chains of different lengths in 1⋅2 H2O after First Order Reversal Curves (FORC) analyses. A detailed DFT analysis allowed us to propose the normal mode assignment of the Raman peaks in the low-spin and high-spin states of 1⋅2 H2O. Vibrational spectra of 1⋅2 H2O reveal that the BF4(-) anions and water molecules play no significant role on the vibrational properties of the [Fe(βAlatrz)3](2+) polymeric chains, although non-coordinated water molecules have a dramatic influence on the emergence of a step in the spin transition curve. The dehydrated material [Fe(βAlatrz)3](BF4)2 (1) reveals indeed a significantly different magnetic behavior with a one-step SCO which was also investigated.

  4. Functional CD1d and/or NKT cell invariant chain transcript in horse, pig, African elephant and guinea pig, but not in ruminants

    PubMed Central

    Looringh van Beeck, Frank A.; Reinink, Peter; Hermsen, Roel; Zajonc, Dirk M.; Laven, Marielle J.; Fun, Axel; Troskie, Milana; Schoemaker, Nico J.; Morar, Darshana; Lenstra, Johannes A.; Vervelde, Lonneke; Rutten, Victor P.M.G.; van Eden, Willem; Van Rhijn, Ildiko

    2009-01-01

    CD1d-restricted invariant natural killer T cells (NKT cells) have been well characterized in humans and mice, but it is unknown whether they are present in other species. Here we describe the invariant TCR α chain and the full length CD1d transcript of pig and horse. Molecular modeling predicts that porcine (po) invariant TCR α chain/poCD1d/α-GalCer and equine (eq) invariant TCR α chain/eqCD1d/α-GalCer form complexes that are highly homologous to the human complex. Since a prerequisite for the presence of NKT cells is the expression of CD1d protein, we performed searches for CD1D genes and CD1d transcripts in multiple species. Previously, cattle and guinea pig have been suggested to lack CD1D genes. The CD1D genes of European taurine cattle (Bos taurus) are known to be pseudogenes because of disrupting mutations in the start codon and in the donor splice site of the first intron. Here we show that the same mutations are found in six other ruminants: African buffalo, sheep, bushbuck, bongo, N’Dama cattle, and roe deer. In contrast, intact CD1d transcripts were found in guinea pig, African elephant, horse, rabbit, and pig. Despite the discovery of a highly homologous NKT/CD1d system in pig and horse, our data suggest that functional CD1D and CD1d-restricted NKT cells are not universally present in mammals. PMID:19185921

  5. The structure of nanocomposite 1D cationic conductor crystal@SWNT.

    PubMed

    Kiselev, N A; Kumskov, A S; Zakalyukin, R M; Vasiliev, A L; Chernisheva, M V; Eliseev, A A; Krestinin, A V; Freitag, B; Hutchison, J L

    2012-06-01

    Nanocomposites consisting of one-dimensional (1D) crystals of the cationic conductors CuI, CuBr and AgBr inside single-walled carbon nanotubes, mainly (n, 0), were obtained using the capillary technique. 1D crystal structure models were proposed based on the high resolution transmission electron microscopy performed on a FEI Titan 80-300 at 80 kV with aberration correction. According to the models and image simulations there are two modifications of 1D crystal: hexagonal close-packed bromine (iodine) anion sublattice (growth direction <001>) and 1D crystal cubic structure (growth direction <112>) compressed transversely to the nanotube (D(m) ∼1.33 nm) axis. Tentatively this kind of 1D crystal can be considered as monoclinic. One modification of the anion sublattice reversibly transforms into the other inside the nanotube, probably initiated by electron beam heating. As demonstrated by micrographs, copper or silver cations can occupy octahedral positions or are statistically distributed across two tetrahedral positions. A 1DAgBr@SWNT (18, 0; 19, 0) pseudoperiodic 'lattice distortion' is revealed resulting from convolution of the nanotube wall function image with 1D cubic crystal function image.

  6. Structural resistance of chemically modified 1-D nanostructured titanates in inorganic acid environment

    SciTech Connect

    Marinkovic, Bojan A.; Fredholm, Yann C.; Morgado, Edisson

    2010-10-15

    Sodium containing one-dimensional nanostructured layered titanates (1-D NSLT) were produced both from commercial anatase powder and Brazilian natural rutile mineral sands by alkali hydrothermal process. The 1-D NSLT were chemically modified with proton, cobalt or iron via ionic exchange and all products were additionally submitted to intensive inorganic acid aging (pH = 0.5) for 28 days. The morphology and crystal structure transformations of chemically modified 1-D NSLT were followed by transmission electron microscopy, powder X-ray diffraction, selected area electron diffraction and energy dispersive spectroscopy. It was found that the original sodium rich 1-D NSLT and cobalt substituted 1-D NSLT were completely converted to rutile nanoparticles, while the protonated form was transformed in a 70%-30% (by weight) anatase-rutile nanoparticles mixture, very similar to that of the well-known TiO{sub 2}-photocatalyst P25 (Degussa). The iron substituted 1-D NSLT presented better acid resistance as 13% of the original structure and morphology remained, the rest being converted in rutile. A significant amount of remaining 1-D NSLT was also observed after the acid treatment of the product obtained from rutile sand. The results showed that phase transformation of NSLT into titanium dioxide polymorph in inorganic acid conditions were controllable by varying the exchanged cations. Finally, the possibility to transform, through acid aging, 1-D NSLT obtained from Brazilian natural rutile sand into TiO{sub 2}-polymorphs was demonstrated for the first time to the best of authors' knowledge, opening path for producing TiO{sub 2}-nanoproducts with different morphologies through a simple process and from a low cost precursor.

  7. Synthesis of Hollow Sphere and 1D Structural Materials by Sol-Gel Process.

    PubMed

    Li, Fa-Liang; Zhang, Hai-Jun

    2017-08-25

    The sol-gel method is a simple and facile wet chemical process for fabricating advanced materials with high homogeneity, high purity, and excellent chemical reactivity at a relatively low temperature. By adjusting the processing parameters, the sol-gel technique can be used to prepare hollow sphere and 1D structural materials that exhibit a wide application in the fields of catalyst, drug or gene carriers, photoactive, sensors and Li-ion batteries. This feature article reviewed the development of the preparation of hollow sphere and 1D structural materials using the sol-gel method. The effects of calcination temperature, soaking time, pH value, surfactant, etc., on the preparation of hollow sphere and 1D structural materials were summarized, and their formation mechanisms were generalized. Finally, possible future research directions of the sol-gel technique were outlined.

  8. Synthesis of Hollow Sphere and 1D Structural Materials by Sol-Gel Process

    PubMed Central

    Li, Fa-Liang; Zhang, Hai-Jun

    2017-01-01

    The sol-gel method is a simple and facile wet chemical process for fabricating advanced materials with high homogeneity, high purity, and excellent chemical reactivity at a relatively low temperature. By adjusting the processing parameters, the sol-gel technique can be used to prepare hollow sphere and 1D structural materials that exhibit a wide application in the fields of catalyst, drug or gene carriers, photoactive, sensors and Li-ion batteries. This feature article reviewed the development of the preparation of hollow sphere and 1D structural materials using the sol-gel method. The effects of calcination temperature, soaking time, pH value, surfactant, etc., on the preparation of hollow sphere and 1D structural materials were summarized, and their formation mechanisms were generalized. Finally, possible future research directions of the sol-gel technique were outlined. PMID:28841188

  9. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

    PubMed

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent

    2016-02-05

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

  10. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

    PubMed Central

    2016-01-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  11. Formation of 1D adsorbed water structures on CaO(001)

    NASA Astrophysics Data System (ADS)

    Zhao, Xunhua; Bhattacharya, Saswata; Ghiringhelli, Luca M.; Levchenko, Sergey V.; Scheffler, Matthias

    2015-03-01

    Understanding the interaction of water with oxide surfaces is of fundamental importance for basic and engineering sciences. Recently, a spontaneous formation of one-dimensional (1D) adsorbed water structures have been observed on CaO(001). Interestingly, at other alkaline earth metal oxides, in particular MgO(001) and SrO(001), such structures have not been found experimentally. We calculate the relative stability of adsorbed water structures on the three oxides using density-functional theory combined with the ab initio atomistic thermodynamics. Low-energy structures at different coverages are obtained with a first-principles genetic algorithm. Finite-temperature vibrational spectra are calculated using ab initio molecular dynamics. We find a range of (T, p) conditions where 1D structures are thermodynamically stable on CaO(001). The orientation and vibrational spectra of the 1D structures are in agreement with the experiments. The formation of the 1D structures is found to be actuated by a symmetry breaking in the adsorbed water tetramer, as well as by a balance between water-water and water-substrate interactions, determined by the lattice constant of the oxide.

  12. 1D pixelated MV portal imager with structured privacy film: a feasibility study

    NASA Astrophysics Data System (ADS)

    Baturin, Pavlo; Shedlock, Daniel; Myronakis, Marios; Berbeco, Ross; Star-Lack, Josh

    2017-03-01

    Modern amorphous silicon flat panel-based electronic portal imaging devices that utilize thin gadolinium oxysulfide scintillators suffer from low quantum efficiencies (QEs). Thick two dimensionally (2D) pixelated scintillator arrays offer an effective but expensive option for increasing QE. To reduce costs, we have investigated the possibility of combining a thick one dimensional (1D) pixelated scintillator (PS) with an orthogonally placed 1D structured optical filter to provide for overall good 2D spatial resolution. In this work, we studied the potential for using a 1D video screen privacy film (PF) to serve as a directional optical attenuator and filter. A Geant4 model of the PF was built based on reflection and transmission measurements taken with a laser-based optical reflectometer. This information was incorporated into a Geant4-based x-ray detector simulator to generate modulation transfer functions (MTFs), noise power spectra (NPS), and detective quantum efficiencies (DQEs) for various 1D and 2D configurations. It was found that the 1D array with PF can provide the MTFs and DQEs of 2D arrays. Although the PF significantly reduced the amount of optical photons detected by the flat panel, we anticipate using a scintillator with an inherently high optical yield (e.g. cesium iodide) for MV imaging, where fluence rates are inherently high, will still provide adequate signal intensities for the imaging tasks associated with radiotherapy.

  13. A novel 1D chain of azido bridged copper(II) with a salen-type di-Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Biswas, Saptarshi; Ghosh, Ashutosh

    2012-07-01

    One new complex of Cu(II), [(CuL)2Cu3(N3)6]n (1) has been synthesized by reacting the "ligand complex", [CuL] with copper acetate and sodium azide (NaN3) in methanol-water where the di-Schiff base ligand H2L = N,N‧-bis(α-methylsalicylidene)-1,3-propanediamine. The X-ray single crystal structural analysis shows that complex 1 consists of an incomplete face-sharing double cube of four Cu(II) ions with the formula of [(CuL)2Cu2(N3)2]2+ which are connected by [Cu(N3)4]2- unit to form a novel 1D chain.

  14. Multi-dimensional transition-metal coordination polymers of 4,4'-bipyridine-N,N'-dioxide: 1D chains and 2D sheets.

    PubMed

    Jia, Junhua; Blake, Alexander J; Champness, Neil R; Hubberstey, Peter; Wilson, Claire; Schröder, Martin

    2008-10-06

    Reaction of 4,4'-bipyridine -N, N' -dioxide (L) with a variety of transition-metal salts in MeOH affords a range of coordination polymer products. For the complexes [FeCl 3(mu-L)] infinity, 1, and ([Cu(L) 2(OHMe) 2(mu-L)].2PF 6. n(solv)) infinity, 2, 1D chain structures are observed, whereas ([Mn(mu-L) 3].2ClO 4) infinity, 3, and ([Cu(mu-L) 3].2BF 4) infinity, 4, both show 2D sheet architectures incorporating an unusual 3 (6)- hxl topology. The more common 4 (4)- sql topology is observed in [Cd(ONO 2) 2(mu-L) 2] infinity, 5, ([Cu(OHMe) 2(mu-L) 2].2ZrF 5) infinity, 6, ([Cu(L) 2(mu-L) 2].2EF 6) infinity ( 7 E = P; 8 E = Sb), and ([Et 4N][Cu(OHMe) 0.5(mu-L) 2(mu-FSiF 4F) 0.5].2SbF 6. n(solv)) infinity, 9. In 6, the [ZrF 5] (-) anion, formed in situ from [ZrF 6] (2-), forms 1D anionic chains ([ZrF 5] (-)) infinity of vertex-linked octahedra, and these chains thread through a pair of inclined polycatenated ([Cu(OHMe) 2(mu-L) 2] (2+)) infinity 4 (4)- sql grids to give a rare example of a triply intertwined coordination polymer. 9 also shows a 3D matrix structure with 4 (4)- sql sheets of stoichiometry ([Cu(L) 2] (2+)) infinity coordinatively linked by bridging [SiF 6] (2-) anions to give a structure of 5-c 4 (4).6 (6)- sqp topology. The mononuclear [Cu(L) 6].2BF 4 ( 10) and [Cd(L) 6].2NO 3 ( 11) and binuclear complexes [(Cu(L)(OH 2)) 2(mu-L) 2)].2SiF 6. n(solv), 12, are also reported. The majority of the coordination polymers are free of solvent and are nonporous. Thermal treatment of materials that do contain solvent results in structural disintegration of the complex structures giving no permanent porosity.

  15. Investigation of 1-D crustal velocity structure beneath Izmir Gulf and surroundings by using local earthquakes

    SciTech Connect

    Polat, Orhan; Özer, Çaglar

    2016-04-18

    In this study; we examined one dimensional crustal velocity structure of Izmir gulf and surroundings. We used nearly one thousand high quality (A and B class) earthquake data which recorded by Disaster and Emergency Management Presidency (AFAD) [1], Bogazici University (BU-KOERI) [2] and National Observatory of Athens (NOA) [3,4]. We tried several synthetic tests to understand power of new velocity structure, and examined phase residuals, RMS values and shifting tests. After evaluating these tests; we decided one dimensional velocity structure and minimum 1-D P wave velocities, hypocentral parameter and earthquake locations from VELEST algorithm. Distribution of earthquakes was visibly improved by using new minimum velocity structure.

  16. Investigation of 1-D crustal velocity structure beneath Izmir Gulf and surroundings by using local earthquakes

    NASA Astrophysics Data System (ADS)

    Polat, Orhan; Özer, Ćaglar

    2016-04-01

    In this study; we examined one dimensional crustal velocity structure of Izmir gulf and surroundings. We used nearly one thousand high quality (A and B class) earthquake data which recorded by Disaster and Emergency Management Presidency (AFAD) [1], Bogazici University (BU-KOERI) [2] and National Observatory of Athens (NOA) [3,4]. We tried several synthetic tests to understand power of new velocity structure, and examined phase residuals, RMS values and shifting tests. After evaluating these tests; we decided one dimensional velocity structure and minimum 1-D P wave velocities, hypocentral parameter and earthquake locations from VELEST algorithm. Distribution of earthquakes was visibly improved by using new minimum velocity structure.

  17. Adaptability of the semi-invariant natural killer T-cell receptor towards structurally diverse CD1d-restricted ligands

    PubMed Central

    Florence, William C; Xia, Chengfeng; Gordy, Laura E; Chen, Wenlan; Zhang, Yalong; Scott-Browne, James; Kinjo, Yuki; Yu, Karl O A; Keshipeddy, Santosh; Pellicci, Daniel G; Patel, Onisha; Kjer-Nielsen, Lars; McCluskey, James; Godfrey, Dale I; Rossjohn, Jamie; Richardson, Stewart K; Porcelli, Steven A; Howell, Amy R; Hayakawa, Kyoko; Gapin, Laurent; Zajonc, Dirk M; Wang, Peng George; Joyce, Sebastian

    2009-01-01

    The semi-invariant natural killer (NK) T-cell receptor (NKTcr) recognises structurally diverse glycolipid antigens presented by the monomorphic CD1d molecule. While the α-chain of the NKTcr is invariant, the β-chain is more diverse, but how this diversity enables the NKTcr to recognise diverse antigens, such as an α-linked monosaccharide (α-galactosylceramide and α-galactosyldiacylglycerol) and the β-linked trisaccharide (isoglobotriaosylceramide), is unclear. We demonstrate here that NKTcrs, which varied in their β-chain usage, recognised diverse glycolipid antigens with a similar binding mode on CD1d. Nevertheless, the NKTcrs recognised distinct epitopic sites within these antigens, including α-galactosylceramide, the structurally similar α-galactosyldiacylglycerol and the very distinct isoglobotriaosylceramide. We also show that the relative roles of the CDR loops within the NKTcr β-chain varied as a function of the antigen. Thus, while NKTcrs characteristically use a conserved docking mode, the NKTcr β-chain allows these cells to recognise unique aspects of structurally diverse CD1d-restricted ligands. PMID:19816402

  18. Synthesis, characterization and comparison of polyaniline 1D-structure controlled by poly(L-lactide) and poly(D-lactide)

    NASA Astrophysics Data System (ADS)

    Gu, Zhou-Jie; Shen, Qing

    2016-01-01

    1D-structural polyaniline (PANI) was controllably synthesized by utilizing the poly(L-lactide) (PLLA) and poly(D-lactide) (PDLA) as controllers. FESEM images showed that the morphology of 1D-structural PANI controlled by PDLA likes a joint obviously unlike PLLA controlled vertebra structure reported previously. To set the ratio of ANI/PLLA (ml/g) at 0.45/0.135, 0.45/0.270 and 0.45/0.540, the formed PANI 1D structure was changed in the cross-section as four round leaves, four non-round leaves and four sharp leaves, respectively. FTIR and XRD analysis indicated that the PLLA and PDLA both were doped in PANI chains while the PLLA was strongly in the electrons delocalization than that of the PDLA due probably to the L-type stronger in crystal polymorphism than that of the D-type.

  19. Structural mapping and framework interconversions in 1D, 2D, and 3D divalent metal R,S-hydroxyphosphonoacetate hybrids.

    PubMed

    Colodrero, Rosario M P; Olivera-Pastor, Pascual; Cabeza, Aurelio; Papadaki, Maria; Demadis, Konstantinos D; Aranda, Miguel A G

    2010-01-18

    Reactions of divalent cations (Mg(2+), Co(2+), Ni(2+), and Zn(2+)) with R,S-hydroxyphosphonoacetic acid (HPAA) in aqueous solutions (pH values ranging 1.0-4.0) yielded a range of crystalline hydrated M-HPAA hybrids. One-dimensional (1D) chain compounds were formed at room temperature whereas reactions conducted under hydrothermal conditions resulted in two-dimensional (2D) layered frameworks or, in some cases, three-dimensional (3D) networks incorporating various alkaline cations. 1D phases with compositions [M{HO(3)PCH(OH)CO(2)}(H(2)O)(2)].2H(2)O (M = Mg, Co, and Zn) were isolated. These compounds were dehydrated in liquid water to yield the corresponding [M{HO(3)PCH(OH)CO(2)}(H(2)O)(2)] compounds lacking the lattice water between the 1D chains. [M{HO(3)PCH(OH)CO(2)}(H(2)O)(2)] (M = Mg, Ni, Co, Zn) compounds were formed by crystallization at room temperature (at higher pH values) or also by partial dehydration of 1D compounds with higher hydration degrees. Complete dehydration of these 1D solids at 240-270 degrees C led to 3D phases, [M{HO3PCH(OH)CO(2)}]. The 2D layered compound [Mg{HO(3)PCH(OH)CO(2)}(H(2)O)(2)] was obtained under hydrothermal conditions. For both synthesis methods, addition of alkali metal hydroxides to adjust the pH usually led to mixed phase materials, whereas direct reactions between the metal oxides and the hydroxyphosphonoacetic acid gave single phase materials. On the other hand, adjusting the pH with acetate salts and increasing the ratio M(2+)/HPAA and/or the A(+)/M(2+) ratio (A = Na, K) resulted in 3D networks, where the alkali cations were incorporated within the frameworks for charge compensation. The crystal structures of eight new M(II)-HPAA hybrids are reported herein and the thermal behavior related to dehydration/rehydration of some compounds are studied in detail.

  20. Structural and mechanistic insights into regulation of the retromer coat by TBC1d5

    PubMed Central

    Jia, Da; Zhang, Jin-San; Li, Fang; Wang, Jing; Deng, Zhihui; White, Mark A.; Osborne, Douglas G.; Phillips-Krawczak, Christine; Gomez, Timothy S.; Li, Haiying; Singla, Amika; Burstein, Ezra; Billadeau, Daniel D.; Rosen, Michael K.

    2016-01-01

    Retromer is a membrane coat complex that is recruited to endosomes by the small GTPase Rab7 and sorting nexin 3. The timing of this interaction and consequent endosomal dynamics are thought to be regulated by the guanine nucleotide cycle of Rab7. Here we demonstrate that TBC1d5, a GTPase-activating protein (GAP) for Rab7, is a high-affinity ligand of the retromer cargo selective complex VPS26/VPS29/VPS35. The crystal structure of the TBC1d5 GAP domain bound to VPS29 and complementary biochemical and cellular data show that a loop from TBC1d5 binds to a conserved hydrophobic pocket on VPS29 opposite the VPS29–VPS35 interface. Additional data suggest that a distinct loop of the GAP domain may contact VPS35. Loss of TBC1d5 causes defective retromer-dependent trafficking of receptors. Our findings illustrate how retromer recruits a GAP, which is likely to be involved in the timing of Rab7 inactivation leading to membrane uncoating, with important consequences for receptor trafficking. PMID:27827364

  1. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    SciTech Connect

    Zhang, Yingjie; Bhadbhade, Mohan; Karatchevtseva, Inna; Price, Jason R.; Liu, Hao; Zhang, Zhaoming; Kong, Linggen; Čejka, Jiří; Lu, Kim; Lumpkin, Gregory R.

    2015-03-15

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.

  2. Synthesis and characterization of a 1D chain-like Cu{sub 6} substituted sandwich-type phosphotungstate with pendant dinuclear Cu–azido complexes

    SciTech Connect

    Li, Yan-Ying; Zhao, Jun-Wei; Wei, Qi; Yang, Bai-Feng; Yang, Guo-Yu

    2014-02-15

    A novel Cu–azido complex modified hexa-Cu{sup II} substituted sandwich-type phosphotungstate [Cu(en){sub 2}]([Cu{sub 2}(en){sub 2}(μ-1,1-N{sub 3}){sub 2}(H{sub 2}O)]{sub 2}[Cu{sub 6}(en){sub 2}(H{sub 2}O){sub 2}(B-α-PW{sub 9}O{sub 34}){sub 2}])·6H{sub 2}O (1) (en=ethylene-diamine) has been prepared under hydrothermal conditions and structurally characterized by elemental analyses, IR spectra, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. 1 displays a beautiful 1-D chain architecture constructed from sandwich-type [Cu{sub 2}(en){sub 2}(μ-1,1-N{sub 3}){sub 2}(H{sub 2}O)]{sub 2}[Cu{sub 6}(en){sub 2}(H{sub 2}O){sub 2}(B-α-PW{sub 9}O{sub 34}){sub 2}]{sup 2−} units and [Cu(en){sub 2}]{sup 2+} linkers. To our knowledge, 1 represents the first hexa-Cu{sup II} sandwiched phosphotungstate with supporting Cu–azido complexes. - Graphical abstract: The first hexa-Cu{sup II} sandwiched phosphotungstate with supporting Cu–azido complexes has been prepared and characterized. Display Omitted - Highlights: • Hexa-copper-substituted phosphotungstate. • Cu–azido complexes modified hexa-Cu{sup II} substituted sandwich-type polyoxometalate. • 1-D chain architecture built by hexa-copper-substituted polyoxotungstate units.

  3. Low band gap frequencies and multiplexing properties in 1D and 2D mass spring structures

    NASA Astrophysics Data System (ADS)

    Aly, Arafa H.; Mehaney, Ahmed

    2016-11-01

    This study reports on the propagation of elastic waves in 1D and 2D mass spring structures. An analytical and computation model is presented for the 1D and 2D mass spring systems with different examples. An enhancement in the band gap values was obtained by modeling the structures to obtain low frequency band gaps at small dimensions. Additionally, the evolution of the band gap as a function of mass value is discussed. Special attention is devoted to the local resonance property in frequency ranges within the gaps in the band structure for the corresponding infinite periodic lattice in the 1D and 2D mass spring system. A linear defect formed of a row of specific masses produces an elastic waveguide that transmits at the narrow pass band frequency. The frequency of the waveguides can be selected by adjusting the mass and stiffness coefficients of the materials constituting the waveguide. Moreover, we pay more attention to analyze the wave multiplexer and DE-multiplexer in the 2D mass spring system. We show that two of these tunable waveguides with alternating materials can be employed to filter and separate specific frequencies from a broad band input signal. The presented simulation data is validated through comparison with the published research, and can be extended in the development of resonators and MEMS verification.

  4. Quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya and next-nearest-neighbor interactions

    NASA Astrophysics Data System (ADS)

    Djoufack, Z. I.; Tala-Tebue, E.; Nguenang, J. P.; Kenfack-Jiotsa, A.

    2016-10-01

    We report in this work, an analytical study of quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya Interaction (DMI) and Next-Nearest-Neighbor Interactions (NNNI). By means of the time-dependent Hartree approximation and the semi-discrete multiple-scale method, the equation of motion for the single-boson wave function is reduced to the nonlinear Schrödinger equation. It comes from this present study that the spectrum of the frequencies increases, its periodicity changes, in the presence of NNNI. The antisymmetric feature of the DMI was probed from the dispersion curve while changing the sign of the parameter controlling it. Five regions were identified in the dispersion spectrum, when the NNNI are taken into account instead of three as in the opposite case. In each of these regions, the quantum model can exhibit quantum stationary localized and stable bright or dark soliton solutions. In each region, we could set up quantum localized n-boson Hartree states as well as the analytical expression of their energy level, respectively. The accuracy of the analytical studies is confirmed by the excellent agreement with the numerical calculations, and it certifies the stability of the stationary quantum localized solitons solutions exhibited in each region. In addition, we found that the intensity of the localization of quantum localized n-boson Hartree states increases when the NNNI are considered. We also realized that the intensity of Hartree n-boson states corresponding to quantum discrete soliton states depend on the wave vector.

  5. Quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya and next-nearest-neighbor interactions.

    PubMed

    Djoufack, Z I; Tala-Tebue, E; Nguenang, J P; Kenfack-Jiotsa, A

    2016-10-01

    We report in this work, an analytical study of quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya Interaction (DMI) and Next-Nearest-Neighbor Interactions (NNNI). By means of the time-dependent Hartree approximation and the semi-discrete multiple-scale method, the equation of motion for the single-boson wave function is reduced to the nonlinear Schrödinger equation. It comes from this present study that the spectrum of the frequencies increases, its periodicity changes, in the presence of NNNI. The antisymmetric feature of the DMI was probed from the dispersion curve while changing the sign of the parameter controlling it. Five regions were identified in the dispersion spectrum, when the NNNI are taken into account instead of three as in the opposite case. In each of these regions, the quantum model can exhibit quantum stationary localized and stable bright or dark soliton solutions. In each region, we could set up quantum localized n-boson Hartree states as well as the analytical expression of their energy level, respectively. The accuracy of the analytical studies is confirmed by the excellent agreement with the numerical calculations, and it certifies the stability of the stationary quantum localized solitons solutions exhibited in each region. In addition, we found that the intensity of the localization of quantum localized n-boson Hartree states increases when the NNNI are considered. We also realized that the intensity of Hartree n-boson states corresponding to quantum discrete soliton states depend on the wave vector.

  6. Supramolecular open-framework based on 1-D iron phosphate-diphosphate chains assembled through hydrogen bonding

    SciTech Connect

    Salvado, Miguel A.; Pertierra, Pilar; Trobajo, Camino; Garcia, Jose R.

    2008-05-15

    Fe(H{sub 2}PO{sub 4})(H{sub 2}P{sub 2}O{sub 7}).C{sub 5}H{sub 5}N, a new iron(III) phosphate with an open-framework has been synthesized hydrothermally using pyridine as organic template. The crystal structure was solved ab initio using conventional powder X-ray diffraction data. The unit cell is orthorhombic, a=9.5075(2), b=10.1079(1), c=13.3195(2) A, space group P2{sub 1}2{sub 1}2{sub 1}, Z=4. The structure consists of FeO{sub 6} octahedra joined by H{sub 2}PO{sub 4} and H{sub 2}P{sub 2}O{sub 7} groups forming linear chains interconnected by hydrogen bonding to give rise to a supramolecular framework enclosing tunnels in which the pyridine molecules reside. - Graphical abstract: The low temperature hydrothermal synthesis offers many possibilities in the preparation of new materials with mixed octahedral-tetrahedral open-frameworks. Fe(H{sub 2}PO{sub 4})(H{sub 2}P{sub 2}O{sub 7}).C{sub 5}H{sub 5}N is constituted by linear chains of FeO{sub 6} octahedra joined through of both dihydrogenphosphate and dihydrogendiphosphate bridges, interconnected by hydrogen bonds, originating channels where the pyridine molecules are located.

  7. 1d, 2d, and 3d periodic structures: Electromagnetic characterization, design, and measurement

    NASA Astrophysics Data System (ADS)

    Brockett, Timothy John

    Periodic structures have many useful applications in electromagnetics including phased arrays, frequency selective surfaces, and absorbing interfaces. Their unique properties can be used to provide increased performance in antenna gain, electromagnetic propagation, and electromagnetic absorption. In antenna arrays, repeating elements create a larger eective aperture, increasing the gain of the antenna and the ability to scan the direction of the main beam. Three-dimensional periodic structures, such as an array of shaped pillars such as columns, cones, or prisms have the potential of improving electromagnetic absorption, improving performance in applications such as solar cell eciency and absorbing interfaces. Furthermore, research into periodic structures is a continuing endeavor where novel approaches and analysis in appropriate applications can be sought. This dissertation will address the analysis, diagnostics, and enhancement of 1D, 2D, and 3D periodic structures for antenna array applications and solar cell technology. In particular, a unique approach to array design will be introduced to prevent the appearance of undesirable grating lobes in large antenna arrays that employ subarrays. This approach, named the distortion diagnostic procedure, can apply directly to 1D and 2D periodic structures in the form of planar antenna arrays. Interesting corollaries included here are developments in millimeter-wave antenna measurements including spiral planar scanning, phaseless measurements, and addressing antennas that feature an internal source. Finally, analysis and enhancement of 3D periodic structures in nanostructure photovoltaic arrays and absorbing interfaces will be examined for their behavior and basic operation in regards to improved absorption of electromagnetic waves.

  8. Thermodynamic nature of vitrification in a 1D model of a structural glass former

    SciTech Connect

    Semenov, A. N.

    2015-07-28

    We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.

  9. Thermodynamic nature of vitrification in a 1D model of a structural glass former

    NASA Astrophysics Data System (ADS)

    Semenov, A. N.

    2015-07-01

    We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.

  10. Thermodynamic nature of vitrification in a 1D model of a structural glass former.

    PubMed

    Semenov, A N

    2015-07-28

    We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.

  11. Controlled Self-Assembly of Cyclophane Amphiphiles: From 1D Nanofibers to Ultrathin 2D Topological Structures

    SciTech Connect

    Cai, Zhengxu; Li, Lianwei; Lo, Wai-Yip; Zhao, Donglin; Wu, Qinghe; Zhang, Na; Su, Yu-An; Chen, Wei; Yu, Luping

    2016-07-05

    A novel series of amphiphilic TC-PEG molecules were designed and synthesized based on the orthogonal cyclophane unit. These molecules were able to self-assemble from 1D nanofibers and nanobelts to 2D ultrathin nanosheets (3 nm thick) in a controlled way by tuning the length of PEG side chains. The special structure of the cyclophane moiety allowed control in construction of nanostructures through programmed noncovalent interactions (hydrophobic hydrophilic interaction and pi-pi interaction). The self-assembled nanostructures were characterized by combining real space imaging (TEM, SEM, and AFM) and reciprocal space scattering (GIWAXS) techniques. This unique supramolecular system may provide a new strategy for the design of materials with tunable nanomorphology and functionality.

  12. Kinetic fragility and structure of lithium borophosphate glasses analysed by 1D/2D NMR.

    PubMed

    Muñoz-Senovilla, Laura; Tricot, Gregory; Muñoz, Francisco

    2017-08-30

    The macroscopic and high temperature properties of lithium borophosphate glasses were determined in this contribution. Our data, obtained on 50Li2O-xB2O3-(50-x)P2O5 glasses, confirm a continuous and linear increase of the glass transition temperature with the B/P substitution but show a two-domain evolution of the kinetic fragility with a steep decrease in the low B2O3 region (0 ≤ x ≤ 10) followed by a moderate increase for higher B2O3 contents. In order to understand this different behaviour, the glass structure was investigated in detail using 1D and 2D (11)B/(31)P correlation solid state nuclear magnetic resonance. The local and medium orders of borate units were determined by 1D MAS-NMR, 2D (11)B DQSQ- and (11)B((31)P) D-HMQC NMR experiments. The latter NMR technique was also used to deeply interpret the 1D (31)P MAS-NMR spectra. Altogether the data allow (i) highlighting of the presence of four borate and seven phosphate units, (ii) evaluation of the number of homopolar POP and mixed POB linkages, and (iii) contribute to a better understanding of the Tg and kinetic fragility evolution.

  13. Study of phase transformation and crystal structure for 1D carbon-modified titania ribbons

    SciTech Connect

    Zhou, Lihui Zhang, Fang; Li, Jinxia

    2014-02-15

    One-dimensional hydrogen titanate ribbons were successfully prepared with hydrothermal reaction in a highly basic solution. A series of one-dimensional carbon-modified TiO{sub 2} ribbons were prepared via calcination of the mixture of hydrogen titanate ribbons and sucrose solution under N{sub 2} flow at different temperatures. The phase transformation process of hydrogen titanate ribbons was investigated by in-situ X-ray diffraction at various temperatures. Besides, one-dimensional carbon-modified TiO{sub 2} ribbons calcined at different temperatures were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, nitrogen adsorption isotherms, diffuse reflectance ultraviolet–visible spectroscopy, and so on. Carbon-modified TiO{sub 2} ribbons showed one-dimensional ribbon crystal structure and various crystal phases of TiO{sub 2}. After being modified with carbon, a layer of uniform carbon film was coated on the surface of TiO{sub 2} ribbons, which improved their adsorption capacity for methyl orange as a model organic pollutant. One-dimensional carbon-modified TiO{sub 2} ribbons also exhibited enhanced visible-light absorbance with the increase of calcination temperatures. - Highlights: • The synthesis of 1D carbon-modified TiO{sub 2} ribbons. • The phase transformation of 1D carbon-modified TiO{sub 2} ribbons. • 1D carbon-modified TiO{sub 2} exhibites enhanced visible-light absorbance.

  14. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    SciTech Connect

    Maskaly, Karlene Rosera

    2005-06-01

    increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

  15. Tight-Binding Approximations in 1D and 2D Coupled-Cavity Photonic Crystal Structures

    NASA Astrophysics Data System (ADS)

    Day, Nicole C. L.

    Light confinement and controlling an optical field has numerous applications in the field of telecommunications for optical signals processing. When the wavelength of the electromagnetic field is on the order of the period of a photonic microstructure, the field undergoes reflection, refraction, and coherent scattering. This produces photonic bandgaps, forbidden frequency regions or spectral stop bands where light cannot exist. Dielectric perturbations that break the perfect periodicity of these structures produce what is analogous to an impurity state in the bandgap of a semiconductor. The defect modes that exist at discrete frequencies within the photonic bandgap are spatially localized about the cavity-defects in the photonic crystal. In this thesis the properties of two tight-binding approximations (TBAs) are investigated in one-dimensional and two-dimensional coupled-cavity photonic crystal structures. We require an efficient and simple approach that ensures the continuity of the electromagnetic field across dielectric interfaces in complex structures. In this thesis we develop E- and D-TBAs to calculate the modes in finite 1D and 2D two-defect coupled-cavity photonic crystal structures. In the E- and D-TBAs we expand the coupled-cavity [vector electron]-modes in terms of the individual [vector electron]- and [vector D meson]-modes, respectively. We investigate the dependence of the defect modes, their frequencies and quality factors on the relative placement of the defects in the photonic crystal structures. We then elucidate the differences between the two TBA formulations, and describe the conditions under which these formulations may be more robust when encountering a dielectric perturbation. Our 1D analysis showed that the 1D modes were sensitive to the structure geometry. The antisymmetric D mode amplitudes show that the D. TBA did not capture the correct (tangential [vector electron]-field) boundary conditions. However, the D-TBA did not yield

  16. Computation of 1-D shock structure using nonlinear coupled constitutive relations and generalized hydrodynamic equations

    NASA Astrophysics Data System (ADS)

    Zhao, Wenwen; Jiang, Zhongzheng; Chen, Weifang

    2016-11-01

    The moment methods in rarefied gas dynamics could be divided into generalized hydrodynamic equations (GHE) and extended hydrodynamic equations (EHE), e.g., Burnett equations, Grad equations and R-13 equations, theoretically. Eu firstly developed the GHE based on a non-equilibrium canonical distribution function and demonstrated the thermodynamically consistent of this model. Subsequently, nonlinear coupled constitutive relations (NCCR) was proposed by Myong by omitting the product of heat flux and velocity gradient in GHE to reduce the computational complexity. According to the successful application in 1-D shock wave structure and 2-D flat plate flow, the capability of NCCR has already been demonstrated successfully. The motivation of this study was to investigate the different behavior of NCCR and GHE for monatomic and diatomic gases in one-dimensional shock structure problems. Therefore, argon and nitrogen shock structure was calculated using both GHE and NCCR model up to Ma=50. The 3rd order MUSCL scheme for inviscid term and the 2nd order central difference scheme for viscid scheme were employed to carry out the computations. Finally, the present results including shock wave profile and its qualitative properties by NCCR and GHE are compared with that of DSMC and NS equations. The results showed that the GHE yield 1-D shock wave in much closer agreement with DSMC results than do the NCCR model without considering the computational complexity and efficiency in present cases.

  17. Self-assembly of silver(I) coordination polymers from aminopyrimidyl derivatives and malonate acid: From 1D chain to 2D layer

    NASA Astrophysics Data System (ADS)

    Sun, Di; Zhang, Na; Xu, Qin-Juan; Luo, Geng-Geng; Huang, Rong-Bin; Zheng, Lan-Sun

    2010-04-01

    Two new silver(I) coordination polymers (CPs) of the formula [Ag 2(dmapym) 4(mal)·H 2O] n ( 1) and [Ag 3(apym) 3(mal)NO 3] n ( 2) (dmapym = 2-amino-4,6-dimethylprimidine, apym = 2-aminopyrimidine, H 2mal = malonate) have been synthesized by reactions of AgNO 3 and 2-aminopyrimidyl ligands with malonate under the ammoniacal condition. Both complexes have been characterized by element analysis, IR and single-crystal X-ray diffraction. The monodentate dmapym and tridentate mal ligands link Ag(I) ions to give complex 1 a one-dimensional (1D) H-shaped chain structure. The complex 2 is a two-dimensional (2D) double sheet structure constructed by (4, 4) single sheet. Additionally, the hydrogen-bonding and C-H⋯π interactions also direct the self-assembly of supramolecular architectures. The photoluminescence properties of the 1 and 2 were investigated in the solid state at room temperature.

  18. Observation of ferromagnetic and antiferromagnetic coupling in 1-D and 2-D extended structures of copper(II) terephthalates

    SciTech Connect

    Deakin, L.; Arif, A.M.; Miller, J.S.

    1999-11-01

    The reaction between CuCl{sub 2}{center{underscore}dot}2H{sub 2}O and disodium terephthalate, Na{sub 2}tp, in aqueous solution simultaneously produces chain, bis(aqua)[{mu}-(terephthalato-{kappa}O:{kappa}O{prime})]copper(II), monohydrate, Cutp(OH{sub 2}){sub 2}{center{underscore}dot}H{sub 2}O (1), and layered, bis(aqua)[{mu}-(terephthalato-{kappa}O)]copper(II), Cutp(OH{sub 2}){sub 2} (2), structured materials. 1 (C{sub 8}H{sub 10}CuO{sub 7}) belongs to the orthorhombic P2{sub 1}2{sub 1}2 space group [a = 6.3015(4) {angstrom}, b = 6.8743(4) {angstrom}, c = 22.9972(14) {angstrom}, and Z = 4] and incorporates tp in a bridging bis-monodentate binding mode and Cu(II) in a tetragonally elongated octahedron. 2 (C{sub 8}H{sub 10}CuO{sub 6}) which belongs to the orthorhombic Pmc2{sub 1} space group [a = 10.7421(8) {angstrom}, b = 7.2339(10) {angstrom}, c = 5.7143(13) {angstrom}, and Z = 2] incorporates tp in a mono-bidentate binding mode and Cu(II) in a distorted square pyramid. 1 and 2 exhibit axial X-band powder EPR spectra with G{sub {perpendicular}} = 2.08, g{sub {parallel}} = 2.29 (1) and g{sub {perpendicular}} = 2.07, g{sub {parallel}} = 2.29 (2) at 300 K. 1 obeys the Curie-Weiss law at high temperatures ({theta} = {minus}7.2 K) and at low temperatures behaves as 1-D magnetic chains with an exchange-coupling constant of J/k{sub B} = {minus}9.15 K (H = {minus}2JS{sub 1}{center{underscore}dot}S{sub 2}). This material displays a spontaneous moment below 2 K under small applied magnetic fields, consistent with the presence of spin canting. 2 exhibits ferromagnetic interactions with {theta} = +0.8 K. Along the 1-D chain where coordinated water forms the bridge between metal centers, the coupling between Cu(II) is J/k{sub B} = +0.6 K. The fit of the magnetic susceptibility for 2 using a molecular field correction, which takes into consideration antiferromagnetic interactions between chains via the tp ligand, yields J{prime}/k{sub B} = {minus}0.13 K.

  19. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    NASA Astrophysics Data System (ADS)

    Zhang, Yingjie; Bhadbhade, Mohan; Karatchevtseva, Inna; Price, Jason R.; Liu, Hao; Zhang, Zhaoming; Kong, Linggen; Čejka, Jiří; Lu, Kim; Lumpkin, Gregory R.

    2015-03-01

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H4btca) have been synthesized and structurally characterized. (ED)[(UO2)(btca)]·(DMSO)·3H2O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH4)2[(UO2)6O2(OH)6(btca)]·~6H2O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO2)2(H2O)(btca)]·4H2O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ5-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated.

  20. Crystal structure of TBC1D15 GTPase-activating protein (GAP) domain and its activity on Rab GTPases.

    PubMed

    Chen, Yan-Na; Gu, Xin; Zhou, X Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei; Xu, H Eric; Lv, Zhengbing

    2017-04-01

    TBC1D15 belongs to the TBC (Tre-2/Bub2/Cdc16) domain family and functions as a GTPase-activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark-TBC1D15 and Sus-TBC1D15 belong to the same subfamily of TBC domain-containing proteins, and their GAP-domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost.

  1. Modeling of subsurface structures in Telomoyo Volcano geothermal area, Magelang using 1-D magnetotelluric method

    NASA Astrophysics Data System (ADS)

    Sarjan, Achmad Fajar Narotama; Niasari, Sintia Windhi

    2017-07-01

    There are some of geothermal prospects around Java Island. One of them are located in Telomoyo Volcano area, Magelang, Central Java. The existence of hot spring manifestations in Telomoyo Volcano area shows the presence of geothermal system. The upflow zone of this geothermal system was formed in the caldera of Telomoyo Volcano area, while the outflow zone was formed around Candi Umbul. In addition, from the geological map shows a geological structure assumed as a normal fault with southwest-northeast orientation that was caused by the volcanic activity. The aim of this research is to give a brief introduction about subsurface resistivity beneath Telomoyo Volcano area using 1-D magnetotelluric forward model. Thus, we can determine the possibility of data that will obtained during the acquisition process based on the geological model that was made. The apparent resistivity, phase, and period values were obtained from the forward modeling process. The result from this study is a 1-D resistivity section with synthetics curves of each geothermal model. In each model the presence of clay cap characterized by a low resistivity layer. A layer below the clay cap with a medium resistivity value interpreted as the reservoir of this geothermal system. The heat source of this geothermal area is characterized by a low resistivity that is located at depth 4000-5500m. This study is still in progress to acquire the exact values of resistivity from each layer from the field data acquisition in Telomoyo Volcano area, Magelang.

  2. Method of single expression: an exact solution for wavelength scale 1D photonic structure computer modeling

    NASA Astrophysics Data System (ADS)

    Baghdasaryan, Hovik V.; Knyazyan, Tamara M.

    2003-12-01

    The principles of the method of single expression (MSE) for boundary problems solution in classical electrodynamics are presented. In the MSE the solution of the Helmholtz's equation is presented in the special form of a single expression describing resultant amplitude and phase distributions in the medium. This form of solution presenation permits to pass over the restrictions of the superposition principle and to solve both linear and nonlinear problems with ths same ease. In the MSE the Helmholtz's equation is reformulated to the set of first order differential equations and the boundary problem is solved numerically. No approximations are implied either in Helmholtz's equation or in boundary conditions. Using the MSE steady-state boundary problems are modeled for wavelength scale multilayer and modulated 1D photonic structures including amplification and nonuniformity evoked by intense electromagnetic field.

  3. Structural transformation in monolayer materials: a 2D to 1D transformation.

    PubMed

    Momeni, Kasra; Attariani, Hamed; LeSar, Richard A

    2016-07-20

    Reducing the dimensions of materials to atomic scales results in a large portion of atoms being at or near the surface, with lower bond order and thus higher energy. At such scales, reduction of the surface energy and surface stresses can be the driving force for the formation of new low-dimensional nanostructures, and may be exhibited through surface relaxation and/or surface reconstruction, which can be utilized for tailoring the properties and phase transformation of nanomaterials without applying any external load. Here we used atomistic simulations and revealed an intrinsic structural transformation in monolayer materials that lowers their dimension from 2D nanosheets to 1D nanostructures to reduce their surface and elastic energies. Experimental evidence of such transformation has also been revealed for one of the predicted nanostructures. Such transformation plays an important role in bi-/multi-layer 2D materials.

  4. Structural repertoire of immunoglobulin λ light chains.

    PubMed

    Chailyan, Anna; Marcatili, Paolo; Cirillo, Davide; Tramontano, Anna

    2011-05-01

    The immunoglobulin λ isotype is present in nearly all vertebrates and plays an important role in the human immune system. Despite its importance, few systematic studies have been performed to analyze the structural conformation of its variable regions, contrary to what is the case for κ and heavy chains. We show here that an analysis of the structures of λ chains allows the definition of a discrete set of recurring conformations (canonical structures) of their hypervariable loops and, most importantly, the identification of sequence constraints that can be used to predict their structure. We also show that the structural repertoire of λ chains is different and more varied than that of the κ chains, consistently with the current view of the involvement of the two major light-chain families in complementary strategies of the immune system to ensure a fine tuning between diversity and stability in antigen recognition.

  5. Synthesis, crystal structures, magnetic and luminescent properties of unique 1D p-ferrocenylbenzoate-bridged lanthanide complexes

    SciTech Connect

    Yan, P.F.; Zhang, F.M.; Li, G.M.; Zhang, J.W.; Sun, W.B.; Suda, M.; Einaga, Y.

    2009-07-15

    Treatments of p-ferrocenylbenzoate [p-NaOOCH{sub 4}C{sub 6}Fc, Fc=(eta{sup 5}-C{sub 5}H{sub 5})Fe(eta{sup 5}-C{sub 5}H{sub 4})] with Ln(NO{sub 3}){sub 3}.nH{sub 2}O afford seven p-ferrocenylbenzoate lanthanide complexes {l_brace}[Ln(OOCH{sub 4}C{sub 6}Fc){sub 2}(mu{sub 2}-OOCH{sub 4}C{sub 6}Fc){sub 2}(H{sub 2}O){sub 2}](H{sub 3}O){r_brace}{sub n} [Ln=Ce (1), Pr (2), Sm (3), Eu (4), Gd (5), Tb (6) and Dy (7)]. X-ray crystallographic analysis reveals that the isomorphous complexes {l_brace}[Ce(OOCH{sub 4}C{sub 6}Fc){sub 2}(mu{sub 2}-OOCH{sub 4}C{sub 6}Fc){sub 2}(H{sub 2}O){sub 2}](H{sub 3}O){r_brace}{sub n} (1) and {l_brace}[Pr(OOCH{sub 4}C{sub 6}Fc){sub 2}(mu{sub 2}-OOCH{sub 4}C{sub 6}Fc){sub 2}(H{sub 2}O){sub 2}](H{sub 3}O){r_brace}{sub n} (2) form a unique 1D double-bridged infinite chain structure bridged by mu{sub 2}-OOCH{sub 4}C{sub 6}Fc groups. Each Ln(III) ion adopts a dodecahedron coordination environment with eight coordinated oxygen atoms from two terminal monodentate coordinated FcC{sub 6}H{sub 4}COO{sup -} units, two terminal monodentate coordinated H{sub 2}O molecules and four mu{sub 2}-{sup -}OOCH{sub 4}C{sub 6}Fc units. The luminescent spectra reveal that only 4 and 6 exhibit characteristic emissions of lanthanide ions, Eu(III) and Tb(III) ions, respectively. The variable-temperature magnetic properties of 5 and 7 suggest that a ferromagnetic coupling between spin carriers may exist in 5. - Graphical abstract: Seven p-ferrocenylbenzoate lanthanide coordination polymers were synthesized. Given is the perspective view of a unique 1D double-bridged infinite chain structure of 1, excitation and emission spectra of 6 and plots of chi{sub m}T vs. T and chi{sub m}{sup -1} vs. T of 5.

  6. Four 1-D metal-organic polymers self-assembled from semi-flexible benzimidazole-based ligand: Syntheses, structures and fluorescent properties

    NASA Astrophysics Data System (ADS)

    Zhou, Chun-lin; Wang, Shi-min; Liu, Sai-nan; Yu, Tian-tian; Li, Rui-ying; Xu, Hong; Liu, Zhong-yi; Sun, Huan; Cheng, Jia-jia; Li, Jin-peng; Hou, Hong-wei; Chang, Jun-biao

    2016-08-01

    Four one-dimensional (1-D) metal-organic polymers based on methylene-bis(1,1‧-benzimidazole)(mbbz), namely, {[Hg(mbbz)(SCN)2]·1/3H2O}n (1), [Co(mbbz)(Cl)2]n (2), {[Co(mbbz)(SO4)]·CH3OH}n (3) and {[Zn(mbbz)(SO4)]·CH3OH}n (4) have been successfully synthesized and structurally characterized. Single-crystal X-ray diffraction reveals that polymers 1 and 2 exhibit interesting 1-D double helical chain structures, while polymers 3 and 4 are 1-D double chain structures due to the bridging effect of mbbz ligands and sulfate anions. These polymers containing the mbbz-based ligand have a high degree of dependence on the corresponding counter anions. Furthermore, the fluorescence properties of the four polymers were also investigated in the solid state, showing the fluorescence signal changes in comparing with that of free ligand mbbz.

  7. Switching waves and dissipative structures in a chain of spasers

    SciTech Connect

    Andrianov, E S; Pukhov, A A; Dorofeenko, Aleksandr V; Vinogradov, Aleksei P; Lisyansky, Aleksandr A

    2012-09-30

    We have considered the physical mechanism of optical bistability in a spaser in the field of an external optical wave. We have studied the effect of this phenomenon on the dynamics of a 1D chain of coupled spasers. It is shown that such a chain demonstrates the behaviour typical of open nonlinear systems. In particular, for high Joule losses in a spaser, a nonlinear switching autowave propagates in the chain, thereby evolving the spasers' state from a low population inversion state into a high population inversion state or vice versa. The control parameter that determines the type of switching is the amplitude of the external optical wave. For low Joule losses there emerge quasi-periodic dissipative structures whose formation dynamics is of 'self-assembly' nature. (optical fibres, lasers and amplifiers. properties and applications)

  8. The Role of the Impedivity in the Magnetotelluric Response of 1D and 2D Structures

    NASA Astrophysics Data System (ADS)

    Esposito, Roberta; Giulia Di Giuseppe, Maria; Troiano, Antonio; Patella, Domenico; Mariano Castelo Branco, Raimundo

    2014-05-01

    The influence of the resistivity dispersion on the magnetotelluric (MT) response is analyzed. MT uses the natural electromagnetic (EM) field to determine the electrical resistivity of the subsoil and retrieve the geometry of lithospheric structures, revealing the presence of bodies as metallic deposits, hydrocarbons reservoirs, geothermal fluids. The frequency range of the EM field used varies from 10-4 to 104 Hz. If the soil is polarizable, the dispersion of the resistivity, whose characteristic frequency interval is between 10-2 and 102 Hz, may affect MT responses. Resistivity dispersion is a known phenomenology, which constitutes the basis of the Induced Polarization (IP) prospecting method. In the frequency domain (FD), the dispersion consists in a variation of the resistivity parameter as the frequency of the exciting current is changed. The dispersive resistivity, called impedivity, is a complex function of the frequency. At vanishing frequency, however, the impedivity is real and coincides with the classical resistivity parameter used in DC geoelectrical methods. A real asymptote is also approached as the frequency tends to infinity. The complex physical and chemical fluid-metal-rock interactions may produce induced polarization effects, which are related to the dispersion in rocks. This is manifested on the MT response, creating a distortion on the experimental curves. Disregarding the distortion effect may lead to misleading interpretation of the surveyed structures. We show the results from simulation of the MT responses, when dispersion is assumed to characterize the electrical properties of a region of the explored half-space. Initially, a 1D-layered earth is considered, with intermediate layer assumed to be dispersive. The influence of the dispersion amplitude on the shape of the MT responses is evaluated. The dispersion alters the shape of the curves in a way that, without any external constraints, may make the interpretation of the curves quite

  9. Optical bullets in (2+1)D photonic structures and their interaction with localized defects

    NASA Astrophysics Data System (ADS)

    Dohnal, Tomas

    2005-11-01

    This dissertation studies light propagation in Kerr-nonlinear two dimensional waveguides with a Bragg resonant, periodic structure in the propagation direction. The model describing evolution of the electric field envelopes is the system of 2D Nonlinear Coupled Mode Equations (2D CME). The periodic structure induces a range of frequencies (frequency gap) in which linear waves do not propagate. It is shown that, similarly to the ID case of a fiber grating, the 2D nonlinear system supports localized solitary wave solutions, referred to as 2D gap solitons, which have frequencies inside the linear gap and can travel at, any speed smaller than or equal to the speed of light in the corresponding homogeneous medium. Such solutions are constructed numerically via Newton's iteration. Convergence is obtained only near the upper edge of the gap. Gap solitons with a nonzero velocity are constructed by numerically following a bifurcation curve parameterized by the velocity v. It is shown that gap solitons are saddle points of the corresponding Hamiltonian functional and that no (constrained) local minima of the Hamiltonian exist. The linear stability problem is formulated and reasons for the failure of the standard Hamiltonian PDE approach for determining linear stability are discussed. In the second part of the dissertation interaction of 2D gap solitons with localized defects is studied and trapping of slow enough 2D gap solitons is demonstrated. This study builds on [JOSA B 19, 1635 (2002)], where such trapping of 1D gap solitons is considered. Analogously to this 1D problem trapping in the 2D model is explained as a resonant energy transfer into one or more defect modes existent for the particular defect. For special localized defects exact linear modes are found explicitly via the separation of variables. Numerical computation of linear defect modes is used for more general defects. Corresponding nonlinear modes are then constructed via Newton's iteration by following a

  10. Syntheses, crystal structures and properties of two 1-D cadmium(II) coordination polymers based on 1,1'-(1,3-propanediyl)bis-1H-benzimidazole

    SciTech Connect

    Yang Huaixia; Meng Xiangru; Liu Yun; Hou Hongwei Fan Yaoting; Shen Xiaoqing

    2008-09-15

    The combination of framework-builders 1,1'-(1,3-propanediyl)bis-1H-benzimidazole (pbbm), Cd(II) ion and framework-regulator ClO{sub 4}{sup -} or SO{sub 4}{sup 2-} provides two new coordination polymers [Cd(pbbm){sub 2}(ClO{sub 4}){sub 2}]{sub n}(1) and {l_brace}[Cd(pbbm)SO{sub 4}(H{sub 2}O){sub 2}].CH{sub 3}OH{r_brace}{sub n}(2). Both of them display 1-D chain framework, but their detailed structures are clearly different from each other. 1 displays a 1-D ribbon of rings framework, 2 features an interesting infinite 1-D looped chain structure composed of two kinds of rings, the smaller 8-membered ring and the larger 20-membered ring. The antimicrobial activities of the two polymers were tested by the agar diffusion method and the results indicated that they exhibited antimicrobial activities against bacterial strands. The measurement of the non-isothermal kinetics of the thermal decomposition of 2 reveals that there are at least three steps that occur in its decomposition process. - Graphical abstract: Two new Cd(II)-containing complexes have been synthesized and characterized by single-crystal X-ray diffraction. The antimicrobial activity and the non-isothermal kinetics of the thermal decomposition of the polymers were also investigated. Display Omitted.

  11. Binding of actinomycin C1 (D) and actinomin to base-modified oligonucleotide duplexes with parallel chain orientation.

    PubMed

    Li, Hong; Peng, Xiaohua; Leonard, Peter; Seela, Frank

    2006-06-15

    The binding of actinomycin D (C1, 1) and its analog actinomin (2) was studied on base-modified oligonucleotide duplexes with parallel chain orientation (ps) and with anti-parallel chains (aps) for comparison. Actinomycin D binds not only to aps duplexes containing guanine-cytosine base pairs but also to those incorporating modified bases such as 7-deazaguanine or its 6-deoxo derivative. For this, novel phosphoramidites were prepared. The new building block of 7-deaza-2'-deoxyguanosine is significantly more stable than the one currently used and allows normal oxidation conditions during solid-phase oligonucleotide synthesis. Actinomycin binds weakly to ps duplexes containing guanine-isocytosine base pairs but not to ps-DNA incorporating pairs of isoguanine-cytosine residues. On the contrary, the actinomycin D analog actinomin, which contains positively charged side chains instead of the chiral peptide rings, is strongly bound to both ps- and aps-DNA. Guanines, isoguanine, as well as other 7-deaza derivatives are accepted as nucleobases. Apparently, the pentapeptide lacton rings of actinomycin do not fit nicely into the groove of ps-DNA thereby reducing the binding strength of the antibiotic while the groove size of ps-DNA does not affect actinomin binding notably.

  12. MAGNETIC CORE SHELL STRUCTURES: from 0D to 1D assembling.

    PubMed

    Ficai, Denisa; Ficai, Anton; Dinu, Elena; Oprea, Ovidiu; Sonmez, Maria; Keler, Memduh Kagan; Sahin, Yesim Muge; Ekren, Nazmi; Inan, Ahmet Talat; Daglilar, Sibel; Gunduz, Oguzhan

    2015-01-01

    Material research and development studies are focused on different techniques of bringing out nanomaterials with desired characteristics and properties. From the point of view of materials development, nowadays scientists are strongly focused on obtaining materials with predefined characteristics and properties. The morphology control seems to be a determinant factor and increasing attention is devoted to this aspect. At this moment it is possible to engineer the material's features by using different methods and materials combination for both medical and industrial applications. In the applications of chemistry and synthesis, biology, mechanics, optics solar cells and microelectronics tailoring the adjustable parameters of stoichiometry, chemical structure, shape and segregation are evaluated and opens new fields. Because of the magnetic features of nanoparticles and durable particle size, less than 100 nm, this study is aiming to describe their uses in practical applications. That's why the whole hydrodynamic magnetic core shell topic will be reviewed on this paper. Additionally, the properties acting in general sight in solid-state physics are utilized for material selection and for defining issue connecting the core, shell structure and their producing properties. Here, in the study of core/shell nanoparticle various physical and chemical synthesis routes and the effect of electrospun method are briefly discussed. Starting from a real void of the scientific literature, the existent data related to the 1D magnetic electrospun materials are reviewed. The perspectives in the medical, environmental or energetic sector is great and bring some real advantages related to the 0D core@shell structures because both mechanical and biological properties are dependent on the morphology of the materials.

  13. Structure of Human Ferritin L Chain

    SciTech Connect

    Wang,Z.; Li, C.; Ellenburg, M.; Soistman, E.; Ruble, J.; Wright, B.; Ho, J.; Carter, D.

    2006-01-01

    Ferritin is the major iron-storage protein present in all cells. It generally contains 24 subunits, with different ratios of heavy chain (H) to light chain (L), in the shape of a hollow sphere hosting up to 4500 ferric Fe atoms inside. H-rich ferritins catalyze the oxidation of iron(II), while L-rich ferritins promote the nucleation and storage of iron(III). Several X-ray structures have been determined, including those of L-chain ferritins from horse spleen (HoSF), recombinant L-chain ferritins from horse (HoLF), mouse (MoLF) and bullfrog (BfLF) as well as recombinant human H-chain ferritin (HuHF). Here, structures have been determined of two crystal forms of recombinant human L-chain ferritin (HuLF) obtained from native and perdeuterated proteins. The structures show a cluster of acidic residues at the ferrihydrite nucleation site and at the iron channel along the threefold axis. An ordered Cd{sup 2+} structure is observed within the iron channel, offering further insight into the route and mechanism of iron transport into the capsid. The loop between helices D and E, which is disordered in many other L-chain structures, is clearly visible in these two structures. The crystals generated from perdeuterated HuLF will be used for neutron diffraction studies.

  14. A ferrocenyl-substituted 1,2,4-triazole ligand and its Fe(II), Ni(II) and Cu(II) 1D-chain complexes.

    PubMed

    Scott, Hayley S; Nafady, Ayman; Cashion, John D; Bond, Alan M; Moubaraki, Boujemaa; Murray, Keith S; Neville, Suzanne M

    2013-07-28

    As part of a program aimed at making bifunctional iron(II) spin-crossover (SCO) materials, particularly those having redox/electron transfer as the second function, we have made the new ferrocene-triazole ligand ATF ([(4H-1,2,4-triazol-4-yl)amino]methylferrocene), (1), and a series of M(II) complexes of this ligand with emphasis on iron(II). Polynuclear 1D-chain complexes [Fe(ATF)3](Br)2·0.5(H2O) (2), [Fe(ATF)3](ClO4)2·0.5(H2O) (3), [Ni(ATF)3](ClO4)2·0.5(H2O) (4) and an analogous complex formed with a positively charged ATF ligand [Fe(ATF(+))3](ClO4)5 (6) were formed as polycrystalline powders. Crystals of a mixed ATF/NCS-bridged copper(II) polymer [Cu(ATF)2(NCS)](ClO4)·(Et2O)0.5(MeCN) (5) were formed and structurally characterised. Magnetic and Mössbauer spectral measurements on 2, 3 and 6 indicated that SCO has not been achieved though the Mössbauer data show interesting temperature dependence for doublets of the two iron sites for complexes 2 and 3. Solid state cyclic voltammetric data on the iron(II) complexes 3 and 4 showed well defined, reversible ATF-based electrochemistry, similar to those shown by ATF in solution.

  15. Electronic and structural properties of 3D, 2D and 1D materials

    NASA Astrophysics Data System (ADS)

    Ribeiro, Filipe Joao

    In this work several applications of the ab initio pseudopotential density functional theory method are presented. With this method it is possible to calculate the electronic ground state properties of many systems like bulk solids, surfaces, nanotubes, and nanowires, and draw conclusions about the systems structural and electronic properties. With modifications of this approach excited states can also be treated. The first chapter of this thesis gives a brief description of the computational techniques employed. The second chapter describes results of calculations on the structural and electronic properties of carbon and germanium. We try to shed some light on a still poorly understood structural phase transition of graphite under pressure at low temperatures, which is different from the high temperature regime. Next, we study the phase transition path of germanium under pressure and predict the existence of a new phase. The following chapter explores the possibility of superconductivity in the graphite-like compound BC3 since there are many similarities between the electronic structure of this material and the 39 K superconductor MgB2. Subsequently, results of calculations on the adsorption of indium atoms on carbon nanotubes and graphite-like surfaces are presented. These studies explain some very interesting experimental results of In migration on nanotubes in an electrical potential. In the following chapters the electronic properties of very thin metallic MoSe nanowires are studied, and the different regimes of stability of metallic monatomic chains of Au, Al, Ag, Pd, Rh, and Ru are investigated and compared. Chapter 7 addresses the possible polymerization of C60 molecules inside carbon and boron nitride nanotubes. Finally, the propagation of a light signal in a medium with gains and losses is investigated, and the possibility of a discontinuity in the index of refraction is discussed.

