Method of preparing and utilizing a catalyst system for an oxidation process on a gaseous hydrocarbon stream

DOEpatents

Berry, David A; Shekhawat, Dushyant; Smith, Mark; Haynes, Daniel

2013-07-16

The disclosure relates to a method of utilizing a catalyst system for an oxidation process on a gaseous hydrocarbon stream with a mitigation of carbon accumulation. The system is comprised of a catalytically active phase deposited onto an oxygen conducting phase, with or without supplemental support. The catalytically active phase has a specified crystal structure where at least one catalytically active metal is a cation within the crystal structure and coordinated with oxygen atoms within the crystal structure. The catalyst system employs an optimum coverage ratio for a given set of oxidation conditions, based on a specified hydrocarbon conversion and a carbon deposition limit. Specific embodiments of the catalyst system are disclosed.

Crystallization and preliminary X-ray diffraction study of phosphopantetheine adenylyltransferase from M. tuberculosis crystallizing in space group P3{sub 2}

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

Timofeev, V. I., E-mail: tostars@mail.ru; Chupova, L. A.; Esipov, R. S.

Crystals of M. tuberculosis phosphopantetheine adenylyltransferase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 2.00-Å resolution. The crystals belong to sp. gr. P3{sub 2} and have the following unit-cell parameters: a = b = 106.47 Å, c = 71.32 Å, α = γ = 90°, β = 120°. The structure was solved by the molecular-replacement method. There are six subunits of the enzyme comprising a hexamer per asymmetricmore » unit. The hexamer is a biologically active form of phosphopantetheine adenylyltransferase from M. tuberculosis.« less

Device for calorimetric measurement

DOEpatents

King, William P; Lee, Jungchul

2015-01-13

In one aspect, provided herein is a single crystal silicon microcalorimeter, for example useful for high temperature operation and long-term stability of calorimetric measurements. Microcalorimeters described herein include microcalorimeter embodiments having a suspended structure and comprising single crystal silicon. Also provided herein are methods for making calorimetric measurements, for example, on small quantities of materials or for determining the energy content of combustible material having an unknown composition.

One-dimensional dielectric bi-periodic photonic structures based on ternary photonic crystals

NASA Astrophysics Data System (ADS)

Dadoenkova, Nataliya N.; Dadoenkova, Yuliya S.; Panyaev, Ivan S.; Sannikov, Dmitry G.; Lyubchanskii, Igor L.

2018-01-01

We investigate the transmittivity spectra, fields, and energy distribution of the electromagnetic eigenwaves propagating in a one-dimensional (1D) dielectric photonic crystal [(TiO2/SiO2)NAl2O3]M with two periods formed by unit cells TiO2/SiO2 and (TiO2/SiO2)NAl2O3. Spectra of TE- and TM-modes depend on the geometric parameters of the structure and undergo modifications with the change in the period numbers, layer thicknesses, and incidence angle. Special attention is paid to the applicability of the hybrid effective medium approximation comprising the long-wave approximation and two-dimensional (2 × 2) transfer matrix method. We demonstrate spectral peculiarities of the bi-periodic structure and also show the differences between the band gap spectra of the bi-periodic and ternary 1D dielectric photonic crystals. The presented photonic crystal structure can find its applications in optoelectronics and nanophotonics areas as omnidirectional reflectors, optical ultra-narrow bandpass filters, and antireflection coatings.

Oxides having high energy densities

DOEpatents

Ceder, Gerbrand; Kang, Kisuk

2013-09-10

Certain disclosed embodiments generally relate to oxide materials having relatively high energy and/or power densities. Various aspects of the embodiments are directed to oxide materials having a structure B.sub.i(M.sub.jY.sub.k)O.sub.2, for example, a structure Li.sub.j(Ni.sub.jY.sub.k)O.sub.2 such as Li(Ni.sub.0.5Mn.sub.0.5)O.sub.2. In this structure, Y represents one or more atoms, each independently selected from the group consisting of alkaline earth metals, transition metals, Group 14 elements, Group 15, or Group 16 elements. In some embodiments, such an oxide material may have an O3 crystal structure, and/or a layered structure such that the oxide comprises a plurality of first, repeating atomic planes comprising Li, and a plurality of second, repeating atomic planes comprising Ni and/or Y.

Shear sensitive monomer-polymer laminate structure and method of using same

NASA Technical Reports Server (NTRS)

Singh, Jag J. (Inventor); Eftekhari, Abe (Inventor); Parmar, Devendra S. (Inventor)

1993-01-01

Monomer cholesteric liquid crystals have helical structures which result in a phenomenon known as selective reflection, wherein incident white light is reflected in such a way that its wavelength is governed by the instantaneous pitch of the helix structure. The pitch is dependent on temperature and external stress fields. It is possible to use such monomers in flow visualization and temperature measurement. However, the required thin layers of these monomers are quickly washed away by a flow, making their application time dependent for a given flow rate. The laminate structure according to the present invention comprises a liquid crystal polymer substrate attached to a test surface of an article. A light absorbing coating is applied to the substrate and is thin enough to permit bonding steric interaction between the liquid crystal polymer substrate and an overlying liquid crystal monomer thin film. Light is directed through and reflected by the liquid crystal monomer thin film and unreflected light is absorbed by the underlying coating. The wavelength of the reflected light is indicative of the shear stress experienced by the test surface. Novel aspects of the invention include its firm bonding of a liquid crystal monomer to a model and its use of a coating to reduce interference from light unreflected by the monomer helical structure.

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

DOE PAGES

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; ...

2017-07-13

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAPmore » β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

The ESFRI Instruct Core Centre Frankfurt: automated high-throughput crystallization suited for membrane proteins and more.

PubMed

Thielmann, Yvonne; Koepke, Juergen; Michel, Hartmut

2012-06-01

Structure determination of membrane proteins and membrane protein complexes is still a very challenging field. To facilitate the work on membrane proteins the Core Centre follows a strategy that comprises four labs of protein analytics and crystal handling, covering mass spectrometry, calorimetry, crystallization and X-ray diffraction. This general workflow is presented and a capacity of 20% of the operating time of all systems is provided to the European structural biology community within the ESFRI Instruct program. A description of the crystallization service offered at the Core Centre is given with detailed information on screening strategy, screens used and changes to adapt high throughput for membrane proteins. Our aim is to constantly develop the Core Centre towards the usage of more efficient methods. This strategy might also include the ability to automate all steps from crystallization trials to crystal screening; here we look ahead how this aim might be realized at the Core Centre.

A co-crystal between benzene and ethane: a potential evaporite material for Saturn’s moon Titan

PubMed Central

Maynard-Casely, Helen E.; Hodyss, Robert; Cable, Morgan L.; Vu, Tuan Hoang; Rahm, Martin

2016-01-01

Using synchrotron X-ray powder diffraction, the structure of a co-crystal between benzene and ethane formed in situ at cryogenic conditions has been determined, and validated using dispersion-corrected density functional theory calculations. The structure comprises a lattice of benzene molecules hosting ethane molecules within channels. Similarity between the intermolecular interactions found in the co-crystal and in pure benzene indicate that the C—H⋯π network of benzene is maintained in the co-crystal, however, this expands to accommodate the guest ethane molecules. The co-crystal has a 3:1 benzene:ethane stoichiometry and is described in the space group with a = 15.977 (1) Å and c = 5.581 (1) Å at 90 K, with a density of 1.067 g cm−3. The conditions under which this co-crystal forms identify it is a potential that forms from evaporation of Saturn’s moon Titan’s lakes, an evaporite material. PMID:27158505

Reinvestigation of L-tryptophan picrate: Establishment of the existence of the L-tryptophan L-tryptophanium dimeric cation

NASA Astrophysics Data System (ADS)

Petrosyan, A. M.; Fleck, M.; Ghazaryan, V. V.

2013-03-01

A crystal structure redetermination of the L-tryptophan picrate crystal previously studied by Ishida et al. (Chem. Pharm. Bull. 41 (1993) 433-438) showed that it comprises L-tryptophan L-tryptophanium dimeric cation, one picrate anion and picric acid. The O⋯O distance of the O-H⋯O hydrogen bond in the dimeric cation is equal to 2.470(6) Å. The infrared spectrum of the crystal was registered and analyzed. The infrared spectrum of the crystals contains a broad absorption band centered at ca. 1170 cm-1, which is assigned to the stretching vibration of the O-H bond.

The impact of N,N-dimethyldodecylamine N-oxide (DDAO) concentration on the crystallisation of sodium dodecyl sulfate (SDS) systems and the resulting changes to crystal structure, shape and the kinetics of crystal growth.

PubMed

Summerton, Emily; Hollamby, Martin J; Zimbitas, Georgina; Snow, Tim; Smith, Andrew J; Sommertune, Jens; Bettiol, Jeanluc; Jones, Christopher; Britton, Melanie M; Bakalis, Serafim

2018-05-19

At low temperatures stability issues arise in commercial detergent products when surfactant crystallisation occurs, a process which is not currently well-understood. An understanding of the phase transition can be obtained using a simple binary SDS (sodium dodecyl sulfate) + DDAO (N,N-dimethyldodecylamine N-oxide) aqueous system. It expected that the crystallisation temperature of an SDS system can be lowered with addition of DDAO, thus providing a route to improve detergent stability. Detergent systems are typically comprised of anionic surfactants, non-ionic surfactants and water. This study explores the crystallisation of a three component system consisting of sodium dodecyl sulfate (SDS), N,N-dimethyldodecylamine N-oxide (DDAO), and water using wide-angle X-ray scattering (WAXS), differential scanning calorimetry (DSC) and confocal Raman microscopy. The presence of DDAO lowered the crystallisation temperature of a 20 wt% SDS system. For all aqueous mixtures of SDS + DDAO at low temperatures, SDS hydrated crystals, SDS.1/2H 2 O or SDS·H 2 O, formed. SDS hydrates comprising of layers of SDS separated by water layers. DDAO tended to reside in the vicinity of these SDS crystals. In the absence of DDAO an additional intermediary hydrate structure, SDS.1/8H 2 O, formed whereas for mixed SDS + DDAO systems no such structure was detected during crystallisation. Copyright © 2018. Published by Elsevier Inc.

Barium iodide and strontium iodide crystals andd scintillators implementing the same

DOEpatents

Payne, Stephen A; Cherepy, Nerine J; Hull, Giulia E; Drobshoff, Alexander D; Burger, Arnold

2013-11-12

In one embodiment, a material comprises a crystal comprising strontium iodide providing at least 50,000 photons per MeV. A scintillator radiation detector according to another embodiment includes a scintillator optic comprising europium-doped strontium iodide providing at least 50,000 photons per MeV. A scintillator radiation detector in yet another embodiment includes a scintillator optic comprising SrI.sub.2 and BaI.sub.2, wherein a ratio of SrI.sub.2 to BaI.sub.2 is in a range of between 0:1 A method for manufacturing a crystal suitable for use in a scintillator includes mixing strontium iodide-containing crystals with a source of Eu.sup.2+, heating the mixture above a melting point of the strontium iodide-containing crystals, and cooling the heated mixture near the seed crystal for growing a crystal. Additional materials, systems, and methods are presented.

Efficiency of surface plasmon excitation at the photonic crystal – metal interface

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

Kuznetsova, T I; Raspopov, N A

2015-11-30

We report the results of a theoretical investigation of light wave transformation in a one-dimensional photonic crystal. The scheme considered comprises an incident wave directed in parallel with layers of the photonic crystal under an assumption that the wave vector is far from a forbidden zone. Expressions for propagating and evanescent electromagnetic waves in a periodic medium of the photonic crystal are obtained. It is found that the transverse structure of the propagating wave comprises a strong constant component and a weak oscillating component with a period determined by that of the photonic crystal. On the contrary, the dependence ofmore » evanescent waves on transverse coordinates is presented by a strong oscillating component and a weak constant component. The process of transformation of propagating waves to evanescent waves at a crystal – metal interface is investigated. Parameters of the photonic crystal typical for synthetic opals are used in all numerical simulations. The theoretical approach elaborated yields in an explicit form the dependence of the amplitude of a generated surface wave on the period of the dielectric function modulation in the photonic crystal. The results obtained show that in the conditions close to plasmon resonance the amplitude of the surface wave may be on the order of or even exceed that of the initial incident wave. (light wave transformation)« less

Method For Screening Microcrystallizations For Crystal Formation

DOEpatents

Santarsiero, Bernard D. , Stevens, Raymond C. , Schultz, Peter G. , Jaklevic, Joseph M. , Yegian, Derek T. , Cornell, Earl W. , Nordmeyer, Robert A.

2003-10-07

A method is provided for performing array microcrystallizations to determine suitable crystallization conditions for a molecule, the method comprising: forming an array of microcrystallizations, each microcrystallization comprising a drop comprising a mother liquor solution whose composition varies within the array and a molecule to be crystallized, the drop having a volume of less than 1 microliter; storing the array of microcrystallizations under conditions suitable for molecule crystals to form in the drops in the array; and detecting molecule crystal formation in the drops by taking images of the drops.

Hexadecameric structure of an invertebrate gap junction channel.

PubMed

Oshima, Atsunori; Matsuzawa, Tomohiro; Murata, Kazuyoshi; Tani, Kazutoshi; Fujiyoshi, Yoshinori

2016-03-27

Innexins are invertebrate-specific gap junction proteins with four transmembrane helices. These proteins oligomerize to constitute intercellular channels that allow for the passage of small signaling molecules associated with neural and muscular electrical activity. In contrast to the large number of structural and functional studies of connexin gap junction channels, few structural studies of recombinant innexin channels are reported. Here we show the three-dimensional structure of two-dimensionally crystallized Caenorhabditis elegans innexin-6 (INX-6) gap junction channels. The N-terminal deleted INX-6 proteins are crystallized in lipid bilayers. The three-dimensional reconstruction determined by cryo-electron crystallography reveals that a single INX-6 gap junction channel comprises 16 subunits, a hexadecamer, in contrast to chordate connexin channels, which comprise 12 subunits. The channel pore diameters at the cytoplasmic entrance and extracellular gap region are larger than those of connexin26. Two bulb densities are observed in each hemichannel, one in the pore and the other at the cytoplasmic side of the hemichannel in the channel pore pathway. These findings imply a structural diversity of gap junction channels among multicellular organisms. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Electric field induced structural colour tuning of a silver/titanium dioxide nanoparticle one-dimensional photonic crystal

PubMed Central

Aluicio-Sarduy, Eduardo; Callegari, Simone; Figueroa del Valle, Diana Gisell; Desii, Andrea; Kriegel, Ilka

2016-01-01

Summary An electric field is employed for the active tuning of the structural colour in photonic crystals, which acts as an effective external stimulus with an impact on light transmission manipulation. In this work, we demonstrate structural colour in a photonic crystal device comprised of alternating layers of silver nanoparticles and titanium dioxide nanoparticles, exhibiting spectral shifts of around 10 nm for an applied voltage of only 10 V. The accumulation of charge at the metal/dielectric interface with an applied electric field leads to an effective increase of the charges contributing to the plasma frequency in silver. This initiates a blue shift of the silver plasmon band with a simultaneous blue shift of the photonic band gap as a result of the change in the silver dielectric function (i.e. decrease of the effective refractive index). These results are the first demonstration of active colour tuning in silver/titanium dioxide nanoparticle-based photonic crystals and open the route to metal/dielectric-based photonic crystals as electro-optic switches. PMID:27826514

Electric field induced structural colour tuning of a silver/titanium dioxide nanoparticle one-dimensional photonic crystal.