  16. Structure and Stability of Monatomic Metallic Chains

    NASA Astrophysics Data System (ADS)

    Batra, Inder P.; Sen, Prasenjit; Ciraci, S.

    2001-03-01

    We have investigated atomic and electronic structure of Au and Al monatomic chains by using first-principle plane wave method within density-functional theory. Despite their different valencies, Au and Al form planar zigzag chains with each atom having four nearest neighbors. The zigzag structure is stable against linearization and non-planar deformations. We performed an extensive charge density analysis and finite temperature calculations to reveal the origin of the unusual atomic structure in these one dimensional metallic systems. The implications of the zigzag structure on the electronic properties and the balistic electron conduction have been examined.

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

    PubMed

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

    2003-08-15

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

  18. Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation

    SciTech Connect

    S Park; W Jin; S Shoelson

    2011-12-31

    We have solved the x-ray crystal structures of the RabGAP domains of human TBC1D1 and human TBC1D4 (AS160), at 2.2 and 3.5 {angstrom} resolution, respectively. Like the yeast Gyp1p RabGAP domain, whose structure was solved previously in complex with mouse Rab33B, the human TBC1D1 and TBC1D4 domains both have 16 {alpha}-helices and no {beta}-sheet elements. We expected the yeast Gyp1p RabGAP/mouse Rab33B structure to predict the corresponding interfaces between cognate mammalian RabGAPs and Rabs, but found that residues were poorly conserved. We further tested the relevance of this model by Ala-scanning mutagenesis, but only one of five substitutions within the inferred binding site of the TBC1D1 RabGAP significantly perturbed catalytic efficiency. In addition, substitution of TBC1D1 residues with corresponding residues from Gyp1p did not enhance catalytic efficiency. We hypothesized that biologically relevant RabGAP/Rab partners utilize additional contacts not described in the yeast Gyp1p/mouse Rab33B structure, which we predicted using our two new human TBC1D1 and TBC1D4 structures. Ala substitution of TBC1D1 Met{sup 930}, corresponding to a residue outside of the Gyp1p/Rab33B contact, substantially reduced catalytic activity. GLUT4 translocation assays confirmed the biological relevance of our findings. Substitutions with lowest RabGAP activity, including catalytically dead RK and Met{sup 930} and Leu{sup 1019} predicted to perturb Rab binding, confirmed that biological activity requires contacts between cognate RabGAPs and Rabs beyond those in the yeast Gyp1p RabGAP/mouse Rab33B structure.

  19. Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method

    NASA Astrophysics Data System (ADS)

    Wu, Hong; Li, Peng; Li, Yulong

    2016-02-01

    This paper describes the calculation method for unsteady state conditions in the secondary air systems in gas turbines. The 1D-3D-Structure coupled method was applied. A 1D code was used to model the standard components that have typical geometric characteristics. Their flow and heat transfer were described by empirical correlations based on experimental data or CFD calculations. A 3D code was used to model the non-standard components that cannot be described by typical geometric languages, while a finite element analysis was carried out to compute the structural deformation and heat conduction at certain important positions. These codes were coupled through their interfaces. Thus, the changes in heat transfer and structure and their interactions caused by exterior disturbances can be reflected. The results of the coupling method in an unsteady state showed an apparent deviation from the existing data, while the results in the steady state were highly consistent with the existing data. The difference in the results in the unsteady state was caused primarily by structural deformation that cannot be predicted by the 1D method. Thus, in order to obtain the unsteady state performance of a secondary air system more accurately and efficiently, the 1D-3D-Structure coupled method should be used.

  20. Synthesis, crystal structures, magnetic and luminescent properties of unique 1D p-ferrocenylbenzoate-bridged lanthanide complexes

    NASA Astrophysics Data System (ADS)

    Yan, P. F.; Zhang, F. M.; Li, G. M.; Zhang, J. W.; Sun, W. B.; Suda, M.; Einaga, Y.

    2009-07-01

    Treatments of p-ferrocenylbenzoate [ p-NaOOCH 4C 6Fc, Fc=( η5-C 5H 5)Fe( η5-C 5H 4)] with Ln(NO 3) 3· nH 2O afford seven p-ferrocenylbenzoate lanthanide complexes {[ Ln(OOCH 4C 6Fc) 2( μ2-OOCH 4C 6Fc) 2(H 2O) 2](H 3O)} n [ Ln=Ce ( 1), Pr ( 2), Sm ( 3), Eu ( 4), Gd ( 5), Tb ( 6) and Dy ( 7)]. X-ray crystallographic analysis reveals that the isomorphous complexes {[Ce(OOCH 4C 6Fc) 2( μ2-OOCH 4C 6Fc) 2(H 2O) 2](H 3O)} n ( 1) and {[Pr(OOCH 4C 6Fc) 2( μ2-OOCH 4C 6Fc) 2(H 2O) 2](H 3O)} n ( 2) form a unique 1D double-bridged infinite chain structure bridged by μ2-OOCH 4C 6Fc groups. Each Ln(III) ion adopts a dodecahedron coordination environment with eight coordinated oxygen atoms from two terminal monodentate coordinated FcC 6H 4COO - units, two terminal monodentate coordinated H 2O molecules and four μ2- -OOCH 4C 6Fc units. The luminescent spectra reveal that only 4 and 6 exhibit characteristic emissions of lanthanide ions, Eu(III) and Tb(III) ions, respectively. The variable-temperature magnetic properties of 5 and 7 suggest that a ferromagnetic coupling between spin carriers may exist in 5.

  1. Synthesis, structure and magnetic properties of 5-(4-Sulfophenylazo) salicylate-bridged 1D coordination polymers containing linear trinuclear metal clusters

    NASA Astrophysics Data System (ADS)

    Liu, Hong; Song, Li-jun; Ju, Zhan-feng; Li, Wei; Zhang, Jie

    2008-03-01

    Three new trinuclear metal complexes with an azobenzene-containing ligand [M 3(Sasa) 2(Py) 2(H 2O) 8] (Na 2HSasa = 5-(4-Sulfophenylazo) salicylic acid disodium salt; Py = pyridine; M = Cu, Co, Zn), are synthesized through the interface diffusion and structurally characterized by single crystal X-ray diffraction, XRPD analysis and spectral methods. The metal ions in distorted octahedral coordination environments are connected by Sasa ligands to form 1D coordination polymer chain containing the linear trinuclear units with single syn-anti carboxylate bridges. The extensive hydrogen bonding interactions hold these chains together into 3D supramolecular network. Weak antiferromagnetic interactions between adjacent metal ions with J = -1.85 cm -1 and J = -2.81 cm -1 dominate the magnetic properties of Cu(II) and Co(II) complexes, separately.

  2. Structural Origins of Martian Pit Chains

    NASA Astrophysics Data System (ADS)

    Wyrick, D.; Ferrill, D. A.; Morris, A. P.; Colton, S. L.; Sims, D. W.

    2003-12-01

    Pit craters are circular to elliptical depressions found in alignments (chains), which in many cases coalesce into linear troughs, and are common on the surface of Mars. Pit craters lack an elevated rim, ejecta deposits, or lava flows that are associated with impact craters or calderas. It is generally agreed that these features are formed by collapse into a subsurface cavity. Hypotheses regarding the formation of pit crater chains require development of a substantial subsurface void to accommodate collapse of the overlying sediments. Suggested mechanisms of formation include: collapsed lava tubes, dike swarms, collapsed magma chamber, karst dissolution, fissuring beneath loose material, and dilational faulting. The research described here is intended to constrain current interpretations of pit crater chain formation by analyzing their distribution and morphology. The western hemisphere of Mars was systematically mapped using Mars Orbiter Camera (MOC) images to generate ArcView Geographic Information System (GIS) coverages. All visible pit crater chains were mapped, including their orientations and associations with other structures. We found that pit chains commonly occur in areas that show regional extension or local fissuring. There is a strong correlation between pit chains and fault-bounded grabens. Frequently, there are transitions along strike from (i) visible faulting to (ii) faults and pits to (iii) pits alone. We performed a detailed quantitative analysis of pit crater morphology using MOC narrow angle images, Thermal Emission Imaging System (THEMIS) visual images and Mars Orbiter Laser Altimeter (MOLA) data. This allowed us to interpret a pattern of pit chain evolution and calculate pit depth, slope, and volume. The information collected in the study was then compared with non-Martian examples of pit chains and physical analog models. We evaluated the various mechanisms for pit chain development based on the data collected and conclude that dilational

  3. Comparison between GW and Wave-Function-Based Approaches: Calculating the Ionization Potential and Electron Affinity for 1D Hubbard Chains.

    PubMed

    Ou, Qi; Subotnik, Joseph E

    2016-07-07

    We calculate the ionization potential and electron affinity of 1D Hubbard chains with a variety of different site energies from two perspectives: (i) the physics-based GW approximation and (ii) the chemistry-based configuration interaction (CI) approach. Results obtained from all methods are compared against the exact values for three classes of systems: metallic, impurity doped, and molecular (semiconducting/insulating) systems. Although all methods are reasonably accurate for weakly correlated systems, the GW method is significantly more reliable for strongly correlated systems with little disorder unless explicit double excitations are included in the CI. In principle, our results should offer some intuition about the choice of methodologies as well as state references for different classes of physical systems.

  4. Structure of confined films of chain alcohols

    SciTech Connect

    Mugele, Friedrich; Baldelli, Steven; Somorjai, Gabor A.; Salmeron, Miquel

    1999-09-30

    The structure of thin films of simple chain alcohols (1-octanol and 1-undecanol) confined between two atomically smooth mica surfaces has been investigated using a surface forces apparatus (SFA). In both systems, the substrate-molecule interaction leads to a strongly bound first layer on each surface. Additional liquid organizes into highly compressible bilayers, which could be expelled by applying sufficiently high pressure.

  5. Supramolecular assembled of hexameric water clusters into a 1D chain containing (H2O)6 and [(H2O)4O2] stabilized by hydrogen bonding in a copper complex

    PubMed Central

    2012-01-01

    Background Various water clusters including hexamers, heptamers, octamers, decamers and 1D or 2D infinite water chains in a number of organic and inorganic-organic hybrid hosts, have been reported. Results {[Cu(pydc)(amp)].3H2O}n has been hydrothermally synthesized and characterized by elemental analysis and by IR spectroscopy. A wide range of hydrogen bonds (of the O-H...O, N-H...O and N-H...N type) are present in the crystal structure. Hydrogen bond interactions between the co-crystallized water molecules led to formation of six-membered rings with chair conformation. Conclusion In {[Cu(pydc)(amp)].3H2O}n, there are three uncoordinated water molecules. Thermal methods confirm number of co-crystallized water molecules in polymer. Hydrogen bond interactions between the co-crystallized water molecules led to the formation of a six-membered ring with the chair conformation. These rings are part of a 1D chain containing six-membered O6 rings, which are alternately made from (H2O)6 and [(H2O)4O2] rings. [(H2O)4O2] rings are also in chair conformation. PMID:22264401

  6. Far-Infrared Studies of 2D and 1D Electrons in Ultra High-Mobility Gated Semiconductor Structures

    NASA Astrophysics Data System (ADS)

    Heron, R. J.; Lewis, R. A.; Rickel, D. G.; Clark, R. G.; Starrett, R. P.; Kane, B. E.; Facer, G. R.; Lumpkin, N. E.; Dzurak, A. S.; Pfeiffer, L. N.; West, K. W.

    1998-03-01

    Far-infrared (FIR) photoconductivity experiments are reported for extremely high-mobility gated GaAs-AlGaAs 1D and 2D structures in which the electron density and confining potential are separately adjustable by surface gates. Unprecedented mean free paths in excess of 100 μm are observed in ballistic transport measurements in 2D, and conductance quantisation is observed in 5 μm long 1D quantum wires. The electron density is tunable over two orders of magnitude. This allows detailed studies of cyclotron resonance (CR) at differing Landau level filling factors, ν. The samples are undoped, carriers being introduced by a top-gate, so comparisons can be drawn with similar studies in modulation-doped structures, in particular CR measurements in the extreme quantum limit (ν<<1) where a splitting of the CR line has previously been used to probe correlated electron physics. The extension of this work to FIR studies of quantum wires at milli-Kelvin temperatures is expected to provide a spectroscopic probe of 2D-1D coupling and correlation effects in 1D (Luttinger liquid), where the absence of random disorder becomes increasingly important.

  7. Structure, electrochemical properties and capacitance performance of polypyrrole electrodeposited onto 1-D crystals of iridium complex

    NASA Astrophysics Data System (ADS)

    Wysocka-Żołopa, Monika; Winkler, Krzysztof

    2015-12-01

    Composites of polypyrrole and one-dimensional iridium complex crystals [(C2H5)4N]0.55[IrCl2(CO)2] were prepared by in situ two-step electrodeposition. Initially, iridium complex crystals were formed during [IrCl2(CO)2]- complex oxidation. Next, pyrrole was electropolymerized on the surface of the iridium needles. The morphology of the composite was investigated by scanning and transmission electron microscopy. At positive potentials, the iridium complex crystals and the polypyrrole were oxidized. In aprotic solvents, oxidation of the iridium complex crystals resulted in their dissolution. In water containing tetra(n-butyl)ammonium chlorides, the 1-D iridium complex crystals were reversibly oxidized. The product of the iridium complex oxidation remained on the electrode surface in crystalline form. The iridium complex needles significantly influenced the redox properties of the polymer. The polypyrrole involved electrode processes become more reversible in presence of crystals of iridium complex. The current of polypyrrole oxidation was higher compared to that of pure polypyrrole and the capacitance properties of the polymer were significantly enhanced. A specific capacitance as high as 590 F g-1 was obtained for a composite of polypyrrole and 1-D crystals of the iridium complex in water containing tetra(n-butyl)ammonium chloride. This value is approximately twice as high as the capacitance of the pure polymer deposited onto the electrode surface.

  8. Detonation Structure Under Chain Branching Kinetics

    NASA Astrophysics Data System (ADS)

    Liang, Z.; Bauwens, L.

    2006-07-01

    Hydrogen-oxygen chemistry is characterized by a chain branching mechanism that yields three explosion limits. While a detailed kinetic scheme appropriate for hydrogen-oxygen should produce correct results, in many circumstances, a simpler yet reasonably realistic model will be warranted. In particular, it is easier to develop a clear understanding of the reaction zone structure using a simpler model, that includes only the key mechanisms. To that effect, we consider a four-step chain branching scheme that exhibits an explosion behavior with three limits, which behaves at least qualitatively like hydrogen chemistry. We focus in particular on the structure of the initiation and chain branching zones, using a combination between numerical simulation and analysis. Numerical simulations using this chemical model show distinctive keystone figures in the flow field, close to observations in hydrogen-oxygen detonation experiments. The structure of the chain branching zone is resolved using a perturbation analysis, which clarifies the differences between explosion and no-explosion regions and allows for an evaluation of the induction length in the steady wave. The analysis assumes both high activation energy and a slow initiation. Three cases are identified, respectively, with pressure and temperature located within the explosion region, close to the explosion limit and within the no-explosion region. The induction length is shorter and the reaction rate is faster by several orders of magnitude in the explosion region.

  9. Final COMPASS results on the deuteron spin-dependent structure function g1d and the Bjorken sum rule

    NASA Astrophysics Data System (ADS)

    Adolph, C.; Aghasyan, M.; Akhunzyanov, R.; Alexeev, M. G.; Alexeev, G. D.; Amoroso, A.; Andrieux, V.; Anfimov, N. V.; Anosov, V.; Augsten, K.; Augustyniak, W.; Austregesilo, A.; Azevedo, C. D. R.; Badełek, B.; Balestra, F.; Ball, M.; Barth, J.; Beck, R.; Bedfer, Y.; Bernhard, J.; Bicker, K.; Bielert, E. R.; Birsa, R.; Bodlak, M.; Bordalo, P.; Bradamante, F.; Braun, C.; Bressan, A.; Büchele, M.; Chang, W.-C.; Chatterjee, C.; Chiosso, M.; Choi, I.; Chung, S.-U.; Cicuttin, A.; Crespo, M. L.; Curiel, Q.; Dalla Torre, S.; Dasgupta, S. S.; Dasgupta, S.; Denisov, O. Yu.; Dhara, L.; Donskov, S. V.; Doshita, N.; Dreisbach, Ch.; Duic, V.; Dünnweber, W.; Dziewiecki, M.; Efremov, A.; Eversheim, P. D.; Eyrich, W.; Faessler, M.; Ferrero, A.; Finger, M.; Finger, M.; Fischer, H.; Franco, C.; du Fresne von Hohenesche, N.; Friedrich, J. M.; Frolov, V.; Fuchey, E.; Gautheron, F.; Gavrichtchouk, O. P.; Gerassimov, S.; Giarra, J.; Giordano, F.; Gnesi, I.; Gorzellik, M.; Grabmüller, S.; Grasso, A.; Grosse Perdekamp, M.; Grube, B.; Grussenmeyer, T.; Guskov, A.; Haas, F.; Hahne, D.; Hamar, G.; von Harrach, D.; Heinsius, F. H.; Heitz, R.; Herrmann, F.; Horikawa, N.; d'Hose, N.; Hsieh, C.-Y.; Huber, S.; Ishimoto, S.; Ivanov, A.; Ivanshin, Yu.; Iwata, T.; Jary, V.; Joosten, R.; Jörg, P.; Kabuß, E.; Kerbizi, A.; Ketzer, B.; Khaustov, G. V.; Khokhlov, Yu. A.; Kisselev, Yu.; Klein, F.; Klimaszewski, K.; Koivuniemi, J. H.; Kolosov, V. N.; Kondo, K.; Königsmann, K.; Konorov, I.; Konstantinov, V. F.; Kotzinian, A. M.; Kouznetsov, O. M.; Krämer, M.; Kremser, P.; Krinner, F.; Kroumchtein, Z. V.; Kulinich, Y.; Kunne, F.; Kurek, K.; Kurjata, R. P.; Lednev, A. A.; Lehmann, A.; Levillain, M.; Levorato, S.; Lian, Y.-S.; Lichtenstadt, J.; Longo, R.; Maggiora, A.; Magnon, A.; Makins, N.; Makke, N.; Mallot, G. K.; Marianski, B.; Martin, A.; Marzec, J.; Matoušek, J.; Matsuda, H.; Matsuda, T.; Meshcheryakov, G. V.; Meyer, M.; Meyer, W.; Mikhailov, Yu. V.; Mikhasenko, M.; Mitrofanov, E.; Mitrofanov, N.; Miyachi, Y.; Nagaytsev, A.; Nerling, F.; Neyret, D.; Nový, J.; Nowak, W.-D.; Nukazuka, G.; Nunes, A. S.; Olshevsky, A. G.; Orlov, I.; Ostrick, M.; Panzieri, D.; Parsamyan, B.; Paul, S.; Peng, J.-C.; Pereira, F.; Pešek, M.; Peshekhonov, D. V.; Pierre, N.; Platchkov, S.; Pochodzalla, J.; Polyakov, V. A.; Pretz, J.; Quaresma, M.; Quintans, C.; Ramos, S.; Regali, C.; Reicherz, G.; Riedl, C.; Roskot, M.; Rossiyskaya, N. S.; Ryabchikov, D. I.; Rybnikov, A.; Rychter, A.; Salac, R.; Samoylenko, V. D.; Sandacz, A.; Santos, C.; Sarkar, S.; Savin, I. A.; Sawada, T.; Sbrizzai, G.; Schiavon, P.; Schmidt, K.; Schmieden, H.; Schönning, K.; Seder, E.; Selyunin, A.; Silva, L.; Sinha, L.; Sirtl, S.; Slunecka, M.; Smolik, J.; Srnka, A.; Steffen, D.; Stolarski, M.; Subrt, O.; Sulc, M.; Suzuki, H.; Szabelski, A.; Szameitat, T.; Sznajder, P.; Takekawa, S.; Tasevsky, M.; Tessaro, S.; Tessarotto, F.; Thibaud, F.; Thiel, A.; Tosello, F.; Tskhay, V.; Uhl, S.; Vauth, A.; Veloso, J.; Virius, M.; Vondra, J.; Wallner, S.; Weisrock, T.; Wilfert, M.; Windmolders, R.; ter Wolbeek, J.; Zaremba, K.; Zavada, P.; Zavertyaev, M.; Zemlyanichkina, E.; Zhuravlev, N.; Ziembicki, M.; Zink, A.

    2017-06-01

    Final results are presented from the inclusive measurement of deep-inelastic polarised-muon scattering on longitudinally polarised deuterons using a 6LiD target. The data were taken at 160 GeV beam energy and the results are shown for the kinematic range 1(GeV / c) 2 4GeV /c2 in the mass of the hadronic final state. The deuteron double-spin asymmetry A1d and the deuteron longitudinal-spin structure function g1d are presented in bins of x and Q2. Towards lowest accessible values of x, g1d decreases and becomes consistent with zero within uncertainties. The presented final g1d values together with the recently published final g1p values of COMPASS are used to again evaluate the Bjorken sum rule and perform the QCD fit to the g1 world data at next-to-leading order of the strong coupling constant. In both cases, changes in central values of the resulting numbers are well within statistical uncertainties. The flavour-singlet axial charge a0, which is identified in the MS ‾ renormalisation scheme with the total contribution of quark helicities to the nucleon spin, is extracted at next-to-leading order accuracy from only the COMPASS deuteron data: a0 (Q2 = 3(GeV / c) 2) = 0.32 ±0.02stat ±0.04syst ±0.05evol. Together with the recent results on the proton spin structure function g1p, the results on g1d constitute the COMPASS legacy on the measurements of g1 through inclusive spin-dependent deep inelastic scattering.

  10. Magnetic structure and exchange interactions in quasi-1D MnCl2(urea)2

    PubMed Central

    Manson, Jamie L.; Huang, Qing-zhen; Brown, Craig M.; Lynn, Jeffrey W.; Stone, Matthew B.; Singleton, John; Xiao, Fan

    2016-01-01

    MnCl2(urea)2 is a new linear chain coordination polymer that exhibits slightly counter-rotated MnCl4 rhomboids along the chain-axis. The material crystallizes in the non-centrosymmetric orthorhombic space group Iba2, with each Mn(II) ion equatorially surrounded by four Cl− that lead to bi-bridged ribbons. Urea ligands coordinate via O-atoms in the axial positions. Hydrogen bonds of the Cl⋯H-N and O⋯H-N type link the chains into a quasi-3D network. Magnetic susceptibility data reveal a broad maximum at 9 K that is consistent with short-range magnetic order. Pulsed-field magnetization measurements conducted at 0.6 K show that a fully polarized magnetic state is achieved at Bsat = 19.6 T with a field-induced phase transition occurring at 2.8 T. Neutron diffraction studies made on a powdered sample of MnCl2(urea)2 reveal that long-range magnetic order occurs below TN = 3.2(1) K. Additional Bragg peaks due to antiferromagnetic (AFM) ordering can be indexed according to the Ib’a2’ magnetic space group and propagation vector τ = [0, 0, 0]. Rietveld profile analysis of these data reveal a Néel-type collinear ordering of Mn(II) ions with an ordered magnetic moment of 4.06(6) μB (5 μB is expected for isotropic S = 5/2) oriented along the b-axis, i.e., perpendicular to the chain-axis that runs along the c-direction. Owing to potential for spatial exchange anisotropy and the pitfalls in modeling bulk magnetic data, we analyzed inelastic neutron scattering data to retrieve the exchange constants; Jc = 2.22 K (intrachain), Ja = −0.10 K (interchain) and D = −0.14 K with J > 0 assigned to AFM coupling. This J configuration is most unusual and contrasts the more commonly observed case of AFM-coupled FM-chains. PMID:26645988

  11. 3D and 2D structural characterization of 1D Al/Al2 O3 biphasic nanostructures.

    PubMed

    Miró, M Martinez; Veith, M; Lee, J; Soldera, F; Mücklich, F; Bennewitz, R; Aktas, C

    2015-05-01

    1D Al/Al2 O3 nanostructures have been synthesized by chemical vapour deposition (CVD) of the molecular precursor [(t) BuOAlH2 ]2 . The deposited nanostructures grow chaotically on the substrate forming a layer with a high porosity (80%). Depending on the deposition time, diverse nanostructured surfaces with different distribution densities were achieved. A three-dimensional (3D) reconstruction has been evaluated for every nanostructure density using the Focus Ion Beam (FIB) tomography technique and reconstruction software tools. Several structural parameters such as porosity, Euler number, geometrical tortuosity and aspect ratio have been quantified through the analysis with specified software of the reconstructions. Additionally roughness of the prepared surfaces has been characterized at micro- and nanoscale using profilometry and AFM techniques, respectively. While high aspects ratio around 20-30 indicates a strong anisotropy in the structure, high porosity values (around 80%) is observed as a consequence of highly tangled geometry of such 1D nanostructures.

  12. Free-standing guided-mode resonance band-pass filters: from 1D to 2D structures.

    PubMed

    Sakat, Emilie; Vincent, Grégory; Ghenuche, Petru; Bardou, Nathalie; Dupuis, Christophe; Collin, Stéphane; Pardo, Fabrice; Haïdar, Riad; Pelouard, Jean-Luc

    2012-06-04

    We study experimentally and theoretically band-pass filters based on guided-mode resonances in free-standing metal-dielectric structures with subwavelength gratings. A variety of filters are obtained: polarizing filters with 1D gratings, and unpolarized or selective filters with 2D gratings, which are shown to behave as two crossed-1D structures. In either case, a high transmission (up to ≈ 79 %) is demonstrated, which represents an eight-fold enhancement compared to the geometrical transmission of the grating. We also show that the angular sensitivity strongly depends on the rotation axis of the sample. This behavior is explained with a detailed description of the guided-mode transmission mechanism.

  13. Temperature tuning of band-structure of 1D periodic elastic composites

    NASA Astrophysics Data System (ADS)

    Sadeghi, H.; Srivastava, A.; Griswold, R.; Nemat-Nasser, S.

    2012-04-01

    In this paper we show that the bandstructure of a periodic elastic composite, in addition to being dependent upon the micro-constituents and their microarchitecture, may also be controlled by changing the temperature. The essential idea is to fabricate a periodic composite with constituent materials which have temperature dependent elastic properties. As temperature is changed, such a composite is expected to exhibit a bandstructure which changes with the temperature dependent properties of its micro-constituents. For our purpose, we use polyurea and steel to make a 1-D periodic composite. Ultrasonic measurements are done on the sample from 0.5 kHz to 1.5 MHz under changing temperature and the change in the second passband is studied. It is observed that the change in the bandstructure is significant when the temperature is changed from -50°C to 50°C. Experimental results are compared with the theoretical calculations and it is shown that good agreement exists for the observed bandstructure.

  14. New coordination polymers from 1D chain, 2D layer to 3D framework constructed from 1,2-phenylenediacetic acid and 1,3-bis(4-pyridyl)propane flexible ligands

    SciTech Connect

    Xin Lingyun; Liu Guangzhen; Wang Liya

    2011-06-15

    The hydrothermal reactions of Cd, Zn, or Cu(II) acetate salts with H{sub 2}PHDA and BPP flexible ligands afford three new coordination polymers, including [Cd(PHDA)(BPP)(H{sub 2}O)]{sub n}(1), [Zn(PHDA)(BPP)]{sub n}(2), and [Cu{sub 2}(PHDA){sub 2}(BPP)]{sub n}(3) (H{sub 2}PHDA=1,2-phenylenediacetic acid, BPP=1,3-bis(4-pyridyl)propane). The single-crystal X-ray diffractions reveal that all three complexes feature various metal carboxylate subunits extended further by the BPP ligands to form a diverse range of structures, displaying a remarked structural sensitivity to metal(II) cation. Complex 1 containing PHDA-bridged binuclear cadmium generates 1D double-stranded chain, complex 2 results in 2D{yields}2D interpenetrated (4,4) grids, and complex 3 displays a 3D self-penetrated framework with 4{sup 8}6{sup 6}8 rob topology. In addition, fluorescent analyses show that both 1 and 2 exhibit intense blue-violet photoluminescence in the solid state. - Graphical Abstract: We show diverse supramolecular frameworks based on the same ligands (PHDA and BPP) and different metal acetate salts including 1D double-stranded chain, 2D {yields} 2D twofold interpenetrated layer, and 3D self-penetration networks. Highlights: > Three metal(II = 2 /* ROMAN ) coordination polymers were synthesized using H{sub 2}PHDA and BPP. > The diversity of structures show a remarked sensitivity to metal(II) center. > Complexes show the enhancement of fluorescence compared to that of free ligand.

  15. Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands

    SciTech Connect

    Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

    2014-10-15

    Three new 1D to 3D complexes, namely, ([Ni(btec)(Himb){sub 2}(H{sub 2}O){sub 2}]·6H{sub 2}O){sub n} (1), ([Cd(btec){sub 0.5}(imb)(H{sub 2}O)]·1.5H{sub 2}O){sub n} (2), and ([Zn(btec){sub 0.5}(imb)]·H{sub 2}O){sub n} (3) (H{sub 4}btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (5{sup 3}·6{sup 2}·7)(5{sup 2}·6{sup 4}). Complex 3 presents a 3D framework with a point symbol of (4·6{sup 4}·8)(4{sup 2}·6{sup 2}·8{sup 2}). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature. - Graphical abstract: Three new 1D to 3D complexes with different structural and topological motifs have been obtained by modifying the central metal ions. Additionally, their IR, TG analyses and fluorescent properties are also investigated. - Highlights: • Three complexes based on mixed multidentate N- and O-donor ligands. • The complexes are characterized by IR, luminescence and TGA techniques. • Benzenetetracarboxylates display different coordination modes in complexes 1–3. • Changing the metal ions can result in complexes with completely different structures.

  16. An approach to control tuning range and speed in 1D ternary photonic band gap material nano-layered optical filter structures electro-optically

    SciTech Connect

    Zia, Shahneel Banerjee, Anirudh

    2016-05-06

    This paper demonstrates a way to control spectrum tuning capability in one-dimensional (1D) ternary photonic band gap (PBG) material nano-layered structures electro-optically. It is shown that not only tuning range, but also tuning speed of tunable optical filters based on 1D ternary PBG structures can be controlled Electro-optically. This approach finds application in tuning range enhancement of 1D Ternary PBG structures and compensating temperature sensitive transmission spectrum shift in 1D Ternary PBG structures.

  17. Modification of LED radiation pattern by implementation of 1D Fresnel structure in the surface

    NASA Astrophysics Data System (ADS)

    Lettrichova, Ivana; Pudis, Dusan; Laurencikova, Agata; Gaso, Peter; Suslik, Lubos; Jandura, Daniel; Novak, Jozef

    2017-05-01

    In this contribution, we present modification of far field of light emitting diode (LED) with implemented Fresnel structure in the LED surface. Fresnel structures were prepared in one-dimensional arrangement with two different foci f1 = 12.5 μm and f2 = 1 cm. Structures were etched directly in the LED emitting surface using electron beam lithography with the etched depth for the structure with f1 and f2 app. 200 nm and 400 nm, respectively. Due to application of these structures, LED far field narrowing was observed, which is documented by goniophotometer measurements. For the structure with f1 and f2, the intensity decrease for angles +/-30° - +/-50° is app. 3-4% and 5-6%, respectively, in comparison to the Lambertian profile.

  18. Transmission properties analysis of 1D PT-symmetric photonic structures

    NASA Astrophysics Data System (ADS)

    Mossakowska-Wyszyńska, Agnieszka; Witoński, Piotr; Szczepański, Paweł

    2016-12-01

    The transmission properties of one dimensional PT-symmetric photonic crystal (PC) structure with gain and loss regions are presented. Obtained characteristics illustrate the influence of the structures parameters such as the ratio of the PC period to the operating wavelength, the number of the primitive cells creating PC, the loss and gain level (imaginary part of the refractive indices) on reflection and transmission coefficients. It demonstrates strong nonreciprocal response of the structure.

  19. Structure of confined films of chain alcohols

    SciTech Connect

    Mugele, F.; Baldelli, S.; Somorjai, G.A.; Salmeron, M.

    2000-04-13

    The structure of thin films of simple chain alcohols (1-octanol and 1-undecanol) confined between two atomically smooth mica surfaces has been investigated using a surface forces apparatus. Contact angle measurements and optical sum frequency generation were used for additional characterization. In both systems, the substrate-molecule interaction leads to a strongly bound first layer on each surface. Additional liquid organizes into highly compressible bilayers, which could be expelled by applying sufficiently high pressure.

  20. Modeling structures of 1D PhC for telecommunication applications

    NASA Astrophysics Data System (ADS)

    Zawistowski, Zygmunt J.; Jaskorzyńska, BoŻena

    2016-09-01

    Effective method of modeling 1-dimensional photonic crystals structures is presented. As an illustration of the method a concept of widely tunable narrow band drop filter is described. As an active electro-optic material a liquid crystal is used. Very good parameters are obtained so the presented structure is suitable for fast packet switched wavelength division multiplexing networks (WDM).

  1. Formation of Photonic Structures in Photorefractive Lithium Niobate by 1D and 2D Bessel-like Optical Fields

    NASA Astrophysics Data System (ADS)

    Inyushov, A.; Safronova, P.; Trushnikov, I.; Sarkyt, A.; Shandarov, V.

    2017-06-01

    Both, one-dimensional (1D) and two-dimensional (2D) Bessel-like beams with different topology of 2D beam cross-sections are formed from Gaussian laser beams using the amplitude masks and Fresnel biprisms. These almost diffraction-free light fields with wavelengths of 532 and 633 nm can change the refractive indices of photorefractive lithium niobate samples and form within them the nonlinear photonic diffraction structures. The characteristics of photonic structures induced in this way are studied by diffraction of monochromatic light with wavelengths of 633 and 532 nm.

  2. Exploring group 14 structures: 1D to 2D to 3D.

    PubMed

    Wen, Xiao-Dong; Cahill, Thomas J; Hoffmann, Roald

    2010-06-11

    Various one-, two- and three-dimensional Group 14 (C, Si, Ge, Sn, and Pb) element structures at P = 1 atm are studied in this work. As expected, coordination number (CN)--not an unambiguous concept for extended structures--plays an important part in the stability of structures. Carbon not only favors four-coordination, but also is quite happy with pi-bonding, allowing three- and even two-coordination to compete. Highly coordinated (CN > 4) discrete carbon molecules are rare; that "saturation of valence" is reflected in the instability of C extended structures with CN > 4. Si and Ge are quite similar to each other in their preferences. They are less biased in their coordination than C, allowing (as their molecular structures do) CN = 5 and 6, but tending towards four-coordination. Sn and Pb 3D structures are very flexible in their bonding, so that in these elements four- to twelve-coordinate structures are close in energy. This lack of discrimination among ordered structures also points to an approach to the liquid state, consistent with the low melting point of Sn and Pb. The Group 14 liquid structures we simulate in molecular dynamics calculations show the expected, effective, first coordination number increase from 5.1 for Si to 10.4 for Pb. A special point of interest emerging from our study is the instability of potential multilayer graphene structures down Group 14. Only for C will these be stable; for all the other Group 14 elements pristine, unprotected, bi- and multilayer graphenes should collapse, forming "vertical" bonds as short as the in-plane ones.

  3. o-, m-, and p-Pyridyl isomer effects on construction of 1D loop-and-chains: Silver(I) coordination polymers with Y-type tridentate ligands

    NASA Astrophysics Data System (ADS)

    Kim, Jeong Gyun; Cho, Yoonjung; Lee, Haeri; Lee, Young-A.; Jung, Ok-Sang

    2016-10-01

    Self-assembly of silver(I) hexafluorophosphate with unique Y-type tridentate ligands (2,6-bis[(2-picolinoyloxy-5-methylphenyl)methyl]-p-tolylpicolinate (o-L), 2-nicotinoyloxy- (m-L), and 2-isonicotinoyloxy- (p-L)) produces single crystals consisting of 1D loop-and-chain coordination polymers of [Ag(o-L)](PF6)·Me2CO·CHCl3, [Ag(m-L)](PF6)·Me2CO, and [Ag3(p-L)2](PF6)3·2H2O·2C2H5OH·4CH2Cl2 with quite different trigonal prismatic, trigonal, and linear silver(I) coordination geometry, respectively. Coordinating ability of the three ligands for AgPF6 is in the order of p-L > o-L > m-L. The solvate molecules of [Ag(o-L)](PF6)·Me2CO·CHCl3 can be removed, and be replaced reversibly in the order of acetone ≫ chloroform ≈ dichloromethane ≫ benzene, without destruction of its skeleton.

  4. Optical reflectance and omnidirectional bandgaps in Fibonacci quasicrystals type 1-D multilayer structures containing exponentially graded material

    NASA Astrophysics Data System (ADS)

    Singh, Bipin K.; Thapa, Khem B.; Pandey, Praveen C.

    2013-06-01

    A theoretical study of optical reflectance and reflection bands of 1-D photonic quasi-crystals (Fibonacci type arrangement) composed of exponentially graded material is presented. The proposed structures consist of two different layers, one of them is of constant refractive index (L) and the other one is of exponentially graded refractive index (S) dielectric materials. Four different generations (2nd, 3rd, 4th and 5th) of the Fibonacci sequence for 10 periods in one dimension (1-D) are considered and compared in view of their optical reflectance and bandgaps for both TE and TM polarisations. Also, we proposed some heterostructures made by the combination of different Fibonacci generations and their periods to obtain suitable omnidirectional reflection band. We used the transfer matrix method (TMM) to obtain the reflectance, bandgaps and omnidirectional reflectional bandgaps (ODR) of such structures in near infrared spectrum (800-2200 nm) at different angles of incidence. We show that ODR exists in these types of structures. The number of ODRs and total bandgap depend on the Fibonacci generations. Extraordinary ODR bandgaps are obtained in the case of heterostructures formed by the combination of different generations of the Fibonacci sequence. The ODR for these structures is similar to the ODR of photonic crystals containing left-handed materials. This work would be useful to study the Fibonacci type photonic crystals having graded index materials and also it will open new window to design several photonic crystal devices like sensors, reflectors, etc. in the infrared region.

  5. Antiferromagnetic interactions in 1D Heisenberg linear chains of 7-(4-fluorophenyl) and 7-phenyl-substituted 1,3-diphenyl-1,4-dihydro-1,2,4-benzotriazin-4-yl radicals.

    PubMed

    Constantinides, Christos P; Koutentis, Panayiotis A; Rawson, Jeremy M

    2012-11-26

    7-(4-Fluorophenyl) and 7-phenyl-substituted 1,3-diphenyl-1,4-dihydro-1,2,4-benzotriazin-4-yl radicals were characterized by X-ray diffraction analysis and variable-temperature magnetic susceptibility studies. The radicals pack in 1D π stacks of equally spaced slipped radicals with interplanar distances of 3.59 and 3.67 Å and longitudinal angles of 40.97 and 43.47°, respectively. Magnetic-susceptibility studies showed that both radicals exhibit antiferromagnetic interactions. Fitting the magnetic data revealed that the behavior is consistent with 1D regular linear antiferromagnetic chain with J=-12.9 cm(-1), zJ'=-0.4 cm(-1), g=2.0069 and J=-11.8 cm(-1), zJ'=-6.5 cm(-1), g=2.0071, respectively. Magnetic-exchange interactions in benzotriazinyl radicals are sensitive to the degree of slippage, and inter-radical separation and subtle changes in structure alter the fine balance between ferro- and antiferromagnetic interactions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Building 1D lanthanide chains and non-symmetrical [Ln2] "triple-decker" clusters using salen-type ligands: magnetic cooling and relaxation phenomena.

    PubMed

    Canaj, Angelos B; Siczek, Milosz; Otręba, Marta; Lis, Tadeusz; Lorusso, Giulia; Evangelisti, Marco; Milios, Constantinos J

    2016-11-22

    A solvothermal reaction between Ln(NO3)3·6H2O (Ln: Gd, Tb and Dy), 2-hydroxy-1-naphthaldehyde, 2-OH-naphth, and ethylenediamine, en, in MeOH in the presence of a base, NEt3, led to the formation of the 1D coordination polymers [Ln(L)(MeO)(MeOH)0.5]n·MeOH (Ln = Gd (1·MeOH), Tb(2), Dy (3·MeOH); H2L = 1,1'-((1E,1'E)-(ethane-1,2-diylbis(azanylylidene))bis(methanylylidene))bis(naphthalen-2-ol), the Schiff-base ligand derived from the condensation of 2-OH-naphth and en), while a similar reaction in an excess of NaN3 yielded 1D coordination polymers [Ln(L)(N3)0.75(MeO)0.25(MeOH)]n (Ln = Gd (4), Tb (5), Dy (6)). Finally, upon replacing ethylenediamine with o-phenylenediamine, o-phen, we managed to isolate the discrete dimers [Dy2(L')3(MeOH)]·2MeOH (7·2MeOH) and [Gd2(L')3(MeOH)]·2MeOH (8·2MeOH) (H2L' = 1,1'-((1E,1'E)-(1,2-phenylenebis(azanylylidene))bis(methanylylidene))bis (naphthalen-2-ol), the Schiff-base ligand from the condensation of 2-OH-naphth and o-phen). Polymers 1-3 describe one-dimensional chains, containing alternating seven- and eight-coordinate Ln(III) metal centers, polymers 4-6 contain eight-coordinate lanthanide ions, while in both 7 and 8 the two Ln(III) centers are eight- and seven-coordinate, adopting square antiprismatic and "piano-stool" geometry, respectively. The magnetocaloric properties of the three Gd(III) analogues were determined from magnetic measurements, yielding the magnetic entropy change -ΔSm = 21.8, 23.0 and 16.0 J kg(-1) K(-1) at T = 3.0 K on demagnetization of 7 T to 0, for 1, 4 and 8, respectively. The study of the magnetic properties also revealed that all three Dy(III) analogues (3, 6 and 7) display out-of-phase signals, therefore suggesting slow magnetic relaxation, while such behaviour was not established in the Tb(III) analogues.

  7. Hydrothermal synthesis and crystal structure of a novel 1D molybdenum(V) phosphate with mixed-valence cobalt coordination cations

    NASA Astrophysics Data System (ADS)

    Guo, Hong-Xu; Liu, Shi-Xiong

    2005-05-01

    A novel 1D molybdenum(V) phosphate with mixed-valence cobalt coordination cation, Co II[Mo 6O 12(OH) 3(PO 4)(HPO 4) 3] 2[Co III(H 2O)(2,2'-bpy) 2] 2[Co II3(OH) 2(H 2O) 4]·2H 2O ( 1), has been synthesized by hydrothermal and characterized by single crystal X-ray diffraction. The title complex crystallizes in the triclinic system, space group P1¯, with a=12.8779(6), b=13.6862(10), c=15.1111(8) Å, α=97.141(2)°, β=99.1360(10)°, γ=116.719(4)°. The structure of the title polyoxometalate is based on Co II[Mo 6O 12(OH) 3(PO 4)(HPO 4) 3] 2 clusters connected together via [Co II3(OH) 2(H 2O) 4] trimers to give a new unusual 1D chain-like along the c-axis, where the Co[Mo 6P 4] 2 cluster unit is bonded by [Co III(H 2O)(2,2'-bpy) 2] unit.

  8. Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands

    NASA Astrophysics Data System (ADS)

    Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

    2014-10-01

    Three new 1D to 3D complexes, namely, {[Ni(btec)(Himb)2(H2O)2]·6H2O}n (1), {[Cd(btec)0.5(imb)(H2O)]·1.5H2O}n (2), and {[Zn(btec)0.5(imb)]·H2O}n (3) (H4btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (53·62·7)(52·64). Complex 3 presents a 3D framework with a point symbol of (4·64·8)(42·62·82). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature.

  9. Electrophysiological and Structural Remodeling in Heart Failure Modulate Arrhythmogenesis. 1D Simulation Study

    PubMed Central

    Gomez, Juan F.; Cardona, Karen; Romero, Lucia; Ferrero, Jose M.; Trenor, Beatriz

    2014-01-01

    Background Heart failure is a final common pathway or descriptor for various cardiac pathologies. It is associated with sudden cardiac death, which is frequently caused by ventricular arrhythmias. Electrophysiological remodeling, intercellular uncoupling, fibrosis and autonomic imbalance have been identified as major arrhythmogenic factors in heart failure etiology and progression. Objective In this study we investigate in silico the role of electrophysiological and structural heart failure remodeling on the modulation of key elements of the arrhythmogenic substrate, i.e., electrophysiological gradients and abnormal impulse propagation. Methods Two different mathematical models of the human ventricular action potential were used to formulate models of the failing ventricular myocyte. This provided the basis for simulations of the electrical activity within a transmural ventricular strand. Our main goal was to elucidate the roles of electrophysiological and structural remodeling in setting the stage for malignant life-threatening arrhythmias. Results Simulation results illustrate how the presence of M cells and heterogeneous electrophysiological remodeling in the human failing ventricle modulate the dispersion of action potential duration and repolarization time. Specifically, selective heterogeneous remodeling of expression levels for the Na+/Ca2+ exchanger and SERCA pump decrease these heterogeneities. In contrast, fibroblast proliferation and cellular uncoupling both strongly increase repolarization heterogeneities. Conduction velocity and the safety factor for conduction are also reduced by the progressive structural remodeling during heart failure. Conclusion An extensive literature now establishes that in human ventricle, as heart failure progresses, gradients for repolarization are changed significantly by protein specific electrophysiological remodeling (either homogeneous or heterogeneous). Our simulations illustrate and provide new insights into this

  10. Local duality in spin structure functions g1(p) and g1(d)

    SciTech Connect

    Yelena Prok

    2006-02-01

    Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M

  11. Effects of magnetic site disorder of the 1-D Ising spin chain compounds Ca3(Co,Mn)2O6 with dilute doping

    NASA Astrophysics Data System (ADS)

    Casas, Brian; Lampen, Paula; Phan, Manh-Huong; Srikanth, Hariharan; Kovak, Jozef; Skorvanek, Ivan

    2015-03-01

    The spin chain compound Ca3Co2O6 has been extensively studied due to a number of unusual properties originating from geometrically frustrated Ising-like spin chains arranged in a triangular lattice. These quasi one dimensional structures provide an ideal environment to study dilute magnetic disorder in spin-glass like systems. Disorder controlled via chemical doping has been observed to weaken the spin glass behavior and disrupt a number of metamagnetic transitions found in pristine Ca3Co2O6. We report a systematic study of the effects of dilute Mn doping (x = 0.05 - 0.50) in Ca3Co2-xMnxO6 synthesized via a sol-gel method. Detailed AC and DC magnetization measurements performed on a SQUID magnetometer reveal the suppression of the step-like metamagnetic transitions by a doping of x = 0.25. The relaxation time is found to decrease with increasing Mn content, showing the destruction of the spin-glass like behavior. Our observations yield new insight into the role of site disorder on the glassy behavior in spin chain systems. Research was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award No. DE-FG02-07ER46438.

  12. Mixed 1D-2D inorganic polymeric zinc ferrocenylphosphonate: crystal structure and electrochemical study.

    PubMed

    Oms, Olivier; Le Bideau, Jean; Leroux, Fabrice; van der Lee, Arie; Leclercq, Dominique; Vioux, André

    2004-09-29

    Needs for ferrocene immobilization on robust host structures are considerable since derivative materials may find applications in medical areas, optical devices, or catalysis. Synthesis of phosphonate functionalized ferrocene allowed its subsequent inorganic polymerization with a zinc salt. The crystallographic structure of the compound obtained, Zn(HO(3)PFc)(2).2H(2)O, shows a unique two-dimensional ferrocene arrangement anchored on a one-dimensional Zn-O-P-O-Zn backbone. The ferrocene packing in the title compound is very similar to the packing found in molecular ferrocene. The electroactivity of Zn(HO(3)PFc)(2).2H(2)O is thoroughly studied. It shows a reversible surface oxidation of ferrocene. Mössbauer spectroscopy for the oxidized compound shows an isomer shift of IS(2b) = 0.432 mm x s(-1) and a quadrupolar splitting of QS(2b) = 0.205 mm x s(-1), which is consistent with a stable S = 1/2 ferrocenium state. The magnetic susceptibility study, Mössbauer spectroscopy, and galvanostatic titration show that only the ferrocene moieties present at the surface of the crystallites are reversibly oxidized. This observation is reinforced by a complex impedance study showing mainly resistive behavior and conductivity measurements indicating weak, thermally assisted, conductivity. The general properties of this compound demonstrate that phosphonato functionalization may be a useful approach for all fields concerned by immobilization of ferrocene.

  13. Non-native side chain IR probe in peptides: ab initio computation and 1D and 2D IR spectral simulation.

    PubMed

    Zheng, Michael L; Zheng, David C; Wang, Jianping

    2010-02-18

    Infrared frequency region of 2000-2600 cm(-1) (i.e., ca. 4-5 microm in wavelength) is a well-known open spectral window for peptides and proteins. In this work, six unnatural amino acids (unAAs) were designed to have characteristic absorption bands located in this region. Key chemical groups that served as side chains in these unAAs are C[triple bond]C, Phe-C[triple bond]C, N=C=O, N=C=S, P-H, and Si-H, respectively. Cysteine (a natural AA having S-H in side chain) was also studied for comparison. The anharmonic vibrational properties, including frequencies, anharmonicities, and intermode couplings, were examined using the density functional theory. Broadband linear infrared (IR) and two-dimensional (2D) IR spectra were simulated for each molecule. It is found that all of the side chain modes have significant overtone diagonal anharmonicities. All have moderate transition dipole strengths except the C[triple bond]C and S-H stretching modes, in comparison with the C=O stretching mode. In each case, a collection of 2D IR cross peaks were predicted to appear due to the presence of the side chain groups, whose strengths are closely related to the intramolecular anharmonic interactions, and to the transition dipole strengths of the coupled vibrators. Further, potential energy distribution analysis and high-order anharmonic constant computation showed that these IR probes possess a varying degree of mode localization. The results suggest that these IR probes are potentially useful in complementing the well-studied amide-I mode, to investigate structures and dynamics of peptides and proteins.

  14. Structural, morphological, and wettability study of electrochemically anodized 1D TiO2 nanotube arrays

    NASA Astrophysics Data System (ADS)

    Patil, Jyoti V.; Mali, Sawanta S.; Hong, Chang K.; Kim, Jin H.; Patil, Pramod S.

    2017-10-01

    In the present investigation, anatase titanium dioxide (TiO2) nanotube arrays (NTAs) have been successfully synthesized by a simple and cost-effective electrochemical anodization of titanium (Ti) foil. To investigate the effect of reaction time on the TiO2 NTAs, the reaction time was varied from 6, 12, 18, and 24 h and studied its morphological changes. Furthermore, the synthesized TiO2 NTAs were characterized by X-ray diffraction, FT-Raman spectroscopy, X-ray photospectroscopy, scanning electron microscopy, field-emission scanning electron microscopy, and the wettability measurement to study detailed investigation of structural, morphological, and wettability characteristics. These results demonstrated that the anodization time is strongly affecting on the morphology and wettability of the TiO2 NTAs. In addition, these results will be useful in dye-sensitized solar cell and supercapacitor applications.

  15. Effect of substrate on optical bound states in the continuum in 1D photonic structures

    NASA Astrophysics Data System (ADS)

    Sadrieva, Z. F.; Sinev, I. S.; Samusev, A. K.; Iorsh, I. V.; Koshelev, K. L.; Takayama, O.; Malureanu, R.; Lavrinenko, A. V.; Bogdanov, A. A.

    2017-09-01

    Optical bound states in the continuum (BIC) are localized states with energy lying above the light line and having infinite lifetime. Any losses taking place in real systems result in transformation of the bound states into resonant states with finite lifetime. In this work, we analyze properties of BIC in CMOS-compatible one-dimensional photonic structure based on silicon-on-insulator wafer at telecommunication wavelengths, where the absorption of silicon is negligible. We reveal that a high-index substrate could destroy both off-Γ BIC and in-plane symmetry protected at-Γ BIC turning them into resonant states due to leakage into the diffraction channels opening in the substrate.

  16. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

    NASA Astrophysics Data System (ADS)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

  17. Flow Structure Determined Enhancing and Inhibiting Convective Heat Transfers in Quasi 1D Magnetic Fluid

    NASA Astrophysics Data System (ADS)

    Luo, Weili; Huang, Jun; Liu, Tianshu

    2016-11-01

    We have found previously that the convective flow in magnetic fluid responds to applied magnetic fields differently, depending on the relative direction of the gradient of temperature to that of the field. In this work we report the velocity profiles from these flows obtained from optical flow method. The peculiar magnetic driving force as well as the special configurations give rise to unique flow patterns, distinctly depends on the specific relative orientation of the temperature to that of field. The streamline plots indicate formation of local or global flow structures that explain the different effects of field on the heat transfer in the sample. For one configuration, the magneto-thermo convection causing the "heat" to be localized, stopping the equilibration process in the system. We will discuss the different responses to the applied magnetic fields for two different sample configurations in terms of relative orientation of the temperature and field gradients.

  18. Quark-Hadron Duality in Spin Structure Functions $g_1^p$ and $g_1^d$

    SciTech Connect

    P.E. Bosted; K.V. Dharmawardane; G.E. Dodge; T.A. Forest; S.E. Kuhn; Y. Prok

    2006-07-25

    New measurements of the spin structure functions of the proton and deuteron g{sub 1}{sup p}(x, Q{sup 2}) and g{sub 1}{sup d}(x, Q{sup 2}) in the nucleon resonance region are compared with extrapolations of target-mass-corrected next-to-leading-order (NLO) QCD fits to higher energy data. Averaged over the entire resonance region (W < 2 GeV), the data and QCD fits are in good agreement in both magnitude and Q{sup 2} dependence for Q{sup 2} > 1.7 GeV{sup 2}/c{sup 2}. This ''global'' duality appears to result from cancellations among the prominent ''local'' resonance regions: in particular strong {sigma}{sub 3/2} contributions in the {Delta}(1232) region appear to be compensated by strong {sigma}{sub 1/2} contributions in the resonance region centered on 1.5 GeV. These results are encouraging for the extension of NLO QCD fits to lower W and Q{sup 2} than have been used previously.

  19. Solid-state structural transformations and photoreactivity of 1D-ladder coordination polymers of Pb(II).

    PubMed

    Kole, Goutam Kumar; Peedikakkal, Abdul Malik Puthan; Toh, Belinda Mei Fang; Vittal, Jagadese J

    2013-03-18

    An attempt has been made to design double-stranded ladder-like coordination polymers (CPs) of hemidirected Pb(II) . Four CPs, [Pb(μ-bpe)(O2 C-C6 H5 )2 ]⋅2H2 O (1), [Pb2 (μ-bpe)2 (μ-O2 C-C6 H5 )2 (O2 C-C6 H5 )2 ] (2), [Pb2 (μ-bpe)2 (μ-O2 C-p-Tol)2 (O2 C-p-Tol)2 ]⋅ 1.5 H2 O (3) and [Pb2 (μ-bpe)2 (μ-O2 C-m-Tol)2 (O2 C-m-Tol)2 ] (4) (bpe=1,2-bis(4'-pyridyl)ethylene), have been synthesised and investigated for their solid-state photoreactivity. CPs 2-4, having a parallel orientation of bpe molecules in their ladder structures and being bridged by carboxylates, were found to be photoreactive, whereas CP 1 is a linear one-dimensional (1D) CP with guest water molecules aggregating to form a hydrogen-bonded 1D structure. The linear strands of 1 were found to pair up upon eliminating lattice water molecules by heating, which led to the solid-state structural transformation of photostable linear 1D CP 1 into photoreactive ladder CP 2. In the construction of the double-stranded ladder-like structures, the parallel alignment of CC bonds in 2-4 is dictated by the chelating and μ2 -η(2) :η(1) bridging modes of the benzoate and toluate ligands. The role of solvents in the formation of such double-stranded ladder-like structures has also been investigated. A single-crystal-to-single-crystal transformation occurred when 4 was irradiated under UV light to form [Pb2 (rctt-tpcb)(μ-O2 C-m-Tol)2 (O2 C-m-Tol)2 ] (5). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Exponents of the spectral functions and dynamical structure factor of the 1D Lieb-Liniger Bose gas

    NASA Astrophysics Data System (ADS)

    Carmelo, J. M. P.; Sacramento, P. D.

    2016-06-01

    We study the (k , ω) -plane finite-energy line shape of the zero-temperature one-boson removal spectral function (ω < 0) , one-boson addition spectral function (ω > 0) , and charge dynamical structure factor (ω > 0) of the 1D Lieb-Liniger Bose gas with repulsive boson interaction c > 0. Our analysis of the problem focuses on the line shape at finite excitation energies in the vicinity of these functions spectrum upper (ω < 0) or lower (ω > 0) threshold. Specifically, we derive the exact momentum, interaction, and density dependences of the exponents controlling such a line shape in each of the N = 1 , 2 , 3 , … momentum subdomains k ∈ [(N - 1) 2 πn , N 2 πn ] . Here n = N / L is the boson density, N the boson number, and L the system length. In the thermodynamic limit considered in our study nearly all spectral weight of the dynamical correlation functions is for large values of n / c contained in the N = 1 momentum subdomain k ∈ [ 0 , 2 πn ] . As n / c decreases a small fraction of that weight is transferred to the remaining set of N = 2 , 3 , 4 , … momentum subdomains, particularly to the N = 2 subdomain. In the case of the momentum subdomain k ∈ [ 0 , 2 πn ] , our exact results agree with those of previous studies. For that subdomain the above exponents are plotted as a function of the momentum for several n / c values. Our derivation of the line shapes of the three dynamical correlation functions relies on the use of a simplified form of the pseudofermion dynamical theory of the fermionic 1D Hubbard model suitably modified in this paper for the 1D Bose gas.

  1. Hydrothermal synthesis, crystal structure and properties of a novel chain coordination polymer constructed by tetrafunctional phosphonate anions and cobalt ions

    SciTech Connect

    Guan, Lei; Wang, Ying

    2015-08-15

    A novel cobalt phosphonate, [Co(HL)(H{sub 2}O){sub 3}]{sub n} (1) (L=N(CH{sub 2}PO{sub 3}H){sub 3}{sup 3−}) has been synthesized by hydrothermal reaction at 150 °C and structurally characterized by X-ray diffraction, infrared spectroscopy, elemental and thermogravimetric analysis. Complex 1 features a 1D chain structure with double-channel built from CoO{sub 6} octahedra bridged together by the phosphonate groups. Each cobalt ion is octahedrally coordinated by three phosphonate oxygen atoms and three water molecules. The coordinated water molecules can form the hydrogen bonds with the phosphonate oxygen atoms to link the 1D chains, building a 2D layered structure, further resulting in a 3D network. The luminescence spectrum indicates an emission maximum at 435 nm. The magnetic susceptibility curve exhibits a dominant antiferromagnetic behavior with a weakly ferromagnetic component at low temperatures. - Graphical abstract: The connectivity between cobalt ions and the ligands results in a chain structure with a 1D double-channel structure, which is constructed by A-type subrings and B-type subrings. - Highlights: • The tetrafunctional phosphonate ligand was used as the ligand. • A novel chain structure can be formed by A-type rings and B-type rings. • Two types of rings can form a 1D double-channel structure, along the c-axis.

  2. Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7).

    PubMed

    Qin, Jiayue; Wang, Zhizhi; Hoogeveen-Westerveld, Marianne; Shen, Guobo; Gong, Weimin; Nellist, Mark; Xu, Wenqing

    2016-04-15

    Mutations in TSC1 or TSC2 cause tuberous sclerosis complex (TSC), an autosomal dominant disorder characterized by the occurrence of benign tumors in various vital organs and tissues. TSC1 and TSC2, the TSC1 and TSC2 gene products, form the TSC protein complex that senses specific cellular growth conditions to control mTORC1 signaling. TBC1D7 is the third subunit of the TSC complex, and helps to stabilize the TSC1-TSC2 complex through its direct interaction with TSC1. Homozygous inactivation of TBC1D7 causes intellectual disability and megaencephaly. Here we report the crystal structure of a TSC1-TBC1D7 complex and biochemical characterization of the TSC1-TBC1D7 interaction. TBC1D7 interacts with the C-terminal region of the predicted coiled-coil domain of TSC1. The TSC1-TBC1D7 interface is largely hydrophobic, involving the α4 helix of TBC1D7. Each TBC1D7 molecule interacts simultaneously with two parallel TSC1 helices from two TSC1 molecules, suggesting that TBC1D7 may stabilize the TSC complex by tethering the C-terminal ends of two TSC1 coiled-coils.

  3. New coordination polymers from 1D chain, 2D layer to 3D framework constructed from 1,2-phenylenediacetic acid and 1,3-bis(4-pyridyl)propane flexible ligands

    NASA Astrophysics Data System (ADS)

    Xin, Ling-Yun; Liu, Guang-Zhen; Wang, Li-Ya

    2011-06-01

    The hydrothermal reactions of Cd, Zn, or Cu(II) acetate salts with H 2PHDA and BPP flexible ligands afford three new coordination polymers, including [Cd(PHDA)(BPP)(H 2O)] n(1), [Zn(PHDA)(BPP)] n(2), and [Cu 2(PHDA) 2(BPP)] n(3) (H 2PHDA=1,2-phenylenediacetic acid, BPP=1,3-bis(4-pyridyl)propane). The single-crystal X-ray diffractions reveal that all three complexes feature various metal carboxylate subunits extended further by the BPP ligands to form a diverse range of structures, displaying a remarked structural sensitivity to metal(II) cation. Complex 1 containing PHDA-bridged binuclear cadmium generates 1D double-stranded chain, complex 2 results in 2D→2D interpenetrated (4,4) grids, and complex 3 displays a 3D self-penetrated framework with 4 86 68 rob topology. In addition, fluorescent analyses show that both 1 and 2 exhibit intense blue-violet photoluminescence in the solid state.

  4. Designed Quasi-1D Potential Structures Realized in Compositionally Graded InAs1-xPx Nanowires.

    PubMed

    Nylund, Gustav; Storm, Kristian; Lehmann, Sebastian; Capasso, Federico; Samuelson, Lars

    2016-02-10

    III-V semiconductor heterostructures are important components of many solid-state optoelectronic devices, but the ability to control and tune the electrical and optical properties of these structures in conventional device geometries is fundamentally limited by the bulk dimensionality and the inability to accommodate lattice-mismatched material combinations. Here we demonstrate how semiconductor nanowires may enable the creation of arbitrarily shaped one-dimensional potential structures for new types of designed device functionality. We describe the controlled growth of stepwise compositionally graded InAs1-xPx heterostructures defined along the axes of InAs nanowires, and we show that nanowires with sawtooth-shaped composition profiles behave as near-ideal unipolar diodes with ratchet-like rectification of the electron transport through the nanowires, in excellent agreement with simulations. This new type of designed quasi-1D potential structure represents a significant advance in band gap engineering and may enable fundamental studies of low-dimensional hot-carrier dynamics, in addition to constituting a platform for implementing novel electronic and optoelectronic device concepts.

  5. Photonic Crystals: Tunable Design of Structural Colors Produced by Pseudo-1D Photonic Crystals of Graphene Oxide (Small 25/2016).

    PubMed

    Tong, Liping; Qi, Wei; Wang, Mengfan; Huang, Renliang; Su, Rongxin; He, Zhimin

    2016-07-01

    The production of structural colors based on graphene oxide (GO) pseudo-one-dimensional photonic crystals (p1D-PhCs) in the visible spectrum is reported on page 3433 by W. Qi and co-workers. The structural colors could be tuned by simply changing either the volume or concentration of the aqueous GO dispersion. Moreover, GO p1D-PhCs exhibit visible and rapid responsiveness to humidity.

  6. HOTCFGM-1D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Through-Thickness Functionally Graded Microstructures

    NASA Technical Reports Server (NTRS)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    1998-01-01

    The objective of this three-year project was to develop and deliver to NASA Lewis one-dimensional and two-dimensional higher-order theories, and related computer codes, for the analysis, optimization and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, blisk blades). To satisfy this objective, a quasi one-dimensional version of the higher-order theory, HOTCFGM-1D, and four computer codes based on this theory, for the analysis, design and optimization of cylindrical structural components functionally graded in the radial direction were developed. The theory is applicable to thin multi-phased composite shell/cylinders subjected to macroscopically axisymmetric thermomechanical and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial and circumferential directions, and arbitrarily distributed in the radial direction, thereby allowing functional grading of the internal reinforcement in this direction.