PubMed

Aluicio-Sarduy, Eduardo; Callegari, Simone; Figueroa Del Valle, Diana Gisell; Desii, Andrea; Kriegel, Ilka; Scotognella, Francesco

2016-01-01

An electric field is employed for the active tuning of the structural colour in photonic crystals, which acts as an effective external stimulus with an impact on light transmission manipulation. In this work, we demonstrate structural colour in a photonic crystal device comprised of alternating layers of silver nanoparticles and titanium dioxide nanoparticles, exhibiting spectral shifts of around 10 nm for an applied voltage of only 10 V. The accumulation of charge at the metal/dielectric interface with an applied electric field leads to an effective increase of the charges contributing to the plasma frequency in silver. This initiates a blue shift of the silver plasmon band with a simultaneous blue shift of the photonic band gap as a result of the change in the silver dielectric function (i.e. decrease of the effective refractive index). These results are the first demonstration of active colour tuning in silver/titanium dioxide nanoparticle-based photonic crystals and open the route to metal/dielectric-based photonic crystals as electro-optic switches.

Crystallization of Proteins from Crude Bovine Rod Outer Segments☆

PubMed Central

Baker, Bo Y.; Gulati, Sahil; Shi, Wuxian; Wang, Benlian; Stewart, Phoebe L.; Palczewski, Krzysztof

2015-01-01

Obtaining protein crystals suitable for X-ray diffraction studies comprises the greatest challenge in the determination of protein crystal structures, especially for membrane proteins and protein complexes. Although high purity has been broadly accepted as one of the most significant requirements for protein crystallization, a recent study of the Escherichia coli proteome showed that many proteins have an inherent propensity to crystallize and do not require a highly homogeneous sample (Totir et al., 2012). As exemplified by RPE65 (Kiser, Golczak, Lodowski, Chance, & Palczewski, 2009), there also are cases of mammalian proteins crystallized from less purified samples. To test whether this phenomenon can be applied more broadly to the study of proteins from higher organisms, we investigated the protein crystallization profile of bovine rod outer segment (ROS) crude extracts. Interestingly, multiple protein crystals readily formed from such extracts, some of them diffracting to high resolution that allowed structural determination. A total of seven proteins were crystallized, one of which was a membrane protein. Successful crystallization of proteins from heterogeneous ROS extracts demonstrates that many mammalian proteins also have an intrinsic propensity to crystallize from complex biological mixtures. By providing an alternative approach to heterologous expression to achieve crystallization, this strategy could be useful for proteins and complexes that are difficult to purify or obtain by recombinant techniques. PMID:25950977

Synthesis and crystal structures of three new benzotriazolylpropanamides

PubMed Central

Amenta, Donna S.; Liebing, Phil; Biero, Julia E.; Sherman, Robert J.; Gilje, John W.

2017-01-01

The base-catalyzed Michael addition of 2-methyl­acryl­amide to benzotriazole afforded 3-(1H-benzotriazol-1-yl)-2-methyl­propanamide, C10H12N4O (1), in 32% yield in addition to small amounts of isomeric 3-(2H-benzotriazol-2-yl)-2-methyl­propanamide, C10H12N4O (2). In a similar manner, 3-(1H-benzotriazol-1-yl)-N,N-di­methyl­propanamide, C11H14N4O (3), was prepared from benzotriazole and N,N-di­methyl­acryl­amide. All three products have been structurally characterized by single-crystal X-ray diffraction. The crystal structures of 1 and 2 comprise infinite arrays formed by N—H⋯O and N—H⋯N bridges, as well as π–π inter­actions, while the mol­ecules of 3 are aggregated to simple π-dimers in the crystal. PMID:28638650

Anisotropic surface chemistry properties and adsorption behavior of silicate mineral crystals.

PubMed

Xu, Longhua; Tian, Jia; Wu, Houqin; Fang, Shuai; Lu, Zhongyuan; Ma, Caifeng; Sun, Wei; Hu, Yuehua

2018-03-07

Anisotropic surface properties of minerals play an important role in a variety of fields. With a focus on the two most intensively investigated silicate minerals (i.e., phyllosilicate minerals and pegmatite aluminosilicate minerals), this review highlights the research on their anisotropic surface properties based on their crystal structures. Four surface features comprise the anisotropic surface chemistry of minerals: broken bonds, energy, wettability, and charge. Analysis of surface broken bond and energy anisotropy helps to explain the cleavage and growth properties of mineral crystals, and understanding surface wettability and charge anisotropy is critical to the analysis of minerals' solution behavior, such as their flotation performance and rheological properties. In a specific reaction, the anisotropic surface properties of minerals are reflected in the adsorption strengths of reagents on different mineral surfaces. Combined with the knowledge of mineral crushing and grinding, a thorough understanding of the anisotropic surface chemistry properties and the anisotropic adsorption behavior of minerals will lead to the development of effective relational models comprising their crystal structure, surface chemistry properties, and targeted reagent adsorption. Overall, such a comprehensive approach is expected to firmly establish the connection between selective cleavage of mineral crystals for desired surfaces and designing novel reagents selectively adsorbed on the mineral surfaces. As tools to characterize the anisotropic surface chemistry properties of minerals, DLVO theory, atomic force microscopy (AFM), and molecular dynamics (MD) simulations are also reviewed. Copyright © 2017 Elsevier B.V. All rights reserved.

Conductive Hybrid Crystal Composed from Polyoxomolybdate and Deprotonatable Ionic-Liquid Surfactant

PubMed Central

Kobayashi, Jun; Kawahara, Ryosuke; Uchida, Sayaka; Koguchi, Shinichi; Ito, Takeru

2016-01-01

A polyoxomolybdate inorganic-organic hybrid crystal was synthesized with deprotonatable ionic-liquid surfactant. 1-dodecylimidazolium cation was employed for its synthesis. The hybrid crystal contained δ-type octamolybdate (Mo8) isomer, and possessed alternate stacking of Mo8 monolayers and interdigitated surfactant bilayers. The crystal structure was compared with polyoxomolybdate hybrid crystals comprising 1-dodecyl-3-methylimidazolium surfactant, which preferred β-type Mo8 isomer. The less bulky hydrophilic moiety of the 1-dodecylimidazolium interacted with the δ-Mo8 anion by N–H···O hydrogen bonds, which presumably induced the formation of the δ-Mo8 anion. Anhydrous conductivity of the hybrid crystal was estimated to be 5.5 × 10−6 S·cm−1 at 443 K by alternating current (AC) impedance spectroscopy. PMID:27347926

Structure-property relationships of a biological mesocrystal in the adult sea urchin spine

PubMed Central

Seto, Jong; Ma, Yurong; Davis, Sean A.; Meldrum, Fiona; Gourrier, Aurelien; Kim, Yi-Yeoun; Schilde, Uwe; Sztucki, Michael; Burghammer, Manfred; Maltsev, Sergey; Jäger, Christian; Cölfen, Helmut

2012-01-01

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, show how Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature’s demonstration of how crystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials. PMID:22343283

Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

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

Vognsen, Tina, E-mail: tv@farma.ku.dk; Kristensen, Ole, E-mail: ok@farma.ku.dk

2012-03-30

Highlights: Black-Right-Pointing-Pointer The crystal structure of the NTF2-like domain of Rasputin protein is presented. Black-Right-Pointing-Pointer Differences to known ligand binding sites of nuclear transport factor 2 are discussed. Black-Right-Pointing-Pointer A new ligand binding site for the Rasputin and G3BP proteins is proposed. -- Abstract: The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7 A resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a {beta}-sheet and three {alpha}-helices forming a cone-like shape. However, known binding sites formore » RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.« less

Structure-property relationships of a biological mesocrystal in the adult sea urchin spine.

PubMed

Seto, Jong; Ma, Yurong; Davis, Sean A; Meldrum, Fiona; Gourrier, Aurelien; Kim, Yi-Yeoun; Schilde, Uwe; Sztucki, Michael; Burghammer, Manfred; Maltsev, Sergey; Jäger, Christian; Cölfen, Helmut

2012-03-06

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, show how Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature's demonstration of how crystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials.

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

NASA Astrophysics Data System (ADS)

Lei, Qun-li; Hadinoto, Kunn; Ni, Ran

2017-10-01

Hierarchical self-assembly consisting of local associations of simple building blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building blocks, the association between hemispheres can also induce both reentrant melting and reentrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel reentrant crystallization of identical crystals, which melt only in a certain temperature range. This offers another axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5'-Bistetrazole-1,1'-diolate (TKX-50)

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

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi-Gang

2017-03-06

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. The present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

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

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2017-02-28

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria.

PubMed

Dwivedi, Shweta; Kruparani, Shobha P; Sankaranarayanan, Rajan

2004-09-01

Threonyl-tRNA synthetase (ThrRS) faces a crucial double-discrimination problem during the translation of genetic code. Most ThrRSs from the archaeal kingdom possess a unique editing domain that differs from those of eubacteria and eukaryotes. In order to understand the structural basis of the editing mechanism in archaea, the editing module of ThrRS from Pyrococcus abyssi comprising of the first 183 amino-acid residues was cloned, expressed, purified and crystallized. The crystals belong to the trigonal space group P3(1(2))21, with one molecule in the asymmetric unit.

Understanding Nanocalcification: A Role Suggested for Crystal Ghosts

PubMed Central

Bonucci, Ermanno

2014-01-01

The present survey deals with the initial stage of the calcification process in bone and other hard tissues, with special reference to the organic-inorganic relationship and the transformation that the early inorganic particles undergo as the process moves towards completion. Electron microscope studies clearly exclude the possibility that these particles might be crystalline structures, as often believed, by showing that they are, instead, organic-inorganic hybrids, each comprising a filamentous organic component (the crystal ghost) made up of acidic proteins. The hypothesis is suggested that the crystal ghosts bind and stabilize amorphous calcium phosphate and that their subsequent degradation allows the calcium phosphate, once released, to acquire a hydroxyapatite, crystal-like organization. A conclusive view of the mechanism of biological calcification cannot yet be proposed; even so, however, the role of crystal ghosts as a template of the structures usually called “crystallites” is a concept that has gathered increasing support and can no longer be disregarded. PMID:25056630

Co-crystallization phase transformations in all π-conjugated block copolymers with different main-chain moieties.

PubMed

Lee, Yi-Huan; Chen, Wei-Chih; Yang, Yi-Lung; Chiang, Chi-Ju; Yokozawa, Tsutomu; Dai, Chi-An

2014-05-21

Driven by molecular affinity and balance in the crystallization kinetics, the ability to co-crystallize dissimilar yet self-crystallizable blocks of a block copolymer (BCP) into a uniform domain may strongly affect its phase diagram. In this study, we synthesize a new series of crystalline and monodisperse all-π-conjugated poly(2,5-dihexyloxy-p-phenylene)-b-poly(3-(2-ethylhexyl)thiophene) (PPP-P3EHT) BCPs and investigate this multi-crystallization effect. Despite vastly different side-chain and main-chain structures, PPP and P3EHT blocks are able to co-crystallize into a single uniform domain comprising PPP and P3EHT main-chains with mutually interdigitated side-chains spaced in-between. With increasing P3EHT fraction, PPP-P3EHTs undergo sequential phase transitions and form hierarchical superstructures including predominately PPP nanofibrils, co-crystalline nanofibrils, a bilayer co-crystalline/pure P3EHT lamellar structure, a microphase-separated bilayer PPP-P3EHT lamellar structure, and finally P3EHT nanofibrils. In particular, the presence of the new co-crystalline lamellar structure is the manifestation of the interaction balance between self-crystallization and co-crystallization of the dissimilar polymers on the resulting nanostructure of the BCP. The current study demonstrates the co-crystallization nature of all-conjugated BCPs with different main-chain moieties and may provide new guidelines for the organization of π-conjugated BCPs for future optoelectronic applications.

Asymmetric light transmission based on coupling between photonic crystal waveguides and L1/L3 cavity

NASA Astrophysics Data System (ADS)

Zhang, Jinqiannan; Chai, Hongyu; Yu, Zhongyuan; Cheng, Xiang; Ye, Han; Liu, Yumin

2017-09-01

A compact design of all-optical diode with mode conversion function based on a two-dimensional photonic crystal waveguide and an L1 or L3 cavity is theoretically investigated. The proposed photonic crystal structures comprise a triangular arrangement of air holes embedded in a silicon substrate. Asymmetric light propagation is achieved via the spatial mode match/mismatch in the coupling region. The simulations show that at each cavity's resonance frequency, the transmission efficiency of the structure with the L1 and L3 cavities reach 79% and 73%, while the corresponding unidirectionalities are 46 and 37 dB, respectively. The functional frequency can be controlled by simply adjusting the radii of specific air holes in the L1 and L3 cavities. The proposed structure can be used as a frequency filter, a beam splitter and has potential applications in all-optical integrated circuits.

Review: Serial Femtosecond Crystallography: A Revolution in Structural Biology

PubMed Central

Martin-Garcia, Jose M.; Conrad, Chelsie E.; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-01-01

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. PMID:27143509

Serial femtosecond crystallography: A revolution in structural biology.

PubMed

Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-07-15

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. Published by Elsevier Inc.

Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

USGS Publications Warehouse

Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

1990-01-01

Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

Insight into the defects of cage-type silica mesoporous crystals with Fd3m symmetry: TEM observations and a new proposal of "polyhedron packing" for the crystals.

PubMed

Han, Lu; Sakamoto, Yasuhiro; Che, Shunai; Terasaki, Osamu

2009-01-01

Silica mesoporous crystals were synthesized by using a gemini cationic surfactant (C(18-3-1)) as the directing agent, carboxyethylsilanetriol sodium salt as the co-structure directing agent (CSDA), and varying amounts of HCl. By using transmission electron microscopy (TEM) we observed 1) a structural change from the close-packed structures of spherical micelles--face-centered cubic (Fm3m) and hexagonal close-packed (P6(3)/mmc)--to Fd3m structures with an increase of HCl and 2) a few structural defects in the crystals with Fd3m symmetry. The structure of a crystal with Fd3m symmetry is described as one of the tetrahedrally close-packed (tcp) structures consisting of 5(12) and 5(12)6(4) polyhedra. The observed TEM images of the structural defects were explained well through use of simulated TEM images by introducing new 13-15 polyhedra comprising 5(12)6(2), 5(12)6(3), 4(1)5(10)6(2), 4(2)5(8)6(5), and 4(1)5(10)6(4), which have been observed in bubbles by Matzke. The mesostructural changes and defect formation are discussed in terms of the hardness of micelles composed of surfactant/CSDA/silica species that have formed through a change of the interaction between the surfactant and CSDA, which causes the micelles to change from a regime of close-packing to one of minimum-area packing.

Purification, crystallization, and preliminary X-ray diffraction study of purine nucleoside phosphorylase from E. coli

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

Abramchik, Yu. A., E-mail: inna@ns.crys.ras.ru; Timofeev, V. I., E-mail: espiov@ibch.ru; Zhukhlistova, N. E., E-mail: tostars@mail.ru

2015-07-15

Crystals of E. coli purine nucleoside phosphorylase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 0.99 Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unit-cell parameters: a = 74.1 Å, b = 110.2 Å, c = 88.2 Å, α = γ = 90°, β = 111.08°. The crystal contains six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamermore » is the biological active form of E. coli. purine nucleoside phosphorylase.« less

Crystal Structure of the Frizzled-Like Cysteine-Rich Domain of the Receptor Tyrosine Kinase MuSK

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

Stiegler, A.; Burden, S; Hubbard, S

Muscle-specific kinase (MuSK) is an essential receptor tyrosine kinase for the establishment and maintenance of the neuromuscular junction (NMJ). Activation of MuSK by agrin, a neuronally derived heparan-sulfate proteoglycan, and LRP4 (low-density lipoprotein receptor-related protein-4), the agrin receptor, leads to clustering of acetylcholine receptors on the postsynaptic side of the NMJ. The ectodomain of MuSK comprises three immunoglobulin-like domains and a cysteine-rich domain (Fz-CRD) related to those in Frizzled proteins, the receptors for Wnts. Here, we report the crystal structure of the MuSK Fz-CRD at 2.1 {angstrom} resolution. The structure reveals a five-disulfide-bridged domain similar to CRDs of Frizzled proteinsmore » but with a divergent C-terminal region. An asymmetric dimer present in the crystal structure implicates surface hydrophobic residues that may function in homotypic or heterotypic interactions to mediate co-clustering of MuSK, rapsyn, and acetylcholine receptors at the NMJ.« less

4,4'-Bipyridine-pyroglutamic acid (1/2).

PubMed

Arman, Hadi D; Kaulgud, Trupta; Tiekink, Edward R T

2009-10-31

In the title co-crystal, C(10)H(8)N(2)·2C(5)H(7)NO(3), the 4,4'-bipyridine mol-ecule [dihedral angle between the pyridine rings = 36.33 (11)°] accepts O-H⋯N hydrogen bonds from the two pyroglutamic (pga) acid mol-ecules. The pga mol-ecules at each end of the trimeric aggregate self-associate via centrosymmetric eight-membered amide {⋯HNCO}(2) synthons, so that the crystal structure comprises one-dimensional supra-molecular chains propagating in [13]. C-H⋯O and π-π stacking inter-actions [centroid-centroid separation = 3.590 (2) Å] consolidate the structure.

Large grained perovskite solar cells derived from single-crystal perovskite powders with enhanced ambient stability

DOE PAGES

Yen, Hung -Ju; Liang, Po -Wei; Chueh, Chu -Chen; ...

2016-05-25

In this study, we demonstrate the large grained perovskite solar cells prepared from precursor solution comprising single-crystal perovskite powders for the first time. Here, the resultant large grained perovskite thin film possesses negligible physical (structural) gap between each large grain and are highly crystalline as evidenced by its fan-shaped birefringence observed under polarized light, which is very different to the thin film prepared from the typical precursor route (MAI + PbI 2).

The young person's guide to the PDB.

PubMed

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

Room temperature aluminum antimonide radiation detector and methods thereof

DOEpatents

Lordi, Vincenzo; Wu, Kuang Jen J.; Aberg, Daniel; Erhart, Paul; Coombs, III, Arthur W; Sturm, Benjamin W

2015-03-03

In one embodiment, a method for producing a high-purity single crystal of aluminum antimonide (AlSb) includes providing a growing environment with which to grow a crystal, growing a single crystal of AlSb in the growing environment which comprises hydrogen (H.sub.2) gas to reduce oxide formation and subsequent incorporation of oxygen impurities in the crystal, and adding a controlled amount of at least one impurity to the growing environment to effectively incorporate at least one dopant into the crystal. In another embodiment, a high energy radiation detector includes a single high-purity crystal of AlSb, a supporting structure for the crystal, and logic for interpreting signals obtained from the crystal which is operable as a radiation detector at a temperature of about 25.degree. C. In one embodiment, a high-purity single crystal of AlSb includes AlSb and at least one dopant selected from a group consisting of selenium (Se), tellurium (Te), and tin (Sn).

Solution-grown crystals for neutron radiation detectors, and methods of solution growth

DOEpatents

Zaitseva, Natalia; Carman, M Leslie; Payne, Steve

2014-10-28

An organic crystal according to one embodiment includes an organic crystal comprising diphenylacetylene and stilbene or a stilbene derivative, the crystal having physical characteristics of formation from solution, the organic crystal exhibiting a signal response signature for neutrons from a radioactive source. A system according to one embodiment includes an organic crystal comprising diphenylacetylene and stilbene or a stilbene derivative, the crystal having physical characteristics of formation from solution, the organic crystal exhibiting a signal response signature for neutrons from a radioactive source; and a photodetector for detecting the signal response of the organic crystal. Methods of making such crystals are also provided.

Crystallographic and theoretical studies of an inclusion complex of β-cyclodextrin with fentanyl.

PubMed

Ogawa, Noriko; Nagase, Hiromasa; Loftsson, Thorsteinn; Endo, Tomohiro; Takahashi, Chisato; Kawashima, Yoshiaki; Ueda, Haruhisa; Yamamoto, Hiromitsu

2017-10-15

The crystal structure of an inclusion complex of β-cyclodextrin (β-CD) with fentanyl was determined by single crystal X-ray diffraction analysis. The crystal belongs to the triclinic space group P1 and the complex comprises one fentanyl, two β-CD, and several water molecules. β-CD and fentanyl form a host-guest inclusion complex at a ratio of 2:1 and the asymmetric unit of the complex contains two host molecules (β-CDs) in a head-to-head arrangement that form dimers through hydrogen bonds between the secondary hydroxyl groups of β-CD and one guest molecule. Fentanyl is totally contained within the β-CD cavity and the structure of the phenylethyl part of fentanyl inside the dimeric cavity of the complex is disordered. Furthermore, theoretical molecular conformational calculations were conducted to clarify the mobility of the guest molecule in the β-CD cavity using CONFLEX software. Crystal optimization and crystal energy calculations were also conducted. The results of the theoretical calculations confirmed that the conformation of disorder part 1, which was high in occupancy by crystal structure analysis, was more stable. The phenylethyl part of fentanyl existed in several stable conformations. Copyright © 2017 Elsevier B.V. All rights reserved.

Actinide/beryllium neutron sources with reduced dispersion characteristics

DOEpatents

Schulte, Louis D.

2012-08-14

Neutron source comprising a composite, said composite comprising crystals comprising BeO and AmBe.sub.13, and an excess of beryllium, wherein the crystals have an average size of less than 2 microns; the size distribution of the crystals is less than 2 microns; and the beryllium is present in a 7-fold to a 75-fold excess by weight of the amount of AmBe.sub.13; and methods of making thereof.

Nanomembrane structures having mixed crystalline orientations and compositions

DOEpatents

Lagally, Max G.; Scott, Shelley A.; Savage, Donald E.

2014-08-12

The present nanomembrane structures include a multilayer film comprising a single-crystalline layer of semiconductor material disposed between two other single-crystalline layers of semiconductor material. A plurality of holes extending through the nanomembrane are at least partially, and preferably entirely, filled with a filler material which is also a semiconductor, but which differs from the nanomembrane semiconductor materials in composition, crystal orientation, or both.

A Crystal Structure of the Dengue Virus Non-structural Protein 5 (NS5) Polymerase Delineates Interdomain Amino Acid Residues That Enhance Its Thermostability and de Novo Initiation Activities*

PubMed Central

Lim, Siew Pheng; Koh, Jolene Hong Kiew; Seh, Cheah Chen; Liew, Chong Wai; Davidson, Andrew D.; Chua, Leng Shiew; Chandrasekaran, Ramya; Cornvik, Tobias C.; Shi, Pei-Yong; Lescar, Julien

2013-01-01

The dengue virus (DENV) non-structural protein 5 (NS5) comprises an N-terminal methyltransferase and a C-terminal RNA-dependent RNA polymerase (RdRp) domain. Both enzymatic activities form attractive targets for antiviral development. Available crystal structures of NS5 fragments indicate that residues 263–271 (using the DENV serotype 3 numbering) located between the two globular domains of NS5 could be flexible. We observed that the addition of linker residues to the N-terminal end of the DENV RdRp core domain stabilizes DENV1–4 proteins and improves their de novo polymerase initiation activities by enhancing the turnover of the RNA and NTP substrates. Mutation studies of linker residues also indicate their importance for viral replication. We report the structure at 2.6-Å resolution of an RdRp fragment from DENV3 spanning residues 265–900 that has enhanced catalytic properties compared with the RdRp fragment (residues 272–900) reported previously. This new orthorhombic crystal form (space group P21212) comprises two polymerases molecules arranged as a dimer around a non-crystallographic dyad. The enzyme adopts a closed “preinitiation” conformation similar to the one that was captured previously in space group C2221 with one molecule per asymmetric unit. The structure reveals that residues 269–271 interact with the RdRp domain and suggests that residues 263–268 of the NS5 protein from DENV3 are the major contributors to the flexibility between its methyltransferase and RdRp domains. Together, these results should inform the screening and development of antiviral inhibitors directed against the DENV RdRp. PMID:24025331

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

PubMed Central

2016-01-01

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results. PMID:27983843

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.

PubMed

Hayatshahi, Hamed S; Roe, Daniel R; Galindo-Murillo, Rodrigo; Hall, Kathleen B; Cheatham, Thomas E

2017-01-26

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results.

Field induced heliconical structure of cholesteric liquid crystal

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

Lavrentovich, Oleg D.; Shiyanovsii, Sergij V.; Xiang, Jie

A diffraction grating comprises a liquid crystal (LC) cell configured to apply an electric field through a cholesteric LC material that induces the cholesteric LC material into a heliconical state with an oblique helicoid director. The applied electric field produces diffracted light from the cholesteric LC material within the visible, infrared or ultraviolet. The axis of the heliconical state is in the plane of the liquid crystal cell or perpendicular to the plane, depending on the application. A color tuning device operates with a similar heliconical state liquid crystal material but with the heliconical director axis oriented perpendicular to themore » plane of the cell. A power generator varies the strength of the applied electric field to adjust the wavelength of light reflected from the cholesteric liquid crystal material within the visible, infrared or ultraviolet.« less

Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from Arabidopsis thaliana in complex with AMP.

PubMed

Kim, Do Jin; Bitto, Eduard; Bingman, Craig A; Kim, Hyun-Jung; Han, Byung Woo; Phillips, George N

2015-07-01

Members of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contains 44 USP domain-containing proteins, and USP domain is found either in a small protein with unknown physiological function or in an N-terminal portion of a multi-domain protein, usually a protein kinase. Here, we report the first crystal structure of a eukaryotic USP-like protein encoded from the gene At3g01520. The crystal structure of the protein At3g01520 was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 21.8% (Rfree = 26.1%) at 2.5 Å resolution. The crystal structure includes three At3g01520 protein dimers with one AMP molecule bound to each protomer, comprising a Rossmann-like α/β overall fold. The bound AMP and conservation of residues in the ATP-binding loop suggest that the protein At3g01520 also belongs to the ATP-binding USP subfamily members. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

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

Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de; Brosi, Richard W. W.; Steinmetz, Andrea

2013-08-01

The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein,more » but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.« less

Barium iodide and strontium iodide crystals and scintillators implementing the same

DOEpatents

Payne, Stephen A.; Cherepy, Nerine; Pedrini, Christian; Burger, Arnold

2016-09-13

In one embodiment, a crystal includes at least one metal halide; and an activator dopant comprising ytterbium. In another general embodiment, a scintillator optic includes: at least one metal halide doped with a plurality of activators, the plurality of activators comprising: a first activator comprising europium, and a second activator comprising ytterbium. In yet another general embodiment, a method for manufacturing a crystal suitable for use in a scintillator includes mixing one or more salts with a source of at least one dopant activator comprising ytterbium; heating the mixture above a melting point of the salt(s); and cooling the heated mixture to a temperature below the melting point of the salts. Additional materials, systems, and methods are presented.

4,4′-Bipyridine–pyroglutamic acid (1/2)

PubMed Central

Arman, Hadi D.; Kaulgud, Trupta; Tiekink, Edward R. T.

2009-01-01

In the title co-crystal, C10H8N2·2C5H7NO3, the 4,4′-bipyridine mol­ecule [dihedral angle between the pyridine rings = 36.33 (11)°] accepts O—H⋯N hydrogen bonds from the two pyroglutamic (pga) acid mol­ecules. The pga mol­ecules at each end of the trimeric aggregate self-associate via centrosymmetric eight-membered amide {⋯HNCO}2 synthons, so that the crystal structure comprises one-dimensional supra­molecular chains propagating in [13]. C—H⋯O and π–π stacking inter­actions [centroid–centroid separation = 3.590 (2) Å] consolidate the structure. PMID:21578523

The young person’s guide to the PDB*

PubMed Central

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2017-01-01

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120,000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview. PMID:28132477

Structural and dielectric behaviors of Bi4Ti3O12 - lyotropic liquid crystalline nanocolloids

NASA Astrophysics Data System (ADS)

Shukla, Ravi K.; Raina, K. K.

2018-03-01

We investigated the structural and dielectric dynamics of nanocolloids comprising lyotropic liquid crystals and bismuth titanate (Bi4Ti3O12) spherical nanoparticles (≈16-18 nm) of varying concentration 0.05 and 0.1 wt%. The lyotropic liquid crystalline mixture was prepared by a binary mixture of cetylpyridinuium chloride and ethylene glycol mixed in 5:95 wt% ratio. Binary lyotropic mixture exhibited hexagonal lyotropic phase. Structural and textural characterizations of nanocolloids infer that the nanoparticles were homogeneously dispersed in the liquid crystalline matrix and did not perturb the hexagonal ordering of the lyotropic phase. The dielectric constant and dielectric strength were found to be increased with the rise in the Bi4Ti3O12 nanoparticles concertation in the lyotropic matrix. A significant increase of one order was observed in the ac conductivity of colloidal systems as compared to the non-doped lyotropic liquid crystal. Relaxation parameters of the non-doped lyotropic liquid crystal and colloidal systems were computed and correlated with other parameters.

Crystal structure of mitochondrial respiratory membrane protein complex II.