  7. Ionothermal synthesis and crystal structures of metal phosphate chains

    SciTech Connect

    Wragg, David S.; Le Ouay, Benjamin; Beale, Andrew M.; O'Brien, Matthew G.; Slawin, Alexandra M.Z.; Warren, John E.; Prior, Timothy J.; Morris, Russell E.

    2010-07-15

    We have prepared isostructural aluminium and gallium phosphate chains by ionothermal reactions in 1-ethyl-3-methylimidazolium bromide and 1-ethylpyridinium bromide under a variety of conditions. The chains can be prepared as pure phases or along with three dimensional framework phases. The chains are favoured at shorter heating times and the crystallinity can be improved by addition of transition metal acetates and amines which are not included in the final structure. The chain can be prepared with or without the presence of hydrofluoric acid. - Graphical abstract: Chain structures prepared from ionic liquid solvents under a wide variety of synthesis conditions.

  8. Syntheses, structures, and photoluminescence of d 10 coordination architectures: From 1D to 3D complexes based on mixed ligands

    NASA Astrophysics Data System (ADS)

    Yuan, Gang; Shao, Kui-Zhan; Du, Dong-Ying; Wang, Xin-Long; Su, Zhong-Min

    2011-05-01

    Six new compounds, namely, {[Cd 3(Himpy) 3(tda) 2]·3H 2O} n ( 1), {[Zn 3(bipy) 2(tda) 2(H 2O) 2]·4H 2O} n ( 2), {[Cd 3(bipy) 3(tda) 2]·4H 2O} n ( 3), {[Cd 3(tda) 2(H 2O) 3Cl]·H 2O} n ( 4), {[Zn 2(tz)(tda)(H 2O) 2]·H 2O} n ( 5) and {[Cd 7(pz)(tda) 4(OAc)(H 2O) 7]·3H 2O} n ( 6) [H 3tda = 1H-1,2,3-triazole-4,5-dicarboxylic acid, Himpy = 2-(1H-imidazol-2-yl)pyridine, bipy = 2,2'-bipyridine, Htz = 1H-1,2,4-triazole, H 2pz = piperazine] have been prepared under hydrothermal condition and characterized by elemental analyses, infrared spectroscopy, powder X-ray diffraction and single-crystal X-ray diffraction analyses. Compound 1 is a 1D column-like structure and displays a 3D supramolecular network via the π···π stacking interaction. The compounds 2 and 3 exhibit similar 2D layer-like structure, which further extend to 3D supermolecular structure by the π···π stacking interaction. All of compounds 4- 6 display 3D framework with diverse topology constructed from the tda 3- ligands in different coordination modes and secondary ligands (or bridging atom) connecting metal ions. Furthermore, the thermal stabilities and photoluminescent properties of compounds 1- 6 were studied.

  9. Molecular cable-like 1-D iodic spiral chains covered with triple helices stabilized in guest-included chiral porous framework.

    PubMed

    Tadokoro, Makoto; Tanaka, Yasuko; Noguchi, Khoichiro; Sugaya, Tomoaki; Isoda, Kyosuke

    2012-07-21

    The supramolecular crystal {[Pr(DMFA)](3)[Ni(II)(Hbim)(3)](2)I}(n) with intricate chiral networks of [Ni(II)(Hbim)(3)](-) molecules is reported. It includes a cationic architecture as a guest, constructed from chiral nanotubes that penetrate I(-) chains with spiral channels wrapped by triple helices. The I(-) chains have AC conductivity in crystals like a molecular cable.

  10. Quantifying side-chain conformational variations in protein structure.

    PubMed

    Miao, Zhichao; Cao, Yang

    2016-11-15

    Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

  11. Quantifying side-chain conformational variations in protein structure

    NASA Astrophysics Data System (ADS)

    Miao, Zhichao; Cao, Yang

    2016-11-01

    Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

  12. Quantifying side-chain conformational variations in protein structure

    PubMed Central

    Miao, Zhichao; Cao, Yang

    2016-01-01

    Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs. PMID:27845406

  13. Nonequilibrium generalised Langevin equation for the calculation of heat transport properties in model 1D atomic chains coupled to two 3D thermal baths

    NASA Astrophysics Data System (ADS)

    Ness, H.; Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2017-04-01

    We use a generalised Langevin equation scheme to study the thermal transport of low dimensional systems. In this approach, the central classical region is connected to two realistic thermal baths kept at two different temperatures [H. Ness et al., Phys. Rev. B 93, 174303 (2016)]. We consider model Al systems, i.e., one-dimensional atomic chains connected to three-dimensional baths. The thermal transport properties are studied as a function of the chain length N and the temperature difference Δ T between the baths. We calculate the transport properties both in the linear response regime and in the non-linear regime. Two different laws are obtained for the linear conductance versus the length of the chains. For large temperatures (T ≳500 K) and temperature differences (Δ T ≳500 K), the chains, with N >18 atoms, present a diffusive transport regime with the presence of a temperature gradient across the system. For lower temperatures (T ≲500 K) and temperature differences (Δ T ≲400 K), a regime similar to the ballistic regime is observed. Such a ballistic-like regime is also obtained for shorter chains (N ≤15 ). Our detailed analysis suggests that the behaviour at higher temperatures and temperature differences is mainly due to anharmonic effects within the long chains.

  14. Nonequilibrium generalised Langevin equation for the calculation of heat transport properties in model 1D atomic chains coupled to two 3D thermal baths.

    PubMed

    Ness, H; Stella, L; Lorenz, C D; Kantorovich, L

    2017-04-28

    We use a generalised Langevin equation scheme to study the thermal transport of low dimensional systems. In this approach, the central classical region is connected to two realistic thermal baths kept at two different temperatures [H. Ness et al., Phys. Rev. B 93, 174303 (2016)]. We consider model Al systems, i.e., one-dimensional atomic chains connected to three-dimensional baths. The thermal transport properties are studied as a function of the chain length N and the temperature difference ΔT between the baths. We calculate the transport properties both in the linear response regime and in the non-linear regime. Two different laws are obtained for the linear conductance versus the length of the chains. For large temperatures (T≳500 K) and temperature differences (ΔT≳500 K), the chains, with N>18 atoms, present a diffusive transport regime with the presence of a temperature gradient across the system. For lower temperatures (T≲500 K) and temperature differences (ΔT≲400 K), a regime similar to the ballistic regime is observed. Such a ballistic-like regime is also obtained for shorter chains (N≤15). Our detailed analysis suggests that the behaviour at higher temperatures and temperature differences is mainly due to anharmonic effects within the long chains.

  15. Controlled structures of a 1D chiral metallosalen polymer by photo- and solvent-induced partial depolymerization.

    PubMed

    Xi, Xiaobing; Dong, Taiwei; Li, Gao; Cui, Yong

    2011-04-07

    A 1D chiral metallosalen polymer with free pyridine groups is self-assembled and its molecular weight, conformation, architecture and optical property are controlled by depolymerization through sunlight irradiation or alcohol inclusions.

  16. Molecular tectonics: self-complementary supramolecular Se...N synthons directing assembly of 1D silver chains into 3D porous molecular architectures.

    PubMed

    Zhou, Ai-Ju; Zheng, Shao-Liang; Fang, Yue; Tong, Ming-Liang

    2005-06-27

    Reaction of 2,1,3-benzoselenadiazole (bsd) with AgNO3 results in the formation of a novel model example of a Se...N synthon directed molecular network of different polymorphs at different temperatures. Alpha-[Ag(bsd)2(NO3)] x 0.5bsd formed at ambient temperature, has a 3D porous molecular network constructed with monomeric [Ag(bsd)2(NO3)] motif, and has 1D channels that are encapsulated with 1D arrays of two-fold-disordered dimeric (bsd)2 guests aggregated by the self-complementary nonbonded Se...N interactions. This is the first molecular net directed by supramolecular Se...N synthons. The second polymorph, beta-[Ag(bsd)2(NO3)] x 0.5bsd, formed from an analogous reaction at 50 degrees C, contains a similar 3D molecular network constructed with tetrameric [Ag4(bsd)8(NO3)4] motif and 1D arrays of well-ordered dimeric (bsd)2 guests are encapsulated in the channels. Such ordered (bsd)2 dimers provide an excellent simplified dimeric model for MO calculations of intermolecular nonbonded Se...N interactions.

  17. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2012-04-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  18. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2011-10-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  19. Satellite-derived light extinction coefficient and its impact on thermal structure simulations in a 1-D lake model

    NASA Astrophysics Data System (ADS)

    Zolfaghari, Kiana; Duguay, Claude R.; Kheyrollah Pour, Homa

    2017-01-01

    A global constant value of the extinction coefficient (Kd) is usually specified in lake models to parameterize water clarity. This study aimed to improve the performance of the 1-D freshwater lake (FLake) model using satellite-derived Kd for Lake Erie. The CoastColour algorithm was applied to MERIS satellite imagery to estimate Kd. The constant (0.2 m-1) and satellite-derived Kd values as well as radiation fluxes and meteorological station observations were then used to run FLake for a meteorological station on Lake Erie. Results improved compared to using the constant Kd value (0.2 m-1). No significant improvement was found in FLake-simulated lake surface water temperature (LSWT) when Kd variations in time were considered using a monthly average. Therefore, results suggest that a time-independent, lake-specific, and constant satellite-derived Kd value can reproduce LSWT with sufficient accuracy for the Lake Erie station. A sensitivity analysis was also performed to assess the impact of various Kd values on the simulation outputs. Results show that FLake is sensitive to variations in Kd to estimate the thermal structure of Lake Erie. Dark waters result in warmer spring and colder fall temperatures compared to clear waters. Dark waters always produce colder mean water column temperature (MWCT) and lake bottom water temperature (LBWT), shallower mixed layer depth (MLD), longer ice cover duration, and thicker ice. The sensitivity of FLake to Kd variations was more pronounced in the simulation of MWCT, LBWT, and MLD. The model was particularly sensitive to Kd values below 0.5 m-1. This is the first study to assess the value of integrating Kd from the satellite-based CoastColour algorithm into the FLake model. Satellite-derived Kd is found to be a useful input parameter for simulations with FLake and possibly other lake models, and it has potential for applicability to other lakes where Kd is not commonly measured.

  20. Relationships between Th1 or Th2 iNKT Cell Activity and Structures of CD1d-Antigen Complexes: Meta-analysis of CD1d-Glycolipids Dynamics Simulations

    PubMed Central

    Laurent, Xavier; Renault, Nicolas; Farce, Amaury; Chavatte, Philippe; Hénon, Eric

    2014-01-01

    A number of potentially bioactive molecules can be found in nature. In particular, marine organisms are a valuable source of bioactive compounds. The activity of an α-galactosylceramide was first discovered in 1993 via screening of a Japanese marine sponge (Agelas mauritanius). Very rapidly, a synthetic glycololipid analogue of this natural molecule was discovered, called KRN7000. Associated with the CD1d protein, this α-galactosylceramide 1 (KRN7000) interacts with the T-cell antigen receptor to form a ternary complex that yields T helper (Th) 1 and Th2 responses with opposing effects. In our work, we carried out molecular dynamics simulations (11.5 µs in total) involving eight different ligands (conducted in triplicate) in an effort to find out correlation at the molecular level, if any, between chemical modulation of 1 and the orientation of the known biological response, Th1 or Th2. Comparative investigations of human versus mouse and Th1 versus Th2 data have been carried out. A large set of analysis tools was employed including free energy landscapes. One major result is the identification of a specific conformational state of the sugar polar head, which could be correlated, in the present study, to the biological Th2 biased response. These theoretical tools provide a structural basis for predicting the very different dynamical behaviors of α-glycosphingolipids in CD1d and might aid in the future design of new analogues of 1. PMID:25376021

  1. Surface-micromachined chain for use in microelectromechanical structures

    SciTech Connect

    Vernon, Sr., George E.

    2001-01-01

    A surface-micromachined chain and a microelectromechanical (MEM) structure incorporating such a chain are disclosed. The surface-micromachined chain can be fabricated in place on a substrate (e.g. a silicon substrate) by depositing and patterning a plurality of alternating layers of a chain-forming material (e.g. polycrystalline silicon) and a sacrificial material (e.g. silicon dioxide or a silicate glass). The sacrificial material is then removed by etching to release the chain for movement. The chain has applications for forming various types of MEM devices which include a microengine (e.g. an electrostatic motor) connected to rotate a drive sprocket, with the surface-micromachined chain being connected between the drive sprocket and one or more driven sprockets.

  2. Finite Markov Chains and Random Discrete Structures

    DTIC Science & Technology

    1994-07-26

    arrays with fixed margins 4. Persi Diaconis and Susan Holmes, Three Examples of Monte- Carlo Markov Chains: at the Interface between Statistical Computing...solutions for a math- ematical model of thermomechanical phase transitions in shape memory materials with Landau- Ginzburg free energy 1168 Angelo Favini

  3. Synthesis, crystal structure and magnetic properties of an alternating manganese chain

    SciTech Connect

    Ramos Silva, Manuela . E-mail: manuela@pollux.fis.uc.pt; Matos Beja, Ana; Antonio Paixao, Jose; Martin-Gil, Jesus

    2006-07-15

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Mn(II) ions assemble in alternating chains with Mn-Mn distances of 3.8432(13) and 4.4428(14) A. A 3D network of hydrogen bonds links the chains together. The temperature dependence of the magnetic susceptibility reveals that this compound undergoes a magnetic transition and exhibits an antiferromagnetic interaction in the low-temperature phase with two alternating exchange interactions of -2.32(1) and -5.55(1) cm{sup -1}. - Graphical abstract: Portion of the dimeric manganese chain showing the two alternating exchange interactions paths.

  4. New 1-D and 3-D thiocyanatocadmates modified by various amine molecules and Cl(-)/CH3COO(-) ions: synthesis, structural characterization, thermal behavior and photoluminescence properties.

    PubMed

    Guo, Bing; Zhang, Xiao; Wang, Yan-Ning; Huang, Jing-Jing; Yu, Jie-Hui; Xu, Ji-Qing

    2015-03-21

    Under ambient conditions, reactions of CdCl2/Cd(CH3COO)2, SCN(-) and various organic amine molecules in strongly acidic solutions afforded the five new thiocyanatocadmates [H2(abpy)][CdCl2(SCN)2] (abpy = azobispyridine) 1, [H(apy)][Cd(SCN)3] (apy = 4-aminopyridine) 2, [H(ba)]2[CdCl2(SCN)2] (ba = tert-butylamine) 3, [H2(tmen)][Cd3Cl6(SCN)2] (tmen = N,N,N',N'-tetramethylethylenediamine) 4, and [H(dba)]2[Cd2(CH3COO)2(SCN)4] (dba = dibutylamine) 5. In compound 2 only, the CH3COO(-) ions in Cd(CH3COO)2 were completely displaced by SCN(-), producing a chained thiocyanatocadmate [Cd(SCN)3](-). In the other four compounds, the Cl(-) or CH3COO(-) ions appeared in the final inorganic anion frameworks. In compound 1, the Cl(-) ions doubly bridge the Cd(2+) centers, forming a one-dimensional (1-D) infinite chain, and the SCN(-) group exists in a terminal form, whereas in compound 3, the reverse situation is observed. Due to a trans-mode arrangement for two terminal Cl(-) or SCN(-) ions around each Cd(2+) center, the inorganic anion chains in compounds 1 and 3 both show a linear shape. In compound 4, Cd(2+) and Cl(-) first aggregate to form a 1-D endless chain with a composition of Cd3Cl6, which can be described as a linear arrangement of the open double cubanes. SCN(-) serves as the second connector, propagating the Cd3Cl6 chain into a three-dimensional (3-D) network with the occluded H2(tmen)(2+) cations. In compound 5, the SCN(-) groups doubly bridge the Cd(2+) centers, forming a 1-D zigzag-shape chain. The formation of the zigzag chain likely derives from chelation of the CH3COO(-) group to the Cd(2+) center. The thermal behavior and the photoluminescence properties of the title compounds were also investigated.

  5. Ligh chain cardiomyopathy - structural analysis of the light chain tissue deposits.

    SciTech Connect

    Gallo, G.; Goni, F.; Boctor, F.; Vidal, R.; Kumar, A.; Stevens, F. J.; Frangione, B.; Ghiso, J.; Center for Mechanistic Biology and Biotechnology; New York Univ. Medical Center

    1996-01-01

    Cardiomyopathy due to monoclonal light chain deposits is a complication of plasma cell disorders. The deposits may be either fibrillar as in light chain amyloid or nonfibrillar as in light chain deposition disease. The reasons for these structural differences are still unknown. We characterized the myocardial deposits by immunohistochemical examination of sections and extraction and biochemical analysis of the tissue deposits in a patient (MCM) who died of myeloma and systemic light chain deposition disease. Amino acid sequence analysis of the extracted nonfibrillar MCM {kappa}-light chain reveals that it belongs to the L12a germline subset of the {kappa}{sub I} protein and contains five distinctive amino acid substitutions (three in the framework region III and two in the complementarity-determining region III) that have not been reported previously in the same positions in other {kappa}I light chains. The theoretically determined isoelectric point (pI 8.21) of the MCM light chain is high compared with the low isoelectric point of other Bence Jones proteins from subjects without light chain deposition disease. The diffuse binding to basement membranes and the high isoelectric point of the MCM {kappa}-light chain suggest electrostatic interaction as a possible mechanism of tissue deposition. The spatial locations of the five distinctive residues and a sixth rare substitution of the MCM protein modeled on the backbone structure of REI, a {kappa}{sub I}-soluble Bence Jones light chain of known three-dimensional structure, may be responsible for protein destabilization, partial unfolding, and aggregation leading to tissue deposition.

  6. Gold-induced nanowires on the Ge(100) surface yield a 2D and not a 1D electronic structure

    NASA Astrophysics Data System (ADS)

    de Jong, N.; Heimbuch, R.; Eliëns, S.; Smit, S.; Frantzeskakis, E.; Caux, J.-S.; Zandvliet, H. J. W.; Golden, M. S.

    2016-06-01

    Atomic nanowires on semiconductor surfaces induced by the adsorption of metallic atoms have attracted a lot of attention as possible hosts of the elusive, one-dimensional Tomonaga-Luttinger liquid. The Au/Ge(100) system in particular is the subject of controversy as to whether the Au-induced nanowires do indeed host exotic, 1D (one-dimensional) metallic states. In light of this debate, we report here a thorough study of the electronic properties of high quality nanowires formed at the Au/Ge(100) surface. The high-resolution ARPES data show the low-lying Au-induced electronic states to possess a dispersion relation that depends on two orthogonal directions in k space. Comparison of the E (kx,ky) surface measured using high-resolution ARPES to tight-binding calculations yields hopping parameters in the two different directions that differ by approximately factor of two. Additionally, by pinpointing the Au-induced surface states in the first, second, and third surface Brillouin zones and analyzing their periodicity in k||, the nanowire propagation direction seen clearly in STM can be imported into the ARPES data. We find that the larger of the two hopping parameters corresponds, in fact, to the direction perpendicular to the nanowires (tperp). This proves that the Au-induced electron pockets possess a two-dimensional, closed Fermi surface, and this firmly places the Au/Ge(100) nanowire system outside potential hosts of a Tomonaga-Luttinger liquid. We combine these ARPES data with scanning tunneling spectroscopic measurements of the spatially resolved electronic structure and find that the spatially straight—wirelike—conduction channels observed up to energies of order one electron volt below the Fermi level do not originate from the Au-induced states seen in the ARPES data. The former are rather more likely to be associated with bulk Ge states that are localized to the subsurface region. Despite our proof of the 2D (two-dimentional) nature of the Au

  7. Dinuclear and 1D iron(III) Schiff base complexes bridged by 4-salicylideneamino-1,2,4-triazolate: X-ray structures and magnetic properties.

    PubMed

    Herchel, Radovan; Pavelek, Lubomír; Trávníček, Zdeněk

    2011-11-28

    Four new iron(III) complexes were obtained by the reaction of 4-salicylideneamino-1,2,4-triazole (Hsaltrz) and selected dinuclear μ-oxo-bridged iron(III) Schiff base complexes [{FeL(4)}(2)(μ-O)], where L(4) represents a terminal tetradentate dianionic Schiff-base ligand. X-ray structural analysis revealed a novel bridging mode of κN,κO of the saltrz ligand to form dinuclear complexes [{Fe(salen)(μ-saltrz)}(2)]·CH(3)OH (1) (H(2)salen = N,N'-ethylenebis(salicylimine)) and [{Fe(salpn)(μ-saltrz)}(2)] (2) (H(2)salpn = N,N'-1,2-propylenbis(salicylimine)), whereas one-dimensional (1D) zig-zag chains were formed in the case of [{Fe(salch)(μ-saltrz)}·0.5CH(3)OH](n) (3) (H(2)salch = N,N'-cyclohexanebis(salicylimine)) and [Fe(salophen)(μ-saltrz)](n) (4) (H(2)salophen = N,N'-o-phenylenebis(salicylimine)). It was also shown that the rigidity of the terminal ligand L(4) can be considered as the key factor for the molecular dimensionality of the products. The thorough magnetic analysis based on SQUID experiments, including the isotropic exchange and the zero-field splitting of both temperature and field dependent data, was performed for dimeric (1 and 2) and also for polymeric compounds (3 and 4) and revealed weak antiferromagnetic exchange mediated by the saltrz anions with much larger D-parameter (|D|≫|J|).

  8. A new magnetic phase diagram for the quasi-one-dimensional (1D) spin chain compound Ca3Co2O6

    NASA Astrophysics Data System (ADS)

    Srikanth, Hari; Lampen, P.; Bingham, N. S.; Phan, M. H.; Yi, H. T.; Cheong, S. W.

    2015-03-01

    The spin chain cobaltite system Ca3Co2O6 combines geometric frustration with intrinsic low-dimensionality, giving rise to complex physical phenomena that continue to attract a great deal of interest. A long-wavelength spin-density wave (SDW) has recently been observed in Ca3Co2O6 at zero field, stabilized by a helical exchange pathway among neighboring chains. We establish a new and more comprehensive phase diagram for this exotic system through the evolution of the magnetic entropy change ΔSM (T,H) associated with the magnetocaloric effect. ΔSM measurements in a single crystal of Ca3Co2O6 prepared by the flux method demonstrate the suppression of the SDW modulation by small applied magnetic fields (<1T). Metamagnetic transitions to a ferrimagnetic up-up-down spin chain arrangement and full ferromagnetic alignment are observed below 25 K. Short-range ordered (SRO) correlations with an antiferromagnetic character grow in volume as the temperature is lowered below 15 K, resulting in a crossover from ΔSM (H) <0 to ΔSM (H) >0 at 12 K. Our entropy-based analysis reflects current understanding of the role of SDW and SRO phases in Ca3Co2O6, resolves new sub-features of the ferrimagnetic phase, and extends previous results below the onset of slow dynamics (~ 10 K). USF authors acknowledge DoE BES under Award # DE-FG02-07ER46438 (magnetic measurements and analysis).

  9. Nuclear structure notes on element 115 decay chains

    SciTech Connect

    Rudolph, D. Sarmiento, L. G.; Forsberg, U.

    2015-10-15

    Hitherto collected data on more than hundred α-decay chains stemming from element 115 are combined to probe some aspects of the underlying nuclear structure of the heaviest atomic nuclei yet created in the laboratory.

  10. Stabilization of Ca1-dFe2-xMnxO4 (0.44 lt x lt 2) with CaFe2O4-type Structure and Ca2plus Defects in 1D Channels

    SciTech Connect

    T Yang; M Croft; A Ignatov; I Nowik; R Cong; M Greenblatt

    2011-12-31

    Solid solutions of Ca{sub 1-{delta}}Fe{sub 2-x}Mn{sub x}O{sub 4} (0.45 {<=} x {<=} 2) were synthesized from CaCl{sub 2} as flux at 850 C in air. The entire series, even with x = 2, crystallizes in the CaFe{sub 2}O{sub 4}-type structure (Pnma), rather than in the CaMn{sub 2}O{sub 4}-type structure (Pbcm). Rietveld refinements confirmed mixed-valency Mn{sup 3+}/Mn{sup 4+} and a substantial level of Ca{sup 2+} deficiency ({delta} {approx} 0.25) at high x. With increasing x, the unit-cell dimensions a and b decrease, while that of c increases. Detailed structural analyses, together with Mn K-edge X-ray absorption and {sup 57}Fe Moessbauer spectroscopy studies, revealed that the stabilization of CaFe{sub 2}O{sub 4}-type structure, even at high values of x, is due to the existence of non-Jahn-Teller active Mn{sup 4+} (and Fe{sup 3+}), which is compensated by the formation of the Ca{sup 2+} deficiencies in the one-dimensional (1D) channels of Ca{sub 1-{delta}}Fe{sub 2-x}Mn{sub x}O{sub 4} during the flux synthesis. Antiferromagnetic (AFM) long-range ordering is achieved for all compounds at low temperature, because of strong AFM interactions between Mn{sup 3+}/Mn{sup 4+} and Fe{sup 3+}. In addition, a spin (or cluster) glass component was also observed, as expected, because of the extensive Mn/Fe structural and Mn{sup 3+}/Mn{sup 4+} charge disordering.

  11. From 2D graphene to 1D graphene nanoribbons: dimensional crossover signals in the structural thermal fluctuations

    NASA Astrophysics Data System (ADS)

    Dobry, Ariel; Costamagna, Sebastián

    2011-03-01

    I this work, by analyzing the thermal excited rippling in the graphene honeycomb lattice, we find clear signals of an existing dimensional crossover from 2D to 1D while reducing one of the dimensions of the graphene layer. Trough a joint study, using montecarlo atomistic simulations and analytical calculation based, we find that the normal-normal correlation function G (q) does not change the power law behavior valid on the long wavelength limit, however the system size dependency of the quadratic out of plane displacement h2 shows a breakdown of its corresponding scaling law. In this case we show that a new scaling law appear which correspond to a truly 1D system. On the basis of these results, and having explored a wide number of realistic systems size, we conclude that narrow nanoribbons presents strongest corrugations than the square graphene sheets. This result could have important consequences on the electron transport properties of freestanding graphene systems.

  12. Synthesis, crystal structure, near-IR photoelectric response of two 1-D selenides: [Cu2MSe5]·[Mn(H+-en)2(en)] (M=Ge, Sn)

    NASA Astrophysics Data System (ADS)

    Zhang, Yingying; Hu, Dandan; Yang, Huajun; Lin, Jian; Wu, Tao

    2017-07-01

    Reported here are two solvothermally synthesized metal selenides, namely [Cu2MSe5][Mn(H+-en)2(en)] (M = Ge (1) and Sn (2), and en=ethanediamine). The two isostructural compounds feature a 1-D anionic chain of [Cu2MSe5]4- with the existence of strong Cu•••Cu interaction. The estimated optical band gap was determined to be 1.69 eV for 1 and 1.49 eV for 2, indicating their semiconducting nature. Interestingly, 2 exhibits NIR-triggered photoelectric response, which make it potential semiconductor sensor used in photoelectric devices.

  13. On constitutive functions for hindered settling velocity in 1-D settler models: Selection of appropriate model structure.

    PubMed

    Torfs, Elena; Balemans, Sophie; Locatelli, Florent; Diehl, Stefan; Bürger, Raimund; Laurent, Julien; François, Pierre; Nopens, Ingmar

    2017-03-01

    Advanced 1-D models for Secondary Settling Tanks (SSTs) explicitly account for several phenomena that influence the settling process (such as hindered settling and compression settling). For each of these phenomena a valid mathematical expression needs to be selected and its parameters calibrated to obtain a model that can be used for operation and control. This is, however, a challenging task as these phenomena may occur simultaneously. Therefore, the presented work evaluates several available expressions for hindered settling based on long-term batch settling data. Specific attention is paid to the behaviour of these hindered settling functions in the compression region in order to evaluate how the modelling of sludge compression is influenced by the choice of a certain hindered settling function. The analysis shows that the exponential hindered settling forms, which are most commonly used in traditional SST models, not only account for hindered settling but partly lump other phenomena (compression) as well. This makes them unsuitable for advanced 1-D models that explicitly include each phenomenon in a modular way. A power-law function is shown to be more appropriate to describe the hindered settling velocity in advanced 1-D SST models. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. 1D μ-glycine-briged copper (II) chain in complex [Cu(μ-Gly)Im(ClO4)]n and ferromagnetic interactions among copper (II)

    NASA Astrophysics Data System (ADS)

    Pan, Lu; Lv, Xue-Chuan; Luo, Guan-Hua; Gao, Xiao-Han; Tan, Zhi-Cheng

    2016-12-01

    Complex [Cu(μ-Gly)Im(ClO4)]n(Im = imidazole, and Gly = glycine) with μ-glycine-briged copper (II) chain, containing six-coordination distorted elongated octahedron, was synthesized and characterized. The complex belongs to space group P 21/c measured by X-ray single crystal diffraction. In the cluster, each Cu2+ ion are six-coordination by one nitrogen atom and two oxygen atoms of glycine, one nitrogen atoms of imidazole, and two of oxygen atoms of two perchlorate. Each Cu2+ ion has an N2O4 donor set, which forms the distorted elongated octahedron due to the Jahn-Teller (JT) effect. The magnetic and thermodynamic properties were researched. Magnetic susceptibilities of the complex showed that ferromagnetic interactions occurred between the Cu (II) atoms. The Curie-Weiss constant C = 0.565 cm3 K·mol-1 and the Weiss constant θ = 1.0585 K were given by the Curie-Weiss law The ferromagnetic nature of the interaction could be deduced as the exchange pathway of Cusbnd Osbnd Csbnd Osbnd Cu, which involved an equatorial position at one copper (II) ion and an axial position of the nearest copper (II). The complex decomposed from 511 to 538 K as two steps.

  15. Dynamics and supramolecular organization of the 1D spin transition polymeric chain compound [Fe(NH2trz)3](NO3)2. Muon spin relaxation.

    PubMed

    Garcia, Yann; Campbell, Stewart J; Lord, James S; Boland, Yves; Ksenofontov, Vadim; Gütlich, Philipp

    2007-09-27

    The thermal spin transition that occurs in the polymeric chain compound [Fe(NH(2)trz)3](NO3)2 above room temperature has been investigated by zero-field muon spin relaxation (microSR) over the temperature range approximately 8-402 K. The depolarization curves are best described by a Lorentzian and a Gaussian line that represent fast and slow components, respectively. The spin transition is associated with a hysteresis loop of width DeltaT = 34 K (T1/2 upward arrow = 346 K and T1/2 downward arrow = 312 K) that has been delineated by the temperature variation of the initial asymmetry parameter, in good agreement with previously published magnetic measurements. Zero-field and applied field (20-2000 Oe) microSR measurements show the presence of diamagnetic muon species and paramagnetic muonium radical species (A = 753 +/- 77 MHz) over the entire temperature range. Fast dynamics have been revealed in the high-spin state of [Fe(NH(2)trz)3](NO3)2 with the presence of a Gaussian relaxation mode that is mostly due to the dipolar interaction with static nuclear moments. This situation, where the muonium radicals are totally decoupled and not able to sense paramagnetic fluctuations, implies that the high-spin dynamics fall outside the muon time scale. Insights to the origin of the cooperative effects associated with the spin transition of [Fe(NH(2)trz)3](NO3)2 through muon implantation are presented.

  16. Inhibition of Human Steroid 5β-Reductase (AKR1D1) by Finasteride and Structure of the Enzyme-Inhibitor Complex*

    PubMed Central

    Drury, Jason E.; Di Costanzo, Luigi; Penning, Trevor M.; Christianson, David W.

    2009-01-01

    The Δ4-3-ketosteroid functionality is present in nearly all steroid hormones apart from estrogens. The first step in functionalization of the A-ring is mediated in humans by steroid 5α- or 5β-reductase. Finasteride is a mechanism-based inactivator of 5α-reductase type 2 with subnanomolar affinity and is widely used as a therapeutic for the treatment of benign prostatic hyperplasia. It is also used for androgen deprivation in hormone-de pend ent prostate carcinoma, and it has been examined as a chemopreventive agent in prostate cancer. The effect of finasteride on steroid 5β-reductase (AKR1D1) has not been previously reported. We show that finasteride competitively inhibits AKR1D1 with low micromolar affinity but does not act as a mechanism-based inactivator. The structure of the AKR1D1·NADP+·finasteride complex determined at 1.7 Å resolution shows that it is not possible for NADPH to reduce the Δ1-2-ene of finasteride because the cofactor and steroid are not proximal to each other. The C3-ketone of finasteride accepts hydrogen bonds from the catalytic residues Tyr-58 and Glu-120 in the active site of AKR1D1, providing an explanation for the competitive inhibition observed. This is the first reported structure of finasteride bound to an enzyme involved in steroid hormone metabolism. PMID:19515843

  17. Structural insight for chain selection and stagger control in collagen

    PubMed Central

    Boudko, Sergei P.; Bächinger, Hans Peter

    2016-01-01

    Collagen plays a fundamental role in all known metazoans. In collagens three polypeptides form a unique triple-helical structure with a one-residue stagger to fit every third glycine residue in the inner core without disturbing the poly-proline type II helical conformation of each chain. There are homo- and hetero-trimeric types of collagen consisting of one, two or three distinct chains. Thus there must be mechanisms that control composition and stagger during collagen folding. Here, we uncover the structural basis for both chain selection and stagger formation of a collagen molecule. Three distinct chains (α1, α2 and α3) of the non-collagenous domain 2 (NC2) of type IX collagen are assembled to guide triple-helical sequences in the leading, middle and trailing positions. This unique domain opens the door for generating any fragment of collagen in its native composition and stagger. PMID:27897211

  18. 3-D imaging of large scale buried structure by 1-D inversion of very early time electromagnetic (VETEM) data

    USGS Publications Warehouse

    Aydmer, A.A.; Chew, W.C.; Cui, T.J.; Wright, D.L.; Smith, D.V.; Abraham, J.D.

    2001-01-01

    A simple and efficient method for large scale three-dimensional (3-D) subsurface imaging of inhomogeneous background is presented. One-dimensional (1-D) multifrequency distorted Born iterative method (DBIM) is employed in the inversion. Simulation results utilizing synthetic scattering data are given. Calibration of the very early time electromagnetic (VETEM) experimental waveforms is detailed along with major problems encountered in practice and their solutions. This discussion is followed by the results of a large scale application of the method to the experimental data provided by the VETEM system of the U.S. Geological Survey. The method is shown to have a computational complexity that is promising for on-site inversion.

  19. Topological and geometric measurements of force-chain structure.

    PubMed

    Giusti, Chad; Papadopoulos, Lia; Owens, Eli T; Daniels, Karen E; Bassett, Danielle S

    2016-09-01

    Developing quantitative methods for characterizing structural properties of force chains in densely packed granular media is an important step toward understanding or predicting large-scale physical properties of a packing. A promising framework in which to develop such methods is network science, which can be used to translate particle locations and force contacts into a graph in which particles are represented by nodes and forces between particles are represented by weighted edges. Recent work applying network-based community-detection techniques to extract force chains opens the door to developing statistics of force-chain structure, with the goal of identifying geometric and topological differences across packings, and providing a foundation on which to build predictions of bulk material properties from mesoscale network features. Here we discuss a trio of related but fundamentally distinct measurements of the mesoscale structure of force chains in two-dimensional (2D) packings, including a statistic derived using tools from algebraic topology, which together provide a tool set for the analysis of force chain architecture. We demonstrate the utility of this tool set by detecting variations in force-chain architecture with pressure. Collectively, these techniques can be generalized to 3D packings, and to the assessment of continuous deformations of packings under stress or strain.

  20. Topological and geometric measurements of force-chain structure

    NASA Astrophysics Data System (ADS)

    Giusti, Chad; Papadopoulos, Lia; Owens, Eli T.; Daniels, Karen E.; Bassett, Danielle S.

    2016-09-01

    Developing quantitative methods for characterizing structural properties of force chains in densely packed granular media is an important step toward understanding or predicting large-scale physical properties of a packing. A promising framework in which to develop such methods is network science, which can be used to translate particle locations and force contacts into a graph in which particles are represented by nodes and forces between particles are represented by weighted edges. Recent work applying network-based community-detection techniques to extract force chains opens the door to developing statistics of force-chain structure, with the goal of identifying geometric and topological differences across packings, and providing a foundation on which to build predictions of bulk material properties from mesoscale network features. Here we discuss a trio of related but fundamentally distinct measurements of the mesoscale structure of force chains in two-dimensional (2D) packings, including a statistic derived using tools from algebraic topology, which together provide a tool set for the analysis of force chain architecture. We demonstrate the utility of this tool set by detecting variations in force-chain architecture with pressure. Collectively, these techniques can be generalized to 3D packings, and to the assessment of continuous deformations of packings under stress or strain.

  1. Forward waveform modelling procedure for 1-D crustal velocity structure and its application to the southern Korean Peninsula

    NASA Astrophysics Data System (ADS)

    Kim, Seongryong; Rhie, Junkee; Kim, Geunyoung

    2011-04-01

    We propose a full-grid search procedure for broad-band waveform modelling to determine a 1-D crustal velocity model. The velocity model can be more constrained because of the use of broad-band waveforms instead of traveltimes for the crustal phases, although only a small number of event-station pairs were employed. Despite the time-consuming nature of the full-grid search method to search the whole model parameter space, the use of an empirical relationship between the P- and S-wave velocities can significantly reduce computation time. The proposed method was applied to a case in the southern Korean Peninsula. Broad-band waveforms obtained from two inland earthquakes that occurred on 2007 January 20 (Mw 4.6) and 2004 April 26 (Mw 3.6) were used to test the method. The three-layers over half-space crustal velocity model of the P- and S-wave velocities was estimated. Comparisons of waveform fitness between the final model and previously published models demonstrate advancements in the average value of waveform fitness for the inland earthquakes. In addition, 1-D velocity models were determined for three distinct tectonic regions, namely, the Gyonggi Massif, the Okcheon Belt and the Gyeongsang Basin, which are all located inside the study area. A comparison between the three models demonstrates that the crustal thickness of the southern Korean Peninsula increases from NW to SE and that the lower crustal composition of the Okcheon belt differs from that of the other tectonic regions.

  2. Structural Basis for Specific Recognition and Cleavage of Polyubiquitin Chains

    NASA Astrophysics Data System (ADS)

    Fukai, Shuya; Sato, Yusuke

    Ubiquitin is a conserved 76-residue protein that is reversibly conjugated with substrate proteins to regulate various cellular processes. The terminal carboxyl group of ubiquitin can be bonded to lysine residues of substrate proteins including ubiquitin itself. All seven lysine residues (K6, K11, K27, K29, K33, K48 and K63) and the N-terminal Met can act as receptors for the conjugation, producing polyubiquitin chains. For instance, the most abundant K48-linked chains serve as signals for proteasomal degradation, whereas K63-linked chains function in other proteasome-independent processes. Here we show how these functionally and structurally distinct chains are discriminated by linkage-specific deubiquitinating enzymes and binding proteins.

  3. Versatile structures of group 13 metal halide complexes with 4,4'-bipy: from 1D coordination polymers to 2D and 3D metal-organic frameworks.

    PubMed

    Sevastianova, Tatiana N; Bodensteiner, Michael; Maulieva, Albina F; Davydova, Elena I; Virovets, Alexander V; Peresypkina, Eugenia V; Balázs, Gábor; Graßl, Christian; Seidl, Michael; Scheer, Manfred; Frenking, Gernot; Berezovskaya, Ekaterina A; Kazakov, Igor V; Khoroshilova, Olesya V; Timoshkin, Alexey Y

    2015-12-21

    A systematic structural study of complexes formed by aluminium and gallium trihalides with 4,4'-bipyridine (bipy) in 2 : 1, 1 : 1, and 1 : 2 stoichiometric ratios has been performed. Molecular structures of 11 complexes in the solid state have been determined for the first time. Complexes of 2 : 1 composition are molecular, while complexes of 1 : 1 composition form metal-organic frameworks of different kinds: an ionic 3D network (three interpenetrated lvt nets for AlCl3bipy), an ionic 2D network for AlBr3bipy and GaBr3bipy and a 1D coordination polymer in the case of GaCl3bipy. Thus, the nature of the Lewis acid plays a critical role in the structural type of the complex in the solid state. Incorporation of excess bipy molecules into (GaCl3bipy)∞ (formation of crystallosolvate) leads to an unprecedented change of the molecular structure from a non-ionic 1D coordination polymer to an ionic 2D metal organic framework [GaCl2bipy2](+)[GaCl4](-)·2bipy. As indicated by the temperature-dependent XRD study, removal of bipy by heating in a vacuum restores the non-ionic 1D structure. Quantum chemical computations for simple cluster model systems (up to eight Al and Ga atoms) reveal that ionic forms are slightly favourable, although the energy differences between the ionic and non-ionic structures are not large. These theoretical predictions are in good agreement with experimental findings. Thus, even relatively simple cluster models may be used to indicate the structural preferences in the solid state. Both experimental and computational IR frequency shifts of the in-plane ring bending mode of bipy upon complexation correlate well with the M-N bond distances in the complexes.

  4. Direct Printing of 1-D and 2-D Electronically Conductive Structures by Molten Lead-Free Solder

    PubMed Central

    Wang, Chien-Hsun; Tsai, Ho-Lin; Hwang, Weng-Sing

    2016-01-01

    This study aims to determine the effects of appropriate experimental parameters on the thermophysical properties of molten micro droplets, Sn-3Ag-0.5Cu solder balls with an average droplet diameter of 50 μm were prepared. The inkjet printing parameters of the molten micro droplets, such as the dot spacing, stage velocity and sample temperature, were optimized in the 1D and 2D printing of metallic microstructures. The impact and mergence of molten micro droplets were observed with a high-speed digital camera. The line width of each sample was then calculated using a formula over a temperature range of 30 to 70 °C. The results showed that a metallic line with a width of 55 μm can be successfully printed with dot spacing (50 μm) and the stage velocity (50 mm∙s−1) at the substrate temperature of 30 °C. The experimental results revealed that the height (from 0.63 to 0.58) and solidification contact angle (from 72° to 56°) of the metallic micro droplets decreased as the temperature of the sample increased from 30 to 70 °C. High-speed digital camera (HSDC) observations showed that the quality of the 3D micro patterns improved significantly when the droplets were deposited at 70 °C. PMID:28772361

  5. Structural and Thermodynamic Characterization of a Cytoplasmic Dynein Light Chain-Intermediate Chain Complex

    SciTech Connect

    Williams,J.; Roulhac, P.; Roy, A.; Vallee, R.; Fitzgerald, M.; Hendrickson, W.

    2007-01-01

    Cytoplasmic dynein is a microtubule-based motor protein complex that plays important roles in a wide range of fundamental cellular processes, including vesicular transport, mitosis, and cell migration. A single major form of cytoplasmic dynein associates with membranous organelles, mitotic kinetochores, the mitotic and migratory cell cortex, centrosomes, and mRNA complexes. The ability of cytoplasmic dynein to recognize such diverse forms of cargo is thought to be associated with its several accessory subunits, which reside at the base of the molecule. The dynein light chains (LCs) LC8 and TcTex1 form a subcomplex with dynein intermediate chains, and they also interact with numerous protein and ribonucleoprotein partners. This observation has led to the hypothesis that these subunits serve to tether cargo to the dynein motor. Here, we present the structure and a thermodynamic analysis of a complex of LC8 and TcTex1 associated with their intermediate chain scaffold. The intermediate chains effectively block the major putative cargo binding sites within the light chains. These data suggest that, in the dynein complex, the LCs do not bind cargo, in apparent disagreement with a role for LCs in dynein cargo binding interactions.

  6. Interpolatory fixed-point algorithm for an efficient computation of TE and TM modes in arbitrary 1D structures at oblique incidence

    NASA Astrophysics Data System (ADS)

    Pérez Molina, Manuel; Francés Monllor, Jorge; Álvarez López, Mariela; Neipp López, Cristian; Carretero López, Luis

    2010-05-01

    We develop the Interpolatory Fixed-Point Algorithm (IFPA) to compute efficiently the TE and TM reflectance and transmittance coefficients for arbitrary 1D structures at oblique incidence. For this purpose, we demonstrate that the semi-analytical solutions of the Helmholtz equation provided by the fixed-point method have a polynomial dependence on variables that are related to the essential electromagnetic parameters -incidence angle and wavelength-, which allows a drastic simplification of the required calculations taking the advantage of interpolation for a few parameter values. The first step to develop the IFPA consists of stating the Helmholtz equation and boundary conditions for TE and TM plane incident waves on a 1D finite slab with an arbitrary permittivity profile surrounded by two homogeneous media. The Helmholtz equation and boundary conditions are then transformed into a second-order initial value problem which is written in terms of transfer matrices. By applying the fixed-point method, the coefficients of such transfer matrices are obtained as polynomials on several variables that can be characterized by a reduced set of interpolating parameters. We apply the IFPA to specific examples of 1D diffraction gratings, optical rugate filters and quasi-periodic structures, for which precise solutions for the TE and TM modes are efficiently obtained by computing less than 20 interpolating parameters.

  7. Sequence and structure of VH domain from naturally occurring camel heavy chain immunoglobulins lacking light chains.

    PubMed

    Muyldermans, S; Atarhouch, T; Saldanha, J; Barbosa, J A; Hamers, R

    1994-09-01

    We cloned 17 different PCR fragments encoding VH genes of camel (Camelus dromedarius). These clones were derived from the camel heavy chain immunoglobulins lacking the light chain counterpart of normal immunoglobulins. Insight into the camel VH sequences and structure may help the development of single domain antibodies. The most remarkable difference in the camel VH, consistent with the absence of the VL interaction, is the substitution of the conserved Leu45 by an Arg or Cys. Another noteworthy substitution is the Leu11 to Ser. This amino acid normally interacts with the CH1 domain, a domain missing in the camel heavy chain immunoglobulins. The nature of these substitutions agrees with the increased solubility behavior of an isolated camel VH domain. The VH domains of the camels are also characterized by a long CDR3, possibly compensating for the absence of the VL contacts with the antigen. The CDR3 lacks the salt bridge between Arg94 and Asp101. However, the frequent occurrence of additional Cys residues in both the CDR1 and CDR3 might lead to the formation of a second internal disulfide bridge, thereby stabilizing the CDR structure as in the DAW antibody. Within CDRs of the camel VH domains we observe a broad size distribution and a different amino acid pattern compared with the mouse or human VH. Therefore the camel hypervariable regions might adopt structures which differ substantially from the known canonical structures, thereby increasing the repertoire of the camel antigen binding sites within a VH.

  8. Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures.

    PubMed

    Eswar, N; Ramakrishnan, C

    2000-04-01

    A total of 19 835 polar residues from a data set of 250 non-homologous and highly resolved protein crystal structures were used to identify side-chain main-chain (SC-MC) hydrogen bonds. The ratio of the number of SC-MC hydrogen bonds to the total number of polar residues is close to 1:2, indicating the ubiquitous nature of such hydrogen bonds. Close to 56% of the SC-MC hydrogen bonds are local involving side-chain acceptor/donor ('i') and a main-chain donor/acceptor within the window i-5 to i+5. These short-range hydrogen bonds form well defined conformational motifs characterized by specific combinations of backbone and side-chain torsion angles. (a) The Ser/Thr residues show the greatest preference in forming intra-helical hydrogen bonds between the atoms O(gamma)(i) and O(i-4). More than half the examples of such hydrogen bonds are found at the middle of alpha-helices rather than at their ends. The most favoured motif of these examples is alpha(R)alpha(R)alpha(R)alpha(R)(g(-)). (b) These residues also show great preference to form hydrogen bonds between O(gamma)(i) and O(i-3), which are closely related to the previous type and though intra-helical, these hydrogen bonds are more often found at the C-termini of helices than at the middle. The motif represented by alpha(R)alpha(R)alpha(R)alpha(R)(g(+)) is most preferred in these cases. (c) The Ser, Thr and Glu are the most frequently found residues participating in intra-residue hydrogen bonds (between the side-chain and main-chain of the same residue) which are characterized by specific motifs of the form beta(g(+)) for Ser/Thr residues and alpha(R)(g(-)g(+)t) for Glu/Gln. (d) The side-chain acceptor atoms of Asn/Asp and Ser/Thr residues show high preference to form hydrogen bonds with acceptors two residues ahead in the chain, which are characterized by the motifs beta (tt')alphaR and beta(t)alpha(R), respectively. These hydrogen bonded segments, referred to as Asx turns, are known to provide stability to type I

  9. Crystal structure, infrared spectra and luminescence of a 1D Cd coordination polymer with 4-nitrophthalic acid and 1,10-phenanthroline monohydrate ligands

    NASA Astrophysics Data System (ADS)

    Han, Li-Juan; Kong, Ya-Jie; Sheng, Ning

    2015-01-01

    A new one-dimensional (1D) coordination polymer, [Cd(NPTA)(1,10-phen)(H2O)] n ( 1) (H2NPTA = 4-nitrophthalic acid; 1,10-phen = 1,10-phenanthroline monohydrate), has been synthesized under hydrothermal conditions and characterized by elemental analysis, single-crystal X-ray diffraction, solid state emission spectra, FT-IR spectra, and thermogravimetric analyses. The compound belongs to triclinic system with space group , and exhibits a one-dimensional linear chain. Each Cd with a strongly distorted octahedral coordination geometry is six-coordinated by two N atoms from one 1,10-phenanthroline ligand, three O atoms from two carboxylate groups of two different NPTA2- ligands and one O atoms from lattice water. Layer supramolecular architecture is formed by medium π-π stacking interactions between two neighboring phenanthroline rings from two independent linear chains. Studies on luminescent property of 1 exhibit the solid state emission originating from an intra ligand π → π* transition of NPTA2- ligand.

  10. CX, DPX, and PCW: Web Servers for the Visualization of Interior and Protruding Regions of Protein Structures in 3D and 1D.

    PubMed

    Ligeti, Balázs; Vera, Roberto; Juhász, János; Pongor, Sándor

    2017-01-01

    The CX and DPX web-based servers at http://pongor.itk.ppke.hu/bioinfoservices are dedicated to the analysis of protein 3D structures submitted by the users as Protein Data Bank (PDB) files. CX computes an atomic protrusion index, cx that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index, dpx for buried atoms, and allows one to visualize the distribution of buried residues. CX and DPX visualize 3D structures colored according to the calculated indices and return PDB files that can be visualized using standard programs. A combined server site, the Protein Core Workbench allows visualization of dpx, cx, solvent-accessible area as well as the number of atomic contacts as 3D plots and 1D sequence plots. Online visualization of the 3D structures and 1D sequence plots are available in all three servers. Mirror sites are available at http://hydra.icgeb.trieste.it/protein/ .

  11. The dependence of lipid asymmetry upon phosphatidylcholine acyl chain structure[S

    PubMed Central

    Son, Mijin; London, Erwin

    2013-01-01

    Lipid asymmetry, the difference in inner and outer leaflet lipid composition, is an important feature of biomembranes. By utilizing our recently developed MβCD-catalyzed exchange method, the effect of lipid acyl chain structure upon the ability to form asymmetric membranes was investigated. Using this approach, SM was efficiently introduced into the outer leaflet of vesicles containing various phosphatidylcholines (PC), but whether the resulting vesicles were asymmetric (SM outside/PC inside) depended upon PC acyl chain structure. Vesicles exhibited asymmetry using PC with two monounsaturated chains of >14 carbons; PC with one saturated and one unsaturated chain; and PC with phytanoyl chains. Vesicles were most weakly asymmetric using PC with two 14 carbon monounsaturated chains or with two polyunsaturated chains. To define the origin of this behavior, transverse diffusion (flip-flop) of lipids in vesicles containing various PCs was compared. A correlation between asymmetry and transverse diffusion was observed, with slower transverse diffusion in vesicles containing PCs that supported lipid asymmetry. Thus, asymmetric vesicles can be prepared using a wide range of acyl chain structures, but fast transverse diffusion destroys lipid asymmetry. These properties may constrain acyl chain structure in asymmetric natural membranes to avoid short or overly polyunsaturated acyl chains. PMID:23093551

  12. From 1D and 2D ZnO nanostructures to 3D hierarchical structures with enhanced gas sensing properties.

    PubMed

    Alenezi, Mohammad R; Henley, Simon J; Emerson, Neil G; Silva, S Ravi P

    2014-01-07

    Facile and low cost hydrothermal routes are developed to fabricate three-dimensional (3D) hierarchical ZnO structures with high surface-to-volume ratios and an increased fraction of (0001) polar surfaces. Hierarchical ZnO nanowires (ZNWs) and nanodisks (ZNDs) assembled from initial ZnO nanostructures are prepared from sequential nucleation and growth following a hydrothermal process. These hierarchical ZnO structures display an enhancement of gas sensing performance and exhibit significantly improved sensitivity and fast response to acetone in comparison to other mono-morphological ZnO, such as nanoparticles, NWs, or NDs. In addition to the high surface-to-volume ratio due to its small size, the nanowire building blocks show the enhanced gas sensing properties mainly ascribed to the increased proportion of exposed active (0001) planes, and the formation of many nanojunctions at the interface between the initial ZnO nanostructure and secondary NWs. This work provides the route for structure induced enhancement of gas sensing performance by designing a desirable nanostructure, which could also be extended to synthesize other metal oxide nanostructures with superior gas sensing performance.

  13. Tailoring the spin waves band structure of 1D magnonic crystals consisting of L-shaped iron/permalloy nanowires

    NASA Astrophysics Data System (ADS)

    Gubbiotti, G.; Silvani, R.; Tacchi, S.; Madami, M.; Carlotti, G.; Yang, Z.; Adeyeye, A. O.; Kostylev, M.

    2017-03-01

    We have investigated both experimentally and numerically the magnonic band structure of arrays of closely spaced Fe/permalloy nanowires (NWs) with an L-shape cross-section using the Brillouin light scattering technique and GPU-based micromagnetic simulations. NWs consist of a 340 nm wide and 10 nm thick permalloy layer covered by a 170 nm wide Fe overlayer. The thickness of the latter was varied in the range from 0 to 10 nm in order to analyze its influence on the magnonic band structure. We found that both the frequency and the spatial profile of the most intense and dispersive mode, can be efficiently tuned by the presence of the thin Fe NW overlayer. In particular, by increasing the Fe thickness, one observes a substantial frequency increase, while the spatial profile of the mode narrows and moves to the permalloy NW portion not covered by Fe. In addition, the presence of the Fe overlayer causes a significant increase of the number of detected modes and a change of their intensity in the Brillouin spectra as a function of the Bloch wave number. These results show that it is possible to engineer the band structure of magnonic crystals consisting of bi-layered, L-shaped, NWs by a careful control of the overlayer thickness.

  14. Crystal Structure of Human Liver delta {4}-3-Ketosteroid 5 beta-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis

    SciTech Connect

    Di Costanzo,L.; Drury, J.; Penning, T.; Christianson, D.

    2008-01-01

    AKR1D1 (steroid 5{beta}-reductase) reduces all 4-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an a,{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a 4-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90 bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human 4-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP+ at 1.79- and 1.35- Angstroms resolution (HEPES bound in the active site), NADP+ and cortisone at 1.90- Angstroms resolution, NADP+ and progesterone at 2.03- Angstroms resolution, and NADP+ and testosterone at 1.62- Angstroms resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP+. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr58 and Glu120. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

  15. Propagation of the Ultra-Short Laser Pulses Through the Helical 1D Photonic Crystal Structure with Twist Defect

    NASA Astrophysics Data System (ADS)

    Antonov, Dmitrii V.; Iegorov, Roman

    2016-02-01

    The presence of the photonic band-gap is a featured property of the cholesteric liquid crystals (CLC). It can be practically realized for almost any reasonable wavelengths with very high degree of tunability. We have investigated theoretically the influence of the twist defect of the CLC helical structure onto the bandwidth-limited ultra-short laser pulse propagating inside the photonic band-gap. The changes of both pulse duration and peak power with defect angle were observed together with pulse acceleration and retardation for a case of normal incidence of the light.

  16. CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure

    PubMed Central

    2012-01-01

    Background One aim of the in silico characterization of proteins is to identify all residue-positions, which are crucial for function or structure. Several sequence-based algorithms exist, which predict functionally important sites. However, with respect to sequence information, many functionally and structurally important sites are hard to distinguish and consequently a large number of incorrectly predicted functional sites have to be expected. This is why we were interested to design a new classifier that differentiates between functionally and structurally important sites and to assess its performance on representative datasets. Results We have implemented CLIPS-1D, which predicts a role in catalysis, ligand-binding, or protein structure for residue-positions in a mutually exclusive manner. By analyzing a multiple sequence alignment, the algorithm scores conservation as well as abundance of residues at individual sites and their local neighborhood and categorizes by means of a multiclass support vector machine. A cross-validation confirmed that residue-positions involved in catalysis were identified with state-of-the-art quality; the mean MCC-value was 0.34. For structurally important sites, prediction quality was considerably higher (mean MCC = 0.67). For ligand-binding sites, prediction quality was lower (mean MCC = 0.12), because binding sites and structurally important residue-positions share conservation and abundance values, which makes their separation difficult. We show that classification success varies for residues in a class-specific manner. This is why our algorithm computes residue-specific p-values, which allow for the statistical assessment of each individual prediction. CLIPS-1D is available as a Web service at http://www-bioinf.uni-regensburg.de/. Conclusions CLIPS-1D is a classifier, whose prediction quality has been determined separately for catalytic sites, ligand-binding sites, and structurally important sites. It generates hypotheses about

  17. Magnetism and structure in chains of copper dinuclear paddlewheel units.

    PubMed

    Perec, Mireille; Baggio, Ricardo; Sartoris, Rosana P; Santana, Ricardo C; Peña, Octavio; Calvo, Rafael

    2010-01-18

    An anhydrous copper carboxylate compound of formula [Cu(trans-2-butenoate)(2)](n) has been characterized. X-ray analysis reveals a structure built by paddlewheel units bridged by pairs of Cu...O axial bonds to give infinite chains arranged in a new topological motif. Susceptibility measurements in the 10-300 K temperature range, and isothermal magnetization curves at 2, 5, 10, and 50 K with fields up to 5 T, were obtained. Electron Paramagnetic Resonance (EPR) spectra of powder samples were measured at 33.9 GHz at 300 K, and at 9.60 GHz at temperatures in the range 90 chain model of alternating paddlewheel and [Cu(mu-O)(2)Cu] dinuclear units yielded exchange interactions J(1) = -330.6(1) cm(-1) and J(2) = 5.9(2) cm(-1). The EPR spectra reflect the usual antiferromagnetic dinuclear behavior, with zero field splitting parameters of the excited spin triplet, D = -0.329(3) cm(-1) and E approximately 0, plus a central peak not expected for isolated dinuclear units. We interpret this peak as arising from the stochastic spin dynamics of the chain introduced by exchange couplings between spins in neighbor dinuclear units, which averages out the zero field splitting. Interactions of the units with the rest of the chain acting as a spin bath give rise to a quantum transition between localized dinuclear states and states of the spin chain. This effect competes with the condensation of the antiferromagnetic dinuclear units into the singlet ground state, producing a characteristic temperature dependence of the shape of the powder EPR spectra. We interpret these features in terms of basic theories of magnetic resonance in coupled spin systems applied to the chain array of dinuclear units.

  18. A Comparison of Long-Period SKS Datasets And What They Reveal About 1D Outer Core Structure

    NASA Astrophysics Data System (ADS)

    Houser, C. T.; Ritsema, J. E.; Grand, S.

    2010-12-01

    Seismology is the most direct tool for documenting the presences or absence of outer core stratification. The outermost core is most effectively sampled by SKS, S2KS, S3KS, S4KS, etc.) which have bottoming depths at the top of the outermost core. In order to incorporate modern data sets (e.g., USArray, Europe, China, etc), we need to sift through massive amounts of seismic data to identify the smaller portion of quality signals in a time-efficient manner. We evaluate the application of a cluster analysis technique (Houser et al., 2008) toward identifying and evaluating the SKS phases that traverse the outer core. Cluster analysis is a semi-automated method for interrogating large datasets by processing all the data for an earthquake while allowing the user to graphically interact with the data to remove low quality records. The Houser et al. (2008) cluster analysis method has already been applied to diffracted S waves (Manners et al., 2004), and here we will expand the cluster analysis to the radial component core phases. These newly measured SKS arrival times will be compared with SKS arrival time measurements used in previous mantle tomographic models, namely, S20RTS (Ritsema and van Heist, 2002) using a purely automated method and TXBW (Grand, 2002) using a purely manual method. We find that the arrival times collected by the three methods (automated, clustered, and manual) during overlapping time frames are in agreement within the measurement error bars. Therefore, the SKS data from these studies can be combined to constrain the radial structure of the outermost core. Thus, cluster analysis is an ideal tool for developing a large compilation of SKS arrival times from modern global seismic data, while simultaneously providing a measure of data quality.

  19. Study of the electronic structure of short chain oligothiophenes

    NASA Astrophysics Data System (ADS)

    Grazioli, C.; Baseggio, O.; Stener, M.; Fronzoni, G.; de Simone, M.; Coreno, M.; Guarnaccio, A.; Santagata, A.; D'Auria, M.

    2017-02-01

    The electronic structure of short-chain thiophenes (thiophene, 2,2'-bithiophene, and 2,2':5',2″-terthiophene) in the gas phase has been investigated by combining the outcomes of Near-Edge X-ray-Absorption Fine-Structure (NEXAFS) and X-ray Photoemission Spectroscopy (XPS) at the C K-edge with those of density functional theory (DFT) calculations. The calculated NEXAFS spectra provide a comprehensive description of the main experimental features and allow their attribution. The evolution of the C1s NEXAFS spectral features is analyzed as a function of the number of thiophene rings; a tendency to stabilization for increasing chain length is found. The computation of the binding energy allows to assign the experimental XPS peaks to the different carbon sites on the basis of both the inductive effects generated by the presence of the S atom as well as of the differential aromaticity effects.

  20. Tertiary structure of human {Lambda}6 light chains.

    SciTech Connect

    Pokkuluri, P. R.; Solomon, A.; Weiss, D. T.; Stevens, F. J.; Schiffer, M.; Center for Mechanistic Biology and Biotechnology; Univ. of Tennessee Medical Center /Graduate School of Medicine

    1999-01-01

    AL amyloidosis is a disease process characterized by the pathologic deposition of monoclonal light chains in tissue. To date, only limited information has been obtained on the molecular features that render such light chains amyloidogenic. Although protein products of the major human V kappa and V lambda gene families have been identified in AL deposits, one particular subgroup--lambda 6--has been found to be preferentially associated with this disease. Notably, the variable region of lambda 6 proteins (V lambda 6) has distinctive primary structural features including the presence in the third framework region (FR3) of two additional amino acid residues that distinguish members of this subgroup from other types of light chains. However, the structural consequences of these alterations have not been elucidated. To determine if lambda 6 proteins possess unique tertiary structural features, as compared to light chains of other V lambda subgroups, we have obtained x-ray diffraction data on crystals prepared from two recombinant V lambda 6 molecules. These components, isolated from a bacterial expression system, were generated from lambda 6-related cDNAs cloned from bone marrow-derived plasma cells from a patient (Wil) who had documented AL amyloidosis and another (Jto) with multiple myeloma and tubular cast nephropathy, but no evident fibrillar deposits. The x-ray crystallographic analyses revealed that the two-residue insertion located between positions 68 and 69 (not between 66 and 67 as previously surmised) extended an existing loop region that effectively increased the surface area adjacent to the first complementarity determining region (CDR1). Further, an unusual interaction between the Arg 25 and Phe 2 residues commonly found in lambda 6 molecules was noted. However, the structures of V lambda 6 Wil and Jto also differed from each other, as evidenced by the presence in the latter of certain ionic and hydrophobic interactions that we posit increased protein

  1. Assembly of 1D, 2D and 3D lanthanum(iii) coordination polymers with perchlorinated benzenedicarboxylates: positional isomeric effect, structural transformation and ring-opening polymerisation of glycolide.

    PubMed

    Chen, Sheng-Chun; Dai, An-Qi; Huang, Kun-Lin; Zhang, Zhi-Hui; Cui, Ai-Jun; He, Ming-Yang; Chen, Qun

    2016-02-28

    Utilizing a series of positional isomers of tetrachlorinated benzenedicarboxylic acid ligands, seven La(iii)-based coordination polymers were solvothermally synthesized and structurally characterized. Their structural dimensionalities varying from 1D double chains, to the 2D 3,4,5-connected network, to 3D 6-connected pcu topological nets are only governed by the positions of carboxyl groups on the tetrachlorinated benzene ring. A comprehensive analysis and comparison reveals that the size of the carbonyl solvent molecules (DMF, DEF, DMA, and NMP) can affect the coordination geometries around the La(iii) ions, the coordination modes of carboxylate groups, the packing arrangements, and the void volumes of the overall crystal lattices. One as-synthesized framework further shows an unprecedented structural transformation from a 3D 6-connected network to a 3D 4,5-connected net through the dissolution and reformation pathway in water, suggesting that these easily hydrolyzed lanthanide complexes may serve as precursors to produce new high-dimensional frameworks. The bulk solvent-free melt polymerisation of glycolide utilizing these La(iii) complexes as initiators has been reported herein for the first time. All complexes were found to promote the polymerization of glycolide over a temperature range of 200 to 220 °C, producing poly(glycolic acid) (PGA) with a molecular weight up to 93,280. Under the same experimental conditions, the different catalytic activities for these complexes may result from their structural discrepancy.

  2. Structure and Phase Transitions of Alkylammonium Chains on Mica

    NASA Astrophysics Data System (ADS)

    Heinz, Hendrik; Suter, Ulrich W.

    2004-03-01

    The properties of organically modified silicate minerals determine essentially the properties of polymer-clay nanocomposites. We investigate mica sheets with octadecyltrimethylammonium (C_18) ions or dioctadecyldimethylammonium (2C_18) ions, respectively, with periodicity in the xy plane by NVT molecular dynamics simulation at different temperatures (100 % alkali exchange). With increasing temperature, we find rearrangements of C_18 ions on the mica surface (not for 2C_18 ions due to geometric restraints), compute basal-plane spacings, tilt angles and gauche-trans ratios in the alkyl chains, as well as density and pressure profiles [1, 2]. Agreement with available experimental data is very good (AFM, DSC, IR, NMR, XRD) and we explain the phase transitions of the systems on heating. We also investigate shorter chains down to 2C_12 with only 80 % alkali exchange. Using a relation between basal-plane spacing and surface structure (alkylammonium-islands vs homogeneous mixtures with alkali ions), we discuss the preferred self-assembly pattern on the mica surface as a function of surface saturation with alkyl chains and the chain length [3]. [1] H. Heinz, H.-J. Castelijns, U. W. Suter, J. Am. Chem. Soc. 125, 9500 (2003). [2] H. Heinz, W. Paul, U. W. Suter, K. Binder, J. Chem. Phys., in press. [3] H. Heinz, U. W. Suter, Angew. Chem. Int. Ed., accepted for publication.

  3. Crystal Structure of Human Liver [delta][superscript 4]-3-Ketosteroid 5[beta]-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis

    SciTech Connect

    Di Costanzo, Luigi; Drury, Jason E.; Penning, Trevor M.; Christianson, David W.

    2008-07-15

    AKR1D1 (steroid 5{beta}-reductase) reduces all {Delta}{sup 4}-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an {alpha}{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a {Delta}{sup 4}-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90{sup o} bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human {Delta}{sup 4}-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP{sup +} at 1.79- and 1.35-{angstrom} resolution (HEPES bound in the active site), NADP{sup +} and cortisone at 1.90-{angstrom} resolution, NADP{sup +} and progesterone at 2.03-{angstrom} resolution, and NADP{sup +} and testosterone at 1.62-{angstrom} resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP{sup +}. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr{sup 58} and Glu{sup 120}. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

  4. Structural Transition in Atomic Chains Driven by Transient Doping

    NASA Astrophysics Data System (ADS)

    Polei, S.; Snijders, P. C.; Erwin, S. C.; Himpsel, F. J.; Meiwes-Broer, K.-H.; Barke, I.

    2013-10-01

    A reversible structural transition is observed on Si(553)-Au by scanning tunneling microscopy, triggered by electrons injected from the tip into the surface. The periodicity of atomic chains near the step edges changes from the 1×3 ground state to a 1×2 excited state with increasing tunneling current. The threshold current for this transition is reduced at lower temperatures. In conjunction with first-principles density-functional calculations it is shown that the 1×2 phase is created by temporary doping of the atom chains. Random telegraph fluctuations between two levels of the tunneling current provide direct access to the dynamics of the phase transition, revealing lifetimes in the millisecond range.

  5. Simple synthesis of PbSe nanocrystals and their self-assembly into 2D ‘flakes’ and 1D ‘ribbons’ structures

    SciTech Connect

    Díaz-Torres, E.; Ortega-López, M.; Matsumoto, Y.; Santoyo-Salazar, J.

    2016-08-15

    Highlights: • PbSe is obtained in a simple way by the co-precipitation method at low-temperature. • The structural, morphological and optical properties of PbSe were studied. • Adding NH{sub 4}OH to the precursor solutions influences on the morphology. • 2D- and 1D-PbSe structures assemble by oriented attachment. • PbSe can be a potential candidate for thermoelectric applications. - Abstract: This work presents a simple and low-temperature method to prepare a variety of Lead selenide (PbSe) nanostructures, using aqueous solutions of Pb(NO{sub 3}){sub 2} and NaHSe. Nanostructures with different morphology were obtained by varying the Pb:Se molar ratio, as well as the mixing sequence of NH{sub 4}OH with either Pb(NO{sub 3}){sub 2} or NaHSe. Nanoparticles with different shapes (spherical and octahedral), and self-assembled structures (flakes and ribbons) were observed by Transmission Electron Microscopy. X-ray results confirmed that the PbSe rock-salt crystalline structure was obtained for all of the prepared samples. The crystal size is in the order of 7.3 to 8.9 nm for single nanocrystals. The absorption spectra of the samples show exciton absorption bands at 1395 nm and 1660 nm. This material could be used to develop more advanced structures for thermoelectric generators.

  6. Spontaneous nucleation of structural defects in inhomogeneous ion chains

    NASA Astrophysics Data System (ADS)

    De Chiara, Gabriele; del Campo, Adolfo; Morigi, Giovanna; Plenio, Martin B.; Retzker, Alex

    2010-11-01

    Structural defects in ion crystals can be formed during a linear quench of the transverse trapping frequency across the mechanical instability from a linear chain to a zigzag structure. The density of defects after the sweep can be conveniently described by the Kibble-Zurek mechanism (KZM). In particular, the number of kinks in the zigzag ordering can be derived from a time-dependent Ginzburg-Landau equation for the order parameter, here the zigzag transverse size, under the assumption that the ions are continuously laser cooled. In a linear Paul trap, the transition becomes inhomogeneous, since the charge density is larger in the center and more rarefied at the edges. During the linear quench, the mechanical instability is first crossed in the center of the chain, and a front, at which the mechanical instability is crossed during the quench, is identified that propagates along the chain from the center to the edges. If the velocity of this front is smaller than the sound velocity, the dynamics become adiabatic even in the thermodynamic limit and no defect is produced. Otherwise, the nucleation of kinks is reduced with respect to the case in which the charges are homogeneously distributed, leading to a new scaling of the density of kinks with the quenching rate. The analytical predictions are verified numerically by integrating the Langevin equations of motion of the ions, in the presence of a time-dependent transverse confinement. We argue that the non-equilibrium dynamics of an ion chain in a Paul trap constitutes an ideal scenario to test the inhomogeneous extension of the KZM, which lacks experimental evidence to date.

  7. Structural, Electronic, and Mechanical Properties of Chains of Silicon Clusters with Trigonal Bipiramidal Structures

    NASA Astrophysics Data System (ADS)

    Tchernatinsky, Alex; Jayanthi, C. S.; Wu, S. Y.

    2002-03-01

    We report here our investigation of structural, electronic, and mechanical properties of non-trivial silicon chains. These chains are built from elementary blocks of clusters of 5 and 8 silicon atoms, arranged into trigonal bipiramidal structures and periodically continued along the axial direction. The initial configurations are constructed such that there are no dangling bonds associated with any atom along the chains. The stable configurations of the chains are determined by molecular dynamics simulations based on the first-principles method of Sankey and Niklewski [1] using the self-consistency scheme given in Ref. [2]. Mechanical and electronic properties of the resulting stable chains will be presented. 1. O.F.Sankey, and D.J.Niklewski, Phys. Rev. B 40 3979(1989). 2. P.Ordejon, E.Artacho, and J.M.Soler, Phys.Rev. B 53,10441 (1996).

  8. Hydrothermal syntheses, crystal structures and properties of 0-D, 1-D and 2-D organic-inorganic hybrid borotungstates constructed from Keggin-type heteropolyanion [α-BW 12O 40] 5- and transition-metal complexes

    NASA Astrophysics Data System (ADS)

    Zhao, Junwei; Song, Yiping; Ma, Pengtao; Wang, Jingping; Niu, Jingyang

    2009-07-01

    Three novel organic-inorganic hybrid borotungstates {[Ni(phen) 2(H 2O)] 2H(α-BW 12O 40)}·4H 2O ( 1), [Cu I(2,2'-bipy)(4,4'-bipy) 0.5] 2{[Cu I(2,2'-bipy)] 2Cu I(4,4'-bipy) 2(α-BW 12O 40)} ( 2) and {[Cu I(4,4'-bipy)] 3H 2(α-BW 12O 40)}·3.5H 2O ( 3) (phen=1,10-phenanthroline, 2,2'-bipy=2,2'-bipyridine, 4,4'-bipy=4,4'-bipyridine) have been hydrothermally synthesized and structurally characterized by elemental analyses, IR, UV spectra, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), single-crystal X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and photoluminescence. The structural analysis reveals that 1 consists of a 0-D bisupporting polyoxometalate cluster where two [Ni(phen) 2(H 2O)] 2+ cations are grafted on the polyoxoanion [α-BW 12O 40] 5- through two terminal oxygen atoms, 2 shows a 1-D infinite chain constructed from [α-BW 12O 40] 5- polyoxoanions and {[Cu I(2,2'-bipy)] 2Cu I(4,4'-bipy) 2} 3+ cations by means of alternating fashion, and 3 displays an unprecedented 2D extended structure built by [α-BW 12O 40] 5- polyoxoanions and -Cu I-4,4'-bipy- linear chains, in which each [α-BW 12O 40] 5- polyoxoanion acts as a tetradentate inorganic ligand and provides three terminal oxygen atom and one two-bridging oxygen atom. The presence of Ni II and W VI in 1, Cu I ions and W VI in 2 and 3 are identified by XPS spectra. The photoluminescence of 2 and 3 are also investigated.

  9. Community structure of force chains in granular hopper discharge

    NASA Astrophysics Data System (ADS)

    Navakas, Robertas; Džiugys, Algis; Misiulis, Edgaras; StriÅ«gas, Nerijus

    2017-07-01

    We analyse the force chain structure in granular matter during discharge from a hopper using discrete element modeling (DEM). Having obtained the particle configurations and the mechanical forces acting between the particles from DEM simulations, we build interaction graphs for the particle configurations at the respective time moments. The particles are represented as the graph vertices, the vertices are connected by edges if the respective particles are in contact, and the edge weights are proportional to the force moduli between the particle pairs. The community structures of the resulting graphs are then identified using a "walktrap" community detection algorithm. Evolution of the community structures is analysed during the hopper discharge and its dependence on the static friction coefficient between the particles.

  10. Mononuclear, dinuclear and 1-D polymeric complexes of Cd(II) of a pyridyl pyrazole ligand: Syntheses, crystal structures and photoluminescence studies

    NASA Astrophysics Data System (ADS)

    Das, Kinsuk; Konar, Saugata; Jana, Atanu; Barik, Anil Kumar; Roy, Sangita; Kar, Susanta Kumar

    2013-03-01

    The syntheses, crystal structures and photoluminescence properties of four new Cd(II) complexes are reported using strongly coordinating ligand 3,5-dimethyl-1-(2'-pyridyl) pyrazole (L) in presence of anionic ancillary bridging ligands as nitrite, chloride and dicyanamide. Among the complexes two (1 and 2) are monomeric, 3 is μ2 - chloro bridged dimer and the last one (4) is a mixed alternate chloro - end to end (EE) dicyanamide bridged 1D polymer. All the four complexes have been X-ray crystallographically characterized. The ligand L behaves as a potent bidentate neutral N, N donor. Geometrical diversity of Cd(II) complexes is due to no loss or gain of crystal field stability with the variation of geometry. Consequently the stability of a structure depends on steric requirements. The ligand L shows considerable fluorescence and all four complexes in methanol exhibit interesting photoluminescence properties with different emission intensities. The band maxima and fluorescence efficiency (in methanol) are found to be dependent on the coordination chromophore and structural rigidity induced by the incorporated Cd(II) ion. Among the synthesized complexes 1 exhibits the highest fluorescence intensity in methanol.

  11. K2Ca4[(UO2)(Si2O7)2]: A Uranyl Silicate with a One-Dimensional Chain Structure.

    PubMed

    Liu, Chia-Lin; Liu, Hsin-Kuan; Chang, Wen-Jung; Lii, Kwang-Hwa

    2015-09-08

    A new uranyl silicate, K2Ca4[(UO2)(Si2O7)2], with a 1D chain structure has been synthesized from a solution of mixed alkali- and alkaline-earth-metal cations under hydrothermal conditions at 550 °C and 1400 bar and characterized by single-crystal X-ray diffraction and photoluminescence spectroscopy. It crystallizes in the triclinic space group P1̅ (No. 2) with a = 6.6354(2) Å, b = 6.6791(2) Å, c = 9.6987(3) Å, α = 98.324(2)°, β = 93.624(2)°, γ = 112.310(2)°, and Z = 1. Its crystal structure consists of a 1D chain of uranyl disilicate formed of corner-sharing UO6 tetragonal bipyramids and Si2O7 double groups. The adjacent chains are separated by K(+) and Ca(2+) cations. It is the first example of uranyl silicate with a 1D chain structure.

  12. Nanoscale stabilization of zintl compounds: 1D ionic Li-P double helix confined inside a carbon nanotube.

    PubMed

    Ivanov, Alexander S; Kar, Tapas; Boldyrev, Alexander I

    2016-02-14

    One-dimensional (1D) ionic nanowires are extremely rare materials due to the difficulty in stabilizing 1D chains of ions under ambient conditions. We demonstrate here a theoretical prediction of a novel hybrid material, a nanotube encapsulated 1D ionic lithium monophosphide (LiP) chain, featuring a unique double-helix structure, which is very unusual in inorganic chemistry. This nanocomposite has been investigated with density functional theory, including molecular dynamics simulations and electronic structure calculations. We find that the formation of the LiP double-helical nanowire is facilitated by strong interactions between LiP and CNTs resulting in a charge transfer. This work suggests that nanostructured confinement may be used to stabilize other polyphosphide 1D chains, thus opening new ways to study the chemistry of zintl compounds at the nanoscale.

  13. Controlled modulation of 1D ZnO nano/micro structures: Evaluation of the various effects on the photocatalytic activity

    NASA Astrophysics Data System (ADS)

    Arslan, Osman; Abalı, Yüksel

    2017-09-01

    Effects of the concentration, temperature and precursor type on the fabrication of the elongated ZnO nano/micro structures were comprehensively investigated. Analytical investigations such as SEM and statistical analysis of the elongated ZnO nano/micro structures provided wide information about the growth behavior and final geometries. Different temperatures for the 1 D ZnO formation clearly revealed that hexagonally grown ZnO nanorods were obtained. Especially low crystal diffraction characteristics at low temperature (55 °C) implied that ZnO nano/micro rod formation requires some minimum conditions for the formation of an efficient photocatalyst. All XRD investigations together with SEM and TEM supported the ligand ordered elongation conducted by diverse beginning concentrations. Since temperature found as a highly dominant actor for morphology and surface sequence as manifested in crystallinity, morphology and photocatalytic results, we have systematically summarized the growth conditions of the ZnO nano/micro rods from same precursor.

  14. Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides

    NASA Astrophysics Data System (ADS)

    Grossutti, Michael; Dutcher, John

    The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly important example of confined water, with differences in polysaccharide structure providing different spatially confined environments for water adsorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, monodisperse phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA) and chitosan. We find similarities between water structuring in the two linear polysaccharides, and significant differences for phytoglycogen. In particular, the phytoglycogen nanoparticles exhibited high network water connectivity, and a large increase in the fraction of multimer water clusters with increasing RH, whereas the water structure for HA and chitosan was found to be insensitive to changes in RH. These measurements provide unique insight into the relationship between the chain architecture and hydration of polysaccharides.

  15. MR Elastography Studies of the 3D Force Chain Structure in Dense Granular Media: Distribution of Chain Lengths

    NASA Astrophysics Data System (ADS)

    Sanfratello, L.; Fukushima, E.

    2009-06-01

    We recently developed a novel extension of MR Elastograpy (MRE) to image the force chain structure within a dense 3D quasi-static granular assembly. Subsequently, computer codes and algorithms to determine the distribution of the force chain lengths, where a chain is taken to be a relatively straight section between branching points, were developed. Similar tools were used previously to analyze 2D photoelastic data and now have been expanded to analyze our most current 3D MRE force chain data. These investigations reveal that the distribution of the chain lengths in 3D decays exponentially, as was observed in 2D. The exponential decay of the length distribution is consistent with DEM simulation results of Peters, et al. We conclude that the decay length of this distribution is a meaningful quantitative measure that characterizes granular assemblies.

  16. Mechanically interlocked daisy-chain-like structures as multidimensional molecular muscles

    NASA Astrophysics Data System (ADS)

    Chang, Jia-Cheng; Tseng, Shin-Han; Lai, Chien-Chen; Liu, Yi-Hung; Peng, Shie-Ming; Chiu, Sheng-Hsien

    2016-09-01

    Daisy chains (DCs) are garlands of flowers that can be worn as bracelets and necklaces. As a result of their beautiful interlocked structures and possible muscle-like motions, cyclic molecular DCs ([cn]DCs, where n is the number of repeating units) have long been attractive synthetic targets for supramolecular chemists. Herein we report artificial molecular muscles that—unlike one-dimensional (1D) biological muscles—contract and stretch in 2D or 3D. These systems have the structures of [c3]- and [c4]DCs with subcomponents that operate as molecular switches, powered through the addition or removal of Zn2+ ions to impart muscle-like behaviour. We assembled these [c3]- and [c4]DCs selectively by exploiting structural rigidity, coordination geometries and bond rotational barriers that disfavoured the formation of smaller homologues. The switching phenomena of our [c3]- and [c4]DCs resulted in the contracted molecular muscles stretching by approximately 23 and 36%, respectively, comparable to the value (27%) for linear biological muscles.

  17. Mechanically interlocked daisy-chain-like structures as multidimensional molecular muscles

    NASA Astrophysics Data System (ADS)

    Chang, Jia-Cheng; Tseng, Shin-Han; Lai, Chien-Chen; Liu, Yi-Hung; Peng, Shie-Ming; Chiu, Sheng-Hsien

    2017-02-01

    Daisy chains (DCs) are garlands of flowers that can be worn as bracelets and necklaces. As a result of their beautiful interlocked structures and possible muscle-like motions, cyclic molecular DCs ([cn]DCs, where n is the number of repeating units) have long been attractive synthetic targets for supramolecular chemists. Herein we report artificial molecular muscles that—unlike one-dimensional (1D) biological muscles—contract and stretch in 2D or 3D. These systems have the structures of [c3]- and [c4]DCs with subcomponents that operate as molecular switches, powered through the addition or removal of Zn2+ ions to impart muscle-like behaviour. We assembled these [c3]- and [c4]DCs selectively by exploiting structural rigidity, coordination geometries and bond rotational barriers that disfavoured the formation of smaller homologues. The switching phenomena of our [c3]- and [c4]DCs resulted in the contracted molecular muscles stretching by approximately 23 and 36%, respectively, comparable to the value (27%) for linear biological muscles.

  18. The light chains of muscle myosin: its structure, function, and evolution.

    PubMed

    Matsuda, G

    1983-01-01

    In this review I described the primary structures of myosin light chains contained in fast skeletal muscle, cardiac muscle, and gizzard muscle of chicken. In a comparison of these proteins many more amino acid substitutions than expected were recognized among the primary structures in the muscle from various organs. A fairly high homology was however shown between their primary structure, and this homology is also recognized among the light chains, parvalbumins, troponins C, and calmodulins. On the other hand, the relation between the primary structures and physiological function of these myosin light chains or the interaction between light chains and heavy chains still seems unclear. These problems are important subjects for future study.

  19. A pure inorganic 1D chain based on {Mo8O28} clusters and Mn(II) ions: [Mn(H2O)2Mo8O28 ] n 6 n -

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaofen; Yan, Yonghong; Wu, Lizhou; Yu, Chengxin; Dong, Xinbo; Hu, Huaiming; Xue, Ganglin

    2016-01-01

    A new pure inorganic polymer, (NH4)6n[Mn(H2O)2Mo8O28)]n(H2O)2n(1), has been synthesized and characterized by elemental analyses, IR spectrum, UV-vis absorption spectra, TG-DSC and electrochemical studies. In 1, [Mo8O28]8- anions act as tetradentate ligands and are alternately linked by Mn(H2O)2 2 + ions into a one-dimensional chain structure. It is interesting that 1 represents the first example of pure inorganic-inorganic hybrid based on octamolybdate and transition metal ions. Moreover, it was indicated that 1 had definite catalytic activities on the probe reaction of benzyl alcohol oxidation to benzaldehyde with H2O2.

  20. Chaining sequence/structure seeds for computing RNA similarity.

    PubMed

    Bourgeade, Laetitia; Chauve, Cédric; Allali, Julien

    2015-03-01

    We describe a new method to compare a query RNA with a static set of target RNAs. Our method is based on (i) a static indexing of the sequence/structure seeds of the target RNAs; (ii) searching the target RNAs by detecting seeds of the query present in the target, chaining these seeds in promising candidate homologs; and then (iii) completing the alignment using an anchor-based exact alignment algorithm. We apply our method on the benchmark Bralibase2.1 and compare its accuracy and efficiency with the exact method LocARNA and its recent seeds-based speed-up ExpLoc-P. Our pipeline RNA-unchained greatly improves computation time of LocARNA and is comparable to the one of ExpLoc-P, while improving the overall accuracy of the final alignments.

  1. Nuclear Structure Studies from Hg and Au Alpha Decay Chains

    NASA Astrophysics Data System (ADS)

    Goon, J. Tm.; Bingham, C. R.; Hartley, D. J.; Zhang, Jing-Ye; Riedinger, L. L.; Danchev, M.; Kondev, F. G.; Carpenter, M. P.; Janssens, R. V. F.; Abu Saleem, K. H.; Ahmad, I.; Davids, C. N.; Heinz, A.; Khoo, T. L.; Lauritsen, T.; Lister, C. J.; Poli, G. L.; Seweryniak, D.; Wiedenhover, I.; Ma, W. C.; Amro, H.; Reviol, W.; Cizewski, J. A.; Smith, M.

    2003-04-01

    Neutron deficient nuclei near the Z = 82 shell gap have been a source of great interest. This region is known to exhibit the phenomena of shape-coexistence and triaxiality. Alpha decay study of these nuclei coupled with gamma-rayspectroscopy data can give a better understanding of their nuclear structure properties. The decay chains of ^173-177Au and ^175-179Hg were studied following the bombardment of ^92,94,96Mo targets with ^84Sr beam from the ATLAS accelerator at the Argonne National Laboratory. The experiment utilized the Gammasphere array in conjunction with the Fragment Mass Analyzer (FMA) for mass identification and a Double-sided Silicon Strip Detector (DSSD) that was used to detect the recoiling implants and the alpha particles associated with each nuclide. An array of four Ge detectors and a low-energy photon spectrometer (LEPS) was used at the focal plane of the FMA to detect γ rays in coincidence with the α particles. This information was used to elucidate the α-decay fine structures. Inverse radioactive decay tagging was also useful in assigning certain fine structure α peaks to a particular nuclide. New α decay lines were observed and their energies, and half-lives were measured. These include fine structure lines in the α decays of ^174,176Au and ^173Pt. The decay schemes resulting from the fine structure observations will be presented. The α decay reduced widths are used to suggest spin and parity assignments. The structure of these states will be discussed in the framework of the Nilsson model and alpha decay selection rules. * This work is supported by the Department of Energy through contract numbers DE-FG02-96ER40983 (UT), W-31-109-ENG-38 (ANL), DE-FG02-95ER40939 (MSU), DE-FG05-88ER40406 (WU), and by the National Science Foundation (RU

  2. Forest-atmosphere BVOC exchange in diverse and structurally complex canopies: 1-D modeling of a mid-successional forest in northern Michigan

    SciTech Connect

    Bryan, Alexander M.; Cheng, Susan J.; Ashworth, Kirsti; Guenther, Alex B.; Hardiman, Brady; Bohrer, Gil; Steiner, A. L.

    2015-11-01

    Foliar emissions of biogenic volatile organic compounds (BVOC)dimportant precursors of tropospheric ozone and secondary organic aerosolsdvary widely by vegetation type. Modeling studies to date typi-cally represent the canopy as a single dominant tree type or a blend of tree types, yet many forests are diverse with trees of varying height. To assess the sensitivity of biogenic emissions to tree height vari-ation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homo-geneous or heterogeneous with canopy depth. The heterogeneous canopy emulates the mid-successional forest at the University of Michigan Biological Station (UMBS). In this case, high-isoprene-emitting fo-liage (e.g., aspen and oak) is constrained to the upper canopy, where higher sunlight availability increases the light-dependent isoprene emission, leading to 34% more isoprene and its oxidation products as compared to the homogeneous simulation. Isoprene declines from aspen mortality are 10% larger when heterogeneity is considered. Overall, our results highlight the importance of adequately representing complexities of forest canopy structure when simulating light-dependent BVOC emissions and chemistry.

  3. Structure and Dynamics of Asymmetric Poly(styrene-b-1,4-isoprene) Diblock Copolymer under 1D and 2D Nanoconfinement.

    PubMed

    Kipnusu, Wycliffe K; Elmahdy, Mahdy M; Mapesa, Emmanuel U; Zhang, Jianqi; Böhlmann, Winfried; Smilgies, Detlef-M; Papadakis, Christine M; Kremer, Friedrich

    2015-06-17

    The impact of 1- and 2-dimensional (2D) confinement on the structure and dynamics of poly(styrene-b-1,4-isoprene) P(S-b-I) diblock copolymer is investigated by a combination of Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Grazing-Incidence Small-Angle X-ray Scattering (GISAXS), and Broadband Dielectric Spectroscopy (BDS). 1D confinement is achieved by spin coating the P(S-b-I) to form nanometric thin films on silicon substrates, while in the 2D confinement, the copolymer is infiltrated into cylindrical anodized aluminum oxide (AAO) nanopores. After dissolving the AAO matrix having mean pore diameter of 150 nm, the SEM images of the exposed P(S-b-I) show straight nanorods. For the thin films, GISAXS and AFM reveal hexagonally packed cylinders of PS in a PI matrix. Three dielectrically active relaxation modes assigned to the two segmental modes of the styrene and isoprene blocks and the normal mode of the latter are studied selectively by BDS. The dynamic glass transition, related to the segmental modes of the styrene and isoprene blocks, is independent of the dimensionality and the finite sizes (down to 18 nm) of confinement, but the normal mode is influenced by both factors with 2D geometrical constraints exerting greater impact. This reflects the considerable difference in the length scales on which the two kinds of fluctuations take place.

  4. Forest-atmosphere BVOC exchange in diverse and structurally complex canopies: 1-D modeling of a mid-successional forest in northern Michigan

    NASA Astrophysics Data System (ADS)

    Bryan, Alexander M.; Cheng, Susan J.; Ashworth, Kirsti; Guenther, Alex B.; Hardiman, Brady S.; Bohrer, Gil; Steiner, Allison L.

    2015-11-01

    Foliar emissions of biogenic volatile organic compounds (BVOC)-important precursors of tropospheric ozone and secondary organic aerosols-vary widely by vegetation type. Modeling studies to date typically represent the canopy as a single dominant tree type or a blend of tree types, yet many forests are diverse with trees of varying height. To assess the sensitivity of biogenic emissions to tree height variation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homogeneous or heterogeneous with canopy depth. The heterogeneous canopy emulates the mid-successional forest at the University of Michigan Biological Station (UMBS). In this case, high-isoprene-emitting foliage (e.g., aspen and oak) is constrained to the upper canopy, where higher sunlight availability increases the light-dependent isoprene emission, leading to 34% more isoprene and its oxidation products as compared to the homogeneous simulation. Isoprene declines from aspen mortality are 10% larger when heterogeneity is considered. Overall, our results highlight the importance of adequately representing complexities of forest canopy structure when simulating light-dependent BVOC emissions and chemistry.

  5. Synthesis and crystal structure of 1D polyoxometalate-based composite compound, [{Gd(NMP) 6}(PMo 12O 40)] n (NMP= N-methyl-2-pyrrolidone)

    NASA Astrophysics Data System (ADS)

    Niu, Jing-Yang; Wei, Mei-Lin; Wang, Jing-Ping; Dang, Dong-Bin

    2003-07-01

    A novel compound, [{Gd(NMP) 6}(PMo 12O 40)] n, has been synthesized and characterized by IR, and UV spectroscopy, and single crystal X-ray structural analysis. It forms an unprecedented one-dimensional zigzag chain built from alternating polyanions and cationic units through Mo-O t-Gd-O t-Mo links in the crystal. In the compound, Gd 3+ is eight-coordinated with a bicapped trigonal prism geometry environment of oxygen atoms. The results of the single crystal X-ray diffraction analyses and IR are agreement and both show the metal cation units are coordinately bonded to the Keggin cluster. The UV spectrum of the title compound suggests that the compound is entirely dissociated in dilute solution.

  6. Beta 1D integrin displaces the beta 1A isoform in striated muscles: localization at junctional structures and signaling potential in nonmuscle cells.

    PubMed

    Belkin, A M; Zhidkova, N I; Balzac, F; Altruda, F; Tomatis, D; Maier, A; Tarone, G; Koteliansky, V E; Burridge, K

    1996-01-01

    The cytoplasmic domains of integrins provide attachment of these extracellular matrix receptors to the cytoskeleton and play a critical role in integrin-mediated signal transduction. In this report we describe the identification, expression, localization, and initial functional characterization of a novel form of beta 1 integrin, termed beta 1D. This isoform contains a unique alternatively spliced cytoplasmic domain of 50 amino acids, with the last 24 amino acids encoded by an additional exon. Of these 24 amino acids, 11 are conserved when compared to the beta 1A isoform, but 13 are unique (Zhidkova, N. I., A. M. Belkin, and R. Mayne. 1995. Biochem. Biophys. Res. Commun. 214:279-285; van der Flier, A., I. Kuikman, C. Baudoin, R, van der Neuf, and A. Sonnenberg. 1995. FEBS Lett. 369:340-344). Using an anti-peptide antibody against the beta 1D integrin subunit, we demonstrated that the beta 1D isoform is synthesized only in skeletal and cardiac muscles, while very low amounts of beta 1A were detected by immunoblot in striated muscles. Whereas beta 1A could not be detected in adult skeletal muscle fibers and cardiomyocytes by immunofluorescence, beta 1D was localized to the sarcolemma of both cell types. In skeletal muscle, beta 1D was concentrated in costameres, myotendinous, and neuromuscular junctions. In cardiac muscle this beta 1 isoform was found in costamers and intercalated discs. beta 1D was associated with alpha 7A and alpha 7B in adult skeletal muscle. In cardiomyocytes of adult heart, alpha 7B was the major partner for the beta 1D isoform. beta 1D could not be detected in proliferating C2C12 myoblasts, but it appeared immediately after myoblast fusion and its amount continued to rise during myotube growth and maturation. In contrast, expression of the beta 1A isoform was downregulated during myodifferentiation in culture and it was completely displaced by beta 1D in mature differentiated myotubes. We also analyzed some functional properties of the beta 1D

  7. The DNA d(GGGGGTTTTT)[center dot]d(AAAAACCCCC) and Bam H1 d(GGATCC)[sub 2] structure investigation by 1-D and 2-D NMR spectroscopy. [NMR (nuclear magnetic resonance)

    SciTech Connect

    Chen, Ban-Chin.

    1992-01-01

    Two-dimensional NMR techniques Correlated (COSY) and Nuclear Overhauser Effect Spectroscopy (NOESY) have been used with one-dimensional NMR results to complete the assignment of the proton NMR spectrum of double-stranded B DNA duplex, d(G[sub 5]T[sub 5]).d(A[sub 5]C[sub 5]) and restriction endonuclease Bam H1 duplex d(GGATCC)[sub 2]. A general method of assigning the non-exchangeable and exchangeable protons in the NMR spectra of DNA duplexes in D[sub 2]O or H[sub 2]O respectively is discussed. COSY and NOESY measurements have been combined to systematically assign many of the resonances from the H1[prime], H2[prime], H2[double prime] and H3[prime] sugar protons to specific nucleotides in the duplex. This method relies on the fact that sugar protons within a specific nucleotide are scalar coupled and that base protons H8/H6 in right-handed helices can interact simultaneously with their own H2[prime], H2[double prime] sugar protons and those of the adjacent nucleotide attached to its 5[prime] end. COSY experiments are used to identify sugar resonances within a residue, NOESY experiments determination of linkage to adjacent residues. The base protons H5 and H6 resonances of cytosines in the spectrum can immediately be identified by the COSY experiment. The methyl protons of thymine exhibit strong through-space interbase interaction. This establishes that the nucleotides have an anti conformation of the bases relative to the sugar. The self-complementary decanucleotide sequence d(G[sub 5]T[sub 5])[center dot]d(A[sub 5]C[sub 5]) forms a ten base-paired duplex in solution. The five Watson-Crick imino protons are resolved between 12 and 14 ppm and have been assigned to positions in the sequence using sequential nearest-neighbor NOE connectivity. At 1[degrees]C the imino proton of the terminal base pair 1 has broadened out. The interproton distances obtained from 2-D Nuclear Overhauser Effect (NOESY) data is examined by simulation to derive structures for DNA helices.

  8. 1-D "Platinum Wire" Stacking Structure Built of Platinum(II) Diimine Bis(σ-acetylide) Units with Luminescence in the NIR Region.

    PubMed

    Kang, Jiajia; Zhang, Xiaoxin; Zhou, Huajun; Gai, Xuqiao; Jia, Ting; Xu, Liang; Zhang, Jianjun; Li, Yanqin; Ni, Jun

    2016-10-17

    A square-planar platinum(II) complex, Pt(DiBrbpy)(C≡CC6H4Et-4)2 (1) (DiBrbpy = 4,4-dibromo-2,2'-bipyridine), and crystals of its three solvated forms, namely, 1·DMSO, 1·1/2(CH3CN), and 1·1/8(CH2Cl2), were developed and characterized. 1·DMSO and 1·1/2(CH3CN) contain quasi-dimeric and dimeric structures with luminescence in the visible range, whereas 1·1/8(CH2Cl2) exhibits NIR luminescence at 1022 nm due to its intrinsic 1-D "platinum wire" stacking structure with strong Pt-Pt interactions. 1·1/8(CH2Cl2) represents the first compound based on platinum(II) diimine bis(σ-acetylide) molecular units with the NIR luminescence beyond 1000 nm. 1 selectively responds to DMSO and CH3CN by changing its color and luminescence property and the three solvated forms can be reversibly converted to each other upon exposure to corresponding solvent vapors. Their desolvated forms, namely 1a, 1b, and 1c, obtained after heating 1·DMSO, 1·1/2(CH3CN), and 1·1/8(CH2Cl2), respectively, can also be restored to the original solvated forms upon exposure to corresponding solvent vapors. 1a and 1b emit NIR luminescence peaked at 998 and 1018 nm respectively, suggesting indirect synthetic methods as powerful alternatives to achieve NIR luminescence with long wavelength. In contrast, 1c exhibits a red luminescence with a broad unstructured emission band centered at 667 nm. All the responses to organic solvent vapors and heating are due to the structural transformations which result in the conversion of the lowest energy excited states between (3)MLCT/(3)LLCT and (3)MMLCT in solid-state as supported by time-dependent density functional theory (TD-DFT) calculations.

  9. Structural Electronic and Magnetic Properties of Quasi-1D Quantum Magnets [Ni(HF2)(pyz)2]X (pyz = pyrazine; X = PF6- SbF6-) Exhibiting Ni-FHF-Ni and Ni-pyz-Ni Spin Interactions

    SciTech Connect

    J Manson; S Lapidus; P Stephens; P Peterson; K Carreiro; H Southerland; T Lancaster; S Blundell; A Steele; et al.

    2011-12-31

    [Ni(HF{sub 2})(pyz){sub 2}]X {l_brace}pyz = pyrazine; X = PF{sub 6}{sup -} (1), SbF{sub 6}{sup -} (2){r_brace} were structurally characterized by synchrotron X-ray powder diffraction and found to possess axially compressed NiN{sub 4}F{sub 2} octahedra. At 298 K, 1 is monoclinic (C2/c) with unit cell parameters, a = 9.9481(3), b = 9.9421(3), c = 12.5953(4) {angstrom}, and {beta} = 81.610(3){sup o} while 2 is tetragonal (P4/nmm) with a = b = 9.9359(3) and c = 6.4471(2) {angstrom} and is isomorphic with the Cu-analogue. Infinite one-dimensional (1D) Ni-FHF-Ni chains propagate along the c-axis which are linked via {mu}-pyz bridges in the ab-plane to afford three-dimensional polymeric frameworks with PF{sub 6}{sup -} and SbF{sub 6}{sup -} counterions occupying the interior sites. A major difference between 1 and 2 is that the Ni-F-H bonds are bent (157{sup o}) in 1 but are linear in 2. Ligand field calculations (LFT) based on an angular overlap model (AOM), with comparison to the electronic absorption spectra, indicate greater {pi}-donation of the HF{sub 2}{sup -} ligand in 1 owing to the bent Ni-F-H bonds. Magnetic susceptibility data for 1 and 2 exhibit broad maxima at 7.4 and 15 K, respectively, and {lambda}-like peaks in dxT/dT at 6.2 and 12.2 K that are ascribed to transitions to long-range antiferromagnetic order (TN). Muon-spin relaxation and specific heat studies confirm these TN's. A comparative analysis of x vs T to various 1D Heisenberg/Ising models suggests moderate antiferromagnetic interactions, with the primary interaction strength determined to be 3.05/3.42 K (1) and 5.65/6.37 K (2). However, high critical fields of 19 and 37.4 T obtained from low temperature pulsed-field magnetization data indicate that a single exchange constant (J1D) alone is insufficient to explain the data and that residual terms in the spin Hamiltonian, which could include interchain magnetic couplings (J), as mediated by Ni-pyz-Ni, and single-ion anisotropy (D), must be considered

  10. Low-Dimensional Systems: Structures of Interfaces and Magnetic Chains

    NASA Astrophysics Data System (ADS)

    Shen, Qing

    The solid-solid metal oxide(MO) interface in (100) orientation was modeled and its properties were investigated by molecular Dynamics(MD). MD was used to model temperature dependent geometry in the interface region, using standard interatomic potentials. The lattice structure across the MO-MO interface is found to change continually from one crystal to another. The radial distribution function, average potential energy for each layer, the average interplanar spacing, mean square displacement of the ions and spectrum of the autocorrelation function of velocity were calculated. Results for (100) MgO-CoO and NiO-CoO interfaces are compared with solid-solution and pure-phase data. The solid-solid metal oxide interface of rock -salt structure in (100) orientation was modeled and its properties were investigated by Local Density(LD) theory. Starting with molecular dynamics determined time-average atomic configurations at the interface, self-consistent LD calculations were made to determine electronic structure, spectroscopic and energetic properties of interface atoms. Spectral distributions, bonding mechanisms, charge densities and consequences for the optical band gap were determined. Results are given for (100) MgO-CoO interfaces, rm Mg_{x}Co_{1-x}O alloy and NiO-CoO interface. The magnetic properties of transition-metal based quasi-one dimensional molecular metals show unusual concentration and temperature dependence. Ion magnetization in the one dimensional rm Cu_{1-c}Ni _{c} chain of rm Cu_{1-c}Ni_{c}(pc)I was modeled by Monte Carlo methods, using indirect exchange interaction potentials of variable range. The effects of dilution of Cu spin moments by diamagnetic Ni ions and impurity scattering effects on the electron gas polarization are determined. Results are compared with NMR T-dependent magnetization data for this molecular metal.

  11. Synthesis, magnetic properties and electronic structure of the S  =  ½ uniform spin chain system InCuPO5

    NASA Astrophysics Data System (ADS)

    Koteswararao, B.; Hazra, Binoy K.; Rout, Dibyata; Srinivasarao, P. V.; Srinath, S.; Panda, S. K.

    2017-07-01

    We have studied the structural and magnetic properties and electronic structure of the compound InCuPO5 synthesized by a solid state reaction method. The structure of InCuPO5 comprises S  =  ½ uniform spin chains formed by corner-shared CuO4 units. Magnetic susceptibility (χ(T)) data show a broad maximum at about 65 K, a characteristic feature of one-dimensional (1D) magnetism. The χ(T) data are fitted to the coupled S  =  ½ Heisenberg antiferromagnetic (HAFM) uniform chain model that gives the intra-chain coupling (J/k B) between nearest-neighbor Cu2+ ions as  -100 K and the ratio of inter-chain to intra-chain coupling (J‧/J) as about 0.07. The exchange couplings estimated from the magnetic data analysis are in good agreement with the values computed from the electronic structure calculations based on the density functional theory  +  Hubbard U (DFT  +  U) approach. The combination of theoretical and experimental analysis confirms that InCuPO5 is a candidate material for weakly coupled S  = ½ uniform chains. A detailed theoretical analysis of the electronic structure further reveals that the system is insulating with a gap of 2.4 eV and a local moment of 0.70 µ B/Cu.

  12. Electronic, bonding, and optical properties of 1d [CuCN]n (n = 1-10) chains, 2d [CuCN]n (n = 2-10) nanorings, and 3d [Cun (CN)n ]m (n = 4, m = 2, 3; n = 10, m = 2) tubes studied by DFT/TD-DFT methods.

    PubMed

    Tsipis, Athanassios C; Stalikas, Alexandros V

    2015-06-30

    The electronic, bonding, and photophysical properties of one-dimensional [CuCN](n) (n = 1-10) chains, 2-D [CuCN](n) (n = 2-10) nanorings, and 3-D [Cu(n)(CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes are investigated by means of a multitude of computational methodologies using density functional theory (DFT) and time-dependent-density-functional theory (TD-DFT) methods. The calculations revealed that the 2-D [CuCN](n) (n = 2-10) nanorings are more stable than the respective 1-D [CuCN](n) (n = 2-10) linear chains. The 2-D [CuCN](n) (n = 2-10) nanorings are predicted to form 3-D [Cun (CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes supported by weak stacking interactions, which are clearly visualized as broad regions in real space by the 3D plots of the reduced density gradient. The bonding mechanism in the 1-D [CuCN](n) (n = 1-10) chains, 2-D [CuCN](n) (n = 2-10) nanorings, and 3-D [Cu(n)(CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes are easily recognized by a multitude of electronic structure calculation approaches. Particular emphasis was given on the photophysical properties (absorption and emission spectra) of the [CuCN](n) chains, nanorings, and tubes which were simulated by TD-DFT calculations. The absorption and emission bands in the simulated TD-DFT absorption and emission spectra have thoroughly been analyzed and assignments of the contributing principal electronic transitions associated to individual excitations have been made.

  13. Hydrothermal synthesis and structure of a novel 3D framework based on {xi}-octamolybdate chains: [Cu{sub 2}(quinoxaline){sub 2}Mo{sub 4}O{sub 13}]{sub n}

    SciTech Connect

    Chen Lijuan; Lu Canzhong . E-mail: czlu@ma.fiirsm.ac.cn; He Xiang; Zhang Quanzheng; Yang Wenbin; Lin Xinhua . E-mail: xhlin174@sina.com

    2006-08-15

    An unprecedented three-dimensional (3D) polymer [Cu{sub 2}(quinoxaline){sub 2}Mo{sub 4}O{sub 13}]{sub n}, formed from {xi}-octamolybdate chains as building units and pairs of 1D [Cu(quinoxaline)]{sub n}{sup n+} polymeric chains as linkers, provides the first example of an extended higher dimensional structure based on [Mo{sub 8}O{sub 26}]{sub n}{sup 4n-} octamolybdate chain. The basic building block of the octamolybdate chain included in the title compound is first reported to be constructed from {xi}-isomer of octamolybdate unit.

  14. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2‧ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Mudsainiyan, R. K.; Jassal, Amanpreet Kaur; Chawla, S. K.

    2015-05-01

    The 1-D polymeric complex (I) is having formula [Mn(2,2‧-BP).(N3)2]n, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn-azide-Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J1=64.3 K (45.3 cm-1), and J2=-75.7 K (-53.3 cm-1). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L-L)(N3)2]n type.

  15. Structural changes upon excitation of D1-D2-Cyt b559 photosystem II reaction centers depend on the beta-carotene content.

    PubMed

    Losi, Aba; Yruela, Inmaculada; Reus, Michael; Holzwarth, Alfred R; Braslavsky, Silvia E

    2003-07-01

    Different preparations of D1-D2-Cyt b559 complexes from spinach with different beta-carotene (Car) content [on average from <0.5 to 2 per reaction center (RC)] were studied by means of laser-induced optoacoustic spectroscopy. phiP680(+)Pheo(-) does not depend on the preparation (or on the Car content) inasmuch as the magnitude of the prompt heat (produced within 20 ns) does not vary for the different samples upon excitation at 675 and 620 nm. The energy level of the primary charge-separated state, P680(+)Pheo(-), was determined as EP680(+)Pheo(-) = 1.55 eV. Thus, an enthalpy change accompanying charge separation from excited P680 of deltaH*P680Pheo-->P680(+)Pheo(-) = -0.27 eV is obtained. Calculations using the heat evolved during the time-resolved decay of P680(+)Pheo(-) (< or = 100 ns) affords a triplet (3[P680Pheo]) quantum yield phi3[P680Pheo] = 0.5 +/- 0.14. The structural volume change, deltaV1, corresponding to the formation of P680(+)Pheo(-), strongly depends on the Car content; it is ca. -2.5 A3 molecule(-1) for samples with <0.5 Car on average, decreases (in absolute value) to -0.5 +/- 0.2 A3 for samples with an average of 1 Car, and remains the same for samples with two Cars per RC. This suggests that the Car molecules induce changes in the ground-state RC conformation, an idea which was confirmed by preferential excitation of Car with blue light, which produced different carotene triplet lifetimes in samples with 2 Car compared to those containing less carotene. We conclude that the two beta-carotenes are not structurally equivalent. Upon blue-light excitation (480 nm, preferential carotene absorption) the fraction of energy stored is ca. 60% for the 9Chl-2Car sample, whereas it is 40% for the preparations with one or less Cars on average, indicating different paths of energy distribution after Car excitation in these RCs with remaining chlorophyll antennae.

  16. Structure of self-assembled Mn atom chains on Si(001)

    NASA Astrophysics Data System (ADS)

    Villarreal, Renan; Longobardi, Maria; Koester, Sigrun A.; Kirkham, Christopher J.; Bowler, David; Renner, Christoph

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. The structures and properties of the new two-dimensional inorganic–organic hybrid materials based on the molybdate chains

    SciTech Connect

    Li, Na; Mu, Bao; Cao, Xinyu; Huang, Rudan

    2014-09-15

    A series of inorganic organic hybrid materials based on polyoxometalates(POMs), namely, [M{sup II}(HL){sub 2}(H{sub 2}O){sub 2}][Mo{sup VI}{sub 6}O{sub 20}] [M=Co (1), Ni (2), Cu (3), Zn (4)], [Mn{sup IV}L{sub 2}(H{sub 2}O){sub 2}][Mo{sup VI}{sub 6}O{sub 20}] (5), and (HL){sub 3}PMO{sub 12}O{sub 40} (6) [L=3-(4-pyridyl)pyrazole], have been synthesized. The compounds have been characterized by elemental analysis, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. The results from single-crystal X-ray diffraction indicate that 1–5 are isostructural. It is worth noting that the polyanions are bridged by Mo–O–Mo to form 1D inorganic chains, which are further connected via M ions to form 2D nets. In compound 6, the ligands are used as the positive ions to balance the charge of the compound. Moreover, the magnetic properties of compound 5 have also been investigated in detail. - Graphical abstract: In complex 1, The Co ion is six coordinated by four oxygen atoms from two Mo{sub 6}O{sub 20} and two water molecules, and two N atoms from two different ligand. It is noticeable that there is an one-dimensional chain molybdate, which is combined by O–Mo–O, then the chain parallel with each other, the Mo{sub 6} anion acts as a bidentate ligand providing O7 atoms to bridge CoII ions to form a 2D inorganic layer. Finally every nets become 3D structure by hydrogen bond. - Highlights: • Novel inorganic–organic hybrid materials have been prepared. • Compounds 1–5 contain the 1D molybdate chains composed of (MoO{sub 6}) octahedra. • The 1D chains parallel with each other to form a 2D inorganic layer.

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

    SciTech Connect

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

    2015-06-24

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

  20. Three 1D cyanide-bridged M(Ni, Pd, Pt)-Mn(II) Coordination Polymer: Synthesis, Crystal Structure and Magnetic Properties.

    PubMed

    Shi, Jingwen; Xue, Chongchong; Kong, Lingqian; Zhang, Daopeng

    2017-01-01

    Three tetracyanide-containing building blocks K2[M(CN)4] (M = Ni, Pd, Pt) and one semi-closed macrocycle seven-coordinated manganese(II) compound have been employed to assemble cyanide-bridged heterometallic complexes, resulting in three cyanide-bridged MII-MnII complexes: [Mn(L)][Ni(CN)4] · 2H2O (1) [Mn(L)][Pd(CN)4] (2) and [Mn(L)][Pt(CN)4] (3) (L = 2,6-bis[1-(2-(N-methylamino)ethylimino)ethyl]pyridine). Single-crystal X-ray diffraction analysis shows their similar one-dimensional structure consisting of the alternating [Mn(L)]2+ species and [M(CN)4]2- building blocks, generating a cyanide-bridged neutral polymeric chain. In all three isostructural complexes the coordination geometry of manganese ion is a slightly distorted pentagonal-bipyramidal with the two cyanide nitrogen atoms at the trans positions and N5 coordinating mode at the equatorial plane from ligand L. Investigation over magnetic properties of these complexes reveals very weak antiferromagnetic interaction between neighboring Mn(II) ions bridged by the long NC-M-CN unit. A best-fit to the magnetic susceptibility of complexes 1-3 leads to the magnetic coupling constant of J = -0.081, -0.103 and -0.14 cm-1, respectively.

  1. Homoleptic 1-D iron selenolate complexes-synthesis, structure, magnetic and thermal behaviour of (1)(∞)[Fe(SeR)2] (R=Ph, Mes).

    PubMed

    Eichhöfer, Andreas; Buth, Gernot; Dolci, Francesco; Fink, Karin; Mole, Richard A; Wood, Paul T

    2011-07-14

    The first examples of polymeric homoleptic iron chalcogenolato complexes (1)(∞)[Fe(SePh)(2)] and (1)(∞)[Fe(SeMes)(2)] (Ph = phenyl = C(6)H(5), Mes = mesityl = C(6)H(2)-2,4,6-(CH(3))(3)) have been both prepared by reaction of [Fe(N(SiMe(3))(2))(2)] with two equivalents of HSeR (R = Ph, Mes) while (1)(∞)[Fe(SePh)(2)] was found to be also easily accessible through reactions of either FeCl(2), Fe(OOCCH(3))(2) or FeCl(3) with PhSeSiMe(3) in THF. In the crystal, the two compounds form one-dimensional chains with bridging selenolate ligands comprising distinctly different Fe-Se-Fe bridging angles, namely 71.15-72.57° in (1)(∞)[Fe(SePh)(2)] and 91.80° in (1)(∞)[Fe(SeMes)(2)]. Magnetic measurements supported by DFT calculations reveal that this geometrical change has a pronounced influence on the antiferromagnetic exchange interactions of the unpaired electrons along the chains in the two different compounds with a calculated magnetic exchange coupling constant of J = -137 cm(-1) in (1)(∞)[Fe(SePh)(2)] and J = -20 cm(-1) in (1)(∞)[Fe(SeMes)(2)]. In addition we were able to show that the ring molecule [Fe(SePh)(2)](12) which is a structural isomer of (1)(∞)[Fe(SePh)(2)] behaves magnetically similar to the latter one. Investigations by powder XRD reveal that the ring molecule is only a metastable intermediate which converts in THF completely to form (1)(∞)[Fe(SePh)(2)]. Thermal gravimetric analysis of (1)(∞)[Fe(SePh)(2)] under vacuum conditions shows that the compound is thermally labile and already starts to decompose above 30 °C in a two step process under cleavage of SePh(2) to finally form at 250 °C tetragonal PbO-type FeSe. The reaction of (1)(∞)[Fe(SePh)(2)] with the Lewis base 1,10-phenanthroline yielded, depending on the conditions, the octahedral monomeric complexes [Fe(SePh)(2)(1,10-phen)(2)] and [Fe(1,10-phen)(3)][Fe(SePh)(4)]. This journal is © The Royal Society of Chemistry 2011

  2. Atomic structure, energetics, and dynamicsof topological solitons inindium chains on Si(111) surfaces

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Choi, Jin-Ho; Cho, Jun-Hyung; Zeng, Changgan; Zhang, Zhenyu; Hou, Jianguo

    2012-02-01

    Besides the presence of exotic ground states, potentially more intriguing are the elementary excitations of the One-dimensional charge density waves (1D-CDWs), including the nonlinear topological excitation or soliton. Solitons may possess spin-charge inversion properties, and act as the effective carriers that account for the high conductivity in conducting polymers. Howevercomprehensive quantitative study of topological solitary excitations at the atomic level remains a challenge. In this talk, I will present our recent work on the quantitative haracterization of solitons in In chains grown on Si(111) surfaces at atomic scale. The precise atomic structure of the topological soliton in In/Si(111) is determined based on scanning tunneling microscopy and first-principles calculations.Variable emperature measurements of the soliton population allow us to determine the soliton formation energy to be ˜60 meV, smaller than one-half of the band gap of ˜200 meV. Once created, these solitons have very low mobility; the sluggish nature is attributed to the exceptionally low attempt frequency for soliton migration. We furtherdemonstrate local electric ?eld enhanced soliton dynamics, and the feasibility of aggregating solitonsinto soliton polymers.

  3. The role of cellular structure on increasing the detonability limits of three-step chain-branching detonations

    SciTech Connect

    Short, Mark; Kiyanda, Charles B; Quirk, James J; Sharpe, Gary J

    2011-01-27

    In [1], the dynamics of a pulsating three-step chain-branching detonation were studied. The reaction model consists of, sequentially, chain-initiation, chain-branching and chain-termination steps. The chain-initiation and chain-branching steps are taken to be thermally neutral, with chemical energy release occuring in the chain-termination stage. The purpose of the present study is to examine whether cellular detonation structure can increase the value of the chain-branching cross-over temperature T{sub b} at which fully coupled detonation solutions are observed over those in 1 D. The basic concept is straightforward and has been discussed in [1] and [3]; if T{sub s} drops below T{sub b} at the lead shock, the passage of a transverse shock can increase both the lead shock temperature and the temperature behind the transverse wave back above T{sub b}, thus sustaining an unstable cellular detonation for values of T{sub b} for which a one-dimensional pulsating detonation will fail. Experiments potentially supporting this hypothesis with irregular detonations have been shown in [3] in a shock tube with acoustically absorbing walls. Removal of the transverse waves results in detonation failure, giving way to a decoupled shock-flame complex. A number of questions remain to be addressed regarding the possibility of such a mechanism, and, if so, about the precise mechanisms driving the cellular structure for large T{sub b}. For instance, one might ask what sets the cell size in a chain-branching detonation, particularly could the characteristic cell size be set by the chain-branching cross-over temperature T{sub b}: after a transverse wave shock collision, the strength of the transverse wave weakens as it propagates along the front. If the spacing between shock collisions is too large (cell size), then the transverse shocks may weaken to the extent that the lead shock temperature or that behind the transverse waves is not raised above T{sub b}, losing chemical energy to

  4. Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field

    NASA Astrophysics Data System (ADS)

    Carmelo, J. M. P.; Sacramento, P. D.; Machado, J. D. P.; Campbell, D. K.

    2015-10-01

    We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the ‘pseudofermion dynamical theory’ (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents {{\\zeta}τ}(k) controlling the singularities for both the longitudinal ≤ft(τ =l\\right) and transverse ≤ft(τ =t\\right) dynamical structure factors for the whole momentum range k\\in ]0,π[ , in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

  5. Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field.

    PubMed

    Carmelo, J M P; Sacramento, P D; Machado, J D P; Campbell, D K

    2015-10-14

    We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the 'pseudofermion dynamical theory' (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents ζ(τ)(k) controlling the singularities for both the longitudinal (τ = l) and transverse (τ = t) dynamical structure factors for the whole momentum range k ∈ ]0,π[, in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

  6. Ammonia detection of 1-D ZnO/polypyrrole nanocomposite: Effect of CSA doping and their structural, chemical, thermal and gas sensing behavior

    NASA Astrophysics Data System (ADS)

    Jain, Shilpa; Karmakar, Narayan; Shah, Akshara; Kothari, D. C.; Mishra, Satyendra; Shimpi, Navinchandra G.

    2017-02-01

    Nanocomposites of polypyrrole (PPy) with varying concentration of ZnO nanorods (ZnO NRs) were synthesized using in-situ oxidative polymerization technique. The prepared nanocomposites (PPy, PPy-ZnO and CSA doped PPy-ZnO) were studied for various oxidizing and reducing gases at room temperature and found to be more selective towards ammonia gas. Various concentrations of ZnO NRs in Ppy matrix were studied and 15% was found to be optimum in terms of sensor response (66% towards 120 ppm NH3). Further, with 15% doping of camphor sulphonic acid (CSA) in PPy-ZnO nanocomposite for 15% ZnO NRs in Ppy matrix, sensor response increased from 66 to 79% towards 120 ppm of NH3. Structural, Optical and thermal behavior of nanocomposites were studied using powder X-ray diffraction (XRD), Fourier Transform Infra-Red (FTIR) spectroscopy, X-ray Photoelectron Spectroscopy (XPS), UV-vis (UV-vis) absorption spectroscopy, room temperature Photoluminescence (PL) Spectroscopy, Thermo-gravimetric analysis (TGA) and Field Emission Scanning Electron Microscopy (FESEM). ZnO has been completely embedded inside the polymeric chains as observed from in SEM. Meanwhile, FT-IR spectra indicate better conjugation and interaction in nanocomposites. With CSA doping interaction grows stronger due to extended delocalization over π electrons leading to higher sensor response and with response time and recovery time of 24 s and 34 s respectively. CSA doped PPy-ZnO (15%) nanocomposites observed to be a potential candidate for ammonia detection at lower ppm level.

  7. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2′ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    SciTech Connect

    Mudsainiyan, R.K. Jassal, Amanpreet Kaur; Chawla, S.K.

    2015-05-15

    The 1-D polymeric complex (I) is having formula [Mn(2,2′-BP).(N{sub 3}){sub 2}]{sub n}, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn–azide–Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J{sub 1}=64.3 K (45.3 cm{sup −1}), and J{sub 2}=−75.7 K (−53.3 cm{sup −1}). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L–L)(N{sub 3}){sub 2}]{sub n} type. - - Highlights: • Synthesized 1-D polymeric complex of Mn (II) ions with 2, 2′ bipyridyl and azide group. • X-ray data of complex (I) is in a good agreement with TGA and other spectroscopic techniques. • DFT calculations were done and compared with the parameter of experimental and theoretical data. • Intermolecular interactions calculated by Hirshfeld surface analysis

  8. Structurally driven magnetic state transition of biatomic Fe chains on Ir(001)

    NASA Astrophysics Data System (ADS)

    Mokrousov, Yuriy; Thiess, Alexander; Heinze, Stefan

    2009-11-01

    Using first-principles calculations, we demonstrate that the magnetic exchange interaction and the magnetocrystalline anisotropy of biatomic Fe chains grown in the trenches of the (5×1) reconstructed Ir(001) surface depend sensitively on the atomic arrangement of the Fe atoms. Two structural configurations have been considered which are suggested from recent experiments. They differ by the local symmetry and the spacing between the two strands of the biatomic Fe chain. Since both configurations are very close in total energy they may coexist in experiment. We have investigated collinear ferro- and antiferromagnetic solutions as well as a collinear state with two moments in one direction and one in the opposite direction ( ↑↓↑ -state). For the structure with a small interchain spacing, there is a strong exchange interaction between the strands and the ferromagnetic state is energetically favorable. In the structure with larger spacing, the two strands are magnetically nearly decoupled and exhibit antiferromagnetic order along the chain. In both cases, due to hybridization with the Ir substrate the exchange interaction along the chain axis is relatively small compared to free-standing biatomic iron chains. The easy magnetization axis of the Fe chains also switches with the structural configuration and is out-of-plane for the ferromagnetic chains with small spacing and along the chain axis for the antiferromagnetic chains with large spacing between the two strands. Calculated scanning tunneling microscopy images and spectra suggest the possibility to experimentally distinguish between the two structural and magnetic configurations.

  9. The study of the structure factor of a wormlike chain in an orientational external field

    NASA Astrophysics Data System (ADS)

    Jiang, Ying; Zhang, Xinghua; Miao, Bing; Yan, Dadong

    2015-04-01

    A precise representation of the structure factor of a wormlike chain for the arbitrary chain flexibility in an orientational external field is obtained by virtue of the numerical solution to the modified diffusion equation satisfied by the Green's function. The model is built from a standard wormlike chain formalism in a continuous version which crossovers from the rigid-rod limit to the flexible chain limit and the Maier-Saupe interaction which describes the orientational effects from the nematic field. The behaviors of the structure factor in the distinct wavevector k regimes are numerically investigated as functions of chain flexibility and tilt angle between the directors of the nematic field and k. The radius of gyration extracted from the structure factor in small-k regime is also carefully analysed in both the directions along and perpendicular to the nematic axis. Our calculations exactly recover the prediction of the structure factor undergoing an orientational field in the rigid rod limit.

  10. The magnetization curve of spin chains with superlattice structure

    NASA Astrophysics Data System (ADS)

    Silva-Valencia, J.; Franco, R.

    2006-10-01

    The magnetization curve of the spin superlattices composed of repeat pattern of two spin- {1}/{2} XXZ chains with different anisotropy parameters was calculated using density matrix renormalization group. We observe a nontrivial plateau with magnetization value given by the relative sizes of the subchains.

  11. Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA

    NASA Astrophysics Data System (ADS)

    Muramatsu, Akira; Shimizu, Yuta; Yoshikawa, Yuko; Fukuda, Wakao; Umezawa, Naoki; Horai, Yuhei; Higuchi, Tsunehiko; Fujiwara, Shinsuke; Imanaka, Tadayuki; Yoshikawa, Kenichi

    2016-12-01

    We studied the effect of branched-chain polyamines on the folding transition of genome-sized DNA molecules in aqueous solution by the use of single-molecule observation with fluorescence microcopy. Detailed morphological features of polyamine/DNA complexes were characterized by atomic force microscopy (AFM). The AFM observations indicated that branched-chain polyamines tend to induce a characteristic change in the higher-order structure of DNA by forming bridges or crosslinks between the segments of a DNA molecule. In contrast, natural linear-chain polyamines cause a parallel alignment between DNA segments. Circular dichroism measurements revealed that branched-chain polyamines induce the A-form in the secondary structure of DNA, while linear-chain polyamines have only a minimum effect. This large difference in the effects of branched- and linear-chain polyamines is discussed in relation to the difference in the manner of binding of these polyamines to negatively charged double-stranded DNA.