PubMed

Sun, Fei; Huo, Xia; Zhai, Yujia; Wang, Aojin; Xu, Jianxing; Su, Dan; Bartlam, Mark; Rao, Zihe

2005-07-01

The mitochondrial respiratory Complex II or succinate:ubiquinone oxidoreductase (SQR) is an integral membrane protein complex in both the tricarboxylic acid cycle and aerobic respiration. Here we report the first crystal structure of Complex II from porcine heart at 2.4 A resolution and its complex structure with inhibitors 3-nitropropionate and 2-thenoyltrifluoroacetone (TTFA) at 3.5 A resolution. Complex II is comprised of two hydrophilic proteins, flavoprotein (Fp) and iron-sulfur protein (Ip), and two transmembrane proteins (CybL and CybS), as well as prosthetic groups required for electron transfer from succinate to ubiquinone. The structure correlates the protein environments around prosthetic groups with their unique midpoint redox potentials. Two ubiquinone binding sites are discussed and elucidated by TTFA binding. The Complex II structure provides a bona fide model for study of the mitochondrial respiratory system and human mitochondrial diseases related to mutations in this complex.

AgPO2F2 and Ag9(PO2F2)14: the first Ag(i) and Ag(i)/Ag(ii) difluorophosphates with complex crystal structures.

PubMed

Malinowski, Przemysław J; Kurzydłowski, Dominik; Grochala, Wojciech

2015-12-07

The reaction of AgF2 with P2O3F4 yields a mixed valence Ag(I)/Ag(II) difluorophosphate salt with AgAg(PO2F2)14 stoichiometry - the first Ag(ii)-PO2F2 system known. This highly moisture sensitive brown solid is thermally stable up to 120 °C, which points at further feasible extension of the chemistry of Ag(ii)-PO2F2 systems. The crystal structure shows a very complex bonding pattern, comprising of polymeric Ag(PO2F2)14(4-) anions and two types of Ag(I) cations. One particular Ag(II) site present in the crystal structure of Ag9(PO2F2)14 is the first known example of square pyramidal penta-coordinated Ag(ii) in an oxo-ligand environment. Ag(i)PO2F2 - the product of the thermal decomposition of Ag9(PO2F2)14 - has also been characterized by thermal analysis, IR spectroscopy and X-ray powder diffraction. It has a complicated crystal structure as well, which consists of infinite 1D [Ag(I)O4/2] chains which are linked to more complex 3D structures via OPO bridges. The PO2F2(-) anions bind to cations in both compounds as bidentate oxo-ligands. The terminal F atoms tend to point inside the van der Waals cavities in the crystal structure of both compounds. All important structural details of both title compounds were corroborated by DFT calculations.

Purification, crystallization and preliminary crystallographic analysis of the adhesion domain of Epf from Streptococcus pyogenes

PubMed Central

Linke, Christian; Siemens, Nikolai; Middleditch, Martin J.; Kreikemeyer, Bernd; Baker, Edward N.

2012-01-01

The extracellular protein Epf from Streptococcus pyogenes is important for streptococcal adhesion to human epithelial cells. However, Epf has no sequence identity to any protein of known structure or function. Thus, several predicted domains of the 205 kDa protein Epf were cloned separately and expressed in Escherichia coli. The N-terminal domain of Epf was crystallized in space groups P21 and P212121 in the presence of the protease chymotrypsin. Mass spectrometry showed that the species crystallized corresponded to a fragment comprising residues 52–357 of Epf. Complete data sets were collected to 2.0 and 1.6 Å resolution, respectively, at the Australian Synchrotron. PMID:22750867

Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex

PubMed Central

Kim, Kyung Rok; Park, Sang Ho; Kim, Hyoun Sook; Rhee, Kyung Hee; Kim, Byung-Gyu; Kim, Dae Gyu; Park, Mi Seul; Kim, Hyun-Jung; Kim, Sunghoon; Han, Byung Woo

2013-01-01

Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at a resolution of 2.25 Å. DRS is a homodimer with a dimer interface of 3750.5 Å2 which comprises 16.6% of the monomeric surface area. Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNAAsp to elongation factor 1α. From our analyses of the crystal structure and post-translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions. PMID:23609930

Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex.

PubMed

Kim, Kyung Rok; Park, Sang Ho; Kim, Hyoun Sook; Rhee, Kyung Hee; Kim, Byung-Gyu; Kim, Dae Gyu; Park, Mi Seul; Kim, Hyun-Jung; Kim, Sunghoon; Han, Byung Woo

2013-10-01

Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at a resolution of 2.25 Å. DRS is a homodimer with a dimer interface of 3750.5 Å(2) which comprises 16.6% of the monomeric surface area. Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNA(Asp) to elongation factor 1α. From our analyses of the crystal structure and post-translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions. Copyright © 2013 Wiley Periodicals, Inc.

High spatial resolution X-ray and gamma ray imaging system using diffraction crystals

DOEpatents

Smither, Robert K [Hinsdale, IL

2011-05-17

A method and a device for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation are provided. The device comprises a plurality of arrays, with each array comprising a plurality of elements comprising a first collimator, a diffracting crystal, a second collimator, and a detector.

Antioxidative succinobucol-sterol conjugates: Crystal structures and pseudosymmetry in the crystals

NASA Astrophysics Data System (ADS)

Ikonen, Satu; Jurček, Ondřej; Wimmer, Zdeněk; Drašar, Pavel; Kolehmainen, Erkki

2012-03-01

An extensive study to attach succinobucol to sterols has provided conjugates which comprise two pharmaceutically important compounds into one entity where the components are expected to have a synergistic effect. The motivation to design these novel conjugates was the need to broaden the armamentarium of current agents used in the treatment of atherosclerotic diseases and type 2 diabetes. In desire for detailed information of these compounds in solid state, which also have an influence to their physiological activity, systematic crystallization experiments were performed and as a result, X-ray quality single crystals were obtained from four succinobucol-sterol conjugates. All of these compounds crystallized in space group P1 with two or four molecules in an asymmetric unit and the crystallographically independent molecules were found to be related by pseudosymmetry (i.e. by pseudoinversion in 1-3 and by pseudoinversion plus pseudotranslation in 4).

Cutting Edge: Molecular Structure of the IL-1R-Associated Kinase-4 Death Domain and Its Implications for TLR Signaling

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

Lasker, Michael V.; Gajjar, Mark M.; Nair, Satish K.

2010-07-19

IL-1R-associated kinase (IRAK) 4 is an essential component of innate immunity. IRAK-4 deficiency in mice and humans results in severe impairment of IL-1 and TLR signaling. We have solved the crystal structure for the death domain of Mus musculus IRAK-4 to 1.7 {angstrom} resolution. This is the first glimpse of the structural details of a mammalian IRAK family member. The crystal structure reveals a six-helical bundle with a prominent loop, which among IRAKs and Pelle, a Drosophila homologue, is unique to IRAK-4. This highly structured loop contained between helices two and three, comprises an 11-aa stretch. Although innate immune domainmore » recognition is thought to be very similar between Drosophila and mammals, this structural component points to a drastic difference. This structure can be used as a framework for future mutation and deletion studies and potential drug design.« less

Automated preparation method for colloidal crystal arrays of monodisperse and binary colloid mixtures by contact printing with a pintool plotter.

PubMed

Burkert, Klaus; Neumann, Thomas; Wang, Jianjun; Jonas, Ulrich; Knoll, Wolfgang; Ottleben, Holger

2007-03-13

Photonic crystals and photonic band gap materials with periodic variation of the dielectric constant in the submicrometer range exhibit unique optical properties such as opalescence, optical stop bands, and photonic band gaps. As such, they represent attractive materials for the active elements in sensor arrays. Colloidal crystals, which are 3D gratings leading to Bragg diffraction, are one potential precursor of such optical materials. They have gained particular interest in many technological areas as a result of their specific properties and ease of fabrication. Although basic techniques for the preparation of regular patterns of colloidal crystals on structured substrates by self-assembly of mesoscopic particles are known, the efficient fabrication of colloidal crystal arrays by simple contact printing has not yet been reported. In this article, we present a spotting technique used to produce a microarray comprising up to 9600 single addressable sensor fields of colloidal crystal structures with dimensions down to 100 mum on a microfabricated substrate in different formats. Both monodisperse colloidal crystals and binary colloidal crystal systems were prepared by contact printing of polystyrene particles in aqueous suspension. The array morphology was characterized by optical light microscopy and scanning electron microscopy, which revealed regularly ordered crystalline structures for both systems. In the case of binary crystals, the influence of the concentration ratio of the large and small particles in the printing suspension on the obtained crystal structure was investigated. The optical properties of the colloidal crystal arrays were characterized by reflection spectroscopy. To examine the stop bands of the colloidal crystal arrays in a high-throughput fashion, an optical setup based on a CCD camera was realized that allowed the simultaneous readout of all of the reflection spectra of several thousand sensor fields per array in parallel. In agreement with Bragg's relation, the investigated arrays exhibited strong opalescence and stop bands in the expected wavelength range, confirming the successful formation of highly ordered colloidal crystals. Furthermore, a narrow distribution of wavelength-dependent stop bands across the sensor array was achieved, demonstrating the capability of producing highly reproducible crystal spots by the contact printing method with a pintool plotter.

Electro-optic crystal mosaics for the generation of terahertz radiation

DOEpatents

Carrig, Timothy J.; Taylor, Antoinette J.; Stewart, Kevin R.

1996-01-01

Apparatus for the generation of high energy terahertz radiation is presented and comprises laser means effective to produce subpicosecond optical pulses and a mosaic comprising a plurality of planar electro-optic crystals fastened together edge to edge in the form of a grid. The electro-optic crystals are in optical communication with the subpicosecond optical pulses, and behave as a single large electro-optic crystal, producing high energy terahertz radiation by way of optical rectification.

Electro-optic crystal mosaics for the generation of terahertz radiation

DOEpatents

Carrig, T.J.; Taylor, A.J.; Stewart, K.R.

1996-08-06

Apparatus for the generation of high energy terahertz radiation is presented and comprises laser means effective to produce subpicosecond optical pulses and a mosaic comprising a plurality of planar electro-optic crystals fastened together edge to edge in the form of a grid. The electro-optic crystals are in optical communication with the subpicosecond optical pulses, and behave as a single large electro-optic crystal, producing high energy terahertz radiation by way of optical rectification. 5 figs.

Assembly of the most topologically regular two-dimensional micro and nanocrystals with spherical, conical, and tubular shapes

NASA Astrophysics Data System (ADS)

Roshal, D. S.; Konevtsova, O. V.; Myasnikova, A. E.; Rochal, S. B.

2016-11-01

We consider how to control the extension of curvature-induced defects in the hexagonal order covering different curved surfaces. In these frames we propose a physical mechanism for improving structures of two-dimensional spherical colloidal crystals (SCCs). For any SCC comprising of about 300 or less particles the mechanism transforms all extended topological defects (ETDs) in the hexagonal order into the point disclinations. Perfecting the structure is carried out by successive cycles of the particle implantation and subsequent relaxation of the crystal. The mechanism is potentially suitable for obtaining colloidosomes with better selective permeability. Our approach enables modeling the most topologically regular tubular and conical two-dimensional nanocrystals including various possible polymorphic forms of the HIV viral capsid. Different HIV-like shells with an arbitrary number of structural units (SUs) and desired geometrical parameters are easily formed. Faceting of the obtained structures is performed by minimizing the suggested elastic energy.

Symmetric functionalization of polyhedral phenylsilsesquioxanes as a route to nano-building blocks

NASA Astrophysics Data System (ADS)

Roll, Mark Francis

The design and synthesis of nanometer scale structures is of intense current interest. Herein we report on the ability to use symmetric, robust, mutable silsesquioxane ([RSiO3/2]n) nano-building blocks to produce well-defined 3-D structures for electronic or adsorption applications. We are able to show the systematic effects of supermolecular coordination to modulate the density of the molecular packing. This dissertation first describes the synthesis of the elusive decaphenylsilsesquioxane, and the exploration of the substitutionally specific para iodination of the octa-, deca- and dodeca-(p-iodophenyl)-silsesquioxanes, whose single-crystal X-ray diffraction structures are reported. Octa( p-iodophenyl)-silsesquioxane shows supermolecular coordination via Desiraju's halogen-halogen short-contact synthon, forming an open structure with a solvent accessible cavity comprising 40% of the unit cell. The application of palladium, nickel and copper catalyzed cross-coupling techniques using the carbon-iodine bond is explored in order to divergently synthesize crystalline derivatives. These derivatives include the octa(diphenylacetylene)-silsesquioxane and the octa(hexaphenylbenzene)silsesquioxane (56 Aryl), whose single-crystal X-ray diffraction structures are reported. We show that 56 Aryl, which contains more carbon atoms than any other discrete molecule in the Cambridge Structural Database, crystallizes into an extremely open structure with a solvent accessible cavity comprising 55% of the total volume. The supermolecular ordering driven by the bulky hexaphenylbenzene moieties gives nanometer-scale channels along the ab plane. Substitutional specificity is explored in the bromination of octaphenylsilsesquioxane (OPS), and single-crystal X-ray diffraction structures are reported for the octa-, hexadeca- and tetraicosa-brominated derivatives. Precise synthetic control is demonstrated by the unique catalyst-free bromination of OPS, providing the octa(o-bromophenyl)-silsesquioxane in low yield. An iron tribromide catalyzed hexadeca-bromination gives the crystalline octa(2,5-dibromopheny1)silsesquioxane in good yield, with a high density of 2.3 g/cc. Finally, the iron tribromide-catalyzed tetraicosa-bromination of OPS is described, producing a low yield of crystals with a solid solution of substitution patterns coordinated by bromine-bromine short contacts. Lastly, the Scholl-type, dehydrogenative cyclization of the octa(hexaarylbenzene)silsesquioxane systems is explored by the addition of iron trichloride/nitromethane to a refluxing solution of the silsesquioxane in stannic chloride/dichloromethane. The products are analyzed by Proton Nuclear Magnetic Resonance Spectroscopy, Matrix Assisted Laser Desorption and Ionization - Time of Flight Mass Spectroscopy and Diffuse Reflectance Fourier Transform Infra Red Spectroscopy.

Revolving supramolecular chiral structures powered by light in nanomotor-doped liquid crystals

NASA Astrophysics Data System (ADS)

Orlova, Tetiana; Lancia, Federico; Loussert, Charles; Iamsaard, Supitchaya; Katsonis, Nathalie; Brasselet, Etienne

2018-04-01

Molecular machines operated by light have been recently shown to be able to produce oriented motion at the molecular scale1,2 as well as do macroscopic work when embedded in supramolecular structures3-5. However, any supramolecular movement irremediably ceases as soon as the concentration of the interconverting molecular motors or switches reaches a photo-stationary state6,7. To circumvent this limitation, researchers have typically relied on establishing oscillating illumination conditions—either by modulating the source intensity8,9 or by using bespoke illumination arrangements10-13. In contrast, here we report a supramolecular system in which the emergence of oscillating patterns is encoded at the molecular level. Our system comprises chiral liquid crystal structures that revolve continuously when illuminated, under the action of embedded light-driven molecular motors. The rotation at the supramolecular level is sustained by the diffusion of the motors away from a localized illumination area. Above a critical irradiation power, we observe a spontaneous symmetry breaking that dictates the directionality of the supramolecular rotation. The interplay between the twist of the supramolecular structure and the diffusion14 of the chiral molecular motors creates continuous, regular and unidirectional rotation of the liquid crystal structure under non-equilibrium conditions.