  12. Synthesis and characterization of 1D iron(II) spin crossover coordination polymers with hysteresis.

    PubMed

    Bauer, Wolfgang; Lochenie, Charles; Weber, Birgit

    2014-02-07

    Purposeful ligand design was used for the synthesis of eight new 1D iron(II) spin crossover coordination polymers aiming for cooperative spin transitions with hysteresis. The results from magnetic measurements and X-ray structure analysis show that the combination of rigid linkers and a hydrogen bond network between the 1D chains is a promising tool to reach this goal. Five of the eight new samples show a cooperative spin transition with hysteresis with up to 43 K wide hysteresis loops.

  13. Induction of gamma-turn-like structure in ferrocene bearing dipeptide chains via conformational control.

    PubMed

    Moriuchi, Toshiyuki; Nagai, Takayoshi; Hirao, Toshikazu

    2006-01-05

    [structure: see text] A combination of the ferrocene scaffold as a central reverse-turn unit with the dipeptide chains (-L-Pro-L-Ala-NHPy) was demonstrated to induce both inverse gamma-turn-like and antiparallel beta-sheet-like structures. Only the antiparallel beta-sheet-like structure was formed in the ferrocene bearing the heterochiral dipeptide chains (-L-Pro-D-Ala-NHPy), in which highly organized self-assembly was achieved through a network of intermolecular hydrogen bonds.

  14. Amylopectin small chain glucans form structure fingerprint that determines botanical origin of starch.

    PubMed

    Jaiswal, Sarita; Chibbar, Ravindra N

    2017-02-20

    Starch granule size, shape and structure of amylopectin are species specific and influence starch properties and end-use of starch. Amylopectin glucan chain structure was used to predict the starch botanical sources. Mathematical probability for accumulation of small glucan chains DP 6-10 reveal exponential fit curve with maximum R(2) in smallest granule size starches (Chlamydomonas, quinoa, buckwheat). Cereal and cassava showed R(2) of 0.81-0.96 while in pulses and tubers it was less than 0.7. The amylopectin small glucan chains form a unique 'finger print region' that identified starch botanical source. Differential amylopectin chain length distribution (APCLD) graphs between DP 6-80 of all species from Chlamydomonas starch distinguished five structural groups that clustered the 31 analyzed starches into four major patterns. APCLD analyses of amylopectin combined with characteristic pattern of small linear DP (6-9) glucan chains predicted the starch botanical source.

  15. Landscaping the structures of GAVI country vaccine supply chains and testing the effects of radical redesign.

    PubMed

    Lee, Bruce Y; Connor, Diana L; Wateska, Angela R; Norman, Bryan A; Rajgopal, Jayant; Cakouros, Brigid E; Chen, Sheng-I; Claypool, Erin G; Haidari, Leila A; Karir, Veena; Leonard, Jim; Mueller, Leslie E; Paul, Proma; Schmitz, Michelle M; Welling, Joel S; Weng, Yu-Ting; Brown, Shawn T

    2015-08-26

    Many of the world's vaccine supply chains do not adequately provide vaccines, prompting several questions: how are vaccine supply chains currently structured, are these structures closely tailored to individual countries, and should these supply chains be radically redesigned? We segmented the 57 GAVI-eligible countries' vaccine supply chains based on their structure/morphology, analyzed whether these segments correlated with differences in country characteristics, and then utilized HERMES to develop a detailed simulation model of three sample countries' supply chains and explore the cost and impact of various alternative structures. The majority of supply chains (34 of 57) consist of four levels, despite serving a wide diversity of geographical areas and population sizes. These four-level supply chains loosely fall into three clusters [(1) 18 countries relatively more bottom-heavy, i.e., many more storage locations lower in the supply chain, (2) seven with relatively more storage locations in both top and lower levels, and (3) nine comparatively more top-heavy] which do not correlate closely with any of the country characteristics considered. For all three cluster types, our HERMES modeling found that simplified systems (a central location shipping directly to immunization locations with a limited number of Hubs in between) resulted in lower operating costs. A standard four-tier design template may have been followed for most countries and raises the possibility that simpler and more tailored designs may be warranted. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Suspended chains damp wind-induced oscillations of tall flexible structures

    NASA Technical Reports Server (NTRS)

    Reed, W. H., III

    1968-01-01

    Hanging-chain system, which is a form of impact damper, suppresses wind-induced bending oscillations of tall cylindrical antenna masts. A cluster of chains enclosed in a neoprene shroud is suspended inside the tip of the antenna mast, forming a simple method of damping structural vibrations.

  17. Synthesis and structures of ligand-dominated one-dimensional silver(I)-bis(pyridylmethyl)amine coordination chains

    NASA Astrophysics Data System (ADS)

    Lin, Hung-Jui; Liu, Yu-Chiao; Tseng, Yu-Jui; Wu, Jing-Yun

    2016-10-01

    Reactants slow diffusion of Ag(I) salts with 3,4‧-bis(pyridylmethyl)amine (3,4‧-bpma), an unsymmetric bis-pyridyl ligand equipped with a non-innocent amine backbone, afforded polymeric coordination adducts 1-5 having a general formula {[Ag(3,4‧-bpma)(solv)]X}n (solv = H2O, CH3OH, and none; X= CF3CO2-, BF4-, ClO4-, CF3SO3-, and SbF6-). Single-crystal X-ray diffraction (SCXRD) analyses reveal that colorless crystals of Ag(I) coordination polymers (CPs) 1-5 have very similar one-dimensional (1D) non-flat chain structures, which are preferentially depicted as a "zipper-like" rather than a ladder-like or a double-stranded chain topologies. The 3,4‧-bpma ligand in these Ag(I) CPs displays a μ3-bridging mode with a gauche-trans (1,4, and 5) and a trans-trans (2 and 3) conformations. Noteworthy, anions do not show strong influence on structural modulation of Ag(I) CPs in the solid state, but really affect CP conformations and packing fashions, indicative of a ligand-dominated assembly process for such a Ag(I)-3,4‧-bpma system. Thermal stabilities and solid-state photoluminescence properties of crystalline materials 1-5 were investigated.

  18. Novel 1D coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n}: Synthesis, structure, magnetic properties and thermal behavior

    SciTech Connect

    Fomina, Irina; Dobrokhotova, Zhanna; Aleksandrov, Grygory; Emelina, Anna; Bykov, Mikhail; Bogomyakov, Artem; Puntus, Lada; Novotortsev, Vladimir; Eremenko, Igor

    2012-01-15

    The new 1D coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n} (1), where Piv=OOCBu{sup t-}, was synthesized in high yield (>95%) by the reaction of thulium acetate with pivalic acid in air at 100 Degree-Sign S. According to the X-ray diffraction data, the metal atoms in compound 1 are in an octahedral ligand environment unusual for lanthanides. The magnetic and luminescence properties of polymer 1, it's the solid-phase thermal decomposition in air and under argon, and the thermal behavior in the temperature range of -50 Horizontal-Ellipsis +50 Degree-Sign S were investigated. The vaporization process of complex 1 was studied by the Knudsen effusion method combined with mass-spectrometric analysis of the gas-phase composition in the temperature range of 570-680 K. - Graphical Abstract: Novel 1D coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n} was synthesized and studied by X-ray diffraction. The magnetic, luminescence properties, the thermal behavior and the volatility for the compound {l_brace}Tm(Piv){sub 3{r_brace}n} were investigated. Black-Small-Square Highlights: Black-Right-Pointing-Pointer We synthesized the coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n}. Black-Right-Pointing-Pointer Tm atoms in polymer have the coordination number 6. Black-Right-Pointing-Pointer Polymer exhibits blue-color emission at room temperature. Black-Right-Pointing-Pointer Polymer shows high thermal stability and volatility. Black-Right-Pointing-Pointer Polymer has no phase transitions in the range of -50 Horizontal-Ellipsis +50 Degree-Sign S.

  19. Analysis of the rotational structure in the high-resolution infrared spectra of cis,cis- and trans,trans-1,4-difluorobutadiene-1-d1 and trans,trans-1,4-difluorobutadiene-1,4-d2

    SciTech Connect

    Craig, Norman C.; Chen, Yihui; Lu, Yuhua; Neese, Christopher F.; Nemchick, Deacon J.; Blake, Thomas A.

    2013-06-01

    Samples of cis,cis- and trans,trans-1,4-difluorobutadiene-1- d1 and of trans,trans-1,4-difluorobutadiene-1,4-d2 have been synthesized, and high-resolution (≤0.0018 cm-1) infrared spectra of these substances have been recorded in the gas phase. Analysis of the rotational structure, mostly in C-type bands, has yielded ground state rotational constants. For the two 1-d1 species more than one band has been analyzed. For the 1,4-d2 species only one band was available for analysis. However, good agreement between the experimental centrifugal distortion constants and those predicted with a B3LYP/cc-pVTZ model give strong support to the analysis of the very dense spectrum. The ground state rotational constants are a contribution to finding semiexperimental equilibrium structures of the two nonpolar isomers of 1,4- difluorobutadiene.

  20. An experimental disturbance alters fish size structure but not food chain length in streams.

    PubMed

    Walters, Annika W; Post, David M

    2008-12-01

    Streams experience frequent natural disturbance and are undergoing considerable anthropogenic disturbance due to dam construction and water diversion. Disturbance is known to impact community structure, but its effect on food chain length is still a matter of considerable debate. Theoretical models show that longer food chains are less resilient to disturbance, so food chain length is predicted to be shorter following a disturbance event. Here we experimentally test the effect of disturbance on food chain length in streams by diverting stream flow. We found that our experimental low-flow disturbance did not alter food chain length. We did see an effect on body-size structure in our food webs suggesting that food chain length may be an insensitive indicator of disturbance. We suggest that habitat heterogeneity and food web complexity buffer the effect of disturbance on food chain length. The theoretical predictions of disturbance on food chain length are only likely to be seen in homogeneous systems that closely approximate the linear food chains the models are based upon.

  1. Design, synthesis, and functional activity of labeled CD1d glycolipid agonists.

    PubMed

    Jervis, Peter J; Polzella, Paolo; Wojno, Justyna; Jukes, John-Paul; Ghadbane, Hemza; Garcia Diaz, Yoel R; Besra, Gurdyal S; Cerundolo, Vincenzo; Cox, Liam R

    2013-04-17

    Invariant natural killer T cells (iNKT cells) are restricted by CD1d molecules and activated upon CD1d-mediated presentation of glycolipids to T cell receptors (TCRs) located on the surface of the cell. Because the cytokine response profile is governed by the structure of the glycolipid, we sought a method for labeling various glycolipids to study their in vivo behavior. The prototypical CD1d agonist, α-galactosyl ceramide (α-GalCer) 1, instigates a powerful immune response and the generation of a wide range of cytokines when it is presented to iNKT cell TCRs by CD1d molecules. Analysis of crystal structures of the TCR-α-GalCer-CD1d ternary complex identified the α-methylene unit in the fatty acid side chain, and more specifically the pro-S hydrogen at this position, as a site for incorporating a label. We postulated that modifying the glycolipid in this way would exert a minimal impact on the TCR-glycolipid-CD1d ternary complex, allowing the labeled molecule to function as a good mimic for the CD1d agonist under investigation. To test this hypothesis, the synthesis of a biotinylated version of the CD1d agonist threitol ceramide (ThrCer) was targeted. Both diastereoisomers, epimeric at the label tethering site, were prepared, and functional experiments confirmed the importance of substituting the pro-S, and not the pro-R, hydrogen with the label for optimal activity. Significantly, functional experiments revealed that biotinylated ThrCer (S)-10 displayed behavior comparable to that of ThrCer 5 itself and also confirmed that the biotin residue is available for streptavidin and antibiotin antibody recognition. A second CD1d agonist, namely α-GalCer C20:2 4, was modified in a similar way, this time with a fluorescent label. The labeled α-GalCer C20:2 analogue (11) again displayed functional behavior comparable to that of its unlabeled substrate, supporting the notion that the α-methylene unit in the fatty acid amide chain should be a suitable site for attaching

  2. Design, Synthesis, and Functional Activity of Labeled CD1d Glycolipid Agonists

    PubMed Central

    2013-01-01

    Invariant natural killer T cells (iNKT cells) are restricted by CD1d molecules and activated upon CD1d-mediated presentation of glycolipids to T cell receptors (TCRs) located on the surface of the cell. Because the cytokine response profile is governed by the structure of the glycolipid, we sought a method for labeling various glycolipids to study their in vivo behavior. The prototypical CD1d agonist, α-galactosyl ceramide (α-GalCer) 1, instigates a powerful immune response and the generation of a wide range of cytokines when it is presented to iNKT cell TCRs by CD1d molecules. Analysis of crystal structures of the TCR−α-GalCer–CD1d ternary complex identified the α-methylene unit in the fatty acid side chain, and more specifically the pro-S hydrogen at this position, as a site for incorporating a label. We postulated that modifying the glycolipid in this way would exert a minimal impact on the TCR–glycolipid–CD1d ternary complex, allowing the labeled molecule to function as a good mimic for the CD1d agonist under investigation. To test this hypothesis, the synthesis of a biotinylated version of the CD1d agonist threitol ceramide (ThrCer) was targeted. Both diastereoisomers, epimeric at the label tethering site, were prepared, and functional experiments confirmed the importance of substituting the pro-S, and not the pro-R, hydrogen with the label for optimal activity. Significantly, functional experiments revealed that biotinylated ThrCer (S)-10 displayed behavior comparable to that of ThrCer 5 itself and also confirmed that the biotin residue is available for streptavidin and antibiotin antibody recognition. A second CD1d agonist, namely α-GalCer C20:2 4, was modified in a similar way, this time with a fluorescent label. The labeled α-GalCer C20:2 analogue (11) again displayed functional behavior comparable to that of its unlabeled substrate, supporting the notion that the α-methylene unit in the fatty acid amide chain should be a suitable site for

  3. Thermodynamic and structure investigations of new side-chain liquid crystal polymer

    NASA Astrophysics Data System (ADS)

    Danch, A.; Laggner, Peter; Degovics, G.; Sek, D.; Stelzer, F.

    1998-01-01

    Bis [((omega) -(4'-cyanobiphenyl)-4-yl)oxy-n- alkyl]norborn-5-ene-2,3-dicarboxylate was polymerized via ring opening metathesis polymerization. Two distributed polynorbornene derivatives, both of cis configuration, with different length of side-chain were studied. The influence of thermal history on the smectic phase stabilization, position and shape of the glass transition with temperature and on the relaxation process is shown. Glass transition temperatures enthalpies of isotropization and average layer spacing were calculated. Although, the rather flexible spacer between the mesogenic group and the main chain seems to be sufficient to partially decouple the mobility of the main chain from that of the mesogenic group, the influence of a backbone chain structure is still significant for polymer properties, especially in bulk. The measured layer spacing doe not correspond to double length of the side chain which suggests that either the side chains are not fully extended or some overlapping of CN tails occurs.

  4. Dual character of the electronic structure in YBa2Cu4O8: conduction bands of CuO2 planes and CuO chains

    NASA Astrophysics Data System (ADS)

    Kaminski, A.; Kondo, T.; Khasanov, R.; Karpinski, J.; Kazakov, S. M.; Zhigadlo, N. D.; Ohta, T.; Fretwell, H. M.; Palczewski, A. D.; Koll, J. D.; Mesot, J.; Rotenberg, E.; Keller, H.

    2007-03-01

    We use microprobe Angle-Resolved Photoemission Spectroscopy (μARPES) to separately investigate the electronic properties of CuO2 planes and CuO chains in the high temperature superconductor, YBa2Cu4O8. In the CuO2 planes, a two dimensional (2D) electronic structure with nearly momentum independent bilayer splitting is observed. The splitting energy is 150 meV at (π,0), almost 50% larger than in Bi2Sr2CaCu2O8+δ and the electron scattering at the Fermi level in the bonding band is about 1.5 times stronger than in the antibonding band. The CuO chains have a quasi one dimensional (1D) electronic structure. We observe two 1D bands separated by ˜ 550meV: a conducting band and an insulating band with an energy gap of ˜240meV. We find that the conduction electrons are well confined within the planes and chains with a non-trivial hybridization.

  5. Crystal structure of 7,8,9,10-tetra­hydro­benzo[b]naphtho­[2,1-d]furan

    PubMed Central

    Wu, Zhongyuan; Reetz, Manfred T.; Harms, Klaus

    2016-01-01

    In the title compound, C16H14O, the cyclo­hexene ring has a half-chair conformation. The mean plane, calculated through all non-H atoms of the mol­ecule, except for the central CH2 atoms of the cyclo­hexene ring, which deviate by 0.340 (3) and −0.369 (3) Å from this mean plane, has an r.m.s. deviation of 0.012 Å. In the crystal, there are C—H⋯π contacts present, resulting in the formation of zigzag chains propagating along the [010] direction. PMID:26870597

  6. Data mining of supersecondary structure homology between light chains of immunogloblins and MHC molecules: absence of the common conformational fragment in the human IgM rheumatoid factor.

    PubMed

    Izumi, Hiroshi; Wakisaka, Akihiro; Nafie, Laurence A; Dukor, Rina K

    2013-03-25

    It is shown that fuzzy search and data mining techniques of supersecondary structure homology for subunits of proteins using conformational code patterns of α-helix-type (3β5α4β) and β-sheet-type (6α4β4β) fragments can be used to extract correlations between fragments of MHC class I molecules and the light chain of immunoglobulins. The new method of conformational pattern analysis with fuzzy search of structural code homology reflects well the shape of main chain rather than secondary structure in comparison with the DSSP method. Further, the data mining technique using the combination of h- and s-fragment patterns can quantify the supersecondary structure homology between any subunits of proteins with different amino acid sequences. Characteristic fragment patterns (string "shhshss"), which were sandwiched between two identical amino acid sequences His and Pro, were found in light chains of various types of immunogloblins, α-chain and β-2 microglobulin of MHC class I and α-chain and β-chain of MHC class II, but not in heavy chains of Fab immunoglobulin fragments and T cell receptors (TCR). Leukocyte immunoglobulin-like receptors (LILR) are related by the conformational fragment (string "shhshss") to β-2 microglobulins as a type of pair forms (string "sohsss"). Further, human IgM rheumatoid factor, one of the immunogloblins, did not strongly exhibit the conformational fragment pattern. Nonclassic MHC class I molecules CD1D, MIC-A, and MIC-B, which have functions to activate NKT, NK, and T cells, did not also clearly show the patterns. These code-driven mining techniques can be utilized as a metadata-generating tool for systems biology to elucidate the biological function of such conformational fragments of MHC I and II molecules, which come in contact with various signal ligands on the surface of T cells and natural killer cells.

  7. Parameterizing amylose chain-length distributions for biosynthesis-structure-property relations.

    PubMed

    Nada, Sharif S; Zou, Wei; Li, Changfeng; Gilbert, Robert G

    2017-09-25

    Amylose, one of the components of starch, is a glucose polymer consisting largely of long, linear chains with a few long-chain branch points. The chain-length (molecular weight) distribution (CLD) of the component chains of amylose can provide information on amylose biosynthesis-structure-property relations, as has been done previously by fitting amylopectin CLDs to a model with physically meaningful parameters. Due to the presence of long chains, the CLD of amylose can currently best be obtained by size-exclusion chromatography, a technique that suffers from band-broadening effects which alter the observed distribution. The features of the multiple regions present in amylose chain-length distributions are also difficult to resolve, an issue that combines with band broadening to compound the difficulty of analysis and subsequent parameterization of the structural characteristics of amylose. A new method is presented to fit these distributions with biologically meaningful parameters in a way that accounts for band broadening. This is achieved by assuming that band broadening takes the form of a simple Gaussian over a relatively small region and that chain stoppage is a random process independent of the length of the substrate chain over the same region; these assumptions are relatively weak and expected to be frequently applicable. The method provides inbuilt consistency tests for its applicability to a given data set and, in cases where it is applicable, allows for the first nonempirical parameterization of amylose biosynthesis-structure-property relations from CLDs by using parameters directly linked to the activities of the enzymes responsible for chain growth and chain stoppage. Graphical abstract Model calculation illustrating the method described and showing the division between the three characteristic regions of a typical amylose chain-length distribution.

  8. Preparation of Desirable Porous Cell Structure Polylactide/Wood Flour Composite Foams Assisted by Chain Extender

    PubMed Central

    Wang, Youyong; Song, Yongming; Du, Jun; Xi, Zhenhao; Wang, Qingwen

    2017-01-01

    Polylactide (PLA)/wood flour composite foam were prepared through a batch foaming process. The effect of the chain extender on the crystallization behavior and dynamic rheological properties of the PLA/wood flour composites were investigated as well as the crystal structure and cell morphology of the composite foams. The incorporation of the chain extender enhanced the complex viscosity and storage modulus of PLA/wood flour composites, indicating the improved melt elasticity. The chain extender also led to a decreased crystallization rate and final crystallinity of PLA/wood flour composites. With an increasing chain extender content, a finer and more uniform cell structure was formed, and the expansion ratio of PLA/wood flour composite foams was much higher than without the chain extender. Compared to the unfoamed composites, the crystallinity of the foamed PLA/wood flour composites was improved and the crystal was loosely packed. However, the new crystalline form was not evident. PMID:28846604

  9. Effect of the band structure in a rigorous two-body model with long-range interactions in 1D optical lattices

    NASA Astrophysics Data System (ADS)

    Kristensen, Tom; Simoni, Andrea; Launay, Jean-Michel

    2016-05-01

    We compute scattering and bound state properties for two ultracold molecules in a pure 1D optical lattice. We introduce reference functions with complex quasi-momentum that naturally account for the effect of excited energy bands. Our exact results for a short-range interaction are first compared with the simplest version of the standard Bose-Hubbard (BH) model. Such comparison allows us to highlight the effect of the excited bands, of the non-on-site interaction and of tunneling with distant neighbor, that are not taken into account in the BH model. The effective interaction can depend strongly on the particle quasi-momenta and can present a resonant behavior even in a deep lattice. As a second step, we study scattering of two polar particles in the optical lattice. Peculiar Wigner threshold laws stem from the interplay of the long range dipolar interaction and the presence of the energy bands. We finally assess the validity of an extended Bose-Hubbard model for dipolar gases based on our exact two-body calculations. This work was supported by the Agence Nationale de la Recherche (Contract No. ANR-12-BS04-0020-01).

  10. Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs.

    PubMed

    Uto, Takuya; Mawatari, Sho; Yui, Toshifumi

    2014-08-07

    The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iβ, II, and IIII were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively. The cellulose IIII (1-10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models were reflected in the structures of the parent crystal models observed in solvated molecular dynamics (MD) simulations. The minor conformations of the hydroxymethyl groups proposed in the real crystal structures were detected in the MD crystal models and the DFT-optimized (010) model of cellulose II. The crystal chain packing and crystal conversions are interpreted in terms of principal chain sheet stacking.

  11. 3D coordination networks based on supramolecular chains as building units: synthesis and crystal structures of two silver(I) pyridyldiethynides.

    PubMed

    Zhang, Tianle; Kong, Jianxi; Hu, Yuejie; Meng, Xianggao; Yin, Hongbing; Hu, Dongshuang; Ji, Changpeng

    2008-04-21

    Two silver(I) pyridyldiethynides, [Ag2(3,5-C2PyC2).4CF3CO2Ag.4H2O] ( A) and [Ag 2(3,5-C2PyC2).3AgNO3.H2O](B), were synthesized by reactions of 3,5-diethynylpyridine with silver trifluoroacetate and silver nitrate in high yield, respectively. X-ray crystallographic studies revealed that in A pyridyldiethynide groups connect Ag 11 cluster units to generate 1D supramolecular chains as bridging ligands, where each ethynide group interacts with four silver atoms. These supramolecular chains bearing pyridyl groups are linked by silver ions to form wavelike layers, which are further connected by trifluoroacetate ligands to afford a 3D coordination network. However, B exhibits a different structural feature, where two ethynide groups in one pyridyldiethynide ligand coordinate to three and four silver atoms, respectively. These silver ethynide cluster units are linked through silver-ethynide and argentophilic interactions, leading to a double silver chain by sharing silver atoms in these units. In B, the silver double chains are further connected by bridging pyridyldiethynide groups to generate 2D networks, which interact through the Ag-N coordination bonds between silver atoms and pyridyl groups in the adjacent layers to generate a 3D coordination network. In these two compounds, trifluoroacetate and nitrate groups exhibit different bonding modes, indicating that the counterion is an important factor influencing the structures of supramolecular chains and coordination networks.

  12. DESIGN PACKAGE 1D SYSTEM SAFETY ANALYSIS

    SciTech Connect

    L.R. Eisler

    1995-02-02

    The purpose of this analysis is to systematically identify and evaluate hazards related to the Yucca Mountain Project Exploratory Studies Facility (ESF) Design Package 1D, Surface Facilities, (for a list of design items included in the package 1D system safety analysis see section 3). This process is an integral part of the systems engineering process; whereby safety is considered during planning, design, testing, and construction. A largely qualitative approach was used since a radiological System Safety analysis is not required. The risk assessment in this analysis characterizes the accident scenarios associated with the Design Package 1D structures/systems/components in terms of relative risk and includes recommendations for mitigating all identified risks. The priority for recommending and implementing mitigation control features is: (1) Incorporate measures to reduce risks and hazards into the structure/system/component (S/S/C) design, (2) add safety devices and capabilities to the designs that reduce risk, (3) provide devices that detect and warn personnel of hazardous conditions, and (4) develop procedures and conduct training to increase worker awareness of potential hazards, on methods to reduce exposure to hazards, and on the actions required to avoid accidents or correct hazardous conditions. The scope of this analysis is limited to the Design Package 1D structures/systems/components (S/S/Cs) during normal operations excluding hazards occurring during maintenance and ''off normal'' operations.

  13. Monte Carlo simulation of a single ring among linear chains: structural and dynamic heterogeneity.

    PubMed

    Yang, Yong-Biao; Sun, Zhao-Yan; Fu, Cui-Liu; An, Li-Jia; Wang, Zhen-Gang

    2010-08-14

    We perform lattice Monte Carlo simulation using the bond-fluctuation model to examine the conformation and dynamic properties of a single small flexible ring polymer in the matrix of linear chains as functions of the degree of polymerization of the linear chains. The average conformation properties as gauged by the mean-square radius of gyration and asphericity parameter are insensitive to the chain length for all the chain lengths examined (30, 100, 300, and 1000). However, in the longer chain (300 and 1000) samples, there is an increased spread in the distribution of the value of these quantities, suggesting structural heterogeneity. The center-of-mass diffusion of the ring shows a rapid decrease with increasing chain length followed by a more gradual change for the two longer chain systems. In these longer chain systems, a wide spread in the value of the apparent self-diffusion coefficient is also observed, as well as qualitatively different square displacement trajectories among the different samples, suggesting heterogeneity in the dynamics. A primitive path analysis reveals that in these long chain systems, the ring can exist in topologically distinct states with respect to threading by the linear chains. Threading by the linear chain can dramatically slow down and in some cases stall the diffusive motion of the ring. We argue that the life times for these topological conformers can be longer than the disentanglement time of the linear chain matrix, so that the ring exhibits nonergodic behavior on time scales less or comparable to the life time of these conformers. Our results suggest a picture of the ring diffusion as one where the diffusion path consists of distinctive segments, each corresponding to a different conformer, with slow interconversion between the different conformers.

  14. Monte Carlo simulation of a single ring among linear chains: Structural and dynamic heterogeneity

    NASA Astrophysics Data System (ADS)

    Yang, Yong-Biao; Sun, Zhao-Yan; Fu, Cui-Liu; An, Li-Jia; Wang, Zhen-Gang

    2010-08-01

    We perform lattice Monte Carlo simulation using the bond-fluctuation model to examine the conformation and dynamic properties of a single small flexible ring polymer in the matrix of linear chains as functions of the degree of polymerization of the linear chains. The average conformation properties as gauged by the mean-square radius of gyration and asphericity parameter are insensitive to the chain length for all the chain lengths examined (30, 100, 300, and 1000). However, in the longer chain (300 and 1000) samples, there is an increased spread in the distribution of the value of these quantities, suggesting structural heterogeneity. The center-of-mass diffusion of the ring shows a rapid decrease with increasing chain length followed by a more gradual change for the two longer chain systems. In these longer chain systems, a wide spread in the value of the apparent self-diffusion coefficient is also observed, as well as qualitatively different square displacement trajectories among the different samples, suggesting heterogeneity in the dynamics. A primitive path analysis reveals that in these long chain systems, the ring can exist in topologically distinct states with respect to threading by the linear chains. Threading by the linear chain can dramatically slow down and in some cases stall the diffusive motion of the ring. We argue that the life times for these topological conformers can be longer than the disentanglement time of the linear chain matrix, so that the ring exhibits nonergodic behavior on time scales less or comparable to the life time of these conformers. Our results suggest a picture of the ring diffusion as one where the diffusion path consists of distinctive segments, each corresponding to a different conformer, with slow interconversion between the different conformers.

  15. Bent three-{alpha} linear-chain structure of {sup 13}C

    SciTech Connect

    Furutachi, N.; Kimura, M.

    2011-02-15

    The stability of the three-{alpha} linear-chain structure of {sup 13}C has been investigated with a microscopic 3{alpha}+n model. We have found two excited rotational bands that have developed a three-{alpha} cluster structure in {sup 13}C. The lower band built on 3/2{sub 2}{sup -} state at 11.4 MeV has the bent three-{alpha} linear-chain structure, and this structure is stable against the bending motion of three-{alpha} clusters.

  16. Quantitation and structures of oligosaccharide chains in human trachea mucin glycoproteins.

    PubMed

    Sangadala, S; Bhat, U R; Mendicino, J

    1992-12-02

    Human respiratory mucin glycoproteins from patients with cystic fibrosis were purified and oligosaccharide chains were released by treatment with alkaline borohydride. A neutral oligosaccharide alditol fraction was isolated from mucin obtained from a patient with A blood group determinant by chromatography on DEAE-cellulose and individual oligosaccharide chains were then isolated by gel filtration on BioGel P-6 columns and high performance liquid chromatography with gradient and isocratic solvent systems. The structures of the purified oligosaccharides were determined by methylation analysis, sequential glycosidase digestion and 'H-NMR spectroscopy. The amount of each chain was determined by compositional analysis. A wide array of discrete branched oligosaccharide structures that contain from 3 to 22 sugar residues were found. Many of the oligosaccharides are related and appear to be precursors of larger chains. The predominant branched oligosaccharides which accumulate contain terminal blood group H (Fuc alpha 2Ga1 beta 4) or blood group A (Fuc alpha 2(Ga1NAc alpha 3) (Ga1 beta 4) determinants which stop further branching and chain elongation. The elongation of oligosaccharide chains in respiratory mucins occurs on the beta 3-linked G1cNAc at branch points, whereas the beta 6-linked G1cNAc residue ultimately forms short side chains with a Fuc alpha 2(Ga1NAc alpha 3) Ga1 beta 4 G1cNAc beta 6 structure in individuals with A blood group determinant. The results obtained in the current studies further suggest that even higher molecular weight oligosaccharide chains with analogous branched structures are present in some human respiratory mucin glycoproteins. Increasing numbers of the repeating sequence shown in the oligosaccharide below is present in the higher molecular weight chains. [formula: see text] This data in conjunction with our earlier observations on the extensive branching of these oligosaccharide chains helps to define and explain the enormous range of

  17. Prediction of the secondary structure of myosin light chains from comparison of homologous sequences. Implications for the interaction between myosin heavy and light chains.

    PubMed

    Béchet, J J; Houadjeto, M

    1989-07-06

    The primary sequences of seventeen essential and seventeen regulatory myosin light chains were analyzed and compared, using algorithms based on the different structural properties of their amino acid residues. This process allowed estimation of the structural homology between the proteins studied, and improved the prediction of their mean secondary structure and functionally important segments or residues. On the basis of the crystal structure of troponin C, a model of the myosin essential light chain with a fairly compact form is proposed. The possible sites of interaction between myosin light and heavy chains from rabbit skeletal muscle were also investigated by a complementarity method adapted to helix-rich proteins. Segments 139-149 and 65-75 in the essential light chain and segments 27-37, 67-77 and 97-107 in the regulatory light chain are suggested to constitute some of these sites, as most of them were found to have the features of surface-seeking helices.

  18. Structural requirement of the regulatory light chain of smooth muscle myosin as a substrate for myosin light chain kinase.

    PubMed

    Ikebe, M; Reardon, S; Schwonek, J P; Sanders, C R; Ikebe, R

    1994-11-11

    The substrate structure required for skeletal and smooth muscle myosin light chain kinases (MLC kinase) was studied by using various mutant regulatory light chains of smooth muscle myosin. The deletion of the NH2-terminal 10 residues did not greatly affect the kinetic parameters of smooth MLC kinase; however, deletion of an additional 3 residues, Lys11-Arg13, prevented phosphorylation. In contrast, deletion of Lys11-Arg13 did not completely abolish the phosphorylation for skeletal MLC kinase, and deletion of three additional residues was required for complete inhibition. Substitution of Arg16 with Glu markedly decreased Vmax for both smooth and skeletal MLC kinases. Substitution of Lys11-Arg13 with acidic or noncharged residues decreased Vmax, but these changes were much lower than that occurring on substitution of Arg16. Replacement of Lys11-Arg13 with acidic residues reduced the affinity of the free LC20 but had little effect on the myosin-incorporated LC20. These results were different from those previously obtained with synthetic peptide analogs (Kemp, B. E., Pearson, R. B., and House, C. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 7471-7475) and suggest that a cluster of the basic amino acid residues are not fundamentally important for substrate recognition. The structural simulation revealed that the guanidyl group of Arg16 but not the corresponding Glu13 of skeletal light chain resides in close proximity to Ser19, suggesting that the guanidyl group of Arg16 stabilizes the phosphate transfer and that the introduction of Glu at the 16th position would significantly destabilized this reaction.

  19. Discrete hexamer water clusters and 2D water layer trapped in three luminescent Ag/tetramethylpyrazine/benzene-dicarboxylate hosts: 1D chain, 2D layer and 3D network

    NASA Astrophysics Data System (ADS)

    Mei, Hong-Xin; Zhang, Ting; Huang, Hua-Qi; Huang, Rong-Bin; Zheng, Lan-Sun

    2016-03-01

    Three mix-ligand Ag(I) coordination compounds, namely, {[Ag10(tpyz) 5(L1) 5(H2 O)2].(H2 O)4}n (1, tpyz = 2,3,4,5-tetramethylpyrazine, H2 L1 = phthalic acid), [Ag4(tpyz) 2(L2) 2(H2 O)].(H2 O)5}n (2, H2 L2 = isophthalic acid) {[Ag2(tpyz) 2(L3) (H2 O)4].(H2 O)8}n (3, H2 L3 = terephthalic acid), have been synthesized and characterized by elemental analysis, IR, PXRD and X-ray single-crystal diffraction. 1 exhibits a 2D layer which can be simplified as a (4,4) net. 2 is a 3D network which can be simplified as a (3,3)-connected 2-nodal net with a point symbol of {102.12}{102}. 3 consists of linear [Ag(tpyz) (H2 O)2]n chain. Of particular interest, discrete hexamer water clusters were observed in 1 and 2, while a 2D L10(6) water layer exists in 3. The results suggest that the benzene dicarboxylates play pivotal roles in the formation of the different host architectures as well as different water aggregations. Moreover, thermogravimetric analysis (TGA) and emissive behaviors of these compounds were investigated.

  20. Structural and optical properties of self-assembled chains of plasmonic nanocubes

    SciTech Connect

    Klinkova, Anna; Gang, Oleg; Therien-Aubin, Heloise; Ahmed, Aftab; Nykypanchuk, Dmytro; Choueiri, Rachelle M.; Gagnon, Brandon; Muntyanu, Anastasiya; Walker, Gilbert C.; Kumacheva, Eugenia

    2014-10-10

    Solution-based linear self-assembly of metal nanoparticles offers a powerful strategy for creating plasmonic polymers, which, so far, have been formed from spherical nanoparticles and nanorods. Here, we report linear solution-based self-assembly of metal nanocubes (NCs), examine the structural characteristics of the NC chains and demonstrate their advanced optical characteristics. Predominant face-to-face assembly of large NCs coated with short polymer ligands led to a larger volume of hot spots in the chains, a nearly uniform E-field enhancement in the gaps between co-linear NCs and a new coupling mode for NC chains, in comparison with chains of nanospheres with similar dimensions, composition and surface chemistry. The NC chains exhibited a stronger surface enhanced Raman scattering (SERS) signal, in comparison with linear assemblies of nanospheres. The experimental results were in agreement with finite difference time domain (FDTD) simulations.

  1. Structural and optical properties of self-assembled chains of plasmonic nanocubes

    DOE PAGES

    Klinkova, Anna; Gang, Oleg; Therien-Aubin, Heloise; ...

    2014-10-10

    Solution-based linear self-assembly of metal nanoparticles offers a powerful strategy for creating plasmonic polymers, which, so far, have been formed from spherical nanoparticles and nanorods. Here, we report linear solution-based self-assembly of metal nanocubes (NCs), examine the structural characteristics of the NC chains and demonstrate their advanced optical characteristics. Predominant face-to-face assembly of large NCs coated with short polymer ligands led to a larger volume of hot spots in the chains, a nearly uniform E-field enhancement in the gaps between co-linear NCs and a new coupling mode for NC chains, in comparison with chains of nanospheres with similar dimensions, compositionmore » and surface chemistry. The NC chains exhibited a stronger surface enhanced Raman scattering (SERS) signal, in comparison with linear assemblies of nanospheres. The experimental results were in agreement with finite difference time domain (FDTD) simulations.« less

  2. [Study of the antigenic structure of human immunoglobulin lambda-chain using monoclonal antibodies].

    PubMed

    Arsen'eva, E L; Bogacheva, G T; Solomon, A; Weiss, D; Ibragimov, A R; Rokhlin, O V

    1990-01-01

    Nine monoclonals against human Ig lambda chains were produced, 4 antibodies react with C-domain, 5--with V-domain of the lambda chain. Anti-C lambda domain antibodies recognize not less than 3 epitopes and one of them is expressed only on the isolated chain. Anti-V lambda antibodies bind both isolated lambda chain and intact IgG, IgM, IgA. Four epitopes are expressed by few lambda Bence Jones proteins of the III subgroup, the immunogen possessing the same isotype. The 4 mentioned epitopes represent private idiotypic determinants. The epitope 3E10 is characteristic of 50% Bence Jones proteins of the II and III V lambda-subgroups thus representing a common idiotypic determinant. Using anti-V lambda antibodies germ line variability of V lambda III proteins was analysed and the similarity of antigenic structure of normal and myeloma human Ig lambda chains was demonstrated.

  3. Probing atomic structure and Majorana wavefunctions in mono-atomic Fe chains on superconducting Pb surface

    NASA Astrophysics Data System (ADS)

    Pawlak, Rémy; Kisiel, Marcin; Klinovaja, Jelena; Meier, Tobias; Kawai, Shigeki; Glatzel, Thilo; Loss, Daniel; Meyer, Ernst

    2016-11-01

    Motivated by the striking promise of quantum computation, Majorana bound states (MBSs) in solid-state systems have attracted wide attention in recent years. In particular, the wavefunction localisation of MBSs is a key feature and is crucial for their future implementation as qubits. Here we investigate the spatial and electronic characteristics of topological superconducting chains of iron atoms on the surface of Pb(110) by combining scanning tunnelling microscopy and atomic force microscopy. We demonstrate that the Fe chains are mono-atomic, structured in a linear manner and exhibit zero-bias conductance peaks at their ends, which we interpret as signature for a MBS. Spatially resolved conductance maps of the atomic chains reveal that the MBSs are well localised at the chain ends (≲25 nm), with two localisation lengths as predicted by theory. Our observation lends strong support to use MBSs in Fe chains as qubits for quantum-computing devices.

  4. Magnetic properties of cubic FeCo nanoparticles with anisotropic long chain structure

    NASA Astrophysics Data System (ADS)

    Liu, Jinming; Wu, Kai; Wang, Jian-Ping

    2016-05-01

    Cubic FeCo alloy nanoparticles (NPs) with body-centered cubic (bcc) phase were prepared using sputter based gas-condensation method. When the NPs formed long chain assemblies, the magnetic properties were quite different from that of well-dispersed NPs. Most of the well-dispersed NPs were superparamagnetic at room temperature while the long chain NP assemblies were ferromagnetic with coercivities around 765 Oe, which displayed quite different magnetic properties. The ferromagnetism of long chain NPs was from the exchange coupling between NPs, which eventually led to the transition from superparamagnetism (SPM) to superferromagetism (SFM). Zero-field-cooled (ZFC) and field-cooled (FC) curves were obtained and long chain NP assemblies displayed ferromagnetism at the temperature ranging from 10 K to 400 K. Time-dependent remanent magnetic moment curves also indicated that the long chain structure had better thermal stability due to the strong exchange coupling.

  5. Primary structure of chicken cardiac myosin S-1 heavy chain.

    PubMed

    Nakayama, S; Tanaka, H; Yajima, E; Maita, T

    1994-05-01

    The sequence of the NH2-terminal 830 amino acid residues of chicken cardiac ventricular muscle myosin subfragment-1 (S-1) was determined. S-1 was obtained by limited chymotryptic digestion, and cleaved into three characteristics fragments (23, 41, and 22 kDa fragments) by limited tryptic digestion. These fragments were isolated by gel filtration on a Sephadex G-100 column, followed by cation-exchange chromatography on a CM-52 column and reverse-phase HPLC. The isolated fragments were sequenced completely. Peptides overlapping the 23 and 41 kDa fragments and also overlapping the 41 and 22 kDa fragments were obtained by cleaving S-1 with cyanogen bromide, and sequenced completely. We also obtained a minor fragment, the 20 kDa fragment, in addition to the three characteristic fragments. Amino acid compositions of the cyanogen bromide peptides of the 20 kDa fragment indicated that a portion of S-1 heavy chains had lost their COOH-terminal 21 residues during limited tryptic digestion. Methylated amino acid residues were found at four positions: epsilon-N-monomethyllysine at position 32, epsilon-N-trimethyllysine residues at 127 and 549, and 3-N-methylhistidine at 754.

  6. Validation of optimization strategies using the linear structured production chains

    NASA Astrophysics Data System (ADS)

    Kusiak, Jan; Morkisz, Paweł; Oprocha, Piotr; Pietrucha, Wojciech; Sztangret, Łukasz

    2017-06-01

    Different optimization strategies applied to sequence of several stages of production chains were validated in this paper. Two benchmark problems described by ordinary differential equations (ODEs) were considered. A water tank and a passive CR-RC filter were used as the exemplary objects described by the first and the second order differential equations, respectively. Considered in the work optimization problems serve as the validators of strategies elaborated by the Authors. However, the main goal of research is selection of the best strategy for optimization of two real metallurgical processes which will be investigated in an on-going projects. The first problem will be the oxidizing roasting process of zinc sulphide concentrate where the sulphur from the input concentrate should be eliminated and the minimal concentration of sulphide sulphur in the roasted products has to be achieved. Second problem will be the lead refining process consisting of three stages: roasting to the oxide, oxide reduction to metal and the oxidizing refining. Strategies, which appear the most effective in considered benchmark problems will be candidates for optimization of the mentioned above industrial processes.

  7. Glass-based 1-D dielectric microcavities

    NASA Astrophysics Data System (ADS)

    Chiasera, Alessandro; Scotognella, Francesco; Valligatla, Sreeramulu; Varas, Stefano; Jasieniak, Jacek; Criante, Luigino; Lukowiak, Anna; Ristic, Davor; Gonçalves, Rogeria Rocha; Taccheo, Stefano; Ivanda, Mile; Righini, Giancarlo C.; Ramponi, Roberta; Martucci, Alessandro; Ferrari, Maurizio

    2016-11-01

    We have developed a reliable RF sputtering techniques allowing to fabricate glass-based one dimensional microcavities, with high quality factor. This property is strongly related to the modification of the density of states due to the confinement of the gain medium in a photonic band gap structure. In this short review we present some of the more recent results obtained by our team exploiting these 1D microcavities. In particular we present: (1) Er3+ luminescence enhancement of the 4I13/2 → 4I15/2 transition; (2) broad band filters based on disordered 1-D photonic structures; (3) threshold defect-mode lasing action in a hybrid structure.

  8. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions.

    PubMed

    Spassov, Velin Z; Yan, Lisa; Flook, Paul K

    2007-03-01

    The basic differences between the 20 natural amino acid residues are due to differences in their side-chain structures. This characteristic design of protein building blocks implies that side-chain-side-chain interactions play an important, even dominant role in 3D-structural realization of amino acid codes. Here we present the results of a comparative analysis of the contributions of side-chain-side-chain (s-s) and side-chain-backbone (s-b) interactions to the stabilization of folded protein structures within the framework of the CHARMm molecular data model. Contrary to intuition, our results suggest that side-chain-backbone interactions play the major role in side-chain packing, in stabilizing the folded structures, and in differentiating the folded structures from the unfolded or misfolded structures, while the interactions between side chains have a secondary effect. An additional analysis of electrostatic energies suggests that combinatorial dominance of the interactions between opposite charges makes the electrostatic interactions act as an unspecific folding force that stabilizes not only native structure, but also compact random conformations. This observation is in agreement with experimental findings that, in the denatured state, the charge-charge interactions stabilize more compact conformations. Taking advantage of the dominant role of side-chain-backbone interactions in side-chain packing to reduce the combinatorial problem, we developed a new algorithm, ChiRotor, for rapid prediction of side-chain conformations. We present the results of a validation study of the method based on a set of high resolution X-ray structures.

  9. Solution structure of a small protein containing a fluorinated side chain in the core

    PubMed Central

    Cornilescu, Gabriel; Hadley, Erik B.; Woll, Matthew G.; Markley, John L.; Gellman, Samuel H.; Cornilescu, Claudia C.

    2007-01-01

    We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe → F5-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe → F5-Phe mutations are interesting because aryl–perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl–aryl or perfluoroaryl–perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 → F5-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by ∼1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe → F5-Phe mutations offer the possibility of greater tertiary structural stability from side chain–side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability. PMID:17123960

  10. Self-Organized Growth, Structure, and Magnetism of Monatomic Transition-Metal Oxide Chains

    NASA Astrophysics Data System (ADS)

    Ferstl, Pascal; Hammer, Lutz; Sobel, Christopher; Gubo, Matthias; Heinz, Klaus; Schneider, M. Alexander; Mittendorfer, Florian; Redinger, Josef

    2016-07-01

    We report on the self-organized growth of monatomic transition-metal oxide chains of (3 ×1 ) periodicity and unusual M O2 stoichiometry (M =Ni , Co, Fe, Mn) on Ir(100). We analyze their structural and magnetic properties by means of quantitative LEED, STM, and density functional theory (DFT) calculations. LEED analyses reveal a fascinating common atomic structure in which the transition-metal atoms sit above a missing-row structure of the surface and are coupled to the substrate only via oxygen atoms. This structure is confirmed by DFT calculations with structural parameters deviating by less than 1.7 pm. The DFT calculations predict that the NiO2 chains are nonmagnetic, CoO2 chains are ferromagnetic, while FeO2 and MnO2 are antiferromagnetic. All structures show only weak magnetic interchain coupling. Further, we demonstrate the growth of oxide chains of binary alloys of Co and Ni or Fe on Ir(100), which allows us to produce well-controlled ensembles of ferromagnetic chains of different lengths separated by nonmagnetic or antiferromagnetic segments.

  11. Fabrication and investigation of 1D and 2D structures in LiNbO 3 thin films by pulsed laser ablation

    NASA Astrophysics Data System (ADS)

    Meriche, F.; Boudrioua, A.; Kremer, R.; Dogheche, E.; Neiss-Clauss, E.; Mouras, R.; Fischer, A.; Beghoul, M.-R.; Fogarassy, E.; Boutaoui, N.

    2010-09-01

    Lithium niobate thin films were deposited on sapphire substrate by radio-frequency magnetron sputtering technique. One and two dimensional structures have been made using a KrF excimer laser at 248 nm and 6 ns pulse width, under various conditions of ablation, in order to assess the applicability of laser direct-writing of photonic waveguides. The optical and waveguiding properties of LiNbO 3 thin films were studied by prism-coupling technique, while micro-Raman spectroscopy was used for structural and composition characterization, as well as laser processing mechanism investigation. The surface morphology of the processed structures was obtained by a Nomarski optical microscope, an atomic force microscope and a White Light Interferometer Microscope.

  12. Crystal structure of Vδ1 T cell receptor in complex with CD1d-sulfatide shows MHC-like recognition of a self-lipid by human γδ T cells.

    PubMed

    Luoma, Adrienne M; Castro, Caitlin D; Mayassi, Toufic; Bembinster, Leslie A; Bai, Li; Picard, Damien; Anderson, Brian; Scharf, Louise; Kung, Jennifer E; Sibener, Leah V; Savage, Paul B; Jabri, Bana; Bendelac, Albert; Adams, Erin J

    2013-12-12

    The nature of the antigens recognized by γδ T cells and their potential recognition of major histocompatibility complex (MHC)-like molecules has remained unclear. Members of the CD1 family of lipid-presenting molecules are suggested ligands for Vδ1 TCR-expressing γδ T cells, the major γδ lymphocyte population in epithelial tissues. We crystallized a Vδ1 TCR in complex with CD1d and the self-lipid sulfatide, revealing the unusual recognition of CD1d by germline Vδ1 residues spanning all complementarity-determining region (CDR) loops, as well as sulfatide recognition separately encoded by nongermline CDR3δ residues. Binding and functional analysis showed that CD1d presenting self-lipids, including sulfatide, was widely recognized by gut Vδ1+ γδ T cells. These findings provide structural demonstration of MHC-like recognition of a self-lipid by γδ T cells and reveal the prevalence of lipid recognition by innate-like T cell populations. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Self-similar spectral structures and edge-locking hierarchy in open-boundary spin chains

    SciTech Connect

    Haque, Masudul

    2010-07-15

    For an anisotropic Heisenberg (XXZ) spin chain, we show that an open boundary induces a series of approximately self-similar features at different energy scales, high up in the eigenvalue spectrum. We present a nonequilibrium phenomenon related to this fractal structure, involving states in which a connected block near the edge is polarized oppositely to the rest of the chain. We show that such oppositely polarized blocks can be 'locked' to the edge of the spin chain and that there is a hierarchy of edge-locking effects at various orders of the anisotropy. The phenomenon enables dramatic control of quantum-state transmission and magnetization control.

  14. Side chain fluorination and anion effect on the structure of 1-butyl-3-methylimidazolium ionic liquids

    NASA Astrophysics Data System (ADS)

    Weber, Henry; Hollóczki, Oldamur; Pensado, Alfonso S.; Kirchner, Barbara

    2013-08-01

    We present a comprehensive molecular dynamics simulation study on 1-butyl-3-methylimidazolium ionic liquids and their fluorinated analogs. The work focused on the effect of fluorination at varying anions. The main findings are that the fluorination of the cations side chain increases overall structuring, especially the aggregation of cation side chain. Furthermore, large and weakly coordinating anions tend to occupy on-top positions of the cation and decrease the aggregation of cation side chains, most likely due to enhanced alkyl-anion interaction.

  15. An Innovative Supply Chain Management Programme Structure: Broadening the SCM Skill Set

    ERIC Educational Resources Information Center

    Okongwu, Uche

    2007-01-01

    This paper proposes a matrix structure for training Supply Chain Management (SCM) professionals. It is an innovative programme structure that combines two approaches: cross-border and inter-organisational. It enables the students to comprehend complex and specific business environments and to understand the diverse nature of SCM systems in both…

  16. Bone marrow lambda-type light chain crystalline structures associated with multiple myeloma.

    PubMed

    Schvartz, H; Bonhomme, P; Caulet, S; Beorchia, A; Patey, M; Caulet, T

    1985-01-01

    A 58-year-old man showed bone marrow crystalline structures associated with a lambda light chain producing multiple myeloma. Analysis and processing of electron images clearly displayed the periodic structure of the crystals. Immunochemistry suggested that they contained the whole or a fragmented constant portion of immunoglobulin.

  17. An Innovative Supply Chain Management Programme Structure: Broadening the SCM Skill Set

    ERIC Educational Resources Information Center

    Okongwu, Uche

    2007-01-01

    This paper proposes a matrix structure for training Supply Chain Management (SCM) professionals. It is an innovative programme structure that combines two approaches: cross-border and inter-organisational. It enables the students to comprehend complex and specific business environments and to understand the diverse nature of SCM systems in both…

  18. Synthesis, Structure, and Magnetic Properties of A2Cu5(TeO3)(SO4)3(OH)4 (A = Na, K): The First Compounds with a 1D Kagomé Strip Lattice.

    PubMed

    Tang, Yingying; Guo, Wenbin; Xiang, Hongping; Zhang, Suyun; Yang, Ming; Cui, Meiyan; Wang, Nannan; He, Zhangzhen

    2016-01-19

    Two new tellurite-sulfates A2Cu5(TeO3)(SO4)3(OH)4 (A = Na, K) have been synthesized by a conventional hydrothermal method. Both compounds feature 1D kagomé strip structure built by distorted CuO6 octahedra, which can be regarded as the dimensional reduction of kagomé lattice. Magnetic measurements confirmed that the titled compounds possess antiferromagnetic ordering at low temperature, while a field-induced magnetic transition can be observed at critical field. To the best of our knowledge, this is the first time to obtain distorted kagomé strip compounds.

  19. Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

    PubMed Central

    Grechko, Maksim; Zanni, Martin T.

    2012-01-01

    Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I′ band of a polypeptide in its random coil and α-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or α-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D2, which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an α-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D2. When taking into account the angle of the amide I′ transition dipole vector with respect to the helix axis, our measurements indicate that the amide I′ vibrational mode is delocalized across a minimum of 3.5 residues in an α-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine. PMID:23163364

  20. Crystal Structures of T Cell Receptor (Beta) Chains Related to Rheumatoid Arthritis

    SciTech Connect

    Li,H.; van Vranken, S.; Zhao, Y.; Li, Z.; Guo, Y.; Eisele, L.; Li, Y.

    2005-01-01

    The crystal structures of the V{beta}17+ {beta} chains of two human T cell receptors (TCRs), originally derived from the synovial fluid (SF4) and tissue (C5-1) of a patient with rheumatoid arthritis (RA), have been determined in native (SF4) and mutant (C5-1{sub F104{yields}Y/C187{yields}S}) forms, respectively. These TCR {beta} chains form homo-dimers in solution and in crystals. Structural comparison reveals that the main-chain conformations in the CDR regions of the C5-1 and SF4 V{beta}17 closely resemble those of a V{beta}17 JM22 in a bound form; however, the CDR3 region shows different conformations among these three V{beta}17 structures. At the side-chain level, conformational differences were observed at the CDR2 regions between our two ligand-free forms and the bound JM22 form. Other significant differences were observed at the V{beta} regions 8-12, 40-44, and 82-88 between C5-1/SF4 and JM22 V{beta}17, implying that there is considerable variability in the structures of very similar {beta} chains. Structural alignments also reveal a considerable variation in the V{beta}-C{beta} associations, and this may affect ligand recognition. The crystal structures also provide insights into the structure basis of T cell recognition of Mycoplasma arthritidis mitogen (MAM), a superantigen that may be implicated in the development of human RA. Structural comparisons of the V{beta} domains of known TCR structures indicate that there are significant similarities among V{beta} regions that are MAM-reactive, whereas there appear to be significant structural differences among those V{beta} regions that lack MAM-reactivity. It further reveals that CDR2 and framework region (FR) 3 are likely to account for the binding of TCR to MAM.

  1. Structural determination of prunusins A and B, new C-alkylated flavonoids from Prunus domestica, by 1D and 2D NMR spectroscopy.

    PubMed

    Mahmood, Azhar; Fatima, Itrat; Kosar, Shaheen; Ahmed, Rehana; Malik, Abdul

    2010-02-01

    Prunusins A (1) and B (2), the new C-alkylated flavonoids, have been isolated from the seed kernels of Prunus domestica. Their structures were assigned from (1)H and (13)C nuclear magnetic resonating spectra, DEPT and by correlation spectroscopy, HMQC and HMBC experiments. 3, 5, 7, 4'-Tetrahydroxyflavone (3) and 3, 5, 7-trihydroxy-8, 4'-dimethoxyflavone (4) have also been reported from this species. Both compounds (1) and (2) showed significant antifungal activity against pathogenic fungus Trichophyton simmi. Copyright 2009 John Wiley & Sons, Ltd.

  2. Phase Behavior of a Single Structured Ionomer Chain in Solution

    SciTech Connect

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; Grest, Gary S.

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. In hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.

  3. Phase Behavior of a Single Structured Ionomer Chain in Solution

    DOE PAGES

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; ...

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. Inmore » hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.« less

  4. Harnessing graphical structure in Markov chain Monte Carlo learning

    SciTech Connect

    Stolorz, P.E.; Chew P.C.

    1996-12-31

    The Monte Carlo method is recognized as a useful tool in learning and probabilistic inference methods common to many datamining problems. Generalized Hidden Markov Models and Bayes nets are especially popular applications. However, the presence of multiple modes in many relevant integrands and summands often renders the method slow and cumbersome. Recent mean field alternatives designed to speed things up have been inspired by experience gleaned from physics. The current work adopts an approach very similar to this in spirit, but focusses instead upon dynamic programming notions as a basis for producing systematic Monte Carlo improvements. The idea is to approximate a given model by a dynamic programming-style decomposition, which then forms a scaffold upon which to build successively more accurate Monte Carlo approximations. Dynamic programming ideas alone fail to account for non-local structure, while standard Monte Carlo methods essentially ignore all structure. However, suitably-crafted hybrids can successfully exploit the strengths of each method, resulting in algorithms that combine speed with accuracy. The approach relies on the presence of significant {open_quotes}local{close_quotes} information in the problem at hand. This turns out to be a plausible assumption for many important applications. Example calculations are presented, and the overall strengths and weaknesses of the approach are discussed.

  5. Control globular structure formation of a copolymer chain through inverse design.

    PubMed

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-14

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design.

  6. Control globular structure formation of a copolymer chain through inverse design

    NASA Astrophysics Data System (ADS)

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-01

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design.

  7. Carbohydrate Conformation and Lipid Condensation in Monolayers Containing Glycosphingolipid Gb3: Influence of Acyl Chain Structure

    PubMed Central

    Watkins, Erik B.; Gao, Haifei; Dennison, Andrew J.C.; Chopin, Nathalie; Struth, Bernd; Arnold, Thomas; Florent, Jean-Claude; Johannes, Ludger

    2014-01-01

    Globotriaosylceramide (Gb3), a glycosphingolipid found in the plasma membrane of animal cells, is the endocytic receptor of the bacterial Shiga toxin. Using x-ray reflectivity (XR) and grazing incidence x-ray diffraction (GIXD), lipid monolayers containing Gb3 were investigated at the air-water interface. XR probed Gb3 carbohydrate conformation normal to the interface, whereas GIXD precisely characterized Gb3’s influence on acyl chain in-plane packing and area per molecule (APM). Two phospholipids, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), were used to study Gb3 packing in different lipid environments. Furthermore, the impact on monolayer structure of a naturally extracted Gb3 mixture was compared to synthetic Gb3 species with uniquely defined acyl chain structures. XR results showed that lipid environment and Gb3 acyl chain structure impact carbohydrate conformation with greater solvent accessibility observed for smaller phospholipid headgroups and long Gb3 acyl chains. In general, GIXD showed that Gb3 condensed phospholipid packing resulting in smaller APM than predicted by ideal mixing. Gb3’s capacity to condense APM was larger for DSPC monolayers and exhibited different dependencies on acyl chain structure depending on the lipid environment. The interplay between Gb3-induced changes in lipid packing and the lipid environment’s impact on carbohydrate conformation has broad implications for glycosphingolipid macromolecule recognition and ligand binding. PMID:25185550

  8. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    PubMed

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  9. Helix-like structure formation of a semi-flexible chain confined in a cylinder channel

    NASA Astrophysics Data System (ADS)

    Wen, Xiaohui; Sun, Tieyu; Zhang, Wei-Bing; Lam, Chi-Hang; Zhang, Linxi; Zang, Huaping

    2016-09-01

    Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel. A novel helix-like structure is found to form during the simulation. Moreover, the detailed characteristic parameters and formation probability of these helix-like structures under moderate conditions are investigated. We find that the structure is not a perfect helix, but a bundle of elliptical turns. In addition, we conduct a statistical analysis for the chain monomer distribution along the radial direction. This research contributes to our understanding of the microscopic conformation of polymer chains in confined environments filled with a solvent. Project supported by the National Natural Science Foundation of China (Grant Nos. 11504033 and 11404290) and the General Research Fund of Hong Kong Research Council of China (Grant No. 15301014).

  10. Structure and Active Stie Residues of Pg1D, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter jejuni

    SciTech Connect

    Rangarajan,E.; Ruane, K.; Sulea, T.; Watson, D.; Proteau, A.; Leclerc, S.; Cygler, M.; Matte, A.; Young, N.

    2008-01-01

    Campylobacter jejuni is highly unusual among bacteria in forming N-linked glycoproteins. The heptasaccharide produced by its pgl system is attached to protein Asn through its terminal 2, 4-diacetamido-2, 4,6-trideoxy-d-Glc (QuiNAc4NAc or N, N'-diacetylbacillosamine) moiety. The crucial, last part of this sugar's synthesis is the acetylation of UDP-2-acetamido-4-amino-2, 4,6-trideoxy-d-Glc by the enzyme PglD, with acetyl-CoA as a cosubstrate. We have determined the crystal structures of PglD in CoA-bound and unbound forms, refined to 1.8 and 1.75 Angstroms resolution, respectively. PglD is a trimer of subunits each comprised of two domains, an N-terminal {alpha}/{beta}-domain and a C-terminal left-handed {beta}-helix. Few structural differences accompany CoA binding, except in the C-terminal region following the {beta}-helix (residues 189-195), which adopts an extended structure in the unbound form and folds to extend the {beta}-helix upon binding CoA. Computational molecular docking suggests a different mode of nucleotide-sugar binding with respect to the acetyl-CoA donor, with the molecules arranged in an 'L-shape', compared with the 'in-line' orientation in related enzymes. Modeling indicates that the oxyanion intermediate would be stabilized by the NH group of Gly143', with His125' the most likely residue to function as a general base, removing H+ from the amino group prior to nucleophilic attack at the carbonyl carbon of acetyl-CoA. Site-specific mutations of active site residues confirmed the importance of His125', Glu124', and Asn118. We conclude that Asn118 exerts its function by stabilizing the intricate hydrogen bonding network within the active site and that Glu124' may function to increase the pKa of the putative general base, His125'.

  11. A structural ensemble of a ribosome-nascent chain complex during cotranslational protein folding.

    PubMed

    Cabrita, Lisa D; Cassaignau, AnaÏs M E; Launay, Helene M M; Waudby, Christopher A; Wlodarski, Tomasz; Camilloni, Carlo; Karyadi, Maria-Evangelia; Robertson, Amy L; Wang, Xiaolin; Wentink, Anne S; Goodsell, Luke; Woolhead, Cheryl A; Vendruscolo, Michele; Dobson, Christopher M; Christodoulou, John

    2016-04-01

    Although detailed pictures of ribosome structures are emerging, little is known about the structural and cotranslational folding properties of nascent polypeptide chains at the atomic level. Here we used solution-state NMR spectroscopy to define a structural ensemble of a ribosome-nascent chain complex (RNC) formed during protein biosynthesis in Escherichia coli, in which a pair of immunoglobulin-like domains adopts a folded N-terminal domain (FLN5) and a disordered but compact C-terminal domain (FLN6). To study how FLN5 acquires its native structure cotranslationally, we progressively shortened the RNC constructs. We found that the ribosome modulates the folding process, because the complete sequence of FLN5 emerged well beyond the tunnel before acquiring native structure, whereas FLN5 in isolation folded spontaneously, even when truncated. This finding suggests that regulating structure acquisition during biosynthesis can reduce the probability of misfolding, particularly of homologous domains.

  12. Design, synthesis, evaluation, and structure of vitamin D analogues with furan side chains.

    PubMed

    Fraga, Ramón; Zacconi, Flavia; Sussman, Fredy; Ordóñez-Morán, Paloma; Muñoz, Alberto; Huet, Tiphaine; Molnár, Ferdinand; Moras, Dino; Rochel, Natacha; Maestro, Miguel; Mouriño, Antonio

    2012-01-09

    Based on the crystal structures of human vitamin D receptor (hVDR) bound to 1α,25-dihydroxy-vitamin D(3) (1,25 D) and superagonist ligands, we previously designed new superagonist ligands with a tetrahydrofuran ring at the side chain that optimize the aliphatic side-chain conformation through an entropy benefit. Following a similar strategy, four novel vitamin D analogues with aromatic furan side chains (3a, 3b, 4a, 4b) have now been developed. The triene system has been constructed by an efficient stereoselective intramolecular cyclization of an enol triflate (A-ring precursor) followed by a Suzuki-Miyaura coupling of the resulting intermediate with an alkenyl boronic ester (CD-side chain, upper fragment). The furan side chains have been constructed by gold chemistry. These analogues exhibit significant pro-differentiation effects and transactivation potency. The crystal structure of 3a in a complex with the ligand-binding domain of hVDR revealed that the side-chain furanic ring adopts two conformations.

  13. Demonstration of structural polymorphism among MB3 light chains by two-dimensional gel electrophoresis.

    PubMed

    Ishikawa, N; Kasahara, M; Ikeda, H; Ogasawara, K; Hawkin, S; Takenouchi, T; Wakisaka, A; Kikuchi, Y; Aizawa, M

    1985-01-01

    The heavy and light chain subunits of MB3 molecules were isolated from KT2 (DKT2, DR4, MB3 homozygous), ER (Dw4, DR4, MB3 homozygous), JMe (Dw5, DR5, MB3 homozygous), EBV-Sh (DSh, DRw6.2, MB3 homozygous), and EBV-Ky (DKy, DRw9, MB3 homozygous) cells and were compared with one another by two-dimensional gel electrophoresis. The MB3 light chains from KT2, ER, and EBV-Ky cells were clearly different in terms of their isoelectric points, whereas those from ER, JMe, and EBV-Sh cells were indistinguishable. No differences in charge or m.w. were noted for the MB3 heavy chains from the five cell lines. Thus, three out of the five MB3-positive, D/DR-disparate cell lines were found to express structurally distinct MB3 molecules, demonstrating that MB3 is a public serologic specificity shared by at least three structurally distinct MB (human I-A-like) molecules. Because the DR light chain subunits isolated from EBV-Wa, KT2, ER, JMe, EBV-Sh, and EBV-Ky cells differed from one another in their isoelectric points, the DR light chains were apparently more polymorphic than the MB3 light chains.

  14. Isolated Polar Amino Acid Residues Modulate Lipid Binding in the Large Hydrophobic Cavity of CD1d.

    PubMed

    Inuki, Shinsuke; Aiba, Toshihiko; Hirata, Natsumi; Ichihara, Osamu; Yoshidome, Daisuke; Kita, Shunsuke; Maenaka, Katsumi; Fukase, Koichi; Fujimoto, Yukari

    2016-11-18

    The CD1d protein is a nonpolymorphic MHC class I-like protein that controls the activation of natural killer T (NKT) cells through the presentation of self- and foreign-lipid ligands, glycolipids, or phospholipids, leading to the secretion of various cytokines. The CD1d contains a large hydrophobic lipid binding pocket: the A' pocket of CD1d, which recognizes hydrophobic moieties of the ligands, such as long fatty acyl chains. Although lipid-protein interactions typically rely on hydrophobic interactions between lipid chains and the hydrophobic sites of proteins, we showed that the small polar regions located deep inside the hydrophobic A' pocket could be used for the modulation of the lipid binding. A series of the ligands, α-galactosyl ceramide (α-GalCer) derivatives containing polar groups in the acyl chain, was synthesized, and the structure-activity relationship studies demonstrated that simple modification from a methylene to an amide group in the long fatty acyl chain, when introduced at optimal positions, enhanced the CD1d recognition of the glycolipid ligands. Formation of hydrogen bonds between the amide group and the polar residues was supported by molecular dynamics (MD) simulations and WaterMap calculations. The computational studies suggest that localized hydrating water molecules may play an important role in the ligand recognition. Here, the results showed that confined polar residues in the large hydrophobic lipid binding pockets of the proteins could be potential targets to modulate the affinity for its ligands.

  15. Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

    PubMed Central

    Jaeken, Jan W; De Baerdemacker, Stijn; Lejaeghere, Kurt; Van Speybroeck, Veronique

    2014-01-01

    Summary The geometric and electronic structure of the MIL-47(V) metal-organic framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å3. The transition pressure of the pressure-induced large-pore-to-narrow-pore phase transition is calculated to be 82 MPa and 124 MPa for systems with ferromagnetic and antiferromagnetic chains, respectively. For a mixed system, the transition pressure is found to be a weighted average of the ferromagnetic and antiferromagnetic transition pressures. Mapping DFT energies onto a simple-spin Hamiltonian shows both the intra- and inter-chain coupling to be antiferromagnetic, with the latter coupling constant being two orders of magnitude smaller than the former, suggesting the MIL-47(V) to present quasi-1D behavior. The electronic structure of the different spin configurations is investigated and it shows that the band gap position varies strongly with the spin configuration. The valence and conduction bands show a clear V d-character. In addition, these bands are flat in directions orthogonal to VO6 chains, while showing dispersion along the the direction of the VO6 chains, similar as for other quasi-1D materials. PMID:25383285

  16. Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles.

    PubMed

    Vanpoucke, Danny E P; Jaeken, Jan W; De Baerdemacker, Stijn; Lejaeghere, Kurt; Van Speybroeck, Veronique

    2014-01-01

    The geometric and electronic structure of the MIL-47(V) metal-organic framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å(3). The transition pressure of the pressure-induced large-pore-to-narrow-pore phase transition is calculated to be 82 MPa and 124 MPa for systems with ferromagnetic and antiferromagnetic chains, respectively. For a mixed system, the transition pressure is found to be a weighted average of the ferromagnetic and antiferromagnetic transition pressures. Mapping DFT energies onto a simple-spin Hamiltonian shows both the intra- and inter-chain coupling to be antiferromagnetic, with the latter coupling constant being two orders of magnitude smaller than the former, suggesting the MIL-47(V) to present quasi-1D behavior. The electronic structure of the different spin configurations is investigated and it shows that the band gap position varies strongly with the spin configuration. The valence and conduction bands show a clear V d-character. In addition, these bands are flat in directions orthogonal to VO6 chains, while showing dispersion along the the direction of the VO6 chains, similar as for other quasi-1D materials.

  17. Tuning heat transport in trapped-ion chains across a structural phase transition

    NASA Astrophysics Data System (ADS)

    Ruiz, A.; Alonso, D.; Plenio, M. B.; del Campo, A.

    2014-06-01

    We analyze the heat transport in an ion chain that is confined in a strongly anisotropic Paul trap. To drive a heat current across the chain different pairs of counterpropagating laser beams are applied to the ions on the edges. The lasers behave as heat reservoirs operating at different temperatures, and a nonequilibrium heat flow can be sustained. The control of the spatial distribution of the ions in the chain by variation of the trapping frequencies makes ion chains an ideal testbed to study heat transport properties in finite open systems of low dimensionality with tunable nonlinearities. We explore heat transport across a structural phase transition between the linear and zigzag configurations, identifying the condition for optimal heat transport.

  18. Ratchet transport of an active-passive mixture chain in confined structures

    NASA Astrophysics Data System (ADS)

    Lu, Shi-cai; Ou, Ya-li; Ai, Bao-quan

    2017-09-01

    Rectified transport of the active-passive mixture chain is numerically investigated in periodic confined structures. Due to the out-of-equilibrium property of active particles in the chain, the whole chain can be rectified. It is found that the interaction between particles can significantly affect the rectified transport. When all particles in the chain are active, the directed velocity decreases monotonously with increasing the interaction strength. When the particles are mixture, on increasing the interaction strength, the directed velocity firstly decreases to its minimal value, then increases to its maximal value, and finally decreases to zero. In addition, there exist optimal parameters (self-propelled velocity, the natural length of the spring) at which the average velocity is maximal.

  19. A Replica Exchange Molecular Dynamics Simulation of a Single Polyethylene Chain: Temperature Dependence of Structural Properties and Chain Conformational Study at the Equilibrium Melting Temperature.

    PubMed

    Li, Ting; Yang, Xiaozhen; Nies, Erik

    2011-01-11

    The conformational properties of a finite length polyethylene chain were explored over a wide range of temperatures using a replica exchange molecular dynamics simulation providing high quality simulation data representative for the equilibrium behavior of the chain molecule. The radial distribution function (RDF) and the structure factor S(q) of the chain as a function of temperature are analyzed in detail. The different characteristic peaks in the RDF and S(q) were assigned to specific distances in the chain and structural changes occurring with the temperature. In S(q), a peak characteristic for the order in the solid state was found and used to determine the equilibrium melting temperature. A detailed scaling analysis of the structure factor covering the full q range was performed according to the work of Hammouda. In the Θ region, a quantitative analysis of the full structure factor was done using the equivalent Kuhn chain, which enabled us to assign the Θ region of our chain and to demonstrate, in our particular case, the failure of the Gaussian chain approach. The chain conformational properties at the equilibrium melting temperature are discussed using conformational distribution functions, using the largest principal component of the radius of gyration and shape parameters as order parameters. We demonstrate that for the system studied here, the Landau free energy expression based on this conformational distribution information leads to erroneous conclusions concerning the thermodynamic transition behavior. Finally, we focus on the instantaneous conformational properties at the equilibrium melting temperature and give a detailed analysis of the conformational shapes using different shape parameters and a simulation snapshot. We show that the chain does not only take the lamellar rod-like and globular conformational shapes, typical of the solid and liquid states, but can also explore many other conformational states, including the toroidal conformational

  20. The 2012 Ferrara seismic sequence: from a 1D reliable crustal structure for moment tensor solutions to strong implications for seismic hazard

    NASA Astrophysics Data System (ADS)

    Buttinelli, M.; Malagnini, L.; Herrmann, R. B.; Munafò, I.; Anselmi, M.; Akinci, A.; Boschi, E.

    2012-12-01

    On May 20 2012, an event of ML 5.9 (MW 5.6) struck the southern edge of the Po river plain (Pianura Padana). The earthquake was preceded by a foreshock of ML 4.1 (MW 3.8), less than 3 hours before the MW 5.6 main. Hypocentral depths were 6.3 km for both events. Centroid depths were 5 and 6 km, respectively. The activated fault was a reverse one, dipping to the south. Then a complex seismic sequence started, in which more than six earthquakes with ML greater than 5 struck the area, the last one on June 3, 2012. Aftershocks delineated a 50 km-long and 10-15 km-wide zone, approximately elongated in the WE direction. More than 2100 events were located between May 19 and June 25 2012 by the INGV National Seismic Network, 80 of them with ML greater than 3.5. The damage due to the ML 5+ earthquakes was widespread, as they severely hit historical towns and industrial infrastructures. However, a striking inconsistency exists between the relatively small moment magnitudes and the corresponding high level of damage. In order to define a velocity structure for the crust beneath the Pianura Padana, to be used for waveform inversion of moment tensors, we gathered all the geophysical and geological information available for the area. The model is characterized by very thick and shallow Quaternary sediments, to be used for the inversion of broadband waveforms for moment tensor (MT) solutions, in the frequency band between 0.02-0.1 Hz. We calculated moment tensors for 20 events down to MW~3.2. We demonstrate how surface waves dominate the seismograms in the region, which may have played a major role in enhancing the damage to industrial structures observed in the epicentral area. Synthetic seismograms computed using the developed model well reproduced the anomalous durations of the ground motion observed in Pianura Padana, also highlighting important implications for the seismic hazard in the entire area. The present seismic hazard assessment as well as the size of the historical

  1. Angular emission from 1D and 2D meso- and nano-structures: Probed by dual-channel Fourier-plane microscopy

    NASA Astrophysics Data System (ADS)

    Singh, Danveer; Sharma, Deepak Kumar; Chaubey, Shailendra Kumar; Kumar, G. V. Pavan

    2017-09-01

    The optical emission characteristics from individual nanostructures such as organic waveguides, plasmonic nanowires and 2D materials such as MoS2 can vary depending on the nature of interface on which they are grown or deposited. We constructed a dual-channel Fourier-plane microscopy, and studied the directional emission characteristics of an individual organic mesowires, Ag nanowires and MoS2 nanolayers through the glass substrate or air superstrate. Specifically, we show the ability of our microscope to quantitatively probe the radial and azimuthal angular spread in the waveguided PL from the distal ends of the mesowire across the interface without changing its position or orientation. Furthermore, from the guided PL spectral signatures, we show that the finesse of the waveguided Fabry-Perot resonance depends on whether the measurement was performed through the substrate or superstrate. To reveal the versatility of our microscope, we have quantified angular distribution of directional light scattering from the distal end of Ag nanowire at an interface, and angular distribution of excitonic emission from MoS2 nanolayers through a glass substrate. Our work highlights the capability of dual-channel Fourier microscope in quantifying the angular emission characteristics from individual optical antenna structures at an interface, and can be extrapolated to nonlinear organic nanophotonic regimes.

  2. Electrical conductivity of old oceanic mantle in the northwestern Pacific I: 1-D profiles suggesting differences in thermal structure not predictable from a plate cooling model

    NASA Astrophysics Data System (ADS)

    Baba, Kiyoshi; Tada, Noriko; Matsuno, Tetsuo; Liang, Pengfei; Li, Ruibai; Zhang, Luolei; Shimizu, Hisayoshi; Abe, Natsue; Hirano, Naoto; Ichiki, Masahiro; Utada, Hisashi

    2017-08-01

    Seafloor magnetotelluric (MT) experiments were recently conducted in two areas of the northwestern Pacific to investigate the nature of the old oceanic upper mantle. The areas are far from any tectonic activity, and "normal" mantle structure is therefore expected. The data were carefully analyzed to reduce the effects of coastlines and seafloor topographic changes, which are significant boundaries in electrical conductivity and thus distort seafloor MT data. An isotropic, one-dimensional electrical conductivity profile was estimated for each area. The profiles were compared with those obtained from two previous study areas in the northwestern Pacific. Between the four profiles, significant differences were observed in the thickness of the resistive layer beyond expectations based on cooling of homogeneous oceanic lithosphere over time. This surprising feature is now further clarified from what was suggested in a previous study. To explain the observed spatial variation, dynamic processes must be introduced, such as influence of the plume associated with the formation of the Shatsky Rise, or spatially non-uniform, small-scale convection in the asthenosphere. There is significant room of further investigation to determine a reasonable and comprehensive interpretation of the lithosphere-asthenosphere system beneath the northwestern Pacific. The present results demonstrate that electrical conductivity provides key information for such investigation.[Figure not available: see fulltext.

  3. Moments of the Spin Structure Functions g1p and g1d for 0.05 < Q2 < 3.0 GeV2

    SciTech Connect

    Prok, Yelena; Bosted, Peter; Burkert, Volker; Deur, Alexandre; Dharmawardane, Kahanawita; Dodge, Gail; Griffioen, Keith; Kuhn, Sebastian; Minehart, Ralph; Adams, Gary; Amaryan, Moscov; Amaryan, Moskov; Anghinolfi, Marco; Asryan, G.; Audit, Gerard; Avagyan, Harutyun; Baghdasaryan, Hovhannes; Baillie, Nathan; Ball, J.P.; Ball, Jacques; Baltzell, Nathan; Barrow, Steve; Battaglieri, Marco; Beard, Kevin; Bedlinskiy, Ivan; Bektasoglu, Mehmet; Bellis, Matthew; Benmouna, Nawal; Berman, Barry; Biselli, Angela; Blaszczyk, Lukasz; Boyarinov, Sergey; Bonner, Billy; Bouchigny, Sylvain; Bradford, Robert; Branford, Derek; Briscoe, William; Brooks, William; Bultmann, S.; Bueltmann, Stephen; Butuceanu, Cornel; Calarco, John; Careccia, Sharon; Carman, Daniel; Casey, Liam; Cazes, Antoine; Chen, Shifeng; Cheng, Lu; Cole, Philip; Collins, Patrick; Coltharp, Philip; Cords, Dieter; Corvisiero, Pietro; Crabb, Donald; Crede, Volker; Cummings, John; Dale, Daniel; Dashyan, Natalya; De Masi, Rita; De Vita, Raffaella; De Sanctis, Enzo; Degtiarenko, Pavel; Denizli, Haluk; Dennis, Lawrence; Dhuga, Kalvir; Dickson, Richard; Djalali, Chaden; Doughty, David; Dugger, Michael; Dytman, Steven; Dzyubak, Oleksandr; Egiyan, Hovanes; Egiyan, Kim; Elfassi, Lamiaa; Elouadrhiri, Latifa; Eugenio, Paul; Fatemi, Renee; Fedotov, Gleb; Feldman, Gerald; Fersch, Robert; Feuerbach, Robert; Forest, Tony; Fradi, Ahmed; Funsten, Herbert; Garcon, Michel; Gavalian, Gagik; Gevorgyan, Nerses; Gilfoyle, Gerard; Giovanetti, Kevin; Girod, Francois-Xavier; Goetz, John; Golovach, Evgeny; Gothe, Ralf; Guidal, Michel; Guillo, Matthieu; Guler, Nevzat; Guo, Lei; Gyurjyan, Vardan; Hadjidakis, Cynthia; Hafidi, Kawtar; Hakobyan, Hayk; Hanretty, Charles; Hardie, John; Hassall, Neil; Heddle, David; Hersman, F.; Hicks, Kenneth; Hleiqawi, Ishaq; Holtrop, Maurik; Huertas, Marco; Hyde, Charles; Ilieva, Yordanka; Ireland, David; Ishkhanov, Boris; Isupov, Evgeny; Ito, Mark; Jenkins, David; Jo, Hyon-Suk; Johnstone, John; Joo, Kyungseon; Juengst, Henry; Kalantarians, Narbe; Keith, Christopher; Kellie, James; Khandaker, Mahbubul; Kim, Kui; Kim, Kyungmo; Kim, Wooyoung; Klein, Andreas; Klein, Franz; Klusman, Mike; Kossov, Mikhail; Krahn, Zebulun; Kramer, Laird; Kubarovsky, Valery; Kuhn, Joachim; Kuleshov, Sergey; Kuznetsov, Viacheslav; Lachniet, Jeff; Laget, Jean; Langheinrich, Jorn; Lawrence, Dave; Lima, Ana; Livingston, Kenneth; Lu, Haiyun; Lukashin, K.; MacCormick, Marion; Marchand, Claude; Markov, Nikolai; Mattione, Paul; McAleer, Simeon; McKinnon, Bryan; McNabb, John; Mecking, Bernhard; Mestayer, Mac; Meyer, Curtis; Mibe, Tsutomu; Mikhaylov, Konstantin; Mirazita, Marco; Miskimen, Rory; Mokeev, Viktor; Morand, Ludyvine; Moreno, Brahim; Moriya, Kei; Morrow, Steven; Moteabbed, Maryam; Mueller, James; Munevar Espitia, Edwin; Mutchler, Gordon; Nadel-Turonski, Pawel; Nasseripour, Rakhsha; Niccolai, Silvia; Niculescu, Gabriel; Niculescu, Maria-Ioana; Niczyporuk, Bogdan; Niroula, Megh; Niyazov, Rustam; Nozar, Mina; O'Rielly, Grant; Osipenko, Mikhail; Ostrovidov, Alexander; Park, Kijun; Pasyuk, Evgueni; Paterson, Craig; Anefalos Pereira, S.; Philips, Sasha; Pierce, J.; Pivnyuk, Nikolay; Pocanic, Dinko; Pogorelko, Oleg; Popa, Iulian; Pozdnyakov, Sergey; Preedom, Barry; Price, John; Procureur, Sebastien; Protopopescu, Dan; Qin, Liming; Raue, Brian; Riccardi, Gregory; Ricco, Giovanni; Ripani, Marco; Ritchie, Barry; Rosner, Guenther; Rossi, Patrizia; Rowntree, David; Rubin, Philip; Sabatie, Franck; Salamanca, Julian; Salgado, Carlos; Santoro, Joseph; Sapunenko, Vladimir; Schumacher, Reinhard; Seely, Mikell; Serov, Vladimir; Sharabian, Youri; Sharov, Dmitri; Shaw, Jeffrey; Shvedunov, Nikolay; Skabelin, Alexander; Smith, Elton; Smith, Lee; Sober, Daniel; Sokhan, Daria; Stavinskiy, Aleksey; Stepanyan, Samuel; Stepanyan, Stepan; Stokes, Burnham; Stoler, Paul; Strakovski, Igor; Strauch, Steffen; Suleiman, Riad; Taiuti, Mauro; Tedeschi, David; Tkabladze, Avtandil; Tkachenko, Svyatoslav; Todor, Luminita; Ungaro, Maurizio; V

    2009-02-01

    The spin structure functions $g_1$ for the proton and the deuteron have been measured over a wide kinematic range in $x$ and \\Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH$_3$ and ND$_3$ targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for $0.05 < Q^2 < 5 $\\ GeV$^2$ and $W < 3$ GeV. The first moments of $g_1$ for the proton and deuteron are presented -- both have a negative slope at low \\Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first result for the generalized forward spin polarizability of the proton $\\gamma_0^p$ is also reported, and shows evidence of scaling above $Q^2$ = 1.5 GeV$^2$. Although the first moments of $g_1$ are consistent with Chiral Perturbation Theory (\\ChPT) calculations up to approximately $Q^2 = 0.06$ GeV$^2$, a significant discrepancy is observed between the $\\gamma_0^p$ data and \\ChPT\\ for $\\gamma_0^p$,even at the lowest \\Q2.

  4. Chains of type-I radio bursts and drifting pulsation structures

    NASA Astrophysics Data System (ADS)

    Karlický, M.

    2017-06-01

    Aims: Owing to similarities of chains of type-I radio bursts and drifting pulsation structures the question arises as to whether both these radio bursts are generated by similar processes. Methods: Characteristics and parameters of both these radio bursts are compared. Results: We present examples of both types of bursts and show their similarities and differences. Then, for chains of type-I bursts, a similar model as for drifting pulsation structures (DPSs) is proposed. We show that, similar to the DPS model, the chains of type-I bursts can be generated by the fragmented magnetic reconnection associated with plasmoid interactions. To support this new model of chains of type-I bursts, we present an effect of merging two plasmoids to form one larger plasmoid on the radio spectrum of DPS. This process can also explain the `wavy' appearance of some chains of type-I bursts. Further, we show that the chains of type-I bursts with the wavy appearance can be used for estimation of the magnetic field strength in their sources. We think that differences of chains of type-I bursts and DPSs are mainly owing to different regimes of the magnetic field reconnection. While in the case of chains of type-I bursts, the magnetic reconnection and plasmoid interactions are in the quasi-separatrix layer of the active region in more or less quasi-saturated regime, in the case of DPSs, observed in the impulsive phase of eruptive flares, the magnetic reconnection and plasmoid interactions are in the current sheet formed under the flare magnetic rope, which moves upwards and forces this magnetic reconnection.

  5. Chirality organization of ferrocenes bearing podand dipeptide chains: synthesis and structural characterization.

    PubMed

    Moriuchi, T; Nomoto, A; Yoshida, K; Ogawa, A; Hirao, T

    2001-01-10

    A variety of ferrocenes bearing podand dipeptide chains have been synthesized to form an ordered structure in both solid and solution states and have been investigated by 1H NMR, FT-IR, CD, and X-ray crystallographic analyses. Conformational enantiomerization through chirality organization was achieved by the intramolecular hydrogen bondings between the podand dipeptide chains. The single-crystal X-ray structure determination of the ferrocene 2 bearing the podand dipeptide chains (-D-Ala-D-Pro-OEt) revealed two C2-symmetric intramolecular hydrogen bondings between CO (Ala) and NH (another Ala) of each podand dipeptide chain to induce the chirality-organized structure. The molecular structures of the ferrocene 1 composed of the podand L-dipeptide chains (-L-Ala-L-Pro-OEt) and 2 are in a good mirror image relationship, indicating that they are conformational enantiomers. An opposite helically ordered molecular arrangement was formed in the crystal packing of 2 as compared with 1. The ferrocene 2 exhibited induced circular dichroism (CD), which appeared at the absorbance of the ferrocene moiety. The mirror image of the CD signals between 1 and 2 was observed, suggesting that the chirality-organized structure via intramolecular hydrogen bondings is present even in solution. The ferrocene 4 bearing the podand dipeptide chains (-Gly-L-Leu-OEt) also showed an ordered structure in the crystal based on two intramolecular hydrogen bondings between CO (Gly) and NH (another Gly) of each podand dipeptide chain, together with intermolecular hydrogen bondings between CO adjacent to the ferrocene unit and NH (neighboring Leu) to create the highly organized self-assembly. A different self-assembly was observed in the crystal of the ferrocene 5 composed of the podand dipeptide chains (-Gly-L-Phe-OEt), wherein each molecule is bonded to two neighboring molecules through two pairs of symmetrical intermolecular hydrogen bonds to form a 14-membered intermolecularly hydrogen-bonded ring

  6. Topological superconductivity induced by ferromagnetic metal chains

    NASA Astrophysics Data System (ADS)

    Li, Jian; Chen, Hua; Drozdov, Ilya K.; Yazdani, A.; Bernevig, B. Andrei; MacDonald, A. H.

    2014-12-01

    Recent experiments have provided evidence that one-dimensional (1D) topological superconductivity can be realized experimentally by placing transition-metal atoms that form a ferromagnetic chain on a superconducting substrate. We address some properties of this type of system by using a Slater-Koster tight-binding model to account for important features of the electronic structure of the transition-metal chains on the superconducting substrate. We predict that topological superconductivity is nearly universal when ferromagnetic transition-metal chains form straight lines on superconducting substrates and that it is possible for more complex chain structures. When the chain is weakly coupled to the substrate and is longer than superconducting coherence lengths, its proximity-induced superconducting gap is ˜Δ ESO/J where Δ is the s -wave pair potential on the chain, ESO is the spin-orbit splitting energy induced in the normal chain state bands by hybridization with the superconducting substrate, and J is the exchange splitting of the ferromagnetic chain d bands. Because of the topological character of the 1D superconducting state, Majorana end modes appear within the gaps of finite length chains. We find, in agreement with the experiment, that when the chain and substrate orbitals are strongly hybridized, Majorana end modes are substantially reduced in amplitude when separated from the chain end by less than the coherence length defined by the p -wave superconducting gap. We conclude that Pb is a particularly favorable substrate material for ferromagnetic chain topological superconductivity because it provides both strong s -wave pairing and strong Rashba spin-orbit coupling, but that there is an opportunity to optimize properties by varying the atomic composition and structure of the chain. Finally, we note that in the absence of disorder, a new chain magnetic symmetry, one that is also present in the crystalline topological insulators, can stabilize multiple

  7. Synthesis, crystal structure and magnetic properties of a novel heterobimetallic rhenium(IV)-dysprosium(III) chain.

    PubMed

    Pejo, Carolina; Guedes, Guilherme P; Novak, Miguel A; Speziali, Nivaldo L; Chiozzone, Raúl; Julve, Miguel; Lloret, Francesc; Vaz, Maria G F; González, Ricardo

    2015-06-08

    The use of the mononuclear rhenium(IV) precursor [ReBr5 (H2 pydc)](-) (H2 pydc=3,5-pyridinedicarboxylic acid) as a metalloligand towards dysprosium(III) afforded the first heterobimetallic Re(IV) -Dy(III) complex. Crystal structures and static and dynamic magnetic properties of both rhenium-containing species are reported herein. The 5d-4f compound shows an extended 1D structure and the AC magnetic measurements reveal frequency dependence at low temperature suggesting slow relaxation of the magnetization.

  8. Differential Recognition of CD1d-[alpha]-Galactosyl Ceramide by the V[beta]8.2 and V[beta]7 Semi-invariant NKT T Cell Receptors

    SciTech Connect

    Pellicci, Daniel G.; Patel, Onisha; Kjer-Nielsen, Lars; Pang, Siew Siew; Sullivan, Lucy C.; Kyparissoudis, Konstantinos; Brooks, Andrew G.; Reid, Hugh H.; Gras, Stephanie; Lucet, Isabelle S.; Koh, Ruide; Smyth, Mark J.; Mallevaey, Thierry; Matsuda, Jennifer L.; Gapin, Laurent; McCluskey, James; Godfrey, Dale I.; Rossjohn, Jamie; PMCI-A; Monash; UCHSC; Melbourne

    2009-09-02

    The semi-invariant natural killer T cell receptor (NKT TCR) recognizes CD1d-lipid antigens. Although the TCR{alpha} chain is typically invariant, the {beta} chain expression is more diverse, where three V{beta} chains are commonly expressed in mice. We report the structures of V{alpha}14-V{beta}8.2 and V{alpha}14-V{beta}7 NKT TCRs in complex with CD1d-{alpha}-galactosylceramide ({alpha}-GalCer) and the 2.5 {angstrom} structure of the human NKT TCR-CD1d-{alpha}-GalCer complex. Both V{beta}8.2 and V{beta}7 NKT TCRs and the human NKT TCR ligated CD1d-{alpha}-GalCer in a similar manner, highlighting the evolutionarily conserved interaction. However, differences within the V{beta} domains of the V{beta}8.2 and V{beta}7 NKT TCR-CD1d complexes resulted in altered TCR{beta}-CD1d-mediated contacts and modulated recognition mediated by the invariant {alpha} chain. Mutagenesis studies revealed the differing contributions of V{beta}8.2 and V{beta}7 residues within the CDR2{beta} loop in mediating contacts with CD1d. Collectively we provide a structural basis for the differential NKT TCR V{beta} usage in NKT cells.

  9. Structural re-alignment in an immunologic surface region of ricin A chain

    SciTech Connect

    Zemla, A T; Zhou, C E

    2007-07-24

    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  10. Probing structure-induced optical behavior in a new class of self-activated luminescent 0D/1D CaWO₄ metal oxide – CdSe nanocrystal composite heterostructures

    SciTech Connect

    Han, Jinkyu; McBean, Coray; Wang, Lei; Hoy, Jessica; Jaye, Cherno; Liu, Haiqing; Li, Zhuo-Qun; Sfeir, Matthew Y.; Fischer, Daniel A.; Taylor, Gordon T.; Misewich, James A.; Wong, Stanislaus S.

    2015-01-30

    In this report, we synthesize and characterize the structural and optical properties of novel heterostructures composed of (i) semiconducting nanocrystalline CdSe quantum dot (QDs) coupled with (ii) both one and zero-dimensional (1D and 0D) motifs of self-activated luminescence CaWO₄ metal oxides. Specifically, ~4 nm CdSe QDs have been anchored onto (i) high-aspect ratio 1D nanowires, measuring ~230 nm in diameter and ~3 μm in length, as well as onto (ii) crystalline 0D nanoparticles (possessing an average diameter of ~ 80 nm) of CaWO₄ through the mediation of 3-mercaptopropionic acid (MPA) as a connecting linker. Composite formation was confirmed by complementary electron microscopy and spectroscopy (i.e. IR and Raman) data. In terms of luminescent properties, our results show that our 1D and 0D heterostructures evince photoluminescence (PL) quenching and shortened PL lifetimes of CaWO₄ as compared with unbound CaWO₄. We propose that a photo-induced electron transfer process occurs from CaWO₄ to CdSe QDs, a scenario which has been confirmed by NEXAFS measurements and which highlights a decrease in the number of unoccupied orbitals in the conduction bands of CdSe QDs. By contrast, the PL signature and lifetimes of MPA-capped CdSe QDs within these heterostructures do not exhibit noticeable changes as compared with unbound MPA-capped CdSe QDs. The striking difference in optical behavior between CaWO₄ nanostructures and CdSe QDs within our heterostructures can be correlated with the relative positions of their conduction and valence energy band levels. In addition, the PL quenching behaviors for CaWO₄ within the heterostructure configuration were examined by systematically varying (i) the quantities and coverage densities of CdSe QDs as well as (ii) the intrinsic morphology (and by extension, the inherent crystallite size) of CaWO₄ itself.

  11. Dynamic structure of unentangled polymer chains in the vicinity of non-attractive nanoparticles.

    PubMed

    Li, Ying; Kröger, Martin; Liu, Wing Kam

    2014-03-21

    Using coarse-grained molecular dynamics simulation, we study the motion of unentangled polymer chains dynamically confined by non-attractive nanoparticles (NPs). Both normal mode and dynamic structure factor S(q, t) analysis are adopted to analyze chain's dynamics. Relaxation behaviors of chains are found to be significantly slowed down by NPs. The relaxation times of chain's normal modes are monotonically increasing with the NP volume fraction ϕ. At the same time, chains' dynamics are becoming non-Gaussian. Inspection of S(q, t) reveals that chain's dynamics can be attributed to two 'phases', a bulk polymer phase and a confined polymer phase between NPs. The dynamics of a confined polymer is slower than that of a bulk polymer, while still exhibiting high mobility. The amount of the bulk polymer phase is found to exponentially decay with increasing ϕ. With this figure at hand, we establish a simple relationship between NP and confined/interphase polymer volume fractions. This work seems to provide the first quantitative prediction on the relationship between NP and confined/interphase polymer volume fractions.

  12. Structural Distortions and Charge Density Waves in Iodine Chains Encapsulated inside Carbon Nanotubes.

    PubMed

    Komsa, Hannu-Pekka; Senga, Ryosuke; Suenaga, Kazutomo; Krasheninnikov, Arkady V

    2017-06-14

    Atomic chains are perfect systems for getting fundamental insights into the electron dynamics and coupling between the electronic and ionic degrees of freedom in one-dimensional metals. Depending on the band filling, they can exhibit Peierls instabilities (or charge density waves), where equally spaced chain of atoms with partially filled band is inherently unstable, exhibiting spontaneous distortion of the lattice that further leads to metal-insulator transition in the system. Here, using high-resolution scanning transmission electron microscopy, we directly image the atomic structures of a chain of iodine atoms confined inside carbon nanotubes. In addition to long equidistant chains, the ones consisting of iodine dimers and trimers were also observed, as well as transitions between them. First-principles calculations reproduce the experimentally observed bond lengths and lattice constants, showing that the ionic movement is largely unconstrained in the longitudinal direction, while naturally confined by the nanotube in the lateral directions. Moreover, the trimerized chain bears the hallmarks of a charge density wave. The transition is driven by changes in the charge transfer between the chain and the nanotube and is enabled by the charge compensation and additional screening provided by the nanotube.

  13. Structure-selective modification of aromatic side chains with dirhodium metallopeptide catalysts.

    PubMed

    Popp, Brian V; Ball, Zachary T

    2010-05-19

    The combination of peptide molecular recognition and residue-selective dirhodium catalysis allows modification of aromatic side chains that is selective for coil structures. A rate enhancement of >10(3) relative to nonselective dirhodium modification was observed. The increased reactivity of this approach creates the first selective chemical modification of the phenylalanine residue.

  14. Synconset waves and chains: spiking onsets in synchronous populations predict and are predicted by network structure.

    PubMed

    Raghavan, Mohan; Amrutur, Bharadwaj; Narayanan, Rishikesh; Sikdar, Sujit Kumar

    2013-01-01

    Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define 'synconset wave' as a cascade of first spikes within a synchronisation event. Synconset waves would occur in 'synconset chains', which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of our

  15. Crystal structure of the LG1-3 region of the laminin alpha2 chain.

    PubMed

    Carafoli, Federico; Clout, Naomi J; Hohenester, Erhard

    2009-08-21

    Laminins are large heterotrimeric glycoproteins with many essential functions in basement membrane assembly and function. Cell adhesion to laminins is mediated by a tandem of five laminin G-like (LG) domains at the C terminus of the alpha chain. Integrin binding requires an intact LG1-3 region, as well as contributions from the coiled coil formed by the alpha, beta, and gamma chains. We have determined the crystal structure at 2.8-A resolution of the LG1-3 region of the laminin alpha2 chain (alpha 2LG1-3). The three LG domains adopt typical beta-sandwich folds, with canonical calcium binding sites in LG1 and LG2. LG2 and LG3 interact through a substantial interface, but LG1 is completely dissociated from the LG2-3 pair. We suggest that the missing gamma chain tail may be required to stabilize the interaction between LG1 and LG2-3 in the biologically active conformation. A global analysis of N-linked glycosylation sites shows that the beta-sandwich faces of LG1 are free of carbohydrate modifications in all five laminin alpha chains, suggesting that these surfaces may harbor the integrin binding site. The alpha 2LG1-3 structure provides the first atomic view of the integrin binding region of laminins.

  16. Absolute Side-chain Structure at Position 13 Is Required for the Inhibitory Activity of Bromein*

    PubMed Central

    Sawano, Yoriko; Hatano, Ken-ichi; Miyakawa, Takuya; Tanokura, Masaru

    2008-01-01

    Bromelain isoinhibitor (bromein), a cysteine proteinase inhibitor from pineapple stem, has a unique double-chain structure. The bromein precursor protein includes three homologous inhibitor domains, each containing an interchain peptide between the light and heavy chains. The interchain peptide in the single-chain precursor is immediately processed by bromelain, a target proteinase. In the present study, to clarify the essential inhibitory site of bromein, we constructed 44 kinds of site-directed and deletion mutants and investigated the inhibitory activity of each toward bromelain. As a result, the complete chemical structure of Leu13 in the light chain was revealed to be essential for inhibition. Pro12 prior to the leucine residue was also involved in the inhibitory activity and would control the location of the leucine side chain by the fixed φ dihedral angle of proline. Furthermore, the five-residue length of the interchain peptide was strictly required for the inhibitory activity. On the other hand, no inhibitory activity against bromelain was observed by the substitution of proline for the N terminus residue Thr15 of the interchain peptide. In summary, these mutational analyses of bromein demonstrated that the appropriate position and conformation of Leu13 are absolutely crucial for bromelain inhibition. PMID:18948264

  17. Absolute side-chain structure at position 13 is required for the inhibitory activity of bromein.

    PubMed

    Sawano, Yoriko; Hatano, Ken-ichi; Miyakawa, Takuya; Tanokura, Masaru

    2008-12-26

    Bromelain isoinhibitor (bromein), a cysteine proteinase inhibitor from pineapple stem, has a unique double-chain structure. The bromein precursor protein includes three homologous inhibitor domains, each containing an interchain peptide between the light and heavy chains. The interchain peptide in the single-chain precursor is immediately processed by bromelain, a target proteinase. In the present study, to clarify the essential inhibitory site of bromein, we constructed 44 kinds of site-directed and deletion mutants and investigated the inhibitory activity of each toward bromelain. As a result, the complete chemical structure of Leu13 in the light chain was revealed to be essential for inhibition. Pro12 prior to the leucine residue was also involved in the inhibitory activity and would control the location of the leucine side chain by the fixed dihedral angle of proline. Furthermore, the five-residue length of the interchain peptide was strictly required for the inhibitory activity. On the other hand, no inhibitory activity against bromelain was observed by the substitution of proline for the N terminus residue Thr15 of the interchain peptide. In summary, these mutational analyses of bromein demonstrated that the appropriate position and conformation of Leu13 are absolutely crucial for bromelain inhibition.

  18. Structural transitions in short-chain lipid assemblies studied by (31)P-NMR spectroscopy.

    PubMed

    Kleinschmidt, Jörg H; Tamm, Lukas K

    2002-08-01

    The self-assembled supramolecular structures of diacylphosphatidylcholine (diC(n)PC), diacylphosphatidylethanolamine (diC(n)PE), diacylphosphatidyglycerol (diC(n)PG), and diacylphosphatidylserine (diC(n)PS) were investigated by (31)P nuclear magnetic resonance (NMR) spectroscopy as a function of the hydrophobic acyl chain length. Short-chain homologs of these lipids formed micelles, and longer-chain homologs formed bilayers. The shortest acyl chain lengths that supported bilayer structures depended on the headgroup of the lipids. They increased in the order PE (C(6)) < PC (C(9)) < or = PS (C(9) or C(10)) < PG (C(11) or C(12)). This order correlated with the effective headgroup area, which is a function of the physical size, charge, hydration, and hydrogen-bonding capacity of the four headgroups. Electrostatic screening of the headgroup charge with NaCl reduced the effective headgroup area of PS and PG and thereby decreased the micelle-to-bilayer transition of these lipid classes to shorter chain lengths. The experimentally determined supramolecular structures were compared to the assembly states predicted by packing constraints that were calculated from the hydrocarbon-chain volume and effective headgroup area of each lipid. The model accurately predicted the chain-length threshold for bilayer formation if the relative displacement of the acyl chains of the phospholipid were taken into account. The model also predicted cylindrical rather than spherical micelles for all four diacylphospholipid classes and the (31)P-NMR spectra provided evidence for a tubular network that appeared as an intermediate phase at the micelle-to-bilayer transition. The free energy of micellization per methylene group was independent of the structure of the supramolecular assembly, but was -0.95 kJ/mol (-0.23 kcal/mol) for the PGs compared to -2.5 kJ/mol (-0.60 kcal/mol) for the PCs. The integral membrane protein OmpA did not change the bilayer structure of thin (diC(10)PC) bilayers.

  19. 1D polymeric copper(I) complex [Cu2(μ-(2,6-Cl-ba)2en)(μ-I)2]n with exceptionally short Cusbnd Cu distance: Synthesis, characterization, thermal study and crystal structure

    NASA Astrophysics Data System (ADS)

    Khalaji, Aliakbar Dehno; Peyghoun, Seyyed Javad; Akbari, Alireza; Feizi, Nourollah; Dusek, Michal; Eigner, Vaclav

    2017-01-01

    A new 1D polymeric three coordinated copper(I) complex, [Cu2(μ-(2,6-Cl-ba)2en)(μ-I)2]n, with the bidentate Schiff base ligand N,N‧-bis(2,6-dichlorobenzylidene)ethane-1,2-diamine containing a flexible spacer (dbnd NCH2sbnd CH2sbnd Ndbnd) was synthesized and characterized by elemental analyses, UV-Vis, FT-IR and 1H NMR spectroscopy and thermal analaysis. Its molecular structure was determined by single-crystal X-ray diffraction and shows the (2,6-Cl-ba)2en acts as a bis-monodentate bridging ligand forming the dinuclear [Cu2(μ-(2,6-Cl-ba)2en)] groups. Such dinuclear groups are bridged by two iodine anions [(μ-I)2] to form a 1D polymeric copper(I) complex. The copper(I) ions are coordinated in a distorted trigonal planar geometry by two I atoms and one nitrogen atom of Schiff base ligand (2,6-Cl-ba)2en.

  20. Beyond Donor-Acceptor (D-A) Approach: Structure-Optoelectronic Properties-Organic Photovoltaic Performance Correlation in New D-A1 -D-A2 Low-Bandgap Conjugated Polymers.

    PubMed

    Chochos, Christos L; Drakopoulou, Sofia; Katsouras, Athanasios; Squeo, Benedetta M; Sprau, Christian; Colsmann, Alexander; Gregoriou, Vasilis G; Cando, Alex-Palma; Allard, Sybille; Scherf, Ullrich; Gasparini, Nicola; Kazerouni, Negar; Ameri, Tayebeh; Brabec, Christoph J; Avgeropoulos, Apostolos

    2017-04-01

    Low-bandgap near-infrared polymers are usually synthesized using the common donor-acceptor (D-A) approach. However, recently polymer chemists are introducing more complex chemical concepts for better fine tuning of their optoelectronic properties. Usually these studies are limited to one or two polymer examples in each case study so far, though. In this study, the dependence of optoelectronic and macroscopic (device performance) properties in a series of six new D-A1 -D-A2 low bandgap semiconducting polymers is reported for the first time. Correlation between the chemical structure of single-component polymer films and their optoelectronic properties has been achieved in terms of absorption maxima, optical bandgap, ionization potential, and electron affinity. Preliminary organic photovoltaic results based on blends of the D-A1 -D-A2 polymers as the electron donor mixed with the fullerene derivative [6,6]-phenyl-C71 -butyric acid methyl ester demonstrate power conversion efficiencies close to 4% with short-circuit current densities (J sc ) of around 11 mA cm(-2) , high fill factors up to 0.70, and high open-circuit voltages (V oc s) of 0.70 V. All the devices are fabricated in an inverted architecture with the photoactive layer processed in air with doctor blade technique, showing the compatibility with roll-to-roll large-scale manufacturing processes.

  1. Crystal Structures of Mouse CD1d-IGb3 Complex And Its Cognate Valpha14 T Cell Receptor Suggest a Model for Dual Recognition of Foreign And Self Glycolipids

    SciTech Connect

    Zajonc, D.M.; Saveage, P.B.; Bendelac, A.; Wilson, I.A.; Teyton, L.

    2009-05-28

    The semi-invariant Valpha14Jalpha18 T cell receptor (TCR) is expressed by regulatory NKT cells and has the unique ability to recognize chemically diverse ligands presented by CD1d. The crystal structure of CD1d complexed to a natural, endogenous ligand, isoglobotrihexosylceramide (iGb3), illustrates the extent of this diversity when compared to the binding of potent, exogenous ligands, such as alpha-galactosylceramide (alpha-GalCer). A single mode of recognition for these two classes of ligands would then appear problematic for a single T cell receptor. However, the Valpha14 TCR adopts two different conformations in the crystal where, in one configuration, the presence of a larger cavity between the two CDR3 regions could accommodate iGb3 and, in the other, a smaller cavity fits alpha-GalCer more snugly. Alternatively, the extended iGb3 headgroup could be 'squashed' upon docking of the TCR and accommodated between the CD1 and TCR surfaces. Thus, the same TCR may adopt alternative modes of recognition for these foreign and self-ligands for NKT cell activation.

  2. Dependence of the electronic structure on the chain geometry in stereoregular polypropylene: An exploratory theoretical study

    SciTech Connect

    Flamant, I.; Mosley, D.H.; Deleuze, M.

    1994-12-31

    Ab initio RHF/STO-3G band structure calculations are carried out on extended regular polypropylene chains (isotatic helical, syndiotactic helical, and zigzag planar) to assess qualitatively the dependence of the energy band structure and density of states on the molecular geometry. It is found that discrimination between the two syndiotactic forms should be possible from spectral features in the valence region of corresponding PS spectra.

  3. Severe Hypertriglyceridemia in Glut1D on Ketogenic Diet.

    PubMed

    Klepper, Joerg; Leiendecker, Baerbel; Heussinger, Nicole; Lausch, Ekkehart; Bosch, Friedrich

    2016-04-01

    High-fat ketogenic diets are the only treatment available for Glut1 deficiency (Glut1D). Here, we describe an 8-year-old girl with classical Glut1D responsive to a 3:1 ketogenic diet and ethosuximide. After 3 years on the diet a gradual increase of blood lipids was followed by rapid, severe asymptomatic hypertriglyceridemia (1,910 mg/dL). Serum lipid apheresis was required to determine liver, renal, and pancreatic function. A combination of medium chain triglyceride-oil and a reduction of the ketogenic diet to 1:1 ratio normalized triglyceride levels within days but triggered severe myoclonic seizures requiring comedication with sultiam. Severe hypertriglyceridemia in children with Glut1D on ketogenic diets may be underdiagnosed and harmful. In contrast to congenital hypertriglyceridemias, children with Glut1D may be treated effectively by dietary adjustments alone.

  4. The Effect of Plate Structure on Intraplate Volcanism, Kodiak-Bowie Seamount Chain, Gulf of Alaska

    NASA Astrophysics Data System (ADS)

    Reece, R. S.; Christeson, G. L.; Gulick, S. S.; Barth, G. A.; Van Avendonk, H. J.

    2012-12-01

    Newly acquired ocean bottom seismometer (OBS) and multi-channel seismic (MCS) data in the vicinity of the Kodiak-Bowie Seamount Chain and Aja Fracture Zone reveal the character and structure of the Pacific Plate, overlying sediment, and seamounts in the Gulf of Alaska. Our data include two marine wide-angle OBS profiles, two coincident MCS profiles, and several nearby MCS profiles, including lines parallel to and crossing the Seamount Chain and Fracture Zone. This new data may help to reveal the character of the Kodiak-Bowie Seamount Chain and associated intraplate volcanism, much of which is concealed by the Surveyor and Baranof sedimentary fan systems. The Kodiak-Bowie Seamount Chain stretches over 1000 km across the Gulf of Alaska, from the Aleutian Trench in the northwest to offshore Queen Charlotte Islands in the southeast. The ages of the seamounts range from 24 Ma at Kodiak Seamount in the northwest to ≥0.7 Ma at Bowie Seamount in the southeast. Although the seamounts are largely age-progressive, some members of the chain are dated significantly out of sequence. Previous studies suggest the possibility that the majority of seamounts in the chain could be products of the Bowie plume. The Gulf-wide Aja Fracture Zone intersects the Kodiak-Bowie Seamount Chain in the central Gulf at the location of the seismic lines. Preliminary tomographic inversions of the seismic data reveal significant changes in crustal thickness across the Aja Fracture Zone, including at least a 3 km step up in the moho from south to north. Additionally, the region north of the Fracture Zone exhibits a 3 km thick low velocity zone in the upper crust, which is double the thickness of the same feature south of the fracture zone. This low velocity zone in the upper crust may be representative of intraplate volcanism associated with the Kodiak-Bowie Chain; several higher velocity perturbations within this zone are coincident with the locations of major seamounts. We will further refine

  5. BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

    PubMed Central

    Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok-Soo

    2016-01-01

    Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. PMID:27151195

  6. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  7. Structural Basis for Substrate Fatty Acyl Chain Specificity: Crystal Structure of Human Very-Long-Chain Acyl-CoA Dehydrogenase

    SciTech Connect

    McAndrew, Ryan P.; Wang, Yudong; Mohsen, Al-Walid; He, Miao; Vockley, Jerry; Kim, Jung-Ja P.

    2008-08-26

    Very-long-chain acyl-CoA dehydrogenase (VLCAD) is a member of the family of acyl-CoA dehydrogenases (ACADs). Unlike the other ACADs, which are soluble homotetramers, VLCAD is a homodimer associated with the mitochondrial membrane. VLCAD also possesses an additional 180 residues in the C terminus that are not present in the other ACADs. We have determined the crystal structure of VLCAD complexed with myristoyl-CoA, obtained by co-crystallization, to 1.91-{angstrom} resolution. The overall fold of the N-terminal {approx}400 residues of VLCAD is similar to that of the soluble ACADs including medium-chain acyl-CoA dehydrogenase (MCAD). The novel C-terminal domain forms an {alpha}-helical bundle that is positioned perpendicular to the two N-terminal helical domains. The fatty acyl moiety of the bound substrate/product is deeply imbedded inside the protein; however, the adenosine pyrophosphate portion of the C14-CoA ligand is disordered because of partial hydrolysis of the thioester bond and high mobility of the CoA moiety. The location of Glu-422 with respect to the C2-C3 of the bound ligand and FAD confirms Glu-422 to be the catalytic base. In MCAD, Gln-95 and Glu-99 form the base of the substrate binding cavity. In VLCAD, these residues are glycines (Gly-175 and Gly-178), allowing the binding channel to extend for an additional 12{angstrom} and permitting substrate acyl chain lengths as long as 24 carbons to bind. VLCAD deficiency is among the more common defects of mitochondrial {beta}-oxidation and, if left undiagnosed, can be fatal. This structure allows us to gain insight into how a variant VLCAD genotype results in a clinical phenotype.

  8. Design of an active ultrastable single-chain insulin analog: synthesis, structure, and therapeutic implications.

    PubMed

    Hua, Qing-xin; Nakagawa, Satoe H; Jia, Wenhua; Huang, Kun; Phillips, Nelson B; Hu, Shi-quan; Weiss, Michael A

    2008-05-23

    Single-chain insulin (SCI) analogs provide insight into the inter-relation of hormone structure, function, and dynamics. Although compatible with wild-type structure, short connecting segments (<3 residues) prevent induced fit upon receptor binding and so are essentially without biological activity. Substantial but incomplete activity can be regained with increasing linker length. Here, we describe the design, structure, and function of a single-chain insulin analog (SCI-57) containing a 6-residue linker (GGGPRR). Native receptor-binding affinity (130 +/- 8% relative to the wild type) is achieved as hindrance by the linker is offset by favorable substitutions in the insulin moiety. The thermodynamic stability of SCI-57 is markedly increased (DeltaDeltaG(u) = 0.7 +/- 0.1 kcal/mol relative to the corresponding two-chain analog and 1.9 +/- 0.1 kcal/mol relative to wild-type insulin). Analysis of inter-residue nuclear Overhauser effects demonstrates that a native-like fold is maintained in solution. Surprisingly, the glycine-rich connecting segment folds against the insulin moiety: its central Pro contacts Val(A3) at the edge of the hydrophobic core, whereas the final Arg extends the A1-A8 alpha-helix. Comparison between SCI-57 and its parent two-chain analog reveals striking enhancement of multiple native-like nuclear Overhauser effects within the tethered protein. These contacts are consistent with wild-type crystal structures but are ordinarily attenuated in NMR spectra of two-chain analogs, presumably due to conformational fluctuations. Linker-specific damping of fluctuations provides evidence for the intrinsic flexibility of an insulin monomer. In addition to their biophysical interest, ultrastable SCIs may enhance the safety and efficacy of insulin replacement therapy in the developing world.

  9. Magnetism and electronic structure of Fe chains and nano-wires

    NASA Astrophysics Data System (ADS)

    Yang, Tzong-Jer; Zhao, Yu-Jun; Freeman, A. J.

    2004-05-01

    The electronic and magnetic structures of an Fe linear chain and FCC and BCC nano-wires were determined by accurate first-principles self-consistent full potential linearized augmented plane wave calculations. The one-dimensional nature of the systems results in dramatic changes in their properties—as expected from the early predictions of Weinert and Freeman (J. Mag. Magn. Mater. 38 (1983) 23) for linear transition metal chains: a high density of states arising from van Hove singularities, large s-d-exchange splittings (larger in the chain than in the wires) and filled majority d bands (i.e., a "strong Stoner" ferromagnet) and strikingly enhanced Fe magnetic moments that depend on their coordination number. These unusual and distinctive properties are expected to invite somewhat unique experimental characterizations.

  10. Correlation between morphology, electron band structure, and resistivity of Pb atomic chains on the Si(5 5 3)-Au surface.

    PubMed

    Jałochowski, M; Kwapiński, T; Łukasik, P; Nita, P; Kopciuszyński, M

    2016-07-20

    Structural and electron transport properties of multiple Pb atomic chains fabricated on the Si(5 5 3)-Au surface are investigated using scanning tunneling spectroscopy, reflection high electron energy diffraction, angular resolved photoemission electron spectroscopy and in situ electrical resistance. The study shows that Pb atomic chains growth modulates the electron band structure of pristine Si(5 5 3)-Au surface and hence changes its sheet resistivity. Strong correlation between chains morphology, electron band structure and electron transport properties is found. To explain experimental findings a theoretical tight-binding model of multiple atomic chains interacting on effective substrate is proposed.

  11. Correlation between morphology, electron band structure, and resistivity of Pb atomic chains on the Si(5 5 3)-Au surface

    NASA Astrophysics Data System (ADS)

    Jałochowski, M.; Kwapiński, T.; Łukasik, P.; Nita, P.; Kopciuszyński, M.

    2016-07-01

    Structural and electron transport properties of multiple Pb atomic chains fabricated on the Si(5 5 3)-Au surface are investigated using scanning tunneling spectroscopy, reflection high electron energy diffraction, angular resolved photoemission electron spectroscopy and in situ electrical resistance. The study shows that Pb atomic chains growth modulates the electron band structure of pristine Si(5 5 3)-Au surface and hence changes its sheet resistivity. Strong correlation between chains morphology, electron band structure and electron transport properties is found. To explain experimental findings a theoretical tight-binding model of multiple atomic chains interacting on effective substrate is proposed.

  12. Helical structures in vertically aligned dust particle chains in a complex plasma.

    PubMed

    Hyde, Truell W; Kong, Jie; Matthews, Lorin S

    2013-05-01

    Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ(2)=(ω(0h)/ω(0v))(2) (where ω(0h,v) are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. E 85, 016406 (2012)].

  13. Communication: Role of short chain branching in polymer structure and dynamics.

    PubMed

    Kim, Jun Mo; Baig, Chunggi

    2016-02-28

    A comprehensive understanding of chain-branching effects, essential for establishing general knowledge of the structure-property-phenomenon relationship in polymer science, has not yet been found, due to a critical lack of knowledge on the role of short-chain branches, the effects of which have mostly been neglected in favor of the standard entropic-based concepts of long polymers. Here, we show a significant effect of short-chain branching on the structural and dynamical properties of polymeric materials, and reveal the molecular origins behind the fundamental role of short branches, via atomistic nonequilibrium molecular dynamics and mesoscopic Brownian dynamics by systematically varying the strength of the mobility of short branches. We demonstrate that the fast random Brownian kinetics inherent to short branches plays a key role in governing the overall structure and dynamics of polymers, leading to a compact molecular structure and, under external fields, to a lesser degree of structural deformation of polymer, to a reduced shear-thinning behavior, and to a smaller elastic stress, compared with their linear analogues. Their fast dynamical nature being unaffected by practical flow fields owing to their very short characteristic time scale, short branches would substantially influence (i.e., facilitate) the overall relaxation behavior of polymeric materials under various flowing conditions.

  14. Synconset Waves and Chains: Spiking Onsets in Synchronous Populations Predict and Are Predicted by Network Structure

    PubMed Central

    Raghavan, Mohan; Amrutur, Bharadwaj; Narayanan, Rishikesh; Sikdar, Sujit Kumar

    2013-01-01

    Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define ‘synconset wave’ as a cascade of first spikes within a synchronisation event. Synconset waves would occur in ‘synconset chains’, which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of

  15. Conceptual Model of Supply Chain Structure Mapping - A Case of Subsidized LPG Commodity in Yogyakarta

    NASA Astrophysics Data System (ADS)

    Sulistio, Joko; Thoif, Afifuddin; Fitri Alindira, Aulia

    2016-01-01

    — In 2007, the government launched a conversion program of kerosene to LPG by issuing a Presidential Regulation No. 104/2007 on Supply, Distribution and Pricing LPG 3 Kg. Article 2 on the regulation says that setting the supply, distribution, and pricing of LPG 3 Kg include planning an annual sales volume of enterprises, the reference price and the retail price and conditions of export and import of LPG 3 Kg in order to reduce subsidies Kerosene especially to divert the use of kerosene according to government policy. In principle, the purpose of this policy is to reduce energy subsidies on commodities, especially Kerosene. Although the government claimed the conversion program is success, there are few problems arising from conversion program. In 2014, many scarcity and high price of LPG 3 Kg were reported. In this case, Pertamina was given full authority to manage all supply chain and distribution. Because the root of the problem of scarcity that occurred in the supply chain system has not been explained, the proposed solutions will also be partial and not comprehensive. Thus, this research will build a structural map of the causes of supply chain system LPG 3 Kg, as well as providing a comprehensive picture of system dynamics of LPG 3 Kg supply chain system which applied in Indonesia. And the result is expected as in form of Causal Loop Diagram of supply chain system.

  16. First-Principles Analysis on π-bonded Chain Structure on Several Polytypes of SiC Surfaces: Importance of Stacking Sequence on Energetics and Electronic Structures

    NASA Astrophysics Data System (ADS)

    Kaneko, Tomoaki; Tajima, Nobuo; Yamasaki, Takahiro; Ohno, Takahisa

    2017-09-01

    Using first principles calculations based on a density functional theory, the energetics and electronic properties of a (2 × 1) π-bonded chain structure in several polytypes of SiC surfaces are discussed with special attention to the stacking sequence of SiC bilayers. We found that the stacking sequence of the topmost two SiC bilayers plays a decisive role for the stability and electronic structures of the π-bonded chain structure. We showed that the homo-elemental bonds in π-bonded chain structures cause alterations in the electronic structures of both the Si- and C-faces. The energetics of π-bonded chain structures on other group IV and IV-IV compound semiconductors were also investigated. We also showed that the buckling structure in the monolayer honeycomb lattice reflects the buckling of the topmost two atoms in the π-bonded chain structure observed in Si(111) and Ge(111).

  17. Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

    SciTech Connect

    Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; Goswami, Monojoy; Sokolov, Alexei P; Sumpter, Bobby G.

    2015-06-11

    Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z), mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[ni(t,z)•ni(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.

  18. Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

    DOE PAGES

    Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; ...

    2015-06-11

    Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z),more » mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[ni(t,z)•ni(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.« less

  19. Conserved structure of amphibian T-cell antigen receptor beta chain.

    PubMed Central

    Fellah, J S; Kerfourn, F; Guillet, F; Charlemagne, J

    1993-01-01

    All jawed vertebrates possess well-differentiated thymuses and elicit T-cell-like cell-mediated responses; however, no surface T-cell receptor (TCR) molecules or TCR genes have been identified in ectothermic vertebrate species. Here we describe cDNA clones from an amphibian species, Ambystoma mexicanum (the Mexican axolotl), that have sequences highly homologous to the avian and mammalian TCR beta chains. The cloned amphibian beta chain variable region (V beta) shares most of the structural characteristics with the more evolved vertebrate V beta and presents approximately 56% amino acid identities with the murine V beta 14 and human V beta 18 families. The two different cloned axolotl beta chain joining regions (J beta) were found to have conserved all the invariant mammalian J beta residues, and in addition, the presence of a conserved glycine at the V beta-J beta junction suggests the existence of diversity elements. The extracellular domains of the two axolotl beta chain constant region isotypes C beta 1 and C beta 2 show an impressively high degree of identity, thus suggesting that a very efficient mechanism of gene correction has been in operation to preserve this structure at least from the early tetrapod evolution. The transmembrane axolotl C beta domains have been less well conserved when compared to the mammalian C beta but they do maintain the lysine residue that is thought to be involved in the charged interaction between the TCR alpha beta heterodimer and the CD3 complex. Images Fig. 1 PMID:8341702

  20. Quasiparticle band structure of infinite hydrogen fluoride and hydrogen chloride chains.

    PubMed

    Buth, Christian

    2006-10-21

    We study the quasiparticle band structure of isolated, infinite (HF)(infinity) and (HCl)(infinity) bent (zigzag) chains and examine the effect of the crystal field on the energy levels of the constituent monomers. The chains are one of the simplest but realistic models of the corresponding three-dimensional crystalline solids. To describe the isolated monomers and the chains, we set out from the Hartree-Fock approximation, harnessing the advanced Green's function methods local molecular orbital algebraic diagrammatic construction (ADC) scheme and local crystal orbital ADC (CO-ADC) in a strict second order approximation, ADC(2,2) and CO-ADC(2,2), respectively, to account for electron correlations. The configuration space of the periodic correlation calculations is found to converge rapidly only requiring nearest-neighbor contributions to be regarded. Although electron correlations cause a pronounced shift of the quasiparticle band structure of the chains with respect to the Hartree-Fock result, the bandwidth essentially remains unaltered in contrast to, e.g., covalently bound compounds.

  1. Intraglobular structures in multiblock copolymer chains from a Monte Carlo simulation.

    PubMed

    Lewandowski, K; Banaszak, M

    2011-07-01

    Multiblock copolymer chains in implicit nonselective solvents are studied by using a Monte Carlo method, which employs a parallel tempering algorithm. Chains consisting of 120 A and 120 B monomers, arranged in three distinct microarchitectures: (10-10)12, (6-6)20, and (3-3)40, collapse to globular states upon cooling, as expected. By varying both the reduced temperature T* and the compatibility between monomers ω, numerous intraglobular structures are obtained: diclusters (handshake, spiral, torus with a core, etc.), triclusters, and n clusters with n>3 (lamellar and other), which are reminiscent of the block copolymer nanophases for spherically confined geometries. Phase diagrams for various chains in the (T*,ω) space are mapped. The structure factor S(k), for a selected microarchitecture and ω, is calculated. Since S(k) can be measured in scattering experiments, it can be used to relate simulation results to an experiment. Self-assembly in those systems is interpreted in terms of competition between minimization of the interfacial area separating different types of monomers and minimization of contacts between chain and solvent. Finally, the relevance of this model to the protein folding is addressed.