Distribution of Al atoms in the clathrate-I phase Ba8AlxSi46-x at x = 6.9.

PubMed

Bobnar, Matej; Böhme, Bodo; Wedel, Michael; Burkhardt, Ulrich; Ormeci, Alim; Prots, Yurii; Drathen, Christina; Liang, Ying; Nguyen, Hong Duong; Baitinger, Michael; Grin, Yuri

2015-07-28

The clathrate-I phase Ba8AlxSi46-x has been structurally characterized at the composition x = 6.9 (space group Pm3[combining macron]n, no. 223, a = 10.4645(2) Å). A crystal structure model comprising the distribution of aluminium and silicon atoms in the clathrate framework was established: 5.7 Al atoms and 0.3 Si atoms occupy the crystallographic site 6c, while 1.2 Al atoms and 22.8 Si atoms occupy site 24k. The atomic distribution was established based on a combination of (27)Al and (29)Si NMR experiments, X-ray single-crystal diffraction and wavelength-dispersive X-ray spectroscopy.

Manganese oxide nanowires, films, and membranes and methods of making

DOEpatents

Suib, Steven Lawrence [Storrs, CT; Yuan, Jikang [Storrs, CT

2008-10-21

Nanowires, films, and membranes comprising ordered porous manganese oxide-based octahedral molecular sieves, and methods of making, are disclosed. A single crystal ultra-long nanowire includes an ordered porous manganese oxide-based octahedral molecular sieve, and has an average length greater than about 10 micrometers and an average diameter of about 5 nanometers to about 100 nanometers. A film comprises a microporous network comprising a plurality of single crystal nanowires in the form of a layer, wherein a plurality of layers is stacked on a surface of a substrate, wherein the nanowires of each layer are substantially axially aligned. A free standing membrane comprises a microporous network comprising a plurality of single crystal nanowires in the form of a layer, wherein a plurality of layers is aggregately stacked, and wherein the nanowires of each layer are substantially axially aligned.

Crystal growth and annealing method and apparatus

DOEpatents

Gianoulakis, Steven E.; Sparrow, Robert

2001-01-01

A method and apparatus for producing crystals that minimizes birefringence even at large crystal sizes, and is suitable for production of CaF.sub.2 crystals. The method of the present invention comprises annealing a crystal by maintaining a minimal temperature gradient in the crystal while slowly reducing the bulk temperature of the crystal. An apparatus according to the present invention includes a thermal control system added to a crystal growth and annealing apparatus, wherein the thermal control system allows a temperature gradient during crystal growth but minimizes the temperature gradient during crystal annealing. An embodiment of the present invention comprises a secondary heater incorporated into a conventional crystal growth and annealing apparatus. The secondary heater supplies heat to minimize the temperature gradients in the crystal during the annealing process. The secondary heater can mount near the bottom of the crucible to effectively maintain appropriate temperature gradients.

Electrically switchable photonic liquid crystal devices for routing of a polarized light wave

NASA Astrophysics Data System (ADS)

Rushnova, Irina I.; Melnikova, Elena A.; Tolstik, Alexei L.; Muravsky, Alexander A.

2018-04-01

The new mode of LC alignment based on photoalignment AtA-2 azo dye where the refractive interface between orthogonal orientations of the LC director exists without voltage and disappeared or changed with critical voltage has been proposed. The technology to fabricate electrically controlled liquid crystal elements for spatial separation and switching of linearly polarized light beams on the basis of the total internal reflection effect has been significantly improved. Its distinctive feature is the application of a composite alignment material comprising two sublayers of Nylon-6 and AtA-2 photoalignment azo dye offering patterned liquid crystal director orientation with high alignment quality value q = 0 . 998. The fabricated electrically controlled spatially structured liquid crystal devices enable implementation of propagation directions separation for orthogonally polarized light beams and their switching with minimal crosstalk.

Structure of N-acetyl-[beta]-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline

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

Langley, David B.; Harty, Derek W.S.; Jacques, Nicholas A.

2008-09-17

The crystal structure of GcnA, an N-acetyl-{beta}-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal {alpha}-helical domain has not been observed previously and forms a large dimerization interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical ({beta}/{alpha}){sub 8} TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a familymore » 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-{beta}-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.« less

Ab initio solution of macromolecular crystal structures without direct methods.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

2017-04-04

The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

Nanoplate-like tungsten trioxide (hydrate) films prepared by crystal-seed-assisted hydrothermal reaction

NASA Astrophysics Data System (ADS)

Wang, P.; Yang, L.; Dai, B.; Yang, Z.; Guo, S.; Zhu, J.

2017-07-01

Vertically-aligned WO3 nanoplates on transparent conducting fluorine-doped tin oxide (FTO) glass were prepared by a facile template-free crystal-seed-assisted hydrothermal method. The effects of the hydrothermal temperature and reaction time on the crystal structure and morphology of the products were investigated by XRD and SEM. The XRD results showed that the as-prepared thin films obtained below 150∘C comprised orthorhombic WO3 ṡ H2O and completely converted to monoclinic WO3 at 180∘C. It was also noted that there was a phase transformation from orthorhombic to monoclinic by increasing the reaction time from 1 to 12 h. SEM analysis revealed that WO3 thin films are composed of plate-like nanostructures.

Purification, crystallization and preliminary crystallographic analysis of the adhesion domain of Epf from Streptococcus pyogenes.

PubMed

Linke, Christian; Siemens, Nikolai; Middleditch, Martin J; Kreikemeyer, Bernd; Baker, Edward N

2012-07-01

The extracellular protein Epf from Streptococcus pyogenes is important for streptococcal adhesion to human epithelial cells. However, Epf has no sequence identity to any protein of known structure or function. Thus, several predicted domains of the 205 kDa protein Epf were cloned separately and expressed in Escherichia coli. The N-terminal domain of Epf was crystallized in space groups P2(1) and P2(1)2(1)2(1) in the presence of the protease chymotrypsin. Mass spectrometry showed that the species crystallized corresponded to a fragment comprising residues 52-357 of Epf. Complete data sets were collected to 2.0 and 1.6 Å resolution, respectively, at the Australian Synchrotron.

Inhomogeneous field induced magnetoelectric effect in Mott insulators

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

Boulaevskii, Lev N; Batista, Cristian D

2008-01-01

We consider a Mott insulator like HoMnO{sub 3} whose magnetic lattice is geometrically frustrated and comprises a 3D array of triangular layers with magnetic moments ordered in a 120{sup o} structure. We show that the effect of a uniform magnetic field gradient, {gradient}H, is to redistribute the electronic charge of the magnetically ordered phase leading to a unfirom electric field gradient. The resulting voltage difference between the crystal edges is proportional to the square of the crystal thickness, or inter-edge distance, L. It can reach values of several volts for |{gradient}H| {approx} 0.01 T/cm and L {approx_equal} 1mm, as longmore » as the crystal is free of antiferromagnetic domain walls.« less

Matching 4.7-Å XRD Spacing in Amelogenin Nanoribbons and Enamel Matrix

PubMed Central

Sanii, B.; Martinez-Avila, O.; Simpliciano, C.; Zuckermann, R.N.; Habelitz, S.

2014-01-01

The recent discovery of conditions that induce nanoribbon structures of amelogenin protein in vitro raises questions about their role in enamel formation. Nanoribbons of recombinant human full-length amelogenin (rH174) are about 17 nm wide and self-align into parallel bundles; thus, they could act as templates for crystallization of nanofibrous apatite comprising dental enamel. Here we analyzed the secondary structures of nanoribbon amelogenin by x-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) and tested if the structural motif matches previous data on the organic matrix of enamel. XRD analysis showed that a peak corresponding to 4.7 Å is present in nanoribbons of amelogenin. In addition, FTIR analysis showed that amelogenin in the form of nanoribbons was comprised of β-sheets by up to 75%, while amelogenin nanospheres had predominantly random-coil structure. The observation of a 4.7-Å XRD spacing confirms the presence of β-sheets and illustrates structural parallels between the in vitro assemblies and structural motifs in developing enamel. PMID:25048248

An overview of inverted colloidal crystal systems for tissue engineering.

PubMed

João, Carlos Filipe C; Vasconcelos, Joana Marta; Silva, Jorge Carvalho; Borges, João Paulo

2014-10-01

Scaffolding is at the heart of tissue engineering but the number of techniques available for turning biomaterials into scaffolds displaying the features required for a tissue engineering application is somewhat limited. Inverted colloidal crystals (ICCs) are inverse replicas of an ordered array of monodisperse colloidal particles, which organize themselves in packed long-range crystals. The literature on ICC systems has grown enormously in the past 20 years, driven by the need to find organized macroporous structures. Although replicating the structure of packed colloidal crystals (CCs) into solid structures has produced a wide range of advanced materials (e.g., photonic crystals, catalysts, and membranes) only in recent years have ICCs been evaluated as devices for medical/pharmaceutical and tissue engineering applications. The geometry, size, pore density, and interconnectivity are features of the scaffold that strongly affect the cell environment with consequences on cell adhesion, proliferation, and differentiation. ICC scaffolds are highly geometrically ordered structures with increased porosity and connectivity, which enhances oxygen and nutrient diffusion, providing optimum cellular development. In comparison to other types of scaffolds, ICCs have three major unique features: the isotropic three-dimensional environment, comprising highly uniform and size-controllable pores, and the presence of windows connecting adjacent pores. Thus far, this is the only technique that guarantees these features with a long-range order, between a few nanometers and thousands of micrometers. In this review, we present the current development status of ICC scaffolds for tissue engineering applications.

Photonic crystal devices formed by a charged-particle beam

DOEpatents

Lin, Shawn-Yu; Koops, Hans W. P.

2000-01-01

A photonic crystal device and method. The photonic crystal device comprises a substrate with at least one photonic crystal formed thereon by a charged-particle beam deposition method. Each photonic crystal comprises a plurality of spaced elements having a composition different from the substrate, and may further include one or more impurity elements substituted for spaced elements. Embodiments of the present invention may be provided as electromagnetic wave filters, polarizers, resonators, sources, mirrors, beam directors and antennas for use at wavelengths in the range from about 0.2 to 200 microns or longer. Additionally, photonic crystal devices may be provided with one or more electromagnetic waveguides adjacent to a photonic crystal for forming integrated electromagnetic circuits for use at optical, infrared, or millimeter-wave frequencies.

Thermodynamic stability and structural properties of cluster crystals formed by amphiphilic dendrimers

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

Lenz, Dominic A.; Likos, Christos N.; Blaak, Ronald

We pursue the goal of finding real-world examples of macromolecular aggregates that form cluster crystals, which have been predicted on the basis of coarse-grained, ultrasoft pair potentials belonging to a particular mathematical class [B. M. Mladek et al., Phys. Rev. Lett. 46, 045701 (2006)]. For this purpose, we examine in detail the phase behavior and structural properties of model amphiphilic dendrimers of the second generation by means of monomer-resolved computer simulations. On augmenting the density of these systems, a fluid comprised of clusters that contain several overlapping and penetrating macromolecules is spontaneously formed. Upon further compression of the system, amore » transition to multi-occupancy crystals takes place, the thermodynamic stability of which is demonstrated by means of free-energy calculations, and where the FCC is preferred over the BCC-phase. Contrary to predictions for coarse-grained theoretical models in which the particles interact exclusively by effective pair potentials, the internal degrees of freedom of these molecules cause the lattice constant to be density-dependent. Furthermore, the mechanical stability of monodisperse BCC and FCC cluster crystals is restricted to a bounded region in the plane of cluster occupation number versus density. The structural properties of the dendrimers in the dense crystals, including their overall sizes and the distribution of monomers are also thoroughly analyzed.« less

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

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

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

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

Crystal structure of Bombyx mori arylphorins reveals a 3:3 heterohexamer with multiple papain cleavage sites

PubMed Central

Hou, Yong; Li, Jianwei; Li, Yi; Dong, Zhaoming; Xia, Qingyou; Yuan, Y Adam

2014-01-01

In holometabolous insects, the accumulation and utilization of storage proteins (SPs), including arylphorins and methionine-rich proteins, are critical for the insect metamorphosis. SPs function as amino acids reserves, which are synthesized in fat body, secreted into the larval hemolymph and taken up by fat body shortly before pupation. However, the detailed molecular mechanisms of digestion and utilization of SPs during development are largely unknown. Here, we report the crystal structure of Bombyx mori arylphorins at 2.8 Å, which displays a heterohexameric structural arrangement formed by trimerization of dimers comprising two structural similar arylphorins. Our limited proteolysis assay and microarray data strongly suggest that papain-like proteases are the major players for B. mori arylphorins digestion in vitro and in vivo. Consistent with the biochemical data, dozens of papain cleavage sites are mapped on the surface of the heterohexameric structure of B. mori arylphorins. Hence, our results provide the insightful information to understand the metamorphosis of holometabolous insects at molecular level. PMID:24639361

Multicolor photonic crystal laser array

DOEpatents

Wright, Jeremy B; Brener, Igal; Subramania, Ganapathi S; Wang, George T; Li, Qiming

2015-04-28

A multicolor photonic crystal laser array comprises pixels of monolithically grown gain sections each with a different emission center wavelength. As an example, two-dimensional surface-emitting photonic crystal lasers comprising broad gain-bandwidth III-nitride multiple quantum well axial heterostructures were fabricated using a novel top-down nanowire fabrication method. Single-mode lasing was obtained in the blue-violet spectral region with 60 nm of tuning (or 16% of the nominal center wavelength) that was determined purely by the photonic crystal geometry. This approach can be extended to cover the entire visible spectrum.

Annual-ring-type quasi-phase-matching crystal for generation of narrowband high-dimensional entanglement

NASA Astrophysics Data System (ADS)

Hua, Yi-Lin; Zhou, Zong-Quan; Liu, Xiao; Yang, Tian-Shu; Li, Zong-Feng; Li, Pei-Yun; Chen, Geng; Xu, Xiao-Ye; Tang, Jian-Shun; Xu, Jin-Shi; Li, Chuan-Feng; Guo, Guang-Can

2018-01-01

A photon pair can be entangled in many degrees of freedom such as polarization, time bins, and orbital angular momentum (OAM). Among them, the OAM of photons can be entangled in an infinite-dimensional Hilbert space which enhances the channel capacity of sharing information in a network. Twisted photons generated by spontaneous parametric down-conversion offer an opportunity to create this high-dimensional entanglement, but a photon pair generated by this process is typically wideband, which makes it difficult to interface with the quantum memories in a network. Here we propose an annual-ring-type quasi-phase-matching (QPM) crystal for generation of the narrowband high-dimensional entanglement. The structure of the QPM crystal is designed by tracking the geometric divergences of the OAM modes that comprise the entangled state. The dimensionality and the quality of the entanglement can be greatly enhanced with the annual-ring-type QPM crystal.

Prediction of Giant Thermoelectric Efficiency in Crystals with Interlaced Nanostructure.