  2. A novel method of preparing the monoform structure of catalytic antibody light chain.

    PubMed

    Hifumi, Emi; Matsumoto, Shingo; Nakashima, Hiroki; Itonaga, Shogo; Arakawa, Mitsue; Katayama, Yoshiki; Kato, Ryuichi; Uda, Taizo

    2016-02-01

    Along with the development of antibody drugs and catalytic antibodies, the structural diversity (heterogeneity) of antibodies has been given attention. For >20 yr, detailed studies on the subject have not been conducted, because the phenomenon presents many difficult and complex problems. Structural diversity provides some (or many) isoforms of an antibody distinguished by different charges, different molecular sizes, and modifications of amino acid residues. For practical use, the antibody and the subunits must have a defined structure. In recent work, we have found that the copper (Cu) ion plays a substantial role in solving the diversity problem. In the current study, we used several catalytic antibody light chains to examine the effect of the Cu ion. In all cases, the different electrical charges of the molecule converged to a single charge, giving 1 peak in cation-exchange chromatography, as well as a single spot in 2-dimensional gel electrophoresis. The Cu-binding site was investigated by using mutagenesis, ultraviolet-visible spectroscopy, atomic force microscope analysis, and molecular modeling, which suggested that histidine and cysteine residues close to the C-terminus are involved with the binding site. The constant region domain of the antibody light chain played an important role in the heterogeneity of the light chain. Our findings may be a significant tool for preparing a single defined, not multiple, isoform structure.

  3. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  4. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  5. Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations

    NASA Astrophysics Data System (ADS)

    Itoh, Kazuhito; Sasai, Masaki

    2011-03-01

    A statistical mechanical model of allosteric transition of proteins is developed by extending the structure-based model of protein folding to cases that a protein has two different native conformations. Partition function is calculated exactly within the model and free-energy surfaces associated with allostery are derived. In this paper, the model of allosteric transition proposed in a previous paper [Proc. Natl. Acad. Sci. U.S.A 134, 7775 (2010)] is reformulated to describe both fluctuation in side-chain configurations and that in backbone structures in a balanced way. The model is applied to example proteins, Ras, calmodulin, and CheY: Ras undergoes the allosteric transition between guanosine diphosphate (GDP)-bound and guanosine triphosphate (GTP)-bound forms, and the model results show that the GDP-bound form is stabilized enough to prevent unnecessary signal transmission, but the conformation in the GTP-bound state bears large fluctuation in side-chain configurations, which may help to bind multiple target proteins for multiple pathways of signaling. The calculated results of calmodulin show the scenario of sequential ordering in Ca2 + binding and the associated allosteric conformational change, which are realized though the sequential appearing of pre-existing structural fluctuations, i.e., fluctuations to show structures suitable to bind Ca2 + before its binding. Here, the pre-existing fluctuations to accept the second and third Ca2 + ions are dominated by the side-chain fluctuation. In CheY, the calculated side-chain fluctuation of Tyr106 is coordinated with the backbone structural change in the β4-α4 loop, which explains the pre-existing Y-T coupling process in this protein. Ability of the model to explain allosteric transitions of example proteins supports the view that the large entropic effects lower the free-energy barrier of allosteric transition.

  6. Structure of heavy and light chain subunits of type A botulinum neurotoxin analyzed by circular dichroism and fluorescence measurements.

    PubMed

    Singh, B R; DasGupta, B R

    1989-01-23

    The secondary and tertiary structural features of botulinum neurotoxin (NT) serotype A, a dichain protein (Mr 145,000), and its two subunits, the heavy (H) and light (L) chains (Mr 97,000 and 53,000, respectively) were examined using circular dichroism and fluorescence spectorscopy. Nearly 70% of the amino acid residues in each of the three polypeptide preparations were found in ordered structure (sum of alpha helix, beta sheet and beta turns). Also, the alpha helix, beta sheet, beta turns and random coil contents of the dichain NT were nearly equal to the weighted mean of each of these secondary structure parameters of the L and H chains; e.g., sum of alpha helix of L chain (22%) and H chain (18.7%), as weighted mean, 19.8% was similar to that of NT (20%). These agreements suggested that the secondary structures of the subunits of the dichain NT do not significantly change when they are separated as isolated L and H chains. Fluorescence emission maximum of L chain, 4 nm less (blue shift) than that of H chain, suggested relatively more hydrophobic environment of fluorescent tryptophan residue(s) of L chain. Tryptophan fluorescence quantum yields of L chain, H chain and the NT, 0.072, 0.174 and 0.197, respectively, suggested that a) an alteration in the micro-environment of the tryptophan residues was possibly caused by interactions of L and H chain subunits of the NT and b) quantum yields for L and H chains were altered when they are together as subunits of the NT. Possible implications of structural features of the L and H chains, their interactions and the molecular mechanism of action of botulinum NT are assessed.

  7. Energetically unfavorable amide conformations for N6-acetyllysine side chains in refined protein structures.

    PubMed

    Genshaft, Alexander; Moser, Joe-Ann S; D'Antonio, Edward L; Bowman, Christine M; Christianson, David W

    2013-06-01

    The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular "switch" for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations.

  8. Probing structure-induced optical behavior in a new class of self-activated luminescent 0D/1D CaWO₄ metal oxide – CdSe nanocrystal composite heterostructures

    DOE PAGES

    Han, Jinkyu; McBean, Coray; Wang, Lei; ...

    2015-01-30

    In this report, we synthesize and characterize the structural and optical properties of novel heterostructures composed of (i) semiconducting nanocrystalline CdSe quantum dot (QDs) coupled with (ii) both one and zero-dimensional (1D and 0D) motifs of self-activated luminescence CaWO₄ metal oxides. Specifically, ~4 nm CdSe QDs have been anchored onto (i) high-aspect ratio 1D nanowires, measuring ~230 nm in diameter and ~3 μm in length, as well as onto (ii) crystalline 0D nanoparticles (possessing an average diameter of ~ 80 nm) of CaWO₄ through the mediation of 3-mercaptopropionic acid (MPA) as a connecting linker. Composite formation was confirmed by complementarymore » electron microscopy and spectroscopy (i.e. IR and Raman) data. In terms of luminescent properties, our results show that our 1D and 0D heterostructures evince photoluminescence (PL) quenching and shortened PL lifetimes of CaWO₄ as compared with unbound CaWO₄. We propose that a photo-induced electron transfer process occurs from CaWO₄ to CdSe QDs, a scenario which has been confirmed by NEXAFS measurements and which highlights a decrease in the number of unoccupied orbitals in the conduction bands of CdSe QDs. By contrast, the PL signature and lifetimes of MPA-capped CdSe QDs within these heterostructures do not exhibit noticeable changes as compared with unbound MPA-capped CdSe QDs. The striking difference in optical behavior between CaWO₄ nanostructures and CdSe QDs within our heterostructures can be correlated with the relative positions of their conduction and valence energy band levels. In addition, the PL quenching behaviors for CaWO₄ within the heterostructure configuration were examined by systematically varying (i) the quantities and coverage densities of CdSe QDs as well as (ii) the intrinsic morphology (and by extension, the inherent crystallite size) of CaWO₄ itself.« less

  9. Energetic, Structural, and Antimicrobial Analyses of [beta]-Lactam Side Chain Recognition by [beta]-Lactamases

    SciTech Connect

    Caselli, E.; Powers, R.A.; Blaszczak, L.C.; Wu, C.Y.E.; Prati, F.; Shoichet, B.K.

    2010-03-05

    Penicillins and cephalosporins are among the most widely used and successful antibiotics. The emergence of resistance to these {beta}-lactams, most often through bacterial expression of {beta}-lactamases, threatens public health. To understand how {beta}-lactamases recognize their substrates, it would be helpful to know their binding energies. Unfortunately, these have been difficult to measure because {beta}-lactams form covalent adducts with {beta}-lactamases. This has complicated functional analyses and inhibitor design. To investigate the contribution to interaction energy of the key amide (R1) side chain of {beta}-lactam antibiotics, eight acylglycineboronic acids that bear the side chains of characteristic penicillins and cephalosporins, as well as four other analogs, were synthesized. These transition-state analogs form reversible adducts with serine {beta}-lactamases. Therefore, binding energies can be calculated directly from K{sub i} values. The K{sub i} values measured span four orders of magnitude against the Group I {beta}-lactamase AmpC and three orders of magnitude against the Group II {beta}-lactamase TEM-1. The acylglycineboronic acids have K{sub i} values as low as 20 nM against AmpC and as low as 390 nM against TEM-1. The inhibitors showed little activity against serine proteases, such as chymotrypsin. R1 side chains characteristic of {beta}-lactam inhibitors did not have better affinity for AmpC than did side chains characteristic of {beta}-lactam substrates. Two of the inhibitors reversed the resistance of pathogenic bacteria to {beta}-lactams in cell culture. Structures of two inhibitors in their complexes with AmpC were determined by X-ray crystallography to 1.90 {angstrom} and 1.75 {angstrom} resolution; these structures suggest interactions that are important to the affinity of the inhibitors. Acylglycineboronic acids allow us to begin to dissect interaction energies between {beta}-lactam side chains and {beta}-lactamases. Surprisingly

  10. Spin structure factors of Heisenberg spin chain in the presence of anisotropy and magnetic field

    NASA Astrophysics Data System (ADS)

    Rezania, H.

    2017-02-01

    We have theoretically studied the spin structure factors of spin chain in the presence of longitudinal field and transverse anisotropy. The possible effects of easy axis magnetization are investigated in terms of anisotropy in the Heisenberg interactions. This anisotropy is considered for exchange coupling constants perpendicular to magnetic field direction. The original spin model hamiltonian is mapped to a bosonic model via a hard core bosonic transformation where an infinite hard core repulsion is imposed to constrain one boson occupation per site. Using Green's function approach, the energy spectrum of quasiparticle excitation has been obtained. The spectrum of the bosonic gas has been implemented in order to obtain two particle propagator which corresponds to spin structure factor of original Heisenberg chain model Hamiltonian. The results show the position of peak in the longitudinal structure factor at fixed value for anisotropy moves to higher frequency with magnetic field. Also the intensity of dynamical structure factor decreases with magnetic field. A small dependence of longitudinal dynamical spin structure factor on the anisotropy is observed for fixed value of magnetic field. Our results show longitudinal static structure factor is found to be monotonically increasing with magnetic field due to increase of spins aligning along magnetic field. Furthermore the dispersion behaviors of static longitudinal and transverse structure factors for different magnetic fields and anisotropy parameters are addressed.

  11. The single chain limit of structural relaxation in a polyolefin blend

    NASA Astrophysics Data System (ADS)

    May, Andrew F.; Maranas, Janna K.

    2006-07-01

    The influence of composition on component dynamics and relevant static properties in a miscible polymer blend is investigated using molecular dynamics simulation. Emphasis is placed on dynamics in the single chain dilution limit, as this limit isolates the role of inherent component mobility in the polymer's dynamic behavior when placed in a blend. For our systems, a biased local concentration affecting dynamics must arise primarily from chain connectivity, which is quantified by the self-concentration, because concentration fluctuations are minimized due to restraints on chain lengths arising from simulation considerations. The polyolefins simulated [poly(ethylene-propylene) (PEP) and poly(ethylene-butene) (PEB)] have similar structures and glass transition temperatures, and all interactions are dispersive in nature. We find that the dependence of dynamics upon composition differs between the two materials. Specifically, PEB (slower component) is more influenced by the environment than PEP. This is linked to a smaller self-concentration for PEB than PEP. We examine the accuracy of the Lodge-McLeish model (which is based on chain connectivity acting over the Kuhn segment length) in predicting simulation results for effective concentration. The model predicts the simulation results with high accuracy when the model's single parameter, the self-concentration, is calculated from simulation data. However, when utilizing the theoretical prediction of the self-concentration the model is not quantitatively accurate. The ability of the model to link the simulated self-concentration with biased local compositions at the Kuhn segment length provides strong support for the claim that chain connectivity is the leading cause of distinct mobility in polymer blends. Additionally, the direct link between the willingness of a polymer to be influenced by the environment and the value of the self-concentration emphasizes the importance of the chain connectivity. Furthermore, these

  12. Synthesis of 1D Fe₃O₄/P(MBAAm-co-MAA) nanochains as stabilizers for Ag nanoparticles and templates for hollow mesoporous structure, and their applications in catalytic reaction and drug delivery.

    PubMed

    Zhang, Wei; Si, Xiaowei; Liu, Bin; Bian, Guomin; Qi, Yonglin; Yang, Xinlin; Li, Chenxi

    2015-10-15

    One-dimensional (1D) magnetic Fe3O4/P(MBAAm-co-MAA) nanochains were prepared by distillation-precipitation polymerization of MBAAm and MAA in the presence of Fe3O4 nanoparticles as building blocks under a magnetic heating stirrer, which played two critical roles: serving as magnetic field to induce the self-assembly of Fe3O4 nanoparticles into 1D nanochains and providing thermal energy to induce the polymerization of MAA and MBAAm on the surface of the Fe3O4 nanoparticles. The thickness of the P(MBAAm-co-MAA) layer can be easily tuned by adjusting the successive polymerization steps. The polymer layer that contained carboxyl groups was used as stabilizers for loading Ag nanoparticles and the reaction locus for deposition of outer silica layer via a sol-gel method in presence of C18TMS as the pore directing agent for tri-layer nanochains. The corresponding hollow mesoporous silica nanochains with movable maghemite cores (γ-Fe2O3@mSiO2) were produced after removal of the polymer mid-layer and the alkyl groups of the pore directing agent via calcination of the tri-layer nanochains at high temperature. The Fe3O4/P(MBAAm-co-MAA)/Ag nanochains exhibited a highly catalytic efficiency and well reusable property toward the reduction of nitrophenol. Furthermore, the γ-Fe2O3@mSiO2 nanochains possessed hollow mesoporous structure and high specific surface area (197.2 m(2) g(-1)) were used as a drug carrier, which displayed a controlled release property. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Crystal Structure of a Phosphorylated Light Chain Domain of Scallop Smooth-Muscle Myosin

    SciTech Connect

    Kumar, V.S.; Robinson, H.; O-Neall-Hennessey, E.; Reshetnikova, L.; Brown, J. H.; Szent-Gyorgyi, A. G.; Cohen, C.

    2011-11-02

    We have determined the crystal structure of a phosphorylated smooth-muscle myosin light chain domain (LCD). This reconstituted LCD is of a sea scallop catch muscle myosin with its phosphorylatable regulatory light chain (RLC SmoA). In the crystal structure, Arg{sup 16}, an arginine residue that is present in this isoform but not in vertebrate smooth-muscle RLC, stabilizes the phosphorylation site. This arginine interacts with the carbonyl group of the phosphorylation-site serine in the unphosphorylated LCD (determined previously), and with the phosphate group when the serine is phosphorylated. However, the overall conformation of the LCD is essentially unchanged upon phosphorylation. This result provides additional evidence that phosphorylation of the RLC is unlikely to act as an on-switch in regulation of scallop catch muscle myosin.

  14. Fiber Bragg gratings sensing network with a bus chain typology structure

    NASA Astrophysics Data System (ADS)

    Wen, Xiaoyan; Shuai, Huang; Zhu, Fangdong; Zhang, Dongsheng

    2016-06-01

    A fiber Bragg grating (FBG) sensing network with a bus chain typology structure based on time-division multiplexing (TDM) technology has been developed. Each FBG sensor was placed in an isolated branching circuit separated by an optical splitter. By doing this, multiple reflection and spectrum shadow, which are common in a traditional TDM network, were eliminated since incident light reflected by each sensor did not go through the other sensors. Interference among different FBGs was also avoided. The system was experimentally verified by constructing such a network with 17 FBGs involved. Wavelength and position interrogation were successfully realized. Temperature experiment was carried out on four of the FBGs and the sensitivity was 9.87, 9.92, 9.91, and 9.97 pm/°C, respectively. The durability, reliability, and measuring accuracy of the sensing network were effectively improved due to the bus chain typology structure.

  15. Characteristic Features of Molecular Structure and Packing of Organopolysilanes with Asymmetric Side Chains

    NASA Astrophysics Data System (ADS)

    Furukawa, Shoji; Ohta, Hidetaka

    2005-01-01

    The molecular structure and packing of poly(methyl ethyl silane), [(CH3)Si(C2H5)]n, and poly(methyl n-propyl silane), [(CH3)Si(C3H7)]n, have been examined by the X-ray diffraction method. For poly(methyl ethyl silane), several configurations are possible for the arrangement of the C2H5 group, whereas the C3H7 groups stretch along one equivalent direction for poly(methyl n-propyl silane). In both cases, the molecular structure and packing are mostly determined by the intramolecular steric hindrance and van der Waals interaction between side chains, which is the same as that of polysilanes with symmetric side chains.

  16. Cryo-EM reveals the steric zipper structure of a light chain-derived amyloid fibril

    PubMed Central

    Schmidt, Andreas; Annamalai, Karthikeyan; Schmidt, Matthias; Grigorieff, Nikolaus; Fändrich, Marcus

    2016-01-01

    Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a reconstruction of a fibril formed from the pathogenic core of an amyloidogenic immunoglobulin (Ig) light chain. The fibril density shows a lattice-like assembly of face-to-face packed peptide dimers that corresponds to the structure of steric zippers in peptide crystals. Interpretation of the density map with a molecular model enabled us to identify the intermolecular interactions between the peptides and rationalize the hierarchical structure of the fibril based on simple chemical principles. PMID:27185936

  17. Customer involvement in greening the supply chain: an interpretive structural modeling methodology

    NASA Astrophysics Data System (ADS)

    Kumar, Sanjay; Luthra, Sunil; Haleem, Abid

    2013-04-01

    The role of customers in green supply chain management needs to be identified and recognized as an important research area. This paper is an attempt to explore the involvement aspect of customers towards greening of the supply chain (SC). An empirical research approach has been used to collect primary data to rank different variables for effective customer involvement in green concept implementation in SC. An interpretive structural-based model has been presented, and variables have been classified using matrice d' impacts croises- multiplication appliqué a un classement analysis. Contextual relationships among variables have been established using experts' opinions. The research may help practicing managers to understand the interaction among variables affecting customer involvement. Further, this understanding may be helpful in framing the policies and strategies to green SC. Analyzing interaction among variables for effective customer involvement in greening SC to develop the structural model in the Indian perspective is an effort towards promoting environment consciousness.

  18. Alternation of Side-Chain Mesogen Orientation Caused by the Backbone Structure in Liquid-Crystalline Polymer Thin Films.

    PubMed

    Tanaka, Daisuke; Nagashima, Yuki; Hara, Mitsuo; Nagano, Shusaku; Seki, Takahiro

    2015-10-27

    In side-chain-type liquid-crystalline (LC) polymers, the main chain rigidity significantly affects the LC structure and properties. We show herein a relevant new effect regarding the orientation of side-chain mesogenic groups of LC polymers in a thin-film state. A subtle change in the main chain structure, i.e., polyacrylate and polymethacrylate, leads to a clear alternation of mesogens in the homeotropic and planar modes, respectively. This orientational discrimination is triggered from the free surface region (film-air interface) as revealed by surface micropatterning via inkjet printing.

  19. Single chain structure in thin polymer films: corrections to Flory's and Silberberg's hypotheses

    NASA Astrophysics Data System (ADS)

    Cavallo, A.; Müller, M.; Wittmer, J. P.; Johner, A.; Binder, K.

    2005-05-01

    Conformational properties of polymer melts confined between two hard structureless walls are investigated by Monte Carlo simulation of the bond fluctuation model. Parallel and perpendicular components of chain extension, bond-bond correlation function and structure factor are computed and compared with recent theoretical approaches attempting to go beyond Flory's and Silberberg's hypotheses. We demonstrate that for ultrathin films where the thickness, H, is smaller than the excluded volume screening length (blob size), ξ, the chain size parallel to the walls diverges logarithmically, R2/2Napb2+clog(N) with c~1/H. The corresponding bond-bond correlation function decreases like a power law, C(s) = d/sω with s being the curvilinear distance between bonds and ω = 1. Upon increasing the film thickness, H, we find—in contrast to Flory's hypothesis—the bulk exponent ω = 3/2 and, more importantly, a decreasing d(H) that gives direct evidence for an enhanced self-interaction of chain segments reflected at the walls. Systematic deviations from the Kratky plateau as a function of H are found for the single chain form factor parallel to the walls in agreement with the non-monotonic behaviour predicted by theory. This structure in the Kratky plateau might give rise to an erroneous estimation of the chain extension from scattering experiments. For large H the deviations are linear with the wavevector, q, but are very weak. In contrast, for ultrathin films, H<ξ, very strong corrections (albeit logarithmic in q) are found suggesting a possible experimental verification of our results.

  20. Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water.

    PubMed

    Head-Gordon, Teresa; Rick, Steven W

    2007-01-07

    A vast array of experimental data on water provides a global view of the liquid that implicates its tetrahedral hydrogen-bonding network as the unifying molecular connection to its observed structural, thermodynamic, and dielectric property trends with temperature. Recently the classification of water as a tetrahedral liquid has been challenged based on X-ray absorption (XAS) experiments on liquid water (Ph. Wernet et al., Science, 2004, 304, 995), which have been interpreted to show a hydrogen-bonding network that replaces tetrahedral structure with chains or large rings of water molecules. We examine the consequences of tetrahedral vs. chain networks using three different modified water models that exhibit a local hydrogen bonding environment of two hydrogen bonds (2HB) and therefore networks of chains. Using these very differently parameterized models we evaluate their bulk densities, enthalpies of vaporization, heat capacities, isothermal compressibilities, thermal expansion coefficients, and dielectric constants, over the temperature range of 235-323 K. We also evaluate the entropy of the 2HB models at room temperature and whether such models support an ice I(h) structure. All show poor agreement with experimentally measured thermodynamic and dielectric properties over the same temperature range, and behave similarly in most respects to normal liquids.

  1. O-chain structure from the lipopolysaccharide of the human pathogen Halomonas stevensii strain S18214.

    PubMed

    Pieretti, Giuseppina; Carillo, Sara; Kim, Kwang Kyu; Lee, Keun Chul; Lee, Jung-Sook; Lanzetta, Rosa; Parrilli, Michelangelo; Corsaro, M Michela

    2011-02-01

    Halomonas stevensii is a Gram-negative, pathogenic, moderately halophilic bacterium isolated from the blood of a renal care patient. It optimally grows at 30-35°C at pH 8-9 and at a sea salt concentration ranging from 3.0% to 7.5%. Gram-negative bacterial infections are closely associated with the presence of the lipopolysaccharides (LPSs) on the outer membrane. These molecules consist of three regions covalently linked: the glycolipid (lipid A), the oligosaccharide region (core region), and the O-specific polysaccharide (O-chain, O-antigen). O-antigen seems to play an important role in the colonization step (adherence) and the ability to bypass host defense mechanisms. For this reason the structure elucidation of the O-chain repeating unit is important to improve knowledge about the role of LPS in the host-pathogen interaction. In this paper, we report the complete structure of the O-chain from the LPS of H. stevensii. The bacterial cells were cultivated and LPS was extracted by the PCP (phenol-chloroform-petroleum ether) method. After mild acid hydrolysis, the lipid A was removed by centrifugation and the obtained polysaccharide was analyzed by means of chemical analysis and one- and two-dimensional NMR spectroscopy giving the following structure: 2010 Elsevier Ltd. All rights reserved.

  2. Retrobiosynthetic Approach Delineates the Biosynthetic Pathway and the Structure of the Acyl Chain of Mycobacterial Glycopeptidolipids*

    PubMed Central

    Vats, Archana; Singh, Anil Kumar; Mukherjee, Raju; Chopra, Tarun; Ravindran, Madhu Sudhan; Mohanty, Debasisa; Chatterji, Dipankar; Reyrat, Jean-Marc; Gokhale, Rajesh S.

    2012-01-01

    Glycopeptidolipids (GPLs) are dominant cell surface molecules present in several non-tuberculous and opportunistic mycobacterial species. GPLs from Mycobacterium smegmatis are composed of a lipopeptide core unit consisting of a modified C26-C34 fatty acyl chain that is linked to a tetrapeptide (Phe-Thr-Ala-alaninol). The hydroxyl groups of threonine and terminal alaninol are further modified by glycosylations. Although chemical structures have been reported for 16 GPLs from diverse mycobacteria, there is still ambiguity in identifying the exact position of the hydroxyl group on the fatty acyl chain. Moreover, the enzymes involved in the biosynthesis of the fatty acyl component are unknown. In this study we show that a bimodular polyketide synthase in conjunction with a fatty acyl-AMP ligase dictates the synthesis of fatty acyl chain of GPL. Based on genetic, biochemical, and structural investigations, we determine that the hydroxyl group is present at the C-5 position of the fatty acyl component. Our retrobiosynthetic approach has provided a means to understand the biosynthesis of GPLs and also resolve the long-standing debate on the accurate structure of mycobacterial GPLs. PMID:22798073

  3. Layered and molecular-structural control in polyoxomolybdate hybrid crystals by surfactant chain length

    NASA Astrophysics Data System (ADS)

    Ito, Takeru; Nakagawa, Masashi; Kobayashi, Jun; Matsumoto, Takashi; Otobe, Saki; Naruke, Haruo

    2016-02-01

    Polyoxomolybdate-surfactant hybrid layered crystals were synthesized by using single-tailed alkyltrimethylammonium ([CnH2n+1N(CH3)3]+ (Cn), n = 8, 10, 12, 14, 16, and 18) cations. The crystal structures consisted of alternate stacking of octamolybdate ([Mo8O26]4-, Mo8) anionic layers and surfactant cationic layers. The layered distance of the hybrid crystals became longer from 18.5 Å to 26.5 Å with an increase in alkyl chain length. Interestingly, the molecular structures of Mo8, which has several isomers, depended on the alkyl chain length of the employed surfactants. Shorter surfactant (C8 and C10) formed hybrid crystals containing β-type Mo8 isomer, while surfactant with longer alkyl chain (C12, C14, C16, and C18) gave crystals containing δ-type Mo8 isomer. This structural controllability will lead to the precise functional control in the polyoxomolybdate-surfactant hybrid layered crystals.

  4. Cyano-bridged coordination polymer hydrogel-derived Sn-Fe binary oxide nanohybrids with structural diversity: from 3D, 2D, to 2D/1D and enhanced lithium-storage performance.

    PubMed

    Zhang, Weiyu; Zhu, Xiaoshu; Chen, Xuguang; Zhou, Yiming; Tang, Yawen; Ding, Liangxin; Wu, Ping

    2016-05-14

    Metal oxide nanohybrids with uniform dimensions and controlled architectures possess unique compositional and structural superiorities, and thus harbor promising potential for a series of applications in energy, catalysis, and sensing systems. Herein, we propose a facile, general, and scalable cyano-bridged coordination polymer hydrogel-derived thermal-oxidation route for the construction of main-group metal and transition-metal heterometallic oxide nanohybrids with controlled constituents and architectures. The formation of Sn-Fe binary oxide nanohybrids has been demonstrated as an example by using cyano-bridged Sn(iv)-Fe(ii) bimetallic coordination polymer hydrogels (i.e., SnCl4-K4Fe(CN)6 cyanogels, Sn-Fe cyanogels) as precursors. The physicochemical properties of Sn-Fe cyanogels with different Sn/Fe ratios have been systematically examined, and it is found that perfect Sn-Fe cyanogels without unbridged Sn(iv) or Fe(ii) can be formed with Sn/Fe ratios from 2 : 1 to 1 : 2. More importantly, the simple adjustment of Sn/Fe ratios in the Sn-Fe cyanogel precursors can realize flexible dimensional control of the Sn-Fe binary oxide nanohybrids, and 2D/1D SnO2-Fe2O3 hierarchitectures, 2D SnO2-Fe2O3 nanosheets, and 3D SnO2-Fe2O3 networks have been synthesized using the Sn-Fe 1 : 2, Sn-Fe 1 : 1, and Sn-Fe 2 : 1 cyanogels as precursors, respectively. To demonstrate their compositional/structural superiorities and potential applications, the lithium-storage utilization of the Sn-Fe binary oxide nanohybrids has been selected as an objective application, and the nanohybrids exhibit Sn/Fe ratio-dependent lithium-storage performance. As a representative example, the 2D/1D SnO2-Fe2O3 hierarchitectures manifest markedly enhanced Li-storage performance in terms of reversible capacities and cycling stability in comparison with their constituent units, i.e., bare SnO2 nanosheets and Fe2O3 nanorods. The proposed cyanogel-derived thermal-oxidation strategy could

  5. Ricin A-chain structural determinant for binding substrate analogues: a molecular dynamics simulation analysis.

    PubMed

    Olson, M A

    1997-01-01

    Ricin A-chain is a cytotoxic protein that attacks ribosomes by hydrolyzing a specific adenine base from a highly conserved, single-stranded rRNA hairpin containing the tetraloop sequence GAGA. Molecular-dynamics simulation methods are used to analyze the structural determinant for three substrate analogues bound to the ricin A-chain molecule. Simulations were applied to the binding of the dinucleotide adenyl-3',5'-guanosine employing the x-ray crystal structure of the ricin complex and a modeled CGAGAG hexanucleotide loop taken from the NMR solution structure of a 29-mer oligonucleotide hairpin. A third simulation model is also presented describing a conformational search of the docked 29-mer structure by using a simulated-annealing method. Analysis of the structural interaction energies for each model shows the overall binding dominated by nonspecific interactions, which are mediated by specific arginine contracts from the highly basic region on the protein surface. The tetraloop conformation of the 29-mer was found to make specific interactions with conserved protein residues, in a manner that favored the GAGA sequence. A comparison of the two docked loop conformations with the NMR structure revealed significant positional deviations, suggesting that ricin may use an induced fit mechanism to recognize and bind the rRNA substrate. The conserved Tyr-80 may play an important conformational entropic role in the binding and release of the target adenine in the active site.

  6. Synthesis and characterization of metal(II) fluconazole complexes: Chain-like structure and photoluminescence

    NASA Astrophysics Data System (ADS)

    Gong, Yun; Hu, Chang Wen; Xia, Zhi Ning

    2007-06-01

    Three coordination polymers (flu) 2CuBr 2·2H 2O ( 1), (flu) 2Zn(ClO 4) 2·2H 2O ( 2), (flu) 4Ni 2(H 2O) 4(Mo 8O 26) · 6H 2O ( 3), (flu = fluconazole) have been hydrothermally synthesized and characterized by elemental analysis, IR and single-crystal X-ray diffraction. Compounds 1- 3 exhibit similar one dimensional chain-like structures linked by double stranded fluconazole-bridge. In the self-assembly of compounds 1- 3, the introduction of anions with different sizes and geometrical configurations lead to the flexible C-C chain of fluconazole to be rotated for suitable position and angle to hold them. Similar inter-chain hydrogen bonding interactions are observed in compounds 1 and 2, whereas compound 3 exhibits a different three dimensional supramolecular architecture in which different chains are linked by [Mo 8O 26] 4- via hydrogen bonding interactions. Complex 1 is nonemissive at room temperature and compounds 2- 3 exhibit different photoluminescence properties.

  7. Connecting Structural and Transport Properties of Ionic Liquids with Cationic Oligoether Chains

    SciTech Connect

    Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele; Fernandez, Rahonel; Zmich, Nicole; Fernandez, Eddie D.; Dhiman, Surajdevprakash B.; Castner, Edward W.; Wishart, James F.

    2017-01-01

    X-ray diffraction and molecular dynamics simulations were used to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidinium ILs increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. The results point to specific aspects that could be useful for researchers designing ILs for specific applications.

  8. Connecting Structural and Transport Properties of Ionic Liquids with Cationic Oligoether Chains

    DOE PAGES

    Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele; ...

    2017-06-01

    We used X-ray diffraction and molecular dynamics simulations to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Furthermore, their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidiniummore » ILs increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. Our results point to specific aspects that could be useful for researchers designing ILs for specific applications.« less

  9. Molecular structure and rheological properties of short-side-chain heavily glycosylated porcine stomach mucin.

    PubMed

    Yakubov, Gleb E; Papagiannopoulos, Aristeidis; Rat, Elodie; Easton, Richard L; Waigh, Thomas A

    2007-11-01

    The current accepted model for high-molecular-weight gastric mucins of the MUC family is that they adopt a polydisperse coil conformation in bulk solutions. We develop this model using well-characterized highly purified porcine gastric mucin Orthana that is genetically close to the human MUC6 type. It has short side chains and low levels of sialic acid residues and includes minute amounts of cysteine residues that, if abundant, can be responsible for the self-polymerization of mucin. We have established that the mucin structure in bulk solutions corresponds to a daisy-chain random coil. Dynamic light scattering experiments probe the internal dynamics of globular subunits (individual daisies) at the approximately 9 nm length scale, whereas viscosity and light scattering measurements indicate that the size of the whole mucin chains is much larger, approximately 50 nm. The bulk viscosity (eta) scales with mucin concentration (c) in a manner similar to that found for short-side-chain synthetic comb polyelectrolytes and is characterized by a transition between semidilute (eta approximately c1/2) and entangled (eta approximately c3/2) regimes.

  10. Formation of undulated lamellar structure from ABC block terpolymer blends with different chain lengths

    NASA Astrophysics Data System (ADS)

    Matsushita, Yushu; Suzuki, Jiro; Izumi, Yuuki; Matsuoka, Kohei; Takahashi, Shuji; Aoyama, Yoshitaka; Mihira, Tomohiro; Takano, Atsushi

    2010-11-01

    The effect of molecular weight distribution of ABC linear terpolymers on the formation of periodic structures was investigated. Three poly(isoprene-b-styrene-b-2-vinylpridine) triblockterpolymers with molecular weights of 26k, 96k, and 150k were blended variously. Three-phase, four-layer lamellar structures were observed when polydispersity index (PDI) was low, but it has been found that simple lamellar structure with flat surface transforms into an undulated lamellar one, where two interfaces, i.e., I/S and S/P, are both undulated, and they are synchronizing each other if PDI exceeds the critical value. This new structure could be formed due to the periodic and "weak" localization of three chains along the domain interfaces, which produces periodic surfaces with nonconstant mean curvatures. With further increase of PDI, the blend macroscopically phase-separated into different microphase-separated structures.

  11. Medium-chain sugar amphiphiles: a new family of healthy vegetable oil structuring agents.

    PubMed

    Jadhav, Swapnil R; Hwang, Hyeondo; Huang, Qingrong; John, George

    2013-12-11

    Vegetable oils are frequently structured to enhance their organoleptic and mechanical properties. This is usually achieved by increasing the net amount of saturated and/or trans fatty acids in the oil. With the risk of coronary heart diseases associated with these fatty acids, the food industry is looking for better alternatives. In this context, the medium-chain dialkanoates of low-calorie sugars (sugar alcohol dioctanoates) are investigated as a healthy alternative structuring agent. Precursors of sugar amphiphiles, being FDA-approved GRAS materials, exhibited high cell viability at a concentration ~50 μg/mL. They readily formed nanoscale multilayered structures in an oil matrix to form a coherent network at low concentrations (1-3 wt %/v), which immobilized a wide range of oils (canola, soybean, and grapeseed oils). The structuring efficiency of sugar amphiphiles was computed in terms of mechanical, thermal, and structural properties and found to be a function of its type and concentration.

  12. Enzymic and structural studies on Drosophila alcohol dehydrogenase and other short-chain dehydrogenases/reductases.

    PubMed

    Smilda, T; Kamminga, A H; Reinders, P; Baron, W; van Hylckama Vlieg, J E; Beintema, J J

    2001-05-01

    Enzymic and structural studies on Drosophila alcohol dehydrogenases and other short-chain dehydrogenases/reductases (SDRs) are presented. Like alcohol dehydrogenases from other Drosophila species, the enzyme from D. simulans is more active on secondary than on primary alcohols, although ethanol is its only known physiological substrate. Several secondary alcohols were used to determine the kinetic parameters kcat and Km. The results of these experiments indicate that the substrate-binding region of the enzyme allows optimal binding of a short ethyl side-chain in a small binding pocket, and of a propyl or butyl side-chain in large binding pocket, with stereospecificity for R(-) alcohols. At a high concentration of R(-) alcohols substrate activation occurs. The kcat and Km values determined under these conditions are about two-fold, and two orders of magnitude, respectively, higher than those at low substrate concentrations. Sequence alignment of several SDRs of known, and unknown three-dimensional structures, indicate the presence of several conserved residues in addition to those involved in the catalyzed reactions. Structural roles of these conserved residues could be derived from observations made on superpositioned structures of several SDRs with known structures. Several residues are conserved in tetrameric SDRs, but not in dimeric ones. Two halohydrin-halide-lyases show significant homology with SDRs in the catalytic domains of these enzymes, but they do not have the structural features required for binding NAD+. Probably these lyases descend from an SDR, which has lost the capability to bind NAD+, but the enzyme reaction mechanisms may still be similar.

  13. Analysis of the Rotational Structure in the High-Resolution Infrared Spectra of cis,cis- and trans,trans-1,4-DIFLUOROBUTADIENE-1-d_{1} and trans,trans-1,4-DIFLUOROBUTADIENE-1,4-d_{2}

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Chen, Yihui; Lu, Yuhua; Neese, Christopher F.; Nemchick, Deacon J.; Blake, Thomas A.

    2013-06-01

    Samples of cis,cis- and trans,trans-1,4-difluorobutadiene-1-d_{1} (DFBD) and trans,trans-DFBD-1,4-d_{2} have been synthesized and investigated with high-resolution (0.0015 cm^{-1}) infrared spectroscopy. For the first two species the rotational structure in more than one band has been analyzed. For the 1,4-d_{2} species the spectrum of only one C-type band was available in an isotopic mixture. Ground state rotational constants are reported for all three molecules. It is proposed that quartic centrifugal distortion constants computed with a B3LYP/cc-pVTZ model can be used to assess the quality of observed rotational constants. The favorable comparison of predicted and observed ground state rotational constants for all four ^{13}C species of cis,trans-DFBD, which is MW active, demonstrates that the ground state rotational constants for the ^{13}C species of the cis,cis and trans,trans isomers can be successfully predicted with high accuracy. Rotational constants for a full set of isotopologues will be used to determine accurate semiexperimental equilibrium structures of the cis,cis and trans,trans species of DFBD. N. C. Craig, C. M. Oertel, D. C. Oertel, M. J. Tubergen, R. J. Lavrich, A. M Chaka J. Phys. Chem. A 106, 4230-4235 (2002).

  14. Structural investigation of the lipopolysaccharide O-chain isolated from Burkholderia fungorum strain DSM 17061.

    PubMed

    De Felice, Antonia; Di Lorenzo, Flaviana; Scherlach, Kirstin; Ross, Claudia; Silipo, Alba; Hertweck, Christian; Molinaro, Antonio

    2016-10-04

    Gram-negative bacteria exhibit lipopolysaccharides (LPSs) on their outer membrane surface. LPS is considered one of the most potent bacterial virulence factors. Here we report the elucidation of the LPS O-chain structure isolated from Burkholderia fungorum, a bacterium isolated from the white-rot fungus Phanerochaete chrysosporium that can act as a pathogen for plants and domesticated animals. The structure was determined by the employment of detailed chemical and NMR spectroscopy analyses as the following. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Gold Nanoparticle Self-Similar Chain Structure Organized by DNA Origami

    SciTech Connect

    Ding, Baoquan; Deng, Zhengtao; Yan, Hao; Cabrini, Stefano; Zuckermann, Ronald N.; Bokor, Jeffrey

    2010-03-17

    Here we demonstrate Au nanoparticle self-similar chain structure organized by triangle DNA origami with well-controlled orientation and <10 nm spacing. We show for the first time that a large DNA complex (origami) and multiple AuNP conjugates can be well-assembled and purified with reliable yields. The assembled structure could be used to generate high local-field enhancement. The same method can be used to precisely localize multiple components on a DNA template for potential applications in nanophotonic, nanomagnetic, and nanoelectronic devices.

  16. Markov chain models of coupled intracellular calcium channels: Kronecker structured representations and benchmark stationary distribution calculations.

    PubMed

    Deremigio, Hilary; Kemper, Peter; Lamar, M Drew; Smith, Gregory D

    2008-01-01

    Mathematical models of calcium release sites derived from Markov chain models of intracellular calcium channels exhibit collective gating reminiscent of the experimentally observed phenomenon of stochastic calcium excitability (i.e., calcium puffs and sparks). We present a Kronecker structured representation for calcium release site models and perform benchmark stationary distribution calculations using numerical iterative solution techniques that leverage this structure. In this context we find multi-level methods and certain preconditioned projection methods superior to simple Gauss-Seidel type iterations. Response measures such as the number of channels in a particular state converge more quickly using these numerical iterative methods than occupation measures calculated via Monte Carlo simulation.

  17. Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase

    PubMed Central

    Williams, Allison H.; Raetz, Christian R. H.

    2007-01-01

    UDP-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes the first step of lipid A biosynthesis, the reversible transfer of the R-3-hydroxyacyl chain from R-3-hydroxyacyl acyl carrier protein to the glucosamine 3-OH group of UDP-GlcNAc. Escherichia coli LpxA is highly selective for R-3-hydroxymyristate. The crystal structure of the E. coli LpxA homotrimer, determined previously in the absence of lipid substrates or products, revealed that LpxA contains an unusual, left-handed parallel β-helix fold. We have now solved the crystal structures of E. coli LpxA with the bound product UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc at a resolution of 1.74 Å and with bound UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc at 1.85 Å. The structures of these complexes are consistent with the catalytic mechanism deduced by mutagenesis and with a recent 3.0-Å structure of LpxA with bound UDP-GlcNAc. Our structures show how LpxA selects for 14-carbon R-3-hydroxyacyl chains and reveal two modes of UDP binding. PMID:17698807

  18. A 1-D dusty plasma photonic crystal

    SciTech Connect

    Mitu, M. L.; Ticoş, C. M.; Toader, D.; Banu, N.; Scurtu, A.

    2013-09-21

    It is demonstrated numerically that a 1-D plasma crystal made of micron size cylindrical dust particles can, in principle, work as a photonic crystal for terahertz waves. The dust rods are parallel to each other and arranged in a linear string forming a periodic structure of dielectric-plasma regions. The dispersion equation is found by solving the waves equation with the boundary conditions at the dust-plasma interface and taking into account the dielectric permittivity of the dust material and plasma. The wavelength of the electromagnetic waves is in the range of a few hundred microns, close to the interparticle separation distance. The band gaps of the 1-D plasma crystal are numerically found for different types of dust materials, separation distances between the dust rods and rod diameters. The distance between levitated dust rods forming a string in rf plasma is shown experimentally to vary over a relatively wide range, from 650 μm to about 1350 μm, depending on the rf power fed into the discharge.

  19. Cyano-bridged coordination polymer hydrogel-derived Sn-Fe binary oxide nanohybrids with structural diversity: from 3D, 2D, to 2D/1D and enhanced lithium-storage performance

    NASA Astrophysics Data System (ADS)

    Zhang, Weiyu; Zhu, Xiaoshu; Chen, Xuguang; Zhou, Yiming; Tang, Yawen; Ding, Liangxin; Wu, Ping

    2016-05-01

    Metal oxide nanohybrids with uniform dimensions and controlled architectures possess unique compositional and structural superiorities, and thus harbor promising potential for a series of applications in energy, catalysis, and sensing systems. Herein, we propose a facile, general, and scalable cyano-bridged coordination polymer hydrogel-derived thermal-oxidation route for the construction of main-group metal and transition-metal heterometallic oxide nanohybrids with controlled constituents and architectures. The formation of Sn-Fe binary oxide nanohybrids has been demonstrated as an example by using cyano-bridged Sn(iv)-Fe(ii) bimetallic coordination polymer hydrogels (i.e., SnCl4-K4Fe(CN)6 cyanogels, Sn-Fe cyanogels) as precursors. The physicochemical properties of Sn-Fe cyanogels with different Sn/Fe ratios have been systematically examined, and it is found that perfect Sn-Fe cyanogels without unbridged Sn(iv) or Fe(ii) can be formed with Sn/Fe ratios from 2 : 1 to 1 : 2. More importantly, the simple adjustment of Sn/Fe ratios in the Sn-Fe cyanogel precursors can realize flexible dimensional control of the Sn-Fe binary oxide nanohybrids, and 2D/1D SnO2-Fe2O3 hierarchitectures, 2D SnO2-Fe2O3 nanosheets, and 3D SnO2-Fe2O3 networks have been synthesized using the Sn-Fe 1 : 2, Sn-Fe 1 : 1, and Sn-Fe 2 : 1 cyanogels as precursors, respectively. To demonstrate their compositional/structural superiorities and potential applications, the lithium-storage utilization of the Sn-Fe binary oxide nanohybrids has been selected as an objective application, and the nanohybrids exhibit Sn/Fe ratio-dependent lithium-storage performance. As a representative example, the 2D/1D SnO2-Fe2O3 hierarchitectures manifest markedly enhanced Li-storage performance in terms of reversible capacities and cycling stability in comparison with their constituent units, i.e., bare SnO2 nanosheets and Fe2O3 nanorods. The proposed cyanogel-derived thermal-oxidation strategy could open up new

  20. Biobased Fat Mimicking Molecular Structuring Agents for Medium-Chain Triglycerides (MCTs) and Other Edible Oils.

    PubMed

    Silverman, Julian R; John, George

    2015-12-09

    To develop sustainable value-added materials from biomass, novel small-molecule sugar ester gelators were synthesized using biocatalysis. The facile one-step regiospecific coupling of the pro-antioxidant raspberry ketone glucoside and unsaturated or saturated long- and medium-chain fatty acids provides a simple approach to tailor the structure and self-assembly of the amphiphilic product. These low molecular weight molecules demonstrated the ability to self-assemble in a variety of solvents and exhibited supergelation, with a minimum gelation concentration of 0.25 wt %, in numerous organic solvents, as well as in a range of natural edible oils, specifically a relatively unstudied group of liquids: natural medium-chain triglyceride oils, notably coconut oil. Spectroscopic analysis details the gelator structure as well as the intermolecular noncovalent interactions, which allow for gelation. X-ray diffraction studies indicate fatty acid chain packing of gelators is similar to that of natural fats, signifying the crystalline nature may lead to desirable textural properties and mouthfeel.

  1. Beads on a string: structure of bound aggregates of globular particles and long polymer chains.

    PubMed

    Souslov, Anton; Curtis, Jennifer E; Goldbart, Paul M

    2015-11-07

    Macroscopic properties of suspensions, such as those composed of globular particles (e.g., colloidal or macromolecular), can be tuned by controlling the equilibrium aggregation of the particles. We examine how aggregation - and, hence, macroscopic properties - can be controlled in a system composed of both globular particles and long, flexible polymer chains that reversibly bind to one another. We base this on a minimal statistical mechanical model of a single aggregate in which the polymer chain is treated either as ideal or self-avoiding, and, in addition, the globular particles are taken to interact with one another via excluded volume repulsion. Furthermore, each of the globular particles is taken to have one single site to which at most one polymer segment may bind. Within the context of this model, we examine the statistics of the equilibrium size of an aggregate and, thence, the structure of dilute and semidilute suspensions of these aggregates. We apply the model to biologically relevant aggregates, specifically those composed of macromolecular proteoglycan globules and long hyaluronan polymer chains. These aggregates are especially relevant to the materials properties of cartilage and the structure-function properties of perineuronal nets in brain tissue, as well as the pericellular coats of mammalian cells.

  2. Crystal structure and magnetic properties of linear chain potassium aquotetrafluoromanganate(III)

    NASA Astrophysics Data System (ADS)

    Palacio, Fernando; Andres, Mercedes; Esteban-Calderon, C.; Martinez-Ripoll, M.; Garcia-Blanco, S.

    1988-09-01

    The crystal structure and single-crystal ac magnetic susceptibilities of KMnF 4·H 2O are reported. The structure, which is isomorphous to that of RbMnF 4·H 2O, consists of chains of alternating trans-[ MnF 4F {2}/{2}] 2- and trans-[ MnF 2F {2}/{2}( H 2O ) 2] tetragonally elongated octahedra connected to each other by shared apical fluorine atoms. Crystal data: Space group {C2}/{c}, a = 13.907(1) Å, b = 6.2136(2) Å, c = 10.492(1)Å, β = 104.69(1)°, V = 877.0(2) Å 3, Dc = 2.85 g cm -3, Z = 8, R = 0.044. Magnetic susceptibility measurements show a broad maximum around 52 K indicative of lower dimensionality behavior. The data may be fit to a Heisenberg S = 2 linear chain model with {J}/{k B} = -6.5 K and g = 2.05. At 8.45 K a sharp peak in the susceptibility data parallel to the chains indicates weak ferromagnetic behavior.

  3. Surface Structure of Polystyrenes: Comparison of Lattice Chain Simulations and Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Goldbeck-Wood, Gerhard; Bliznyuk, Valery; Burlakov, Victor; Assender, Hazel; Briggs, Andrew; Tsukahara, Yusuke; Anderson, Kelly; Windle, Alan

    2001-03-01

    The understanding of the structural arrangement of polymer chains near surfaces impacts many technological areas. In this study we address surface features on the length scale of 1-100nm (i.e. covering many times the radius of gyration) for a series of polystyrenes with molecular weights Mn from 3*10^3 to 9*10^6. Surface images are generated by scanning probe microscopy in tapping mode. An autocorrelation function analysis of the height data provides information about the lateral correlations in the surface structure. We find that the correlation length converges towards the bulk value of the radius of gyration at larger molecular weights, but lies somewhat above at lower molecular weights. Alongside the experiment we carried out simulations using a face-centred cubic lattice chain model, parameterized for polystyrene. The autocorrelation lengths of the simulated surfaces follow the radius of gyration dependence with chain length. Simulation as well experimental results suggest that the height autocorrelation length converges towards the size and scaling of the radius of gyration for medium to high molecular weight. Further work is required before a conclusion can be reached for low molecular weights.

  4. Structure of IL-22 bound to its high-affinity IL-22R1 chain.

    PubMed

    Jones, Brandi C; Logsdon, Naomi J; Walter, Mark R

    2008-09-10

    IL-22 is an IL-10 family cytokine that initiates innate immune responses against bacterial pathogens and contributes to immune disease. IL-22 biological activity is initiated by binding to a cell-surface complex composed of IL-22R1 and IL-10R2 receptor chains and further regulated by interactions with a soluble binding protein, IL-22BP, which shares sequence similarity with an extracellular region of IL-22R1 (sIL-22R1). IL-22R1 also pairs with the IL-20R2 chain to induce IL-20 and IL-24 signaling. To define the molecular basis of these diverse interactions, we have determined the structure of the IL-22/sIL-22R1 complex. The structure, combined with homology modeling and surface plasmon resonance studies, defines the molecular basis for the distinct affinities and specificities of IL-22 and IL-10 receptor chains that regulate cellular targeting and signal transduction to elicit effective immune responses.

  5. Structure of IL-22 bound to its high affinity IL-22R1 chain

    PubMed Central

    Jones, Brandi C.; Logsdon, Naomi J.; Walter, Mark R.

    2008-01-01

    Summary IL-22 is an IL-10 family cytokine that initiates innate immune responses against bacterial pathogens and contributes to immune disease. IL-22 biological activity is initiated by binding to a cell surface complex composed IL-22R1 and IL-10R2 receptor chains and further regulated by interactions with a soluble binding protein, IL-22BP, which shares sequence similarity with extracellular region of IL-22R1 (sIL-22R1). IL-22R1 also pairs with the IL-20R2 chain to induce IL-20 and IL-24 signaling. To define the molecular basis of these diverse interactions, we have determined structure of the IL-22/sIL-22R1 complex. The structure, combined with homology modeling and surface plasmon resonance studies, define the molecular basis for the distinct affinities and specificities of IL-22 and IL-10 receptor chains that regulate cellular targeting and signal transduction to elicit effective immune responses. PMID:18599299

  6. End States and Subgap Structure in Proximity-Coupled Chains of Magnetic Adatoms.

    PubMed

    Ruby, Michael; Pientka, Falko; Peng, Yang; von Oppen, Felix; Heinrich, Benjamin W; Franke, Katharina J

    2015-11-06

    A recent experiment [Nadj-Perge et al., Science 346, 602 (2014)] provides evidence for Majorana zero modes in iron (Fe) chains on the superconducting Pb(110) surface. Here, we study this system by scanning tunneling microscopy using superconducting tips. This high-resolution technique resolves a rich subgap structure, including zero-energy excitations in some chains. We compare the symmetry properties of the data under voltage reversal against theoretical expectations and provide evidence that the putative Majorana signature overlaps with a previously unresolved low-energy resonance. Interpreting the data within a Majorana framework suggests that the topological gap is smaller than previously extracted from experiment. Aided by model calculations, we also analyze higher-energy features of the subgap spectrum and their relation to high-bias peaks which we associate with the Fe d bands.

  7. Network structure of polyfluorene sheets as a function of alkyl side chain length

    NASA Astrophysics Data System (ADS)

    Knaapila, M.; Bright, D. W.; Stepanyan, R.; Torkkeli, M.; Almásy, L.; Schweins, R.; Vainio, U.; Preis, E.; Galbrecht, F.; Scherf, U.; Monkman, A. P.

    2011-05-01

    The formation of self-organized structures in poly(9,9-di-n-alkylfluorene)s ˜1 vol % methylcyclohexane (MCH) and deuterated MCH (MCH-d14) solutions was studied at room temperature using neutron and x-ray scattering (with the overall q range of 0.000 58-4.29 Å-1) and optical spectroscopy. The number of side chain carbons (N) ranged from 6 to 10. The phase behavior was rationalized in terms of polymer overlap, cross-link density, and blending rules. For N=6-9, the system contains isotropic areas and lyotropic areas where sheetlike assemblies (lateral size of >400 Å) and free polymer chains form ribbonlike agglomerates (characteristic dimension of >1500 Å) leading to a gel-like appearance of the solutions. The ribbons are largely packed together with surface fractal characteristics for N=6-7 but become open networklike structures with mass fractal characteristics for N=8-9, until the system goes through a transition to an isotropic phase of overlapping rodlike polymers for N=10. The polymer order within sheets varies allowing classification for loose membranes and ordered sheets, including the so-called β phase. The polymers within the ordered sheets have restricted motion for N=6-7 but more freedom to vibrate for N=8-9. The nodes in the ribbon network are suggested to contain ordered sheets cross-linking the ribbons together, while the nodes in the isotropic phase appear as weak density fluctuations cross-linking individual chains together. The tendencies for macrophase separation and the formation of non beta sheets decrease while the proportion of free chains increases with increasing N. The fraction of β phase varies nonlinearly, reaching its maximum at N = 8.

  8. Detecting memory and structure in human navigation patterns using Markov chain models of varying order.

    PubMed

    Singer, Philipp; Helic, Denis; Taraghi, Behnam; Strohmaier, Markus

    2014-01-01

    One of the most frequently used models for understanding human navigation on the Web is the Markov chain model, where Web pages are represented as states and hyperlinks as probabilities of navigating from one page to another. Predominantly, human navigation on the Web has been thought to satisfy the memoryless Markov property stating that the next page a user visits only depends on her current page and not on previously visited ones. This idea has found its way in numerous applications such as Google's PageRank algorithm and others. Recently, new studies suggested that human navigation may better be modeled using higher order Markov chain models, i.e., the next page depends on a longer history of past clicks. Yet, this finding is preliminary and does not account for the higher complexity of higher order Markov chain models which is why the memoryless model is still widely used. In this work we thoroughly present a diverse array of advanced inference methods for determining the appropriate Markov chain order. We highlight strengths and weaknesses of each method and apply them for investigating memory and structure of human navigation on the Web. Our experiments reveal that the complexity of higher order models grows faster than their utility, and thus we confirm that the memoryless model represents a quite practical model for human navigation on a page level. However, when we expand our analysis to a topical level, where we abstract away from specific page transitions to transitions between topics, we find that the memoryless assumption is violated and specific regularities can be observed. We report results from experiments with two types of navigational datasets (goal-oriented vs. free form) and observe interesting structural differences that make a strong argument for more contextual studies of human navigation in future work.

  9. Detecting Memory and Structure in Human Navigation Patterns Using Markov Chain Models of Varying Order

    PubMed Central

    Singer, Philipp; Helic, Denis; Taraghi, Behnam; Strohmaier, Markus

    2014-01-01

    One of the most frequently used models for understanding human navigation on the Web is the Markov chain model, where Web pages are represented as states and hyperlinks as probabilities of navigating from one page to another. Predominantly, human navigation on the Web has been thought to satisfy the memoryless Markov property stating that the next page a user visits only depends on her current page and not on previously visited ones. This idea has found its way in numerous applications such as Google's PageRank algorithm and others. Recently, new studies suggested that human navigation may better be modeled using higher order Markov chain models, i.e., the next page depends on a longer history of past clicks. Yet, this finding is preliminary and does not account for the higher complexity of higher order Markov chain models which is why the memoryless model is still widely used. In this work we thoroughly present a diverse array of advanced inference methods for determining the appropriate Markov chain order. We highlight strengths and weaknesses of each method and apply them for investigating memory and structure of human navigation on the Web. Our experiments reveal that the complexity of higher order models grows faster than their utility, and thus we confirm that the memoryless model represents a quite practical model for human navigation on a page level. However, when we expand our analysis to a topical level, where we abstract away from specific page transitions to transitions between topics, we find that the memoryless assumption is violated and specific regularities can be observed. We report results from experiments with two types of navigational datasets (goal-oriented vs. free form) and observe interesting structural differences that make a strong argument for more contextual studies of human navigation in future work. PMID:25013937

  10. Addimer chain structures: Metastable precursors to island formation on Ge Si(0 0 1)-(2 × n) alloyed surface

    NASA Astrophysics Data System (ADS)

    Solis, Kyle J.; Williams, Lance R.; Swartzentruber, B. S.; Han, Sang M.

    2007-01-01

    We have identified addimer chain structures as metastable precursors to compact epitaxial islands on the (2 × n) reconstructed SiGe wetting layer, using polarity-switching scanning tunneling microscopy (STM). These chain structures are comprised of 2-12 addimers residing in the troughs of neighboring substrate dimer rows. The chain structures extend along equivalent <1 3 0> directions across the substrate dimer rows in a zigzag fashion, giving rise to kinked and straight segments. We measure a kink-to-straight ratio of nearly 2:1. This ratio corresponds to a free energy difference of 17 ± 4 meV, favoring the formation of kinked segments. The chain structures convert to compact epitaxial islands at elevated temperatures (⩾90 °C). This conversion suggests that the chain structures are a precursor for compact island formation on the SiGe wetting layer. We digitally process filled- and empty-state STM images to distinguish chain structures from compact islands. By monitoring the populations of both species over time, the chain-to-island conversion rates are measured at substrate temperatures ranging from 90 to 150 °C. The activation energy for the conversion process is measured to be 0.7 ± 0.2 eV with a corresponding pre-exponential factor of 5 × 10 4±2 s -1.

  11. Structure refinement of protein model decoys requires accurate side-chain placement.

    PubMed

    Olson, Mark A; Lee, Michael S

    2013-03-01

    In this study, the application of temperature-based replica-exchange (T-ReX) simulations for structure refinement of decoys taken from the I-TASSER dataset was examined. A set of eight nonredundant proteins was investigated using self-guided Langevin dynamics (SGLD) with a generalized Born implicit solvent model to sample conformational space. For two of the protein test cases, a comparison of the SGLD/T-ReX method with that of a hybrid explicit/implicit solvent molecular dynamics T-ReX simulation model is provided. Additionally, the effect of side-chain placement among the starting decoy structures, using alternative rotamer conformations taken from the SCWRL4 modeling program, was investigated. The simulation results showed that, despite having near-native backbone conformations among the starting decoys, the determinant of their refinement is side-chain packing to a level that satisfies a minimum threshold of native contacts to allow efficient excursions toward the downhill refinement regime on the energy landscape. By repacking using SCWRL4 and by applying the RWplus statistical potential for structure identification, the SGLD/T-ReX simulations achieved refinement to an average of 38% increase in the number of native contacts relative to the original I-TASSER decoy sets and a 25% reduction in values of C(α) root-mean-square deviation. The hybrid model succeeded in obtaining a sharper funnel to low-energy states for a modeled target than the implicit solvent SGLD model; yet, structure identification remained roughly the same. Without meeting a threshold of near-native packing of side chains, the T-ReX simulations degrade the accuracy of the decoys, and subsequently, refinement becomes tantamount to the protein folding problem. Published 2012 Wiley Periodicals, Inc.

  12. A Cardiomyopathy Mutation in the Myosin Essential Light Chain Alters Actomyosin Structure.

    PubMed

    Guhathakurta, Piyali; Prochniewicz, Ewa; Roopnarine, Osha; Rohde, John A; Thomas, David D

    2017-07-11

    We have used site-directed time-resolved fluorescence resonance energy transfer to determine the effect of a pathological mutation in the human ventricular essential light chain (hVELC) of myosin, on the structural dynamics of the actin-myosin complex. The hVELC modulates the function of actomyosin, through the interaction of its N-terminal extension with actin and its C-terminal lobe with the myosin heavy chain. Several mutations in hVELC are associated with hypertrophic cardiomyopathy (HCM). Some biochemical effects of these mutations are known, but further insight is needed about their effects on the structural dynamics of functioning actomyosin. Therefore, we introduced the HCM mutation E56G into a single-cysteine (C16) hVELC construct and substituted it for the VELC of bovine cardiac myosin subfragment 1. Using a donor fluorescent probe on actin (at C374) and an acceptor probe on C16 of hVELC, we performed time-resolved fluorescence resonance energy transfer, directly detecting structural changes within the bound actomyosin complex during function. The E56G mutation has no significant effect on actin-activated ATPase activity or actomyosin affinity in the presence of ATP, or on the structure of the strong-binding S complex in the absence of ATP. However, in the presence of saturating ATP, where both W (prepowerstroke) and S (postpowerstroke) structural states are observed, the mutant increases the mole fraction of the S complex (increasing the duty ratio), while shifting the structure of the remaining W complex toward that of S, indicating a structural redistribution toward the strongly bound (force-generating) complex. We propose that this effect is responsible for the hypercontractile phenotype induced by this HCM mutation in myosin. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  13. Effect of the chain length on the structure of ionic liquids: from spatial heterogeneity to ionic liquid crystals.

    PubMed

    Ji, Yumeng; Shi, Rui; Wang, Yanting; Saielli, Giacomo

    2013-01-31

    Ionic liquids with intermediate nonpolar cationic side-chain lengths are known to have nanoscale spatial heterogeneities with nonpolar tail domains separated by a continuous polar network. In this work, we use coarse-grained molecular dynamics simulations to show that, when the nonpolar cationic side chain is sufficiently long, due to the stronger van der Waals interactions between the side chains, the structure of ionic liquids goes through a transition from spatially heterogeneous to liquid crystalline-like. For XMIm(+)/NO(3)(-) ionic liquids, change occurs when the number of carbon groups on the cationic side chain varies from 14 to 16. In the liquid crystal-like phase, the cationic side chains tend to be parallel to each other, while the cationic head groups and anions, although being mostly layered perpendicularly to the direction along the side chains, still form a continuous polar network.

  14. 1D molecular ladder of the ionic complex of terbium-4-sebacoylbis(1-phenyl-3-methyl-5-pyrazolonate) and sodium dibenzo-18-crown-6: synthesis, crystal structure, and photophysical properties.

    PubMed

    Remya, P N; Biju, S; Reddy, M L P; Cowley, Alan H; Findlater, Michael

    2008-08-18

    On the basis of the novel heterocyclic beta-diketone, 4-sebacoylbis(1-phenyl-3-methyl-5-pyrazolone (H 2SbBP), three new lanthanide complexes Tb 2(SbBP) 3(H 2O) 2 ( 1), Gd 2(SbBP) 3(H 2O) 2 ( 2), and [Tb(SbBP) 2] [Na(DB18C6)H 2O] ( 3) have been synthesized and characterized by various spectroscopic techniques. The single-crystal X-ray diffraction analysis of 3 reveals that the complex crystallizes in the monoclinic space group C2/ c with a = 25.300(6) A, b = 19.204(7) A, c = 15.391(3) A, beta = 93.17(3) degrees , and V = 7466(4) A (3). The crystal structure of 3 is heterodinuclear and features a Tb (3+) center surrounded by two tetradentate bispyrazolone ligands in a somewhat distorted square-antiprismatic geometry. The Na (+) coordination environment is distorted hexagonal pyramidal and involves six oxygen atoms furnished by DB18C6 and one oxygen atom from a water molecule. The X-ray diffraction study of 3 also revealed an interesting 1D molecular ladder structure based on C-H/pi, intra- and intermolecular hydrogen-bonding interactions. The photophysical properties of 1 and 3 in solid state have been investigated, and the quantum yields and (5)D 4 lifetimes were found to be 4.82 +/- 0.01% and 18.13 +/- 0.82% and 1.11 +/- 0.01 and 2.82 +/- 0.02 ms, respectively.