PubMed

Puzyrev, Y S; Shen, X; Pantelides, S T

2016-01-13

We present a theoretical study of the thermoelectric efficiency of "interlaced crystals", recently discovered in hexagonal-CuInS2 nanoparticles. Interlaced crystals are I-III-VI2 or II-IV-V2 tetrahedrally bonded compounds. They have a perfect Bravais lattice in which the two cations have an infinite set of possible ordering patterns within the cation sublattice. The material comprises nanoscale interlaced domains and phases with corresponding boundaries. Here we employ density functional theory and large-scale molecular dynamics calculations based on model classical potentials to demonstrate that the phase and domain boundaries are effective phonon scatterers and greatly suppress thermal conductivity. However, the absence of both structural defects and strain in the interlaced material results in a minimal effect on electronic properties. We predict an increase of thermal resistivity of up to 2 orders of magnitude, which makes interlaced crystals an exceptional candidate for thermoelectric applications.

Excitation enhancement and extraction enhancement with photonic crystals

DOEpatents

Shapira, Ofer; Soljacic, Marin; Zhen, Bo; Chua, Song-Liang; Lee, Jeongwon; Joannopoulos, John

2015-03-03

Disclosed herein is a system for stimulating emission from at least one an emitter, such as a quantum dot or organic molecule, on the surface of a photonic crystal comprising a patterned dielectric substrate. Embodiments of this system include a laser or other source that illuminates the emitter and the photonic crystal, which is characterized by an energy band structure exhibiting a Fano resonance, from a first angle so as to stimulate the emission from the emitter at a second angle. The coupling between the photonic crystal and the emitter may result in spectral and angular enhancement of the emission through excitation and extraction enhancement. These enhancement mechanisms also reduce the emitter's lasing threshold. For instance, these enhancement mechanisms enable lasing of a 100 nm thick layer of diluted organic molecules solution with reduced threshold intensity. This reduction in lasing threshold enables more efficient organic light emitting devices and more sensitive molecular sensing.

Crystal structure and association behaviour of the GluR2 amino-terminal domain

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

Jin, Rongsheng; Singh, Satinder K.; Gu, Shenyan

2009-09-02

Fast excitatory neurotransmission is mediated largely by ionotropic glutamate receptors (iGluRs), tetrameric, ligand-gated ion channel proteins comprised of three subfamilies, AMPA, kainate and NMDA receptors, with each subfamily sharing a common, modular-domain architecture. For all receptor subfamilies, active channels are exclusively formed by assemblages of subunits within the same subfamily, a molecular process principally encoded by the amino-terminal domain (ATD). However, the molecular basis by which the ATD guides subfamily-specific receptor assembly is not known. Here we show that AMPA receptor GluR1- and GluR2-ATDs form tightly associated dimers and, by the analysis of crystal structures of the GluR2-ATD, propose mechanismsmore » by which the ATD guides subfamily-specific receptor assembly.« less

Crystal structure of diaphorin methanol monosolvate isolated from Diaphorina citri Kuwayama, the insect vector of citrus greening disease.

PubMed

Szebenyi, D Marian; Kriksunov, Irina; Howe, Kevin J; Ramsey, John S; Hall, David G; Heck, Michelle L; Krasnoff, Stuart B

2018-04-01

The title compound C 22 H 39 NO 9 ·CH 3 OH [systematic name: ( S )- N -(( S )-{(2 S ,4 R ,6 R )-6-[( S )-2,3-di-hydroxy-prop-yl]-4-hy-droxy-5,5-di-methyl-tetra-hydro-2 H -pyran-2-yl}(hy-droxy)meth-yl)-2-hy-droxy-2-[(2 R ,5 R ,6 R )-2-meth-oxy-5,6-dimeth-yl-4-methyl-ene-tetra-hydro-2 H -pyran-2-yl]acetamide methanol monosolvate], was isolated from the Asian citrus psyllid, Diaphorina citri Kuwayama, and crystallizes in the space group P 2 1 . ' Candidatus Profftella armatura' a bacterial endosymbiont of D. citri , biosynthesizes diaphorin, which is a hybrid polyketide-nonribosomal peptide comprising two highly substituted tetra-hydro-pyran rings joined by an N -acyl aminal bridge [Nakabachi et al. (2013 ▸). Curr. Biol. 23 , 1478-1484]. The crystal structure of the title compound establishes the complete relative configuration of diaphorin, which agrees at all nine chiral centers with the structure of the methanol monosolvate of the di- p -bromo-benzoate derivative of pederin, a biogenically related compound whose crystal structure was reported previously [Furusaki et al. (1968 ▸). Tetra-hedron Lett. 9 , 6301-6304]. Thus, the absolute configuration of diaphorin is proposed by analogy to that of pederin.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1985-01-01

From intermolecular force studies, it is now known that the overall non-additive contribution to the lattice enegy is positive so that analysis based on only pairwise additivity suggests a shallower intermolecular potential than the true value. Two body contributions alone are also known to be categorically unable to even qualitatively describe some configurations of molecular clusters in the gas phase or the general relaxation and reconstruction of fcc crystal surfaces. In addition, the many-body contribution was shown to play a key role in the stability of certain crystal structures. In these recent analyses, a relatively simple potential energy function (PEF), comprising only a two-body Mie-type potential plus a three-body Axilrod-Teller-type potential, was found to be extremely effective. This same parametric PEF is applied to describe the bulk stability and surface energy for the diamond cubic structure. To test the stability condition, the FCC, BCC, diamond cubic, graphite and beta-tin structures were considered.

Hybridization gap in the semiconducting compound SrIr 4In 2Ge 4

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

Calta, Nicholas P.; Im, Jino; Fang, Lei

Here, large single crystals of SrIr 4In 2Ge 4 were synthesized using the In flux method. This compound is a hybridization gap semiconductor with an experimental optical band gap of E g = 0.25(3) eV. It crystallizes in the tetragonal EuIr 4In 2Ge 4 structure type with space group 1more » $$\\overline{4}$$2m and unit cell parameters a = 6.9004(5) Å and c = 8.7120(9) Å. The electronic structure is very similar to both EuIr 4In 2Ge 4 and the parent structure Ca 3Ir 4Ge 4, suggesting that these compounds comprise a new family of hybridization gap materials that exhibit indirect gap, semiconducting behavior at a valence electron count of 60 per formula unit, similar to the Heusler alloys.« less

Hybridization gap in the semiconducting compound SrIr 4In 2Ge 4

DOE PAGES

Calta, Nicholas P.; Im, Jino; Fang, Lei; ...

2016-11-18

Here, large single crystals of SrIr 4In 2Ge 4 were synthesized using the In flux method. This compound is a hybridization gap semiconductor with an experimental optical band gap of E g = 0.25(3) eV. It crystallizes in the tetragonal EuIr 4In 2Ge 4 structure type with space group 1more » $$\\overline{4}$$2m and unit cell parameters a = 6.9004(5) Å and c = 8.7120(9) Å. The electronic structure is very similar to both EuIr 4In 2Ge 4 and the parent structure Ca 3Ir 4Ge 4, suggesting that these compounds comprise a new family of hybridization gap materials that exhibit indirect gap, semiconducting behavior at a valence electron count of 60 per formula unit, similar to the Heusler alloys.« less

Realizing A Mid-Infrared Optically Pumped Molecular Gas Laser Inside Hollow-Core Photonic Crystal Fiber

DTIC Science & Technology

2012-01-01

54  Figure 5.2 External transmission of (a) BK7 glass , (b) CaF2, and (c) Germanium substrates of various thicknesses. The transmission values...a hollow, air-filled core surrounded by cladding structure which is comprised of a periodic array of smaller air holes. Unlike glass capillaries...region of the fiber’s core. The low overlap of the guided light with the HC-PCF’s glass structure together with a higher threshold for the onset of

Synthesis, crystal structure, and protonation behaviour in solution of the recently-discovered drug metabolite, N1,N10-diacetyltriethylenetetramine

NASA Astrophysics Data System (ADS)

Wichmann, Kathrin A.; Söhnel, Tilo; Cooper, Garth J. S.

2012-03-01

N1,N10-diacetyltriethylenetetramine (DAT) is a recently-discovered major in vivo metabolite of triethylenetetramine (TETA), a highly-selective CuII chelator currently under clinical development as a novel first-in-class therapeutic for the cardiovascular, renal and retinal complications of diabetes mellitus. Characterisation of DAT is an integral aspect of the pharmacological work-up required to support this clinical development programme and, to our knowledge, no previous synthesis for it has been published. Here we report the synthesis of DAT dihydrochloride (DAT·2 HCl); its crystal structure as determined by X-ray single-crystal (XRD) and powder diffraction (XRPD); and protonation constants and species distribution in aqueous solution, which represents the different protonation states of DAT at different pH values. The crystal structure of DAT·2 HCl reveals 3D-assemblies of alternating 2D-layers comprising di-protonated DAT strands and anionic species, which form an extensive hydrogen-bond network between amine groups, acetyl groups, and chloride anions. Potentiometric titrations show that HDAT+ is the physiologically relevant state of DAT in solution. These findings contribute to the understanding of TETA's pharmacology and to its development for the experimental therapeutics of the diabetic complications.

Mapping of spin wave propagation in a one-dimensional magnonic crystal

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

Ordóñez-Romero, César L., E-mail: cloro@fisica.unam.mx; Lazcano-Ortiz, Zorayda; Aguilar-Huerta, Melisa

2016-07-28

The formation and evolution of spin wave band gaps in the transmission spectrum of a magnonic crystal have been studied. A time and space resolved magneto inductive probing system has been used to map the spin wave propagation and evolution in a geometrically structured yttrium iron garnet film. Experiments have been carried out using (1) a chemically etched magnonic crystal supporting the propagation of magnetostatic surface spin waves, (2) a short microwave pulsed excitation of the spin waves, and (3) direct spin wave detection using a movable magneto inductive probe connected to a synchronized fast oscilloscope. The results show thatmore » the periodic structure not only modifies the spectra of the transmitted spin waves but also influences the distribution of the spin wave energy inside the magnonic crystal as a function of the position and the transmitted frequency. These results comprise an experimental confirmation of Bloch′s theorem in a spin wave system and demonstrate good agreement with theoretical observations in analogue phononic and photonic systems. Theoretical prediction of the structured transmission spectra is achieved using a simple model based on microwave transmission lines theory. Here, a spin wave system illustrates in detail the evolution of a much more general physical concept: the band gap.« less

Semiconductor crystal high resolution imager

NASA Technical Reports Server (NTRS)

Matteson, James (Inventor); Levin, Craig S. (Inventor)

2011-01-01

A radiation imaging device (10). The radiation image device (10) comprises a subject radiation station (12) producing photon emissions (14), and at least one semiconductor crystal detector (16) arranged in an edge-on orientation with respect to the emitted photons (14) to directly receive the emitted photons (14) and produce a signal. The semiconductor crystal detector (16) comprises at least one anode and at least one cathode that produces the signal in response to the emitted photons (14).

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis

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

Gupta, Vibha; Gupta, Rakesh K.; Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi 110021

2008-05-01

The cloning, purification and crystallization of a bacterioferritin from M. tuberculosis together with preliminary X-ray characterization of its crystals are reported. Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein productmore » was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1 Å resolution and belonged to space group P4{sub 2}, with unit-cell parameters a = 123.0, b = 123.0, c = 174.6 Å.« less

Process for Making Single-Domain Magnetite Crystals

NASA Technical Reports Server (NTRS)

Golden, D. C.; Ming, Douglas W.; Morris, Richard V.; Lofgren, Gary E.; McKay, Gordan A.; Schwandt, Craig S.; Lauer, Howard V., Jr.; Socki, Richard A.

2004-01-01

A process for making chemically pure, single-domain magnetite crystals substantially free of structural defects has been invented as a byproduct of research into the origin of globules in a meteorite found in Antarctica and believed to have originated on Mars. The globules in the meteorite comprise layers of mixed (Mg, Fe, and Ca) carbonates, magnetite, and iron sulfides. Since the discovery of the meteorite was announced in August 1996, scientists have debated whether the globules are of biological origin or were formed from inorganic materials by processes that could have taken place on Mars. While the research that led to the present invention has not provided a definitive conclusion concerning the origin of the globules, it has shown that globules of a different but related chemically layered structure can be grown from inorganic ingredients in a multistep precipitation process. As described in more detail below, the present invention comprises the multistep precipitation process plus a subsequent heat treatment. The multistep precipitation process was demonstrated in a laboratory experiment on the growth of submicron ankerite crystals, overgrown by submicron siderite and pyrite crystals, overgrown by submicron magnesite crystals, overgrown by submicron siderite and pyrite. In each step, chloride salts of appropriate cations (Ca, Fe, and Mg) were dissolved in deoxygenated, CO2- saturated water. NaHCO3 was added as a pH buffer while CO2 was passed continuously through the solution. A 15-mL aliquot of the resulting solution was transferred into each of several 20 mL, poly(tetrafluoroethylene)-lined hydrothermal pressure vessels. The vessels were closed in a CO2 atmosphere, then transferred into an oven at a temperature of 150 C. After a predetermined time, the hydrothermal vessels were removed from the oven and quenched in a freezer. Supernatant solutions were decanted, and carbonate precipitates were washed free of soluble salts by repeated decantations with deionized water.

Surface structures for enhancement of quantum yield in broad spectrum emission nanocrystals

DOEpatents

Schreuder, Michael A.; McBride, James R.; Rosenthal, Sandra J.

2014-07-22

Disclosed are inorganic nanoparticles comprising a body comprising cadmium and/or zinc crystallized with selenium, sulfur, and/or tellurium; a multiplicity of phosphonic acid ligands comprising at least about 20% of the total surface ligand coverage; wherein the nanocrystal is capable of absorbing energy from a first electromagnetic region and capable of emitting light in a second electromagnetic region, wherein the maximum absorbance wavelength of the first electromagnetic region is different from the maximum emission wavelength of the second electromagnetic region, thereby providing a Stokes shift of at least about 20 nm, wherein the second electromagnetic region comprises an at least about 100 nm wide band of wavelengths, and wherein the nanoparticle exhibits has a quantum yield of at least about 10%. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present invention.

Optical trapping apparatus, methods and applications using photonic crystal resonators

DOEpatents

Erickson, David; Chen, Yih-Fan

2015-06-16

A plurality of photonic crystal resonator optical trapping apparatuses and a plurality optical trapping methods using the plurality of photonic crystal resonator optical trapping apparatuses include located and formed over a substrate a photonic waveguide that is coupled (i.e., either separately coupled or integrally coupled) with a photonic crystal resonator. In a particular embodiment, the photonic waveguide and the photonic crystal resonator comprise a monocrystalline silicon (or other) photonic material absent any chemical functionalization. In another particular embodiment, the photonic waveguide and the photonic crystal resonator comprise a silicon nitride material which when actuating the photonic crystal resonator optical trapping apparatus with a 1064 nanometer resonant photonic radiation wavelength (or other resonant photonic radiation wavelength in a range from about 700 to about 1200 nanometers) provides no appreciable heating of an aqueous sample fluid that is analyzed by the photonic crystal resonator optical trapping apparatus.

Crystal structures of three co-crystals of 1,2-bis-(pyridin-4-yl)ethane with 4-alk-oxy-benzoic acids: 4-eth-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), 4-n-propoxybenzoic acid-1,2-bis(pyridin-4-yl)ethane (2/1) and 4-n-but-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1).

PubMed

Tabuchi, Yohei; Gotoh, Kazuma; Ishida, Hiroyuki

2015-11-01

The crystal structures of three hydrogen-bonded co-crystals of 4-alk-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), namely, 2C9H10O3·C12H12N2, (I), 2C10H12O3·C12H12N2, (II), and 2C11H14O3·C12H12N2, (III), have been determined at 93, 290 and 93 K, respectively. In (I), the asymmetric unit consists of one 4-eth-oxy-benzoic acid mol-ecule and one half-mol-ecule of 1,2-bis-(pyridin-4-yl)ethane, which lies on an inversion centre. In (II) and (III), the asymmetric units each comprise two crystallographically independent 4-alk-oxy-benzoic acid mol-ecules and one 1,2-bis-(pyridin-4-yl)ethane mol-ecule. In each crystal, the two components are linked by O-H⋯N hydrogen bonds, forming a linear hydrogen-bonded 2:1unit of the acid and the base. Similar to the structure of 2:1 unit of (I), the units of (II) and (III) adopt nearly pseudo-inversion symmetry. The 2:1 units of (I), (II) and (III) are linked via C-H⋯O hydrogen bonds, forming tape structures.

Crystal structure and Hirshfeld surface analysis of (2E,2'E)-3,3'-(1,4-phenyl-ene)bis-[1-(2,4-di-fluoro-phen-yl)prop-2-en-1-one].

PubMed

Kwong, Huey Chong; Sim, Aijia; Chidan Kumar, C S; Then, Li Yee; Win, Yip-Foo; Quah, Ching Kheng; Naveen, S; Warad, Ismail

2017-12-01

The asymmetric unit of the title compound, C 24 H 14 F 4 O 2 , comprises of one and a half mol-ecules; the half-mol-ecule is completed by crystallographic inversion symmetry. In the crystal, mol-ecules are linked into a three-dimensional network by C-H⋯F and C-H⋯O hydrogen bonds. Some of the C-H⋯F links are unusually short (< 2.20 Å). Hirshfeld surface analyses ( d norm surfaces and two-dimensional fingerprint plots) for the title compound are presented and discussed.

Air electrode composition for solid oxide fuel cell

DOEpatents

Kuo, Lewis; Ruka, Roswell J.; Singhal, Subhash C.

1999-01-01

An air electrode composition for a solid oxide fuel cell is disclosed. The air electrode material is based on lanthanum manganite having a perovskite-like crystal structure ABO.sub.3. The A-site of the air electrode composition comprises a mixed lanthanide in combination with rare earth and alkaline earth dopants. The B-site of the composition comprises Mn in combination with dopants such as Mg, Al, Cr and Ni. The mixed lanthanide comprises La, Ce, Pr and, optionally, Nd. The rare earth A-site dopants preferably comprise La, Nd or a combination thereof, while the alkaline earth A-site dopant preferably comprises Ca. The use of a mixed lanthanide substantially reduces raw material costs in comparison with compositions made from high purity lanthanum starting materials. The amount of the A-site and B-site dopants is controlled in order to provide an air electrode composition having a coefficient of thermal expansion which closely matches that of the other components of the solid oxide fuel cell.

Air electrode composition for solid oxide fuel cell

DOEpatents

Kuo, L.; Ruka, R.J.; Singhal, S.C.

1999-08-03

An air electrode composition for a solid oxide fuel cell is disclosed. The air electrode material is based on lanthanum manganite having a perovskite-like crystal structure ABO{sub 3}. The A-site of the air electrode composition comprises a mixed lanthanide in combination with rare earth and alkaline earth dopants. The B-site of the composition comprises Mn in combination with dopants such as Mg, Al, Cr and Ni. The mixed lanthanide comprises La, Ce, Pr and, optionally, Nd. The rare earth A-site dopants preferably comprise La, Nd or a combination thereof, while the alkaline earth A-site dopant preferably comprises Ca. The use of a mixed lanthanide substantially reduces raw material costs in comparison with compositions made from high purity lanthanum starting materials. The amount of the A-site and B-site dopants is controlled in order to provide an air electrode composition having a coefficient of thermal expansion which closely matches that of the other components of the solid oxide fuel cell. 3 figs.

Delicate crystal structure changes govern the magnetic properties of 1D coordination polymers based on 3d metal carboxylates.

PubMed

Gavrilenko, Konstantin S; Cador, Olivier; Bernot, Kevin; Rosa, Patrick; Sessoli, Roberta; Golhen, Stéphane; Pavlishchuk, Vitaly V; Ouahab, Lahcène

2008-01-01

Homo- and heterometallic 1D coordination polymers of transition metals (Co II, Mn II, Zn II) have been synthesized by an in-situ ligand generation route. Carboxylato-based complexes [Co(PhCOO)2]n (1 a, 1 b), [Co(p-MePhCOO)2]n (2), [ZnMn(PhCOO)4]n (3), and [CoZn(PhCOO)4]n (4) (PhCOOH=benzoic acid, p-MePhCOOH=p-methylbenzoic acid) have been characterized by chemical analysis, single-crystal X-ray diffraction, and magnetization measurements. The new complexes 2 and 3 crystallize in orthorhombic space groups Pnab and Pcab respectively. Their crystal structures consist of zigzag chains, with alternating M(II) centers in octahedral and tetrahedral positions, which are similar to those of 1 a and 1 b. Compound 4 crystallizes in monoclinic space group P2 1/c and comprises zigzag chains of M II ions in a tetrahedral coordination environment. Magnetic investigations reveal the existence of antiferromagnetic interactions between magnetic centers in the heterometallic complexes 3 and 4, while ferromagnetic interactions operate in homometallic compounds (1 a, 1 b, and 2). Compound 1 b orders ferromagnetically at TC=3.7 K whereas 1 a does not show any magnetic ordering down to 330 mK and displays typical single-chain magnet (SCM) behavior with slowing down of magnetization relaxation below 0.6 K. Single-crystal measurements reveal that the system is easily magnetized in the chain direction for 1 a whereas the chain direction coincides with the hard magnetic axis in 1 b. Despite important similarities, small differences in the molecular and crystal structures of these two compounds lead to this dramatic change in properties.

Synthetic thermoelectric materials comprising phononic crystals

DOEpatents

El-Kady, Ihab F; Olsson, Roy H; Hopkins, Patrick; Reinke, Charles; Kim, Bongsang

2013-08-13

Synthetic thermoelectric materials comprising phononic crystals can simultaneously have a large Seebeck coefficient, high electrical conductivity, and low thermal conductivity. Such synthetic thermoelectric materials can enable improved thermoelectric devices, such as thermoelectric generators and coolers, with improved performance. Such synthetic thermoelectric materials and devices can be fabricated using techniques that are compatible with standard microelectronics.

Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.

PubMed

Corradi, Hazel R; Schwager, Sylva L U; Nchinda, Aloysius T; Sturrock, Edward D; Acharya, K Ravi

2006-03-31

Human somatic angiotensin I-converting enzyme (sACE) is a key regulator of blood pressure and an important drug target for combating cardiovascular and renal disease. sACE comprises two homologous metallopeptidase domains, N and C, joined by an inter-domain linker. Both domains are capable of cleaving the two hemoregulatory peptides angiotensin I and bradykinin, but differ in their affinities for a range of other substrates and inhibitors. Previously we determined the structure of testis ACE (C domain); here we present the crystal structure of the N domain of sACE (both in the presence and absence of the antihypertensive drug lisinopril) in order to aid the understanding of how these two domains differ in specificity and function. In addition, the structure of most of the inter-domain linker allows us to propose relative domain positions for sACE that may contribute to the domain cooperativity. The structure now provides a platform for the design of "domain-specific" second-generation ACE inhibitors.

Yb:FAP and related materials, laser gain medium comprising same, and laser systems using same

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

Krupke, William F.; Payne, Stephen A.; Chase, Lloyd L.

An ytterbium doped laser material remarkably superior to all others, including Yb:YAG, comprises Ytterbium doped apatite (Yb:Ca.sub.5 (PO.sub.4).sub.3 F) or Yb:FAP, or ytterbium doped crystals that are structurally related to FAP. The new laser material is used in laser systems pumped by diode pump sources having an output near 0.905 microns or 0.98 microns, such as InGaAs and AlInGaAs, or other narrowband pump sources near 0.905 microns or 0.98 microns. The laser systems are operated in either the conventional or ground state depletion mode.

Yb:FAP and related materials, laser gain medium comprising same, and laser systems using same

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

Krupke, W.F.; Payne, S.A.; Chase, L.L.

An ytterbium doped laser material remarkably superior to all others, including Yb:YAG, comprises ytterbium doped apatite (Yb:Ca[sub 5](PO[sub 4])[sub 3]F) or Yb:FAP, or ytterbium doped crystals that are structurally related to FAP. The new laser material is used in laser systems pumped by diode pump sources having an output near 0.905 microns or 0.98 microns, such as InGaAs and AlInGaAs, or other narrowband pump sources near 0.905 microns or 0.98 microns. The laser systems are operated in either the conventional or ground state depletion mode. 9 figures.

Yb:FAP and related materials, laser gain medium comprising same, and laser systems using same

DOEpatents

Krupke, W.F.; Payne, S.A.; Chase, L.L.; Smith, L.K.

1994-01-18

An ytterbium doped laser material remarkably superior to all others, including Yb:YAG, comprises ytterbium doped apatite (Yb:Ca[sub 5](PO[sub 4])[sub 3]F) or Yb:FAP, or ytterbium doped crystals that are structurally related to FAP. The new laser material is used in laser systems pumped by diode pump sources having an output near 0.905 microns or 0.98 microns, such as InGaAs and AlInGaAs, or other narrowband pump sources near 0.905 microns or 0.98 microns. The laser systems are operated in either the conventional or ground state depletion mode. 9 figures.

Yb:FAP and related materials, laser gain medium comprising same, and laser systems using same

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

Krupke, W.F.; Payne, S.A.; Chase, L.L.

An ytterbium doped laser material remarkably superior to all others, including Yb:YAG, comprises ytterbium doped apatite (Yb:Ca{sub 5}(PO{sub 4}){sub 3}F) or Yb:FAP, or ytterbium doped crystals structurally related to FAP. The new laser material is used in laser systems pumped by diode pump sources having an output near 0.905 microns or 0.98 microns, such as InGaAs and AlInGaAs, or other narrowband pump sources near 0.905 microns or 0.98 microns. The laser systems are operated in either the conventional or ground state depletion mode.

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

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

Rodríguez Guilbe, María M.; Protein Research and Development Center, University of Puerto Rico; Alfaro Malavé, Elisa C.

The genetically encoded fluorescent calcium-indicator protein GCaMP2 was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution and the structure was solved by molecular replacement. Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, thismore » protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way.« less

DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein

PubMed Central

Duan, Ming-Rui; Nan, Jie; Liang, Yu-He; Mao, Peng; Lu, Lu; Li, Lanfen; Wei, Chunhong; Lai, Luhua; Li, Yi; Su, Xiao-Dong

2007-01-01

WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 Å resolution has revealed that this domain is composed of a globular structure with five β strands, forming an antiparallel β-sheet. A novel zinc-binding site is situated at one end of the β-sheet, between strands β4 and β5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at β2 and β3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins. PMID:17264121

Matching 4.7-Å XRD spacing in amelogenin nanoribbons and enamel matrix.

PubMed

Sanii, B; Martinez-Avila, O; Simpliciano, C; Zuckermann, R N; Habelitz, S

2014-09-01

The recent discovery of conditions that induce nanoribbon structures of amelogenin protein in vitro raises questions about their role in enamel formation. Nanoribbons of recombinant human full-length amelogenin (rH174) are about 17 nm wide and self-align into parallel bundles; thus, they could act as templates for crystallization of nanofibrous apatite comprising dental enamel. Here we analyzed the secondary structures of nanoribbon amelogenin by x-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) and tested if the structural motif matches previous data on the organic matrix of enamel. XRD analysis showed that a peak corresponding to 4.7 Å is present in nanoribbons of amelogenin. In addition, FTIR analysis showed that amelogenin in the form of nanoribbons was comprised of β-sheets by up to 75%, while amelogenin nanospheres had predominantly random-coil structure. The observation of a 4.7-Å XRD spacing confirms the presence of β-sheets and illustrates structural parallels between the in vitro assemblies and structural motifs in developing enamel. © International & American Associations for Dental Research.

DNA-mediated nanoparticle crystallization into Wulff polyhedra

NASA Astrophysics Data System (ADS)

Auyeung, Evelyn; Li, Ting I. N. G.; Senesi, Andrew J.; Schmucker, Abrin L.; Pals, Bridget C.; de La Cruz, Monica Olvera; Mirkin, Chad A.

2014-01-01

Crystallization is a fundamental and ubiquitous process much studied over the centuries. But although the crystallization of atoms is fairly well understood, it remains challenging to predict reliably the outcome of molecular crystallization processes that are complicated by various molecular interactions and solvent involvement. This difficulty also applies to nanoparticles: high-quality three-dimensional crystals are mostly produced using drying and sedimentation techniques that are often impossible to rationalize and control to give a desired crystal symmetry, lattice spacing and habit (crystal shape). In principle, DNA-mediated assembly of nanoparticles offers an ideal opportunity for studying nanoparticle crystallization: a well-defined set of rules have been developed to target desired lattice symmetries and lattice constants, and the occurrence of features such as grain boundaries and twinning in DNA superlattices and traditional crystals comprised of molecular or atomic building blocks suggests that similar principles govern their crystallization. But the presence of charged biomolecules, interparticle spacings of tens of nanometres, and the realization so far of only polycrystalline DNA-interconnected nanoparticle superlattices, all suggest that DNA-guided crystallization may differ from traditional crystal growth. Here we show that very slow cooling, over several days, of solutions of complementary-DNA-modified nanoparticles through the melting temperature of the system gives the thermodynamic product with a specific and uniform crystal habit. We find that our nanoparticle assemblies have the Wulff equilibrium crystal structure that is predicted from theoretical considerations and molecular dynamics simulations, thus establishing that DNA hybridization can direct nanoparticle assembly along a pathway that mimics atomic crystallization.

Monoclinic crystal structure of α - RuCl 3 and the zigzag antiferromagnetic ground state

DOE PAGES

Johnson, R. D.; Williams, S. C.; Haghighirad, A. A.; ...

2015-12-10

We have proposed the layered honeycomb magnet α - RuCl 3 as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled j eff = 1/2 Ru 3 + magnetic moments. We report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, inmore » contrast with the currently assumed trigonal three-layer stacking periodicity. We also report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the j eff = 1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below T N ≈ 13 K. Our analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in pulsed field up to 60 T show a single transition around 8 T for in-plane fields followed by a gradual, asymptotic approach to magnetization saturation, as characteristic of strongly anisotropic exchange interactions.« less

Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain

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

Nithianantham, Stanley; Xu, Minghua; Yamada, Mitsunori

2009-04-07

Many bacterial appendages have filamentous structures, often composed of repeating monomers assembled in a head-to-tail manner. The mechanisms of such linkages vary. We report here a novel protein oligomerization motif identified in the FadA adhesin from the Gram-negative bacterium Fusobacterium nucleatum. The 2.0 {angstrom} crystal structure of the secreted form of FadA (mFadA) reveals two antiparallel {alpha}-helices connected by an intervening 8-residue hairpin loop. Leucine-leucine contacts play a prominent dual intra- and intermolecular role in the structure and function of FadA. First, they comprise the main association between the two helical arms of the monomer; second, they mediate the head-to-tailmore » association of monomers to form the elongated polymers. This leucine-mediated filamentous assembly of FadA molecules constitutes a novel structural motif termed the 'leucine chain.' The essential role of these residues in FadA is corroborated by mutagenesis of selected leucine residues, which leads to the abrogation of oligomerization, filament formation, and binding to host cells.« less

Metal Flux Growth, Structural Relations, and Physical Properties of EuCu2Ge2 and Eu3T2In9 (T = Cu and Ag).

PubMed

Subbarao, Udumula; Roy, Soumyabrata; Sarma, Saurav Ch; Sarkar, Sumanta; Mishra, Vidyanshu; Khulbe, Yatish; Peter, Sebastian C

2016-10-17

Single crystals (SCs) of the compounds Eu 3 Ag 2 In 9 and EuCu 2 Ge 2 were synthesized through the reactions run in liquid indium. Eu 3 Ag 2 In 9 crystallizes in the La 3 Al 11 structure type [orthorhombic space group (SG) Immm] with the lattice parameters: a = 4.8370(1) Å, b = 10.6078(3) Å, and c = 13.9195(4) Å. EuCu 2 Ge 2 crystallizes in the tetragonal ThCr 2 Si 2 structure type (SG I4/mmm) with the lattice parameters: a = b = 4.2218(1) Å, and c = 10.3394(5) Å. The crystal structure of Eu 3 Ag 2 In 9 is comprised of edge-shared hexagonal rings consisting of indium. The one-dimensional chains of In 6 rings are shared through the edges, which are further interconnected with other six-membered rings forming a three-dimensional (3D) stable crystal structure along the bc plane. The crystal structure of EuCu 2 Ge 2 can be explained as the complex [CuGe] (2+δ)- polyanionic network embedded with Eu ions. These polyanionic networks present in the crystal structure of EuCu 2 Ge 2 are shared through the edges of the 011 plane containing Cu and Ge atoms, resulting in a 3D network. The structural relationship between Eu 3 T 2 In 9 and EuCu 2 Ge 2 has been discussed in detail, and we conclude that Eu 3 T 2 In 9 is the metal deficient variant of EuCu 2 Ge 2 . The magnetic susceptibilities of Eu 3 T 2 In 9 (T = Cu and Ag) and EuCu 2 Ge 2 were measured between 2 and 300 K. In all cases, magnetic susceptibility data followed Curie-Weiss law above 150 K. Magnetic moment values obtained from the measurements indicate the probable mixed/intermediate valent behavior of the europium atoms, which was further confirmed by X-ray absorption studies and bond distances around the Eu atoms. Electrical resistivity measurements suggest that Eu 3 T 2 In 9 and EuCu 2 Ge 2 are metallic in nature.

Crystal Structure of an Insect Antifreeze Protein and Its Implications for Ice Binding*

PubMed Central

Hakim, Aaron; Nguyen, Jennifer B.; Basu, Koli; Zhu, Darren F.; Thakral, Durga; Davies, Peter L.; Isaacs, Farren J.; Modis, Yorgo; Meng, Wuyi

2013-01-01

Antifreeze proteins (AFPs) help some organisms resist freezing by binding to ice crystals and inhibiting their growth. The molecular basis for how these proteins recognize and bind ice is not well understood. The longhorn beetle Rhagium inquisitor can supercool to below −25 °C, in part by synthesizing the most potent antifreeze protein studied thus far (RiAFP). We report the crystal structure of the 13-kDa RiAFP, determined at 1.21 Å resolution using direct methods. The structure, which contains 1,914 nonhydrogen protein atoms in the asymmetric unit, is the largest determined ab initio without heavy atoms. It reveals a compressed β-solenoid fold in which the top and bottom sheets are held together by a silk-like interdigitation of short side chains. RiAFP is perhaps the most regular structure yet observed. It is a second independently evolved AFP type in beetles. The two beetle AFPs have in common an extremely flat ice-binding surface comprising regular outward-projecting parallel arrays of threonine residues. The more active, wider RiAFP has four (rather than two) of these arrays between which the crystal structure shows the presence of ice-like waters. Molecular dynamics simulations independently reproduce the locations of these ordered crystallographic waters and predict additional waters that together provide an extensive view of the AFP interaction with ice. By matching several planes of hexagonal ice, these waters may help freeze the AFP to the ice surface, thus providing the molecular basis of ice binding. PMID:23486477

Barium iodide and strontium iodide crystals and scintillators implementing the same

DOEpatents

Payne, Stephen A.; Cherepy, Nerine J.; Hull, Giulia E.; Drobshoff, Alexander D.; Burger, Arnold

2016-11-29

In one embodiment, a material comprises a crystal comprising strontium iodide providing at least 50,000 photons per MeV, where the strontium iodide material is characterized by a volume not less than 1 cm.sup.3. In another embodiment, a scintillator optic includes europium-doped strontium iodide providing at least 50,000 photons per MeV, where the europium in the crystal is primarily Eu.sup.2+, and the europium is present in an amount greater than about 1.6%. A scintillator radiation detector in yet another embodiment includes a scintillator optic comprising SrI.sub.2 and BaI.sub.2, where a ratio of SrI.sub.2 to BaI.sub.2 is in a range of between 0:1 and 1.0, the scintillator optic is a crystal that provides at least 50,000 scintillation photons per MeV and energy resolution of less than about 5% at 662 keV, and the crystal has a volume of 1 cm.sup.3 or more; the scintillator optic contains more than about 2% europium.

Two halide-containing cesium manganese vanadates: synthesis, characterization, and magnetic properties

DOE PAGES

Smith Pellizzeri, Tiffany M.; McGuire, Michael A.; McMillen, Colin D.; ...

2018-01-24

In this study, two new halide-containing cesium manganese vanadates have been synthesized by a high-temperature (580 °C) hydrothermal synthetic method from aqueous brine solutions. One compound, Cs 3Mn(VO 3) 4Cl, (1) was prepared using a mixed cesium hydroxide/chloride mineralizer, and crystallizes in the polar noncentrosymmetric space group Cmm2, with a = 16.7820(8) Å, b = 8.4765(4) Å, c = 5.7867(3) Å. This structure is built from sinusoidal zig-zag (VO 3) n chains that run along the b-axis and are coordinated to Mn 2+ containing (MnO 4Cl) square-pyramidal units that are linked together to form layers. The cesium cations reside betweenmore » the layers, but also coordinate to the chloride ion, forming a cesium chloride chain that also propagates along the b-axis. The other compound, Cs 2Mn(VO 3) 3F, (2) crystallizes in space group Pbca with a = 7.4286(2) Å, b = 15.0175(5) Å, c = 19.6957(7) Å, and was prepared using a cesium fluoride mineralizer. The structure is comprised of corner sharing octahedral Mn 2+ chains, with trans fluoride ligands acting as bridging units, whose ends are capped by (VO 3) n vanadate chains to form slabs. The cesium atoms reside between the manganese vanadate layers, and also play an integral part in the structure, forming a cesium fluoride chain that runs along the b-axis. Both compounds were characterized by single-crystal X-ray diffraction, powder X-ray diffraction, and single-crystal Raman spectroscopy. Additionally, the magnetic properties of 2 were investigated. Lastly, above 50 K, it displays behavior typical of a low dimensional system with antiferromagnetic interactions, as to be expected for linear chains of manganese(II) within the crystal structure.« less

Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

PubMed

Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

2013-11-14

We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

Crystal engineering of novel cocrystals of a triazole drug with 1,4-dicarboxylic acids.

PubMed

Remenar, Julius F; Morissette, Sherry L; Peterson, Matthew L; Moulton, Brian; MacPhee, J Michael; Guzmán, Héctor R; Almarsson, Orn

2003-07-16

Cocrystals of the poorly soluble antifungal drug cis-itraconazole (1) with 1,4-dicarboxylic acids have been prepared. The crystal structure of the succinic acid cocrystal with 1 was determined to be a trimer by single-crystal X-ray. The trimer is comprised of two molecules of 1 oriented in antiparallel fashion to form a pocket with a triazole at either end. The extended succinic acid molecule fills the pocket, bridging the triazole groups through hydrogen-bonding interactions rather than interacting with the more basic piperazine nitrogens. The solubility and dissolution rate of some of the cocrystals are approximately the same as those of the amorphous drug in the commercial formulation and are much higher than those for the crystalline free base. The results suggest that cocrystals of drug molecules have the possibility of achieving the higher oral bioavailability common for amorphous forms of water-insoluble drugs while maintaining the long-term chemical and physical stability that crystal forms provide.

Crystallization and preliminary X-ray diffraction studies of the cysteine protease ervatamin A from Ervatamia coronaria

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

Chakraborty, Sibani; Biswas, Sampa; Chakrabarti, Chandana

2005-06-01

Ervatamin A is a papain-family cysteine protease with high activity and stability. It has been isolated and purified from the latex of the medicinal flowering plant E. coronaria and crystallized by the vapour-diffusion technique. Crystals diffracted to 2.1 Å and the structure was solved by molecular replacement. The ervatamins are highly stable cysteine proteases that are present in the latex of the medicinal plant Ervatamia coronaria and belong to the papain family, members of which share similar amino-acid sequences and also a similar fold comprising two domains. Ervatamin A from this family, a highly active protease compared with others frommore » the same source, has been purified to homogeneity by ion-exchange chromatography and crystallized by the vapour-diffusion method. Needle-shaped crystals of ervatamin A diffract to 2.1 Å resolution and belong to space group C222{sub 1}, with unit-cell parameters a = 31.10, b = 144.17, c = 108.61 Å. The solvent content using an ervatamin A molecular weight of 27.6 kDa is 43.9%, with a V{sub M} value of 2.19 Å{sup 3} Da{sup −1} assuming one protein molecule in the asymmetric unit. A molecular-replacement solution has been found using the structure of ervatamin C as a search model.« less

Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

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

Silvian,L.; Jin, P.; Carmillo, P.

2006-01-01

Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangementmore » characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.« less

How to Switch Off a Histidine Kinase: Crystal Structure of Geobacillus Stearothermophilus KinB with the Inhibitor Sda

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

Bick, M.; Lamour, V; Rajashankar, K

2009-01-01

Entry to sporulation in bacilli is governed by a histidine kinase phosphorelay, a variation of the predominant signal transduction mechanism in prokaryotes. Sda directly inhibits sporulation histidine kinases in response to DNA damage and replication defects. We determined a 2.0-Angstroms-resolution X-ray crystal structure of the intact cytoplasmic catalytic core [comprising the dimerization and histidine phosphotransfer domain (DHp domain), connected to the ATP binding catalytic domain] of the Geobacillus stearothermophilus sporulation kinase KinB complexed with Sda. Structural and biochemical analyses reveal that Sda binds to the base of the DHp domain and prevents molecular transactions with the DHp domain to whichmore » it is bound by acting as a simple molecular barricade. Sda acts to sterically block communication between the catalytic domain and the DHp domain, which is required for autophosphorylation, as well as to sterically block communication between the response regulator Spo0F and the DHp domain, which is required for phosphotransfer and phosphatase activities.« less

Typical intellectual engagement and cognition in old age.

PubMed

Dellenbach, Myriam; Zimprich, Daniel

2008-03-01

Typical Intellectual Engagement (TIE) comprises the preference to engage in cognitively demanding activities and has been proposed as a potential explanatory variable of individual differences in cognitive abilities. Little is known, however, about the factorial structure of TIE, its relations to socio-demographic variables, and its influence on intellectual functioning in old age. In the present study, data of 364 adults (65-81 years) from the Zurich Longitudinal Study on Cognitive Aging (ZULU) were used to investigate the factorial structure of TIE and to examine the hypothesis that TIE is associated more strongly with crystallized intelligence than with fluid intelligence in old age. A measurement model of a second order factor based on a structure of four correlated first order factors (Reading, Problem Solving, Abstract Thinking, and Intellectual Curiosity) evinced an excellent fit. After controlling for age, sex, and formal education, TIE was more strongly associated with crystallized intelligence than with fluid intelligence, comparable to results in younger persons. More detailed analyses showed that this association is mostly defined via Reading and Intellectual Curiosity.

Subwavelength photonic crystal waveguide with trapezoidal shaped dielectric pillars in optical systems

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

Xu, Xiaochuan; Chen, Ray T.

2017-02-07

A method for reducing loss in a subwavelength photonic crystal waveguide bend is disclosed. The method comprising: forming the subwavelength photonic crystal waveguide bend with a series of trapezoidal shaped dielectric pillars centered about a bend radius; wherein each of the trapezoidal shaped dielectric pillars comprise a top width, a bottom width, and a trapezoid height; wherein the length of the bottom width is greater than the length of the top width; and wherein the bottom width is closer to the center of the bend radius of the subwavelength photonic crystal waveguide bend than the top width. Other embodiments aremore » described and claimed.« less

Light trapping in thin film solar cells using textured photonic crystal

DOEpatents

Yi, Yasha [Somerville, MA; Kimerling, Lionel C [Concord, MA; Duan, Xiaoman [Amesbury, MA; Zeng, Lirong [Cambridge, MA

2009-01-27

A solar cell includes a photoactive region that receives light. A photonic crystal is coupled to the photoactive region, wherein the photonic crystal comprises a distributed Bragg reflector (DBR) for trapping the light.

Crystal structure of dipotassium N-carbodi­thio­ato-l-prolinate trihydrate

PubMed Central

2017-01-01

The mol­ecular and crystal structure of the l-proline-derived di­thio­carbamate–carboxyl­ate compound poly[tri-μ-aqua-(μ-2-carboxyl­atopyrrolidine-1-carbodi­thio­ato)dipotassium], [K2(C6H7NO2S2)(H2O)3]n or K2(SSC–NC4H7–COO)·3H2O, has been determined. The di­thio­carbamate moiety displays a unique coordination mode, comprising a ‘side-on’ π-coordinated K+ cation besides a commonly σ-chelated K+ cation. By bridging coordination of the CSS group, COO group and water mol­ecules, the K+ cations are linked into a two-dimensional coordination polymer extending parallel to the ab plane. These layers are again inter­connected by O—H⋯S hydrogen bonds. PMID:28932478

Hybrid bandgap engineering for super-hetero-epitaxial semiconductor materials, and products thereof

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang H. (Inventor); King, Glen C. (Inventor); Elliott, James R. (Inventor)

2012-01-01

"Super-hetero-epitaxial" combinations comprise epitaxial growth of one material on a different material with different crystal structure. Compatible crystal structures may be