  15. The crystal structure of 1-D-myo-inosityl 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis reveals a zinc hydrolase with a lactate dehydrogenase fold.

    PubMed

    Maynes, Jason T; Garen, Craig; Cherney, Maia M; Newton, Gerald; Arad, Dorit; Av-Gay, Yossef; Fahey, Robert C; James, Michael N G

    2003-11-21

    Mycothiol (1-D-myo-inosityl 2-(N-acetyl-L-cysteinyl)amido-2-deoxy-alpha-D-glucopyranoside, MSH or AcCys-GlcN-inositol (Ins)) is the major reducing agent in actinomycetes, including Mycobacterium tuberculosis. The biosynthesis of MSH involves a deacetylase that removes the acetyl group from the precursor GlcNAc-Ins to yield GlcN-Ins. The deacetylase (MshB) corresponds to Rv1170 of M. tuberculosis with a molecular mass of 33,400 Da. MshB is a Zn2+ metalloprotein, and the deacetylase activity is completely dependent on the presence of a divalent metal cation. We have determined the x-ray crystallographic structure of MshB, which reveals a protein that folds in a manner resembling lactate dehydrogenase in the N-terminal domain and a C-terminal domain consisting of two beta-sheets and two alpha-helices. The zinc binding site is in the N-terminal domain occupying a position equivalent to that of the NAD+ co-factor of lactate dehydrogenase. The Zn2+ is 5 coordinate with 3 residues from MshB (His-13, Asp-16, His-147) and two water molecules. One water would be displaced upon binding of substrate (GlcNAc-Ins); the other is proposed as the nucleophilic water assisted by the general base carboxylate of Asp-15. In addition to the Zn2+ providing electrophilic assistance in the hydrolysis, His-144 imidazole could form a hydrogen bond to the oxyanion of the tetrahedral intermediate. The extensive sequence identity of MshB, the deacetylase, with mycothiol S-conjugate amidase, an amide hydrolase that mediates detoxification of mycothiol S-conjugate xenobiotics, has allowed us to construct a faithful model of the catalytic domain of mycothiol S-conjugate amidase based on the structure of MshB.

  16. Electronic Structure of Pure Selenium and Tellurium Chains and Selenium Rings and with Impurities

    NASA Astrophysics Data System (ADS)

    Maharjan, N. B.; Cho, Hwa-Suck; Scheicher, R. H.

    2005-03-01

    We have studied the electronic structures of pure chain-structured Selenium and Tellurium and with chalcogen impurities as well as ring-structured Selenium both pure and with Tellurium impurity atoms. The Hartree-Fock Cluster Theory procedure combined with many-body perturbation theory procedure has been used. The accuracy of the calculated electronic wave functions is tested by the investigation of ^77Se and ^125Te nuclear quadrupole interaction parameters. Good agreement is found with experiment for the pure systems. For the impurity systems, the agreement is reasonable but suggests the need for inclusion of more extensive relaxation around the impurity atoms. (*) Current Address: Dept. of Physics, Uppsala University, Sweden (**) Also: Dept. of Physics, University of Central Florida, Orlando, Florida

  17. Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains as structural features of coffee arabinogalactans.

    PubMed

    Nunes, Fernando M; Reis, Ana; Silva, Artur M S; Domingues, M Rosário M; Coimbra, Manuel A

    2008-05-01

    The hot water soluble green coffee arabinogalactans, representing nearly 7% of total coffee bean arabinogalactans, were characterized by (1)H and (13)C NMR and, after partial acid hydrolysis, by ESI-MS/MS. Data obtained showed that these are highly branched type II arabinogalactans covalently linked to proteins (AGP), with a protein moiety containing 10% of 4-hydroxyproline residues. They possess a beta-(1-->3)-Galp/beta-(1-->3,6)-Galp ratio of 0.80, with a sugars composition of Rha:Ara:Gal of 0.25:1.0:1.5, and containing 2mol% of glucuronic acid residues. Beyond the occurrence of single alpha-L-Araf residues and [alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] disaccharide residues as side chains, these AGPs contain unusual side chains at O-3 position of the beta-(1-->6)-linked galactopyranosyl residues composed by [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->] and [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] oligosaccharides. Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains are reported for the first time as structural features of plant arabinogalactan-proteins.

  18. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains.

    PubMed

    Remis, Jonathan P; Wei, Dongguang; Gorur, Amita; Zemla, Marcin; Haraga, Jessica; Allen, Simon; Witkowska, H Ewa; Costerton, J William; Berleman, James E; Auer, Manfred

    2014-02-01

    The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviours, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of outer membrane vesicle chains and membrane tubes that interconnect cells. We observed peritrichous display of vesicles and vesicle chains, and increased abundance in biofilms compared with planktonic cultures. By applying a range of imaging techniques, including three-dimensional (3D) focused ion beam scanning electron microscopy, we determined these structures to range between 30 and 60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine and N-acetylgalactoseamine carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl outer membrane proteins known to be transferable between cells in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and therefore could provide a mechanism for the coordination of social activities.

  19. Bacterial Social Networks: Structure and composition of Myxococcus xanthus outer membrane vesicle chains

    PubMed Central

    Remis, Jonathan P.; Wei, Doug; Gorur, Amita; Zemla, Marcin; Haraga, Jessica; Allen, Simon; Witkowska, H. Ewa; Costerton, J. William; Berleman, James E.; Auer, Manfred

    2014-01-01

    Summary The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviors, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of vesicles and vesicle chains that interconnect cells. We observed peritrichous display of vesicles and vesicle chains and increased abundance in biofilms compared to planktonic cultures. By applying a range of imaging techniques, including 3D Focused Ion Beam Scanning Electron Microscopy (FIB/SEM), we determined these structures to range between 30-60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine (GlcNAc) and N-acetylgalactoseamine (GalNAc) carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl membrane proteins transferred in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and likely provides a mechanism for the coordination of social activities. PMID:23848955

  20. Immunological and structural characterization of a high affinity anti-fluorescein single-chain antibody.

    PubMed

    Bedzyk, W D; Weidner, K M; Denzin, L K; Johnson, L S; Hardman, K D; Pantoliano, M W; Asel, E D; Voss, E W

    1990-10-25

    Single-chain antibody of the (NH2) VL-linker-VH (COOH) design, was constructed based on prototype high affinity anti-fluorescein monoclonal antibody (mAb) 4-4-20. Purified single-chain antibody (SCA) 4-4-20/212 was studied relative to Ig mAb 4-4-20 in terms of ligand binding, kinetics, idiotypy, metatypy, and stability in denaturing agents. Ligand-binding data correlated with metatypic relatedness of the liganded site. Anti-metatypic reagents reacted preferentially with the liganded conformer of the 4-4-20 antibody active site and were unreactive with free ligand and the non-liganded (idiotypic) state. All results were consistent with the conclusion that SCA 4-4-20/212, with a 14-amino acid linker folded into a native conformational state that closely simulated the prototypical mAb. Furthermore, GndHCl unfolding and refolding studies demonstrated H and L chain variable domain intrinsic stability between SCA 4-4-20/212 and a 50 kDa antigen-binding fragment were nearly identical. This suggested CH1 and CL domain interactions may be more prevalent in V region molecular dynamics than structure.

  1. Lipidomic platform for structural identification of skin ceramides with α-hydroxyacyl chains.

    PubMed

    Wu, Zhexue; Shon, Jong Cheol; Lee, Doohyun; Park, Kab-Tae; Park, Chang Seo; Lee, Taeho; Lee, Hye Suk; Liu, Kwang-Hyeon

    2016-03-01

    Skin ceramides are sphingolipids consisting of sphingoid bases, which are linked to fatty acids via an amide bond. Typical fatty acid acyl chains are composed of α-hydroxy fatty acid (A), esterified ω-hydroxy fatty acid (EO), non-hydroxy fatty acid (N), and ω-hydroxy fatty acid (O). We recently established a lipidomic platform to identify skin ceramides with non-hydroxyacyl chains using tandem mass spectrometry. We expanded our study to establish a lipidomic platform to identify skin ceramides with α-hydroxyacyl chains. Tandem mass spectrometry analysis of A-type ceramides using chip-based direct infusion nanoelectrospray-mass spectrometry showed the characteristic fragmentation pattern of both acyl and sphingoid units, which can be applied for structural identification of ceramides. Based on the tandem mass spectrometry fragmentation patterns of A-type ceramides, comprehensive fragmentation schemes were proposed. Our results may be useful for identifying A-type ceramides in the stratum corneum of human skin.

  2. Capturing 1D Channel Network Topology in NetCDF

    NASA Astrophysics Data System (ADS)

    Jagers, B.; van Dam, A.; Mooiman, J.

    2016-12-01

    Traditional Climate and Forecasting conventions for NetCDF files provide support for data on regular grids and data at a set of locations without well defined topology (connectivity). Over the past decade GridSpec, UGRID, and SGRID conventions have been proposed and adopted to capture the topology of numerical models (GridSpec for mosaics of grids, UGRID for unstructured meshes, and SGRID for staggered data on structured grids). UGRID includes conventions for capturing 1D, 2D, and 3D unstructured mesh topologies. The 2D and layered 3D conventions have been adopted by various numerical code developers in the Earth Sciences. The subset of 1D conventions are however less well widely used to this date. In the process of converting our 1D model output to the combined CF and 1D UGRID conventions, we have noticed that it lacks a couple of features. UGRID assumes that the channel geometry between the "nodes" is straight while in most 1D models these channels can be curved. We propose an extension to the UGRID conventions to allow for a two-layered approach in which first a 1D generic channel network topology is defined, and then a 1D mesh topology on that channel network using "branch number" and "branch offset" as coordinate variables.

  3. Structural basis for the RING catalyzed synthesis of K63 linked ubiquitin chains

    PubMed Central

    Branigan, Emma; Plechanovová, Anna; Jaffray, Ellis; Naismith, James H.; Hay, Ronald T.

    2015-01-01

    The RING E3 ligase catalysed formation of lysine 63 linked ubiquitin chains by the Ube2V2–Ubc13 E2 complex is required for many important biological processes. Here we report the structure of the RING domain dimer of rat RNF4 in complex with a human Ubc13~Ub conjugate and Ube2V2. The structure has captured Ube2V2 bound to the acceptor (priming) ubiquitin with Lys63 in a position that could lead to attack on the linkage between the donor (second) ubiquitin and Ubc13 that is held in the active “folded back” conformation by the RING domain of RNF4. The interfaces identified in the structure were verified by in vitro ubiquitination assays of site directed mutants. This represents the first view of the synthesis of Lys63 linked ubiquitin chains in which both substrate ubiquitin and ubiquitin-loaded E2 are juxtaposed to allow E3 ligase mediated catalysis. PMID:26148049

  4. Effect of A Long Chain Carboxylate Acid on Sodium Dodecyl Sulfate Micelle Structure: A SANS Study

    NASA Astrophysics Data System (ADS)

    Patriati, Arum; Giri Rachman Putra, Edy; Seok Seong, Baek

    2010-01-01

    The effect of a different hydrocarbon chain length of carboxylate acid, i.e. dodecanoic acid, CH3(CH)10COOH or lauric acid and hexadecanoic acid, CH3(CH2)14COOH or palmitic acid as a co-surfactant in the 0.3 M sodium dedecyl sulfate, SDS micellar solution has been studied using small angle neutron scattering (SANS). The present of lauric acid has induced the SDS structural micelles. The ellipsoid micelles structures changed significantly in length (major axis) from 22.6 Å to 37.1 Å at a fixed minor axis of 16.7 Å in the present of 0.005 M to 0.1 M lauric acid. Nevertheless, this effect did not occur in the present of palmitic acid with the same concentration range. The present of palmitic acid molecules performed insignificant effect on the SDS micelles growth where the major axis of the micelle was elongated from 22.9 Å to 25.3 Å only. It showed that the appropriate hydrocarbon chain length between surfactant and co-surfactant molecules emerged as one of the determining factors in forming a mixed micelles structure.

  5. Density functional approach to adsorption of simple fluids on surfaces modified with a brush-like chain structure.

    PubMed

    Patrykiejew, A; Sokołowski, S; Tscheliessnig, R; Fischer, J; Pizio, O

    2008-04-17

    A density functional theory to describe adsorption of a simple fluid from a gas phase on a surface modified with pre-adsorbed chains is proposed. The chains are bonded to the surface by one of their ends, so they can form a brush-like structure. Two models are investigated. According to the first model all but the terminating segment of a chain can change the configuration during the adsorption of fluid species. The second model assumes that the chains remain "frozen", and the system is considered as a nonuniform quenched-annealed mixture. We apply simple form of interactions to study adsorption phenomena, microscopic structure, and layering transitions. Our principal findings show that new layering phase transitions can occur because of a chemical modification of the substrate under certain conditions, in comparison with nonmodified surfaces. However, opposite trends, that is, smoothing the adsorption isotherms, can also be observed, depending on the surface density of the grafted chains.

  6. Chain Dynamics and Structure Property Relation in High Impact Strength Polycarbonate Plastic.

    DTIC Science & Technology

    1985-01-04

    AD-fli52 Oil CHAIN DYNAIIICS AND STRUCTURE PROPERTY RELATION IN HIH jTT IMPACT STRENGTH P0.. (U) COLLEGE OF THE HOLY CROSS WORCESTER MR P T...OOO1 C\\J ERFONM’N G ORGANI ATION NAME AND ADDRESS 10. PROGRAM ELEMENT. PROJECT, TASK( AREA & W ORK UNIT NUMBERS ICO CC) IlIoge~ of the !Ho lv Cross ...January 4, 1985 U.S. ARMY RESEARCH OFFICE GRANT NUMBER DAAG 29-82-G-0001 College of the Holy Cross Worcester, Mass. 01610 Approved for Public Release

  7. Pressure dependence of structural and dynamical properties in melt sulfur: Evidence for two successive chain breakages

    NASA Astrophysics Data System (ADS)

    Zhao, G.; Mu, H. F.

    2014-11-01

    Using ab initio molecular dynamics simulations, the pressure dependence of structural and dynamical properties in melt sulfur along 1085 K isotherm was studied with pressure range from 4.18 to 15.8 GPa. It was found that the atomic chains in melt sulfur abruptly break twice with increasing pressure. The electric density of state near EF and the diffusion coefficient both show abrupt increase along with these two times of breakages. These changes would strongly influence the physical properties such as conductivity and viscosity. However, the density discontinuity along the isotherm, indication of a first-order phase transition, was not found.

  8. Crystal structures and thermodynamics/kinetics of Zn(II) coordination polymers with helical chains

    NASA Astrophysics Data System (ADS)

    He, Tian; Yue, Ke-Fen; Zhao, Yi-xing; Chen, San-Ping; Zhou, Chun-sheng; Yan, Ni

    2016-07-01

    Solvothermal reactions of Zn(II) acetates and four V-shaped carboxylates ligands in the presence of 1,4-Bis(2-methyl-imidazol-1-yl)butane afforded four interesting Zn(II) coordination polymers with helical chains, namely, {[Zn(bib)(atibdc)]·2H2O}n (1), {[Zn(bib)(atbip)]·H2O}n (2), [Zn(bib)(2,2‧-tda)]}n (3) and {[Zn(bib)(5-tbipa)]·EtOH}n (4), (H2atibdc=5-amino-2,4,6-triiodoisophthalic acid, H2atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2‧-H2tad=2,2‧-thiodiacetic acid, 5-H2tbipa=5-tert-butyl-isophthalic acid). 1 reveals a 3D chiral framework with three kinds of helical chains along a, b and c axis. 2 shows a 2D step-type chiral framework with right-handed helical chains. 3 displays a wavelike 2D layer network possessing alternate left- and right-handed helical chains. 4 presents a four-connected 3D framework with zigzag and meso-helical chains. The different spacers and substituent group of carboxylic acid ligands may lead to the diverse network structures of 1-4. The fluorescent properties of complexes 1-4 were studied. In addition, the thermal decompositions properties of 1-4 were investigated by simultaneous TG/DTG-DSC technique. The apparent activation energy E and the pre-exponential factor (A) of skeleton collapse for the complexes 1-4 are calculated by the integral Kissinger's method and Ozawa-Doyle's method. The activation energy E (E1=209.658 kJ·mol-1, E2=250.037 kJ mol-1, E3=225.300 kJ mol-1, E4=186.529 kJ·mol-1) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH‡, ΔG‡ and ΔS‡) at the peak temperatures of the DTG curves were also calculated. ΔG‡>0 indicates that the skeleton collapse is not spontaneous. ΔHd>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC curve. The structural stability could be illustrated from the point of thermodynamics and kinetics.

  9. A rational route to SCM materials based on a 1-D cobalt selenocyanato coordination polymer.

    PubMed

    Boeckmann, Jan; Näther, Christian

    2011-07-07

    Thermal annealing of a discrete complex with terminal SeCN anions and monodentate coligands enforces the formation of a 1D cobalt selenocyanato coordination polymer that shows slow relaxation of the magnetization. Therefore, this approach offers a rational route to 1D materials that might show single chain magnetic behaviour.

  10. Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin β1 and γ1 Chains

    PubMed Central

    Carafoli, Federico; Hussain, Sadaf-Ahmahni; Hohenester, Erhard

    2012-01-01

    The heterotrimeric laminins are a defining component of basement membranes and essential for tissue formation and function in all animals. The three short arms of the cross-shaped laminin molecule are composed of one chain each and their tips mediate the formation of a polymeric network. The structural basis for laminin polymerisation is unknown. We have determined crystal structures of the short-arm tips of the mouse laminin β1 and γ1 chains, which are grossly similar to the previously determined structure of the corresponding α5 chain region. The short-arm tips consist of a laminin N-terminal (LN) domain that is attached like the head of a flower to a rod-like stem formed by tandem laminin-type epidermal growth factor-like (LE) domains. The LN domain is a β-sandwich with elaborate loop regions that differ between chains. The γ1 LN domain uniquely contains a calcium binding site. The LE domains have little regular structure and are stabilised by cysteines that are disulphide-linked 1–3, 2–4, 5–6 and 7–8 in all chains. The LN surface is not conserved across the α, β and γ chains, but within each chain subfamily there is a striking concentration of conserved residues on one face of the β-sandwich, while the opposite face invariably is shielded by glycans. We propose that the extensive conserved patches on the β and γ LN domains mediate the binding of these two chains to each other, and that the α chain LN domain subsequently binds to the composite β-γ surface. Mutations in the laminin β2 LN domain causing Pierson syndrome are likely to impair the folding of the β2 chain or its ability to form network interactions. PMID:22860131

  11. Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model.

    PubMed

    Lee, Eric H; Hsin, Jen; Mayans, Olga; Schulten, Klaus

    2007-09-01

    The giant protein titin, which is responsible for passive elasticity in muscle fibers, is built from approximately 300 regular immunoglobulin-like (Ig) domains and FN-III repeats. While the soft elasticity derived from its entropic regions, as well as the stiff mechanical resistance derived from the unfolding of the secondary structure elements of Ig- and FN-III domains have been studied extensively, less is known about the mechanical elasticity stemming from the orientation of neighboring domains relative to each other. Here we address the dynamics and energetics of interdomain arrangement of two adjacent Ig-domains of titin, Z1, and Z2, using molecular dynamics (MD) simulations. The simulations reveal conformational flexibility, due to the domain-domain geometry, that lends an intermediate force elasticity to titin. We employ adaptive biasing force MD simulations to calculate the energy required to bend the Z1Z2 tandem open to identify energetically feasible interdomain arrangements of the Z1 and Z2 domains. The finding is cast into a stochastic model for Z1Z2 interdomain elasticity that is generalized to a multiple domain chain replicating many Z1Z2-like units and representing a long titin segment. The elastic properties of this chain suggest that titin derives so-called tertiary structure elasticity from bending and twisting of its domains. Finally, we employ steered molecular dynamics simulations to stretch individual Z1 and Z2 domains and characterize the so-called secondary structure elasticity of the two domains. Our study suggests that titin's overall elastic response at weak force stems from a soft entropic spring behavior (not described here), from tertiary structure elasticity with an elastic spring constant of approximately 0.001-1 pN/A and, at strong forces, from secondary structure elasticity.

  12. Straight-Chain Alkyl Isocyanides Open the Distal Histidine Gate in Crystal Structures of Myoglobin†

    PubMed Central

    Smith, Rober D.; Blouin, George C.; Johnson, Kenneth A.; Phillips, George N.; Olson, John S.

    2014-01-01

    Crystal structures of methyl, ethyl, propyl and butyl isocyanide bound to sperm whale myoglobin (Mb) reveal two major conformations. In the in conformer, His(E7) is in a “closed” position, forcing the ligand alkyl chain to point inward. In the out conformer, His(E7) is in an “open” position, allowing the ligand side chain to point outward. A progressive increase in the population of the out conformer is observed with increasing ligand length in P21 crystals of native Mb at pH 7.0. This switch from in to out with increasing ligand size also occurs in solution as measured by the decrease in the relative intensity of the low (~2075 cm 1) versus high frequency (~2125 cm 1) isocyano bands. In contrast, all four isocyanides in P6 crystals of wild type recombinant Mb occupy the in conformation. However, mutating either His64 to Ala, creating a “hole” to solvent, or Phe46 to Val, freeing rotation of His64, causes bound butyl isocyanide to point completely outward in P6 crystals. Thus, the unfavorable hindrance caused with crowding a large alkyl side chain into the distal pocket appears to be roughly equal to that for pushing open the His(E7) gate and is easily affected by crystal packing. This structural conclusion supports the “side path” kinetic mechanism for O2 release, in which the dissociated ligand first moves toward the protein interior and then encounters steric resistance, which is roughly equal to that for escaping to solvent through the His(E7) channel. PMID:20481504

  13. Clathrin light chain B: gene structure and neuron-specific splicing.

    PubMed Central

    Stamm, S; Casper, D; Dinsmore, J; Kaufmann, C A; Brosius, J; Helfman, D M

    1992-01-01

    The clathrin light chains are components of clathrin coated vesicles, structural constituents involved in endocytosis and membrane recycling. The clathrin light chain B (LCB) gene encodes two isoforms, termed LCB2 and LCB3, via an alternative RNA splicing mechanism. We have determined the structure of the rat clathrin light chain B gene. The gene consists of six exons that extend over 11.9 kb. The first four exons and the last exon are common to the LCB2 and LCB3 isoforms. The fifth exon, termed EN, is included in the mRNA in brain, giving rise to the brain specific form LCB2 but is excluded in other tissues, generating the LCB3 isoform. Primary rat neuronal cell cultures express predominantly the brain specific LCB2 isoform, whereas primary rat cultures of glia express only the LCB3 isoform, suggesting that expression of the brain-specific LCB2 form is limited to neurons. Further evidence for neuronal localization of the LCB2 form is provided using a teratocarcinoma cell line, P19, which can be induced by retinoic acid to express a neuronal phenotype, concomitant with the induction of the LCB2 form. In order to determine the sequences involved in alternative splice site selection, we constructed a minigene containing the alternative spliced exon EN and its flanking intron and exon sequences. This minigene reflects the splicing pattern of the endogenous gene upon transfection in HeLa cell and primary neuronal cell cultures, indicating that this region of the LCB gene contains all the necessary information for neuron-specific splicing. Images PMID:1408826

  14. Crystal Structure of Botulinum Neurotoxin Type G Light Chain - Serotype Divergence in Substrate Recognition†,‡

    PubMed Central

    Arndt, Joseph W.; Yu, Wayne; Bi, Fay; Stevens, Raymond C.

    2008-01-01

    The seven serotypes (A–G) of botulinum neurotoxins (BoNTs) block neurotransmitter release through their specific proteolysis of one of the three proteins of the soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) complex. BoNTs have stringent substrate specificities that are unique for metalloprotease in that they require exceptionally long substrates (1). In order to understand the molecular reasons for the unique specificities of the BoNTs, we determined the crystal structure of the catalytic light chain (LC) of Clostridium botulinum neurotoxin type G (BoNT/G-LC) at 2.35 Å resolution. The structure of BoNT/G-LC reveals a C-terminal β-sheet that is critical for LC oligomerization and is unlike that seen in the other LC structures. Its structural comparison with thermolysin and the available pool of LC structures reveals important serotype differences that are likely to be involved in substrate recognition of the P1’ residue. In addition, structural and sequence analysis have identified a potential exosite of BoNT/G-LC that recognizes a SNARE recognition motif of VAMP. PMID:16008342

  15. Crystal structure of botulinum neurotoxin type G light chain: serotype divergence in substrate recognition.

    PubMed

    Arndt, Joseph W; Yu, Wayne; Bi, Fay; Stevens, Raymond C

    2005-07-19

    The seven serotypes (A-G) of botulinum neurotoxins (BoNTs) block neurotransmitter release through their specific proteolysis of one of the three proteins of the soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) complex. BoNTs have stringent substrate specificities that are unique for metalloprotease in that they require exceptionally long substrates (1). To understand the molecular reasons for the unique specificities of the BoNTs, we determined the crystal structure of the catalytic light chain (LC) of Clostridium botulinum neurotoxin type G (BoNT/G-LC) at 2.35 A resolution. The structure of BoNT/G-LC reveals a C-terminal beta-sheet that is critical for LC oligomerization and is unlike that seen in the other LC structures. Its structural comparison with thermolysin and the available pool of LC structures reveals important serotype differences that are likely to be involved in substrate recognition of the P1' residue. In addition, structural and sequence analyses have identified a potential exosite of BoNT/G-LC that recognizes a SNARE recognition motif of VAMP.

  16. Insights into Medium-chain Acyl-CoA Dehydrogenase Structure by Molecular Dynamics Simulations.

    PubMed

    Bonito, Cátia A; Leandro, Paula; Ventura, Fátima V; Guedes, Rita C

    2016-08-01

    The medium-chain acyl-CoA dehydrogenase (MCAD) is a mitochondrial enzyme that catalyzes the first step of mitochondrial fatty acid β-oxidation (mFAO) pathway. Its deficiency is the most common genetic disorder of mFAO. Many of the MCAD disease-causing variants, including the most common p.K304E variant, show loss of function due to protein misfolding. Herein, we used molecular dynamics simulations to provide insights into the structural stability and dynamic behavior of MCAD wild-type (MCADwt) and validate a structure that would allow reliable new studies on its variants. Our results revealed that in both proteins the flavin adenine dinucleotide (FAD) has an important structural role on the tetramer stability and also in maintaining the volume of the enzyme catalytic pockets. We confirmed that the presence of substrate changes the dynamics of the catalytic pockets and increases FAD affinity. A comparison between the porcine MCADwt (pMCADwt) and human MCADwt (hMCADwt) structures revealed that both proteins are essentially similar and that the reversion of the double mutant E376G/T255E of hMCAD enzyme does not affect the structure of the protein neither its behavior in simulation. Our validated hMCADwt structure is crucial for complementing and accelerating the experimental studies aiming for the discovery and development of potential stabilizers of MCAD variants as candidates for the treatment of MCAD deficiency (MCADD).

  17. Structure and function of outer dynein arm intermediate and light chain complex

    PubMed Central

    Oda, Toshiyuki; Abe, Tatsuki; Yanagisawa, Haruaki; Kikkawa, Masahide

    2016-01-01

    The outer dynein arm (ODA) is a molecular complex that drives the beating motion of cilia/flagella. Chlamydomonas ODA is composed of three heavy chains (HCs), two ICs, and 11 light chains (LCs). Although the three-dimensional (3D) structure of the whole ODA complex has been investigated, the 3D configurations of the ICs and LCs are largely unknown. Here we identified the 3D positions of the two ICs and three LCs using cryo–electron tomography and structural labeling. We found that these ICs and LCs were all localized at the root of the outer-inner dynein (OID) linker, designated the ODA-Beak complex. Of interest, the coiled-coil domain of IC2 extended from the ODA-Beak to the outer surface of ODA. Furthermore, we investigated the molecular mechanisms of how the OID linker transmits signals to the ODA-Beak, by manipulating the interaction within the OID linker using a chemically induced dimerization system. We showed that the cross-linking of the OID linker strongly suppresses flagellar motility in vivo. These results suggest that the ICs and LCs of the ODA form the ODA-Beak, which may be involved in mechanosignaling from the OID linker to the HCs. PMID:26864626

  18. Primary structure and chain conformation of fucoidan extracted from sea cucumber Holothuria tubulosa.

    PubMed

    Chang, Yaoguang; Hu, Yanfang; Yu, Long; McClements, David Julian; Xu, Xiaoqi; Liu, Guanchen; Xue, Changhu

    2016-01-20

    Knowledge of the structure of polysaccharides is essential for understanding and controlling their functional properties. In this study, fucoidan was extracted from Holothuria tubulosa, a species of sea cucumber that has recently become commercially important. The primary structure of the H. tubulosa fucoidan was clarified using a combination of enzymatic degradation, methylation analysis, and NMR, and its chain conformation was further elucidated by utilizing high performance size exclusion chromatography combined with multiple angle laser light scattering and viscometry. The fucoidan was composed of a tetrafucose repeating unit [ → 3-α-L-Fucp2(OSO3(-))-1 → 3-α-L-Fucp2,4(OSO3(-))-1 → 3-α-L-Fucp-1 → 3-α-L-Fucp2(OSO3(-))-1 → ]. Its sulfate content was determined to be 31.2 ± 1.6% and the weight-average molecular mass was 1567.6 ± 34.1 kDa. The molecule adapted a random coil conformation in 0.15M NaCl solution (pH 7.4) at 25 °C, with a root-mean-square radius of 63.9 ± 1.8 nm and a hydrodynamic radius of 44.5 ± 4.5 nm. This is the first report on the chain conformation of sea cucumber fucoidan.

  19. Influence of HMW tail chains on the structural evolution of HDPE induced by second melt penetration.

    PubMed

    Zhu, Chun-Xia; Xia, Xiao-Chao; Huang, Yan-Hao; Xie, Dan-Dan; Chen, Rui; Yang, Ming-Bo

    2017-07-21

    It is widely accepted that the role of the high molecular weight (HMW) component is cooperative in shear-induced crystallization, owing to entanglements among long chains. However, this paper demonstrates that the HMW component has a novel effect on structural evolution during the process of multi-melt multi-injection molding (M(3)IM), organized as follows. First, the appropriate HDPE system with an incremental concentration of HMW tails was established. Second, the crystalline morphologies and orientation behaviors of the M(3)IM samples were characterized using a combination of scanning electron microscopy (SEM) and two-dimensional small angle X-ray scattering (2D-SAXS), and these suggested that the amount of shish-kebabs was not monotonically promoted with an increasing content of HMW tails but tended to reduce at a certain value. Third, in order to explain this phenomenon, the special temperature and shear profiles of M(3)IM were depicted subsequently, and finally the mechanism of hierarchical structure formation with the influence of various amounts of HMW tail chains was discussed, based on the classical rheological viewpoint.

  20. A one-dimensional chain structure based on unusual tetranuclear manganese(II) clusters.

    PubMed

    Che, Guang Bo; Wang, Jian; Liu, Chun Bo; Li, Xiu Ying; Liu, Bo

    2008-11-01

    The title coordination polymer, poly[bis(mu(4)-biphenyl-2,2'-dicarboxylato)(dipyrido[3,2-a:2',3'-c]phenazine)manganese(II)], [Mn(2)(C(14)H(8)O(4))(2)(C(18)H(10)N(4))](n), was obtained through the reaction of MnCl(2).4H(2)O, biphenyl-2,2'-dicarboxylic acid (H(2)dpdc) and dipyrido[3,2-a:2',3'-c]phenazine (L) under hydrothermal conditions. The asymmetric unit contains two crystallographically unique Mn(II) ions, one unique L ligand and two unique dpdc ligands. One Mn ion is six-coordinated by four O atoms from three different dpdc ligands and two N atoms from one L ligand, adopting a distorted octahedral coordination geometry. The distortions from ideal octahedral geometry are largely due to the presence of chelating ligands and the resulting acute N-Mn-N and O-Mn-O angles. The second Mn ion is coordinated in a distorted trigonal bipyramidal fashion by five O atoms from four distinct dpdc ligands. Four Mn(II) ions are bridged by the carboxylate groups of the dpdc ligands to form an unusual tetranuclear Mn(II) cluster. Clusters are further connected by the aromatic backbone of the dicarboxylate ligands, forming a one-dimensional chain structure along the b axis. The title compound is the first example of a chain structure based on a tetranuclear Mn(II) cluster.

  1. Structure of Amorphous Selenium by 2D (77) Se NMR Spectroscopy: An End to the Dilemma of Chain versus Ring.

    PubMed

    Marple, Maxwell; Badger, Jackson; Hung, Ivan; Gan, Zhehong; Kovnir, Kirill; Sen, Sabyasachi

    2017-08-07

    Amorphous selenium, owing to its tremendous technological importance and perhaps to its chemical simplicity, has been studied for nearly a century and yet an unequivocal structural description of this material remains lacking to date. The primary controversy regarding the structure of amorphous Se relates to the relative fraction of Se atoms residing in ∞1Se chains versus in Se8 rings. Herein we present the results of a two-dimensional solid-state (77) Se nuclear magnetic resonance (NMR) spectroscopic study of the chain and ring crystalline allotropes of Se as well as of amorphous Se to unequivocally demonstrate that 1) the Se8 rings and the ∞1Se chains are characterized by their unique (77) Se NMR signatures and 2) the structure of amorphous Se consists exclusively of ∞1Se chains. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Complete primary structure of a scallop striated muscle myosin heavy chain. Sequence comparison with other heavy chains reveals regions that might be critical for regulation.

    PubMed

    Nyitray, L; Goodwin, E B; Szent-Györgyi, A G

    1991-10-05

    We have determined the primary structure of the myosin heavy chain (MHC) of the striated adductor muscle of the scallop Aequipecten irradians by cloning and sequencing its cDNA. It is the first heavy chain sequence obtained in a directly Ca(2+)-regulated myosin. The 1938-amino acid sequence has an overall structure similar to other MHCs. The subfragment-1 region of the scallop MHC has a 59-62% sequence identity with sarcomeric and a 52-53% identity with nonsarcomeric (smooth and metazoan nonmuscle) MHCs. The heavy chain component of the regulatory domain (Kwon, H., Goodwin, E. B., Nyitray, L., Berliner, E., O'Neall-Hennessey, E., Melandri, F. D., and Szent-Györgyi, A. G. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4771-4775) starts at either Leu-755 or Val-760. Ca(2+)-sensitive Trp residues (Wells, C., Warriner, K. E., and Bagshaw, C. R. (1985) Biochem. J. 231, 31-38) are located near the C-terminal end of this segment (residues 818-827). More detailed sequence comparison with other MHCs reveals that the 50-kDa domain and the N-terminal two-thirds of the 20-kDa domain differ substantially between sarcomeric and nonsarcomeric myosins. In contrast, in the light chain binding region of the regulatory domain (residues 784-844) the scallop sequence shows greater homology with regulated myosins (smooth muscle, nonmuscle, and invertebrate striated muscles) than with unregulated ones (vertebrate skeletal and heart muscles). The N-terminal 25-kDa domain also contains several residues which are preserved only in regulated myosins. These results indicate that certain heavy chain sites might be critical for regulation. The rod has features typical of sarcomeric myosins. It is 52-60% and 30-33% homologous with sarcomeric and nonsarcomeric MHCs, respectively. A Ser-rich tailpiece (residues 1918-1938) is apparently nonhelical.

  3. Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru

    Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.

  4. Crystal structure of Sr2CdPt2 containing linear platinum chains

    PubMed Central

    Nawawi, Effendi; Gulo, Fakhili; Köhler, Jürgen

    2016-01-01

    The ternary inter­metallic title phase, distrontium cadmium diplatinum, was prepared from stoichiometric amounts of the elements at 1123 K for one day. The crystal structure adopts the ortho­rhom­bic Ca2GaCu2 structure type in space group Immm. Its main features are characterized by linear (Pt—Pt⋯Pt—Pt)n chains that are aligned along [010] and condensed through cadmium atoms forming Cd-centred Pt2Cd2/2 rectangles to build up sheets parallel to (001). These sheets are connected to each other via alternating (001) sheets of strontium atoms along [001]. The strontium sheets consists of corrugated Sr4 units that are condensed to each other through edge-sharing parallel to [100]. PMID:26958374

  5. Crystalline structures of polymeric hydrocarbon with 3,4-fold helical chains.

    PubMed

    Lian, Chao-Sheng; Li, Han-Dong; Wang, Jian-Tao

    2015-01-12

    Molecular hydrocarbons are well-known to polymerize under pressure to form covalently bonded frameworks. Here we predict by ab initio calculations two distinct three-dimensional hydrocarbon crystalline structures composed of 3-fold and 4-fold helical CH chains in rhombohedral (R3) and tetragonal (I4₁/a) symmetry, respectively. Both structures with 1:1 stoichiometry are found to be energetically more favorable than solid acetylene and cubane, and even more stable than benzene II solid at high pressure. The calculations on vibrational, electronic, and optical properties reveal that the new chiral hydrocarbons are dynamically stable with large bulk moduli around 200 GPa, and exhibit a transparent insulating behavior with indirect band gaps of 5.9 ~ 6.7 eV and anisotropic adsorption spectra. Such forms of hydrocarbon, once synthesized, would have wide applications in mechanical, optoelectronic, and biological materials.

  6. Crystalline structures of polymeric hydrocarbon with 3,4-fold helical chains

    PubMed Central

    Lian, Chao-Sheng; Li, Han-Dong; Wang, Jian-Tao

    2015-01-01

    Molecular hydrocarbons are well-known to polymerize under pressure to form covalently bonded frameworks. Here we predict by ab initio calculations two distinct three-dimensional hydrocarbon crystalline structures composed of 3-fold and 4-fold helical CH chains in rhombohedral () and tetragonal (I41/a) symmetry, respectively. Both structures with 1:1 stoichiometry are found to be energetically more favorable than solid acetylene and cubane, and even more stable than benzene II solid at high pressure. The calculations on vibrational, electronic, and optical properties reveal that the new chiral hydrocarbons are dynamically stable with large bulk moduli around 200 GPa, and exhibit a transparent insulating behavior with indirect band gaps of 5.9 ~ 6.7 eV and anisotropic adsorption spectra. Such forms of hydrocarbon, once synthesized, would have wide applications in mechanical, optoelectronic, and biological materials. PMID:25579707

  7. Crystal structure of a supercharged variant of the human enteropeptidase light chain.

    PubMed

    Simeonov, Peter; Zahn, Michael; Sträter, Norbert; Zuchner, Thole

    2012-07-01

    The highly specific serine protease human enteropeptidase light chain cleaves the Asp4Lys recognition sequence and represents an interesting enzyme for biotechnological applications. The human enzyme shows 10 times faster kinetics compared to other animal sources but low solubility under low salt conditions, which hampers protein production and crystallization. Therefore, a supercharged variant (N6D/G21D/G22D/N142D/K210E/C112S) with increased solubility was used for crystallization. The structure (resolution, 1.9 Å) displays a typical α/β trypsin-like serine protease-fold. The mutations introduced for protein supercharging generate larger clusters of negative potential on both sites of the active cleft but do not affect the structural integrity of the protein.

  8. Structural differences in the motor domain of temperature-associated myosin heavy chain isoforms from grass carp fast skeletal muscle.

    PubMed

    Tao, Yan; Wang, Sun-Yong; Liang, Chun-Shi; Fukushima, Hideto; Watabe, Shugo

    2009-10-01

    We determined coding sequences for three types of grass carp myosin subfragment-1 (S1) heavy chain by extending 5'-regions of the three known genes encoding light meromyosin isoforms (10 degrees C, intermediate and 30 degrees C types). The primary structures of these three S1 heavy chain isoforms showed 81.4%, 81.2%, and 97.8% identities between the 10 degrees C and intermediate types, between the 10 degrees C and 30 degrees C types, and between the intermediate and 30 degrees C types, respectively. Isoform-specific differences were clearly observed between the 10 degrees C type and the other two types in 97 amino acid residues. Furthermore, among these amino acid mutations, 51 mutations occurred at the conserved residue sites of S1 heavy chain from fish and homoiotherm. Additionally, the 10 degrees C type showed striking differences compared with the other two types in the two surface loops, loop 1 located near the ATP-binding pocket and loop 2, which is one of the actin-binding sites, suggesting that such structural differences possibly affect their motor functions. Interestingly, this 10 degrees C-type myosin heavy chain isolated from adult grass carp skeletal muscle was surprisingly similar to the embryonic fast-type myosin heavy chain from juvenile silver carp in the structure of S1 heavy chain, indicating that it may also function as embryonic fast-type myosin heavy chain in juvenile stage.

  9. Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA

    PubMed Central

    Robins, Lori I.; Williams, Allison H.; Raetz, Christian R. H.

    2009-01-01

    The first step of lipid A biosynthesis is catalyzed by LpxA in Escherichia coli (EcLpxA), an acyltransferase selective for UDP-GlcNAc and R-3-hydroxymyristoyl-acyl carrier protein (ACP). Leptospira interrogans LpxA (LiLpxA) is extremely selective for R-3-hydroxylauroyl-ACP and an analogue of UDP-GlcNAc, designated UDP-GlcNAc3N, in which NH2 replaces the GlcNAc 3-OH group. EcLpxA does not discriminate between UDP-GlcNAc and UDP-GlcNAc3N; however, E. coli does not make UDP-GlcNAc3N. With LiLpxA R-3-hydroxylauroyl-methylphosphopantetheine efficiently substitutes for R-3-hydroxylauroyl-ACP. We now present crystal structures of free LiLpxA, and of its complexes with its product UDP-3-N-(R-3-hydroxylauroyl)-GlcNAc3N and with its substrate R-3-hydroxylauroyl-methylphosphopantetheine. The positions of the acyl chains of the R-3-hydroxylauroyl-methylphosphopantetheine and of the UDP-3-N-(R-3-hydroxylauroyl)-GlcNAc3N are almost identical, and are similar to that of the acyl chain in the EcLpxA/UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc complex. The selectivity of LiLpxA for UDP-GlcNAc3N may be explained by the orientation of the backbone carbonyl group of Q68, which differs by ∼82° from the corresponding Q73 carbonyl group in EcLpxA. This arrangement provides an extra hydrogen bond acceptor for the 3-NH2 group of UDP-GlcNAc3N in LiLpxA. The R-3-hydroxylauroyl-selectivity of LiLpxA is explained by the position of the K171 side chain, which limits the length of the acyl chain-binding groove. Our results support the role of LiLpxA H120 (which corresponds to EcLpxA H125) as the catalytic base and provide the first structural information about the orientation of the phosphopantetheine moiety during LpxA catalysis. PMID:19456129

  10. Crystal structures and thermodynamics/kinetics of Zn(II) coordination polymers with helical chains

    SciTech Connect

    He, Tian; Yue, Ke-Fen; Zhao, Yi-xing; Chen, San-Ping; Zhou, Chun-sheng; Yan, Ni

    2016-07-15

    Solvothermal reactions of Zn(II) acetates and four V-shaped carboxylates ligands in the presence of 1,4-Bis(2-methyl-imidazol-1-yl)butane afforded four interesting Zn(II) coordination polymers with helical chains, namely, {[Zn(bib)(atibdc)]·2H_2O}{sub n} (1), {[Zn(bib)(atbip)]·H_2O}{sub n} (2), {[Zn(bib)(2,2′-tda)]}{sub n} (3) and {[Zn(bib)(5-tbipa)]·EtOH}{sub n} (4), (H{sub 2}atibdc=5-amino-2,4,6-triiodoisophthalic acid, H{sub 2}atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2′-H{sub 2}tad=2,2′-thiodiacetic acid, 5-H{sub 2}tbipa=5-tert-butyl-isophthalic acid). 1 reveals a 3D chiral framework with three kinds of helical chains along a, b and c axis. 2 shows a 2D step-type chiral framework with right-handed helical chains. 3 displays a wavelike 2D layer network possessing alternate left- and right-handed helical chains. 4 presents a four-connected 3D framework with zigzag and meso-helical chains. The different spacers and substituent group of carboxylic acid ligands may lead to the diverse network structures of 1–4. The fluorescent properties of complexes 1−4 were studied. In addition, the thermal decompositions properties of 1–4 were investigated by simultaneous TG/DTG–DSC technique. The apparent activation energy E and the pre-exponential factor (A) of skeleton collapse for the complexes 1–4 are calculated by the integral Kissinger's method and Ozawa–Doyle's method. The activation energy E (E{sub 1}=209.658 kJ·mol{sup −1}, E{sub 2}=250.037 kJ mol{sup −1}, E{sub 3}=225.300 kJ mol{sup −1}, E{sub 4}=186.529 kJ·mol{sup −1}) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH{sup ‡}, ΔG{sup ‡} and ΔS{sup ‡}) at the peak temperatures of the DTG curves were also calculated. ΔG{sup ‡}>0 indicates that the skeleton collapse is not spontaneous. ΔH{sub d}>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC curve. The

  11. Neutral-Type One-Dimensional Mixed-Valence Halogen-Bridged Platinum Chain Complexes with Large Charge-Transfer Band Gaps.

    PubMed

    Otake, Ken-ichi; Otsubo, Kazuya; Sugimoto, Kunihisa; Fujiwara, Akihiko; Kitagawa, Hiroshi

    2016-03-07

    One-dimensional (1D) electronic systems have attracted significant attention for a long time because of their various physical properties. Among 1D electronic systems, 1D halogen-bridged mixed-valence transition-metal complexes (the so-called MX chains) have been thoroughly studied owing to designable structures and electronic states. Here, we report the syntheses, structures, and electronic properties of three kinds of novel neutral MX-chain complexes. The crystal structures consist of 1D chains of Pt-X repeating units with (1R,2R)-(-)-diaminocychlohexane and CN(-) in-plane ligands. Because of the absence of a counteranion, the neutral MX chains have short interchain distances, so that strong interchain electronic interaction is expected. Resonance Raman spectra and diffuse-reflectance UV-vis spectra indicate that their electronic states are mixed-valence states (charge-density-wave state: Pt(2+)···X-Pt(4+)-X···Pt(2+)···X-Pt(4+)-X···). In addition, the relationship between the intervalence charge-transfer (IVCT) band gap and the degree of distortion of the 1D chain shows that the neutral MX chains have a larger IVCT band gap than that of cationic MX-chain complexes. These results provide new insight into the physical and electronic properties of 1D chain compounds.

  12. Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

    PubMed Central

    Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won

    2012-01-01

    Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form “a carboxylate clamp” with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins. PMID:22470497

  13. Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

    SciTech Connect

    Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won

    2012-10-23

    Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.

  14. Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

    PubMed

    Punihaole, David; Hong, Zhenmin; Jakubek, Ryan S; Dahlburg, Elizabeth M; Geib, Steven; Asher, Sanford A

    2015-10-15

    We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) Cβ-Cγ (Cα-Cβ) stretching component of the vibration. The Cβ-Cγ (Cα-Cβ) bond length inversely correlates with the AmIII(P) band frequency. As the Cβ-Cγ (Cα-Cβ) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cβ-Cγ (Cα-Cβ) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cβ-Cγ (Cα-Cβ) σ orbitals. Using a Protein Data Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides. The spectral correlations determined in this study enable important new insights into protein structure in solution, and in Gln- and Asn-rich amyloid-like fibrils and prions.

  15. New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

    SciTech Connect

    Xiong, Kecai; Liu, Wei; Teat, Simon J.; An, Litao; Wang, Hao; Emge, Thomas J.; Li, Jing

    2015-10-15

    Two new hybrid lead halides (H{sub 2}BDA)[PbI{sub 4}] (1) (H{sub 2}BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI{sub 3}] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively. - Graphical abstract: Two new hybrid lead halides built on one-dimensional edge-sharing double chains and two-dimensional corner-sharing perovskite layers are synthesized and their structural and electronic properties are analyzed. - Highlights: • Two new hybrid lead iodides are designed, synthesized, and characterized. • They are closely related to, but different from, perovskite structures. • The electronic properties of both compounds are analyzed by DFT calculations.

  16. Scaffolding, ladders, chains, and rare ferrimagnetism in intermetallic borides: electronic structure calculations and magnetic ordering.

    PubMed

    Brgoch, Jakoah; Goerens, Christian; Fokwa, Boniface P T; Miller, Gordon J

    2011-05-04

    The electronic structures of "Ti(9-n)Fe(2+n)Ru(18)B(8)" (n=0, 0.5, 1, 2, 3), in connection to the recently synthesized Ti(9-n)Fe(2+n)Ru(18)B(8) (n=1, 2), have been investigated and analyzed using LSDA tight-binding calculations to elucidate the distribution of Fe and Ti, to determine the maximum Fe content, and to explore possible magnetic structures to interpret experimental magnetization results. Through a combination of calculations on specific models and using the rigid band approximation, which is validated by the DOS curves for "Ti(9-n)Fe(2+n)Ru(18)B(8)" (n=0, 0.5, 1, 2, 3), mixing of Fe and Ti is anticipated at both the 2b- and 4h-chain sites. The model "Ti(8.5)Fe(2.5)Ru(18)B(8)" (n=0.5) revealed that both Brewer-type Ti-Ru interactions as well as ligand field splitting of the Fe 3d orbitals regulated the observed valence electron counts between 220 and 228 electrons/formula unit. Finally, models of magnetic structures were created using "Ti(6)Fe(5)Ru(18)B(8)" (n=3). A rigid band analysis of the LSDA DOS curves concluded preferred ferromagnetic ordering at low Fe content (n≤0.75) and ferrimagnetic ordering at higher Fe content (n>0.75). Ferrimagnetism arises from antiferromagnetic exchange coupling in the scaffold of Fe1-ladder and 4h-chain sites.

  17. Spectral characteristics of heterocyclic compounds with a chain structure, cooled in an ultrasonic jet

    NASA Astrophysics Data System (ADS)

    Povedailo, V. A.; Yakovlev, D. L.

    2006-11-01

    We have recorded the fluorescence excitation spectra of three heterocyclic compounds with a chain structure [BPO (2-phenyl-5-(4-diphenylyl)oxazole), POPOP (1,4-di[2-(5-phenyloxazolyl)]benzene, and TOPOT (1,4-di[2-(5-n-tolyloxazolyl)]benzene] and the fluorescence spectra of POPOP, under conditions where the molecules were cooled in an ultrasonic helium jet. A line structure is observed in the spectra of POPOP and TOPOT; for the BPO molecules, whose configuration changes considerably during electronic excitation, vibrational structure is apparent only in the low-frequency region of the excitation spectrum, and a diffuse spectrum is recorded starting from ν 0 0 + 200 cm-1. For all the compounds, in the spectra we recorded vibrations with frequencies up to 100 cm-1, arising due to the flexibility of the molecular structure. The rotational contours of the lines for the electronic and vibronic transitions of the POPOP molecules (Trot = 10.5 K) and TOPOT molecules (Trot = 15 K) are structureless and bell-shaped. The degree of polarization of the fluorescence Pfl for the jet-cooled POPOP molecules for excitation of vibrations along the absorption band up to 2000 cm-1 above ν 0 0 is practically constant (˜8.4%) and matches Pfl for high-temperature vapors.

  18. Proton–proton Overhauser NMR spectroscopy with polypeptide chains in large structures

    PubMed Central

    Horst, Reto; Wider, Gerhard; Fiaux, Jocelyne; Bertelsen, Eric B.; Horwich, Arthur L.; Wüthrich, Kurt

    2006-01-01

    The use of 1H–1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H–1H NOE experiments under slow-motion conditions shows that the maximal 1H–1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H–1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution. PMID:17032756

  19. Chemistry of the rock-forming silicates: Multiple-chain, sheet, and framework structures

    NASA Astrophysics Data System (ADS)

    Papike, J. J.

    1988-08-01

    The crystal chemistry of 16 groups of multiple-chain, sheet, and framework silicates is reviewed. Crystal structure drawings are presented to illustrate crystal chemical features necessary to interpret chemical data for each mineral group. The 16 silicate groups considered in this review are the amphibole; nonclassical, ordered pyriboles; mica; pyrophyllite-talc; chlorite; greenalite; minnesotaite; stilpnomelane; prehnite; silica polymorphs; feldspar; nepheline-kalsilite; leucite-analcite; sodalite group; cancrinite group; and scapolite. Electron microprobe analyses should be augmented by independent determinations of Fe2+/Fe3+ and H2O for many of the silicate groups discussed and by determinations of CO32-, SO42-, S2-, and Li in some of the others. However, microprobe data augmented as suggested will still be ambiguous for some of the silicate groups considered here because the structures are not completely determined or are variable, with disparate domains and/or structural modulations, e.g., pyriboles, greenalite, minnesotaite, and stilpnomelane. Nevertheless, the most rigorous way to interpret silicate mineral chemical data is based on the crystal structures involved.

  20. Water structure around hydrophobic amino acid side chain analogs using different water models

    NASA Astrophysics Data System (ADS)

    Hajari, Timir; Bandyopadhyay, Sanjoy

    2017-06-01

    The water structure around hydrophobic groups governs various biochemical processes. There is an ongoing debate on whether water molecules near hydrophobic groups are more ordered with greater participation in water-water hydrogen bonding with respect to water in the pure bulk state. The water structure around six different hydrophobic amino acid side chain analog molecules has been studied in pure water using molecular dynamics simulations. The analysis of water tetrahedral order parameter and the number of hydrogen bonds formed by the individual water molecules in the first hydration shell of the hydrophobic analogs provide evidence that both ordering and hydrogen bonds involving water molecules are to some extent reduced in the hydrophobic hydration shell. It is revealed that the water tetrahedrality in the outer part of the first hydrophobic hydration shell is equivalent to bulk water for all the water models except for the TIP4P-2005 model which shows marginally higher tetrahedrality. However, irrespective of the model employed, water tetrahedrality has always been found to be reduced in the inner part of the first hydration shell, which eventually makes the overall water tetrahedrality in the first hydrophobic hydration shell marginally lower than that observed for pure bulk water. Importantly, it is noticed that the decrease in water structuring exhibits solute size dependencies. Around a small solute like methane, the water tetrahedral ordering or hydrogen bonding propensity is quite similar to that of the bulk state. The effect, reduction in water structuring, is however more pronounced for relatively larger solutes.

  1. Understanding influential factors on implementing green supply chain management practices: An interpretive structural modelling analysis.

    PubMed

    Agi, Maher A N; Nishant, Rohit

    2017-03-01

    In this study, we establish a set of 19 influential factors on the implementation of Green Supply Chain Management (GSCM) practices and analyse the interaction between these factors and their effect on the implementation of GSCM practices using the Interpretive Structural Modelling (ISM) method and the "Matrice d'Impacts Croisés Multiplication Appliquée à un Classement" (MICMAC) analysis on data compiled from interviews with supply chain (SC) executives based in the Gulf countries (Middle East region). The study reveals a strong influence and driving power of the nature of the relationships between SC partners on the implementation of GSCM practices. We especially found that dependence, trust, and durability of the relationship with SC partners have a very high influence. In addition, the size of the company, the top management commitment, the implementation of quality management and the employees training and education exert a critical influence on the implementation of GSCM practices. Contextual elements such as the industry sector and region and their effect on the prominence of specific factors are also highlighted through our study. Finally, implications for research and practice are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Primary structure of myosin heavy chain from fast skeletal muscle of Chum salmon Oncorhynchus keta.

    PubMed

    Iwami, Yuki; Ojima, Takao; Inoue, Akira; Nishita, Kiyoyoshi

    2002-10-01

    The nucleotide sequence of the cDNA encoding myosin heavy chain of chum salmon Oncorhynchus keta fast skeletal muscle was determined. The sequence consists of 5,994 bp, including 5,814 bp of translated region deducing an amino acid sequence of 1,937 residues. The deduced sequence showed 79% homology to that of rabbit fast skeletal myosin and 84-87% homology to those of fast skeletal myosins from walleye pollack, white croaker and carp. The putative binding-sites for ATP, actin and regulatory light-chains in the subfragment-1 region of the salmon myosin showed high homology with the fish myosins (78-100% homology). However, the Loop-1 and Loop-2 showed considerably low homology (31-60%). On the other hand, the deduced sequences of subfragment-2 (533 residues) and light meromyosin (564 residues) showed 88-93% homology to the corresponding regions of the fish myosins. It becomes obvious that several specific residues of the rabbit LMM are substituted to Gly in the salmon LMM as well as the other fish LMMs. This may be involved in the structural instability of the fish myosin tail region.

  3. Selenium dimers and linear chains in one-dimensional cancrinite nanochannels: Structure, dynamics, and optical properties

    NASA Astrophysics Data System (ADS)

    Poborchii, Vladimir V.; Lindner, Gottlieb-Georg; Sato, Mitsuo

    2002-02-01

    Cancrinite crystals possessing parallel nanochannels are attractive for incorporation of guest materials and preparation of one-dimensional structures. In this work, we study variety of cancrinite crystals synthesized with Se inside their channels. Single crystal x-ray diffraction, polarized Raman, optical absorption, and luminescence spectra are investigated. It is shown that Se is stabilized in the form of Se22- and Se2- dimers located in the center of the channel and oriented along the channel. Different absolute and relative concentrations of Se22- and Se2- are obtained for different samples. The Se22- dimers at high concentration show tendency to organize linear chains. At low temperatures, quite strong interdimer bonding for both Se22- and Se2- is observed. Another important low-temperature effect is appearance of additional Raman bands, which are attributed to the vibrations of linear Se22- chains distorted by the incommensurate potential of cancrinite. Strong near-infrared polarized luminescence is observed for all samples. Photoionization of dimers is shown to be important step in the mechanism of the luminescence.

  4. Structured Mono- and Diacylglycerols with a High Content of Medium Chain Fatty Acids.

    PubMed

    Esperón-Rojas, Alaina A; Baeza-Jiménez, R; Cano-Sarmiento, Cynthia; García, Hugo S

    2017-09-01

    In the present work, direct enzyme-catalysed esterification of medium chain fatty acids (MCFA) from three different sources (Medium chain triacylglycerols, MCT; saponified MCT and a mixture of free MCFA) was evaluated to obtain structured mono- and diacylglycerols. The esterifications were carried out mixing the different sources of MCFA with glycerol at two weight ratios (1:1 and 4:1, w/w), using three immobilized lipases: Novozym 435, Lipozyme RM IM and Lipozyme TL IM; different reaction times (t = 0, 15, 30, 60, 120 min); enzyme loadings (5, 10 or 15% with respect to the total weight of substrates). The extent of esterification was determined by gas chromatography (GC) analysis of the acylglycerols produced. The highest incorporation of free MCFA into glycerol was obtained for a 1:1 (w/w) glycerol to free MCFA ratio, 5% of Novozym 435, at 50°C, 300 rpm, 10% of molecular sieves and a commercial MCFA mixture as starting material. Under these conditions, incorporation of at least 90% of MCFA into glycerol was achieved after 30 min of reaction.

  5. Structural identification of skin ceramides containing ω-hydroxy acyl chains using mass spectrometry.

    PubMed

    Wu, Zhexue; Shon, Jong Cheol; Kim, Jong Yei; Cho, Yunhi; Liu, Kwang-Hyeon

    2016-10-01

    The stratum corneum (SC) acts as a barrier that protects organisms against the environment and from transepidermal water loss. It consists of corneocytes embedded in a matrix of lipid metabolites (ceramides, cholesterol, and free fatty acids). Of these lipids, ceramides are sphingolipids consisting of sphingoid bases, linked to fatty acyl chains. Typical fatty acid acyl chains are composed of α-hydroxy fatty acids (A), esterified ω-hydroxy fatty acids (EO), non-hydroxy fatty acids (N), and ω-hydroxy fatty acids (O). Of these, O-type ceramides are ester-linked via their ω-hydroxyl group to proteins in the cornified envelope and can be released and extracted following mild alkaline hydrolysis. Tandem mass spectrometry (MS/MS) analysis of O-type ceramides using chip-based direct infusion nanoelectrospray-ion trap mass spectrometry generated the characteristic fragmentation pattern of both acyl and sphingoid units, suggesting that this method could be applied to the structural identification of O-type ceramides. Based on the MS/MS fragmentation patterns of O-type ceramides, comprehensive fragmentation schemes are proposed. In addition, we have also developed a method for identifying and profiling O-type ceramides in the mouse and guinea pig SC. This information may be used to identify O-type ceramides in the SC of animal skin.

  6. The Role of Interlamellar Chain Entanglement in Deformation-Induced Structure Changes During Uniaxial Stretching of Isotactic Polypropylene

    SciTech Connect

    Zuo,F.; Keum, J.; Chen, X.; Hsiao, B.; Chen, H.; Lai, S.; Wevers, R.; Li, J.

    2007-01-01

    In-situ small-angle X-ray scattering (SAXS), and wide-angle X-ray diffraction (WAXD) were carried out to investigate the deformation-induced structure changes of isotactic polypropylene (iPP) films during uniaxial stretching at varying temperatures (room temperature, 60 C and 160 C). From the WAXD data, mass fractions of amorphous, mesomorphic and crystal phases were estimated. Results indicate that at room temperature, the dominant structure change is the transformation of folded-chain crystal lamellae (monoclinic {alpha}-form) to oriented mesomorphic phase; while at high temperatures (>60 C); the dominant change is the transformation of amorphous phase to oriented folded-chain crystal lamellae. This behavior may be explained by the relative strength between the interlamellar entangled network of amorphous chains, which probably directly influence the tie chain distribution, and the surrounding crystal lamellae. It appears that during stretching at low temperatures, the interlamellar entanglement network is strong and can cause lamellar fragmentation, resulting in the formation of oriented mesomorphic phase. In contrast, during stretching at high temperatures, the chain disentanglement process dominates, resulting in the relaxation of restrained tie chains and the formation of more folded-chain lamellae.

  7. Effect of side-chain asymmetry on the intermolecular structure and order-disorder transition in alkyl-substituted polyfluorenes

    NASA Astrophysics Data System (ADS)

    Knaapila, M.; Stepanyan, R.; Torkkeli, M.; Haase, D.; Fröhlich, N.; Helfer, A.; Forster, M.; Scherf, U.

    2016-04-01

    We study relations among the side-chain asymmetry, structure, and order-disorder transition (ODT) in hairy-rod-type poly(9,9-dihexylfluorene) (PF6) with two identical side chains and atactic poly(9-octyl-9-methyl-fluorene) (PF1-8) with two different side chains per repeat. PF6 and PF1-8 organize into alternating side-chain and backbone layers that transform into an isotropic phase at TODT(PF 6 ) and TbiODT(PF 1 -8 ) . We interpret polymers in terms of monodisperse and bidisperse brushes and predict scenarios TODTchain length above or below the average grafting distance). Calorimetry and x-ray scattering indicate the condition TODT(PF 6 ) ˜TbiODT(PF 1 -8 ) following the low grafting prediction. PF6 side chains coming from the alternating backbone layers appear as two separate layers with thickness H (PF 6 ) , whereas PF1-8 side chains appear as an indistinguishable bilayer with a half thickness Hbilayer(PF 1 -8 ) /2 ≈H (PF 6 ) . The low grafting density region is structurally possible but not certain for PF6 and confirmed for PF1-8.

  8. Glucal-conjugated sterols as novel vascular leakage blocker: structure-activity relationship focusing on the C17-side chain.

    PubMed

    Kim, Kyeojin; Maharjan, Sony; Lim, Changjin; Kim, Nam-Jung; Agrawal, Vijayendra; Han, Young Taek; Lee, Sujin; An, Hongchan; Yun, Hwayoung; Choi, Hyun-Jung; Kwon, Young-Guen; Suh, Young-Ger

    2014-03-21

    A series of glucal-conjugated sterols as novel vascular leakage blocker were identified through design, synthesis and biologically evaluation. In addition, the structure-activity relationship (SAR) of the glucal-conjugated sterols focusing on the C17-side chain was also established. The sterol analogs linked with the rigid C17-side chain side chains exhibited potent cell survival activities. In particular, analog 21l, which possesses a cyclopentyl oxime moiety, was shown to have excellent pharmacological effects on retinal vascular leakage in a diabetic mouse model. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  9. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

    PubMed

    Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

    2015-03-01

    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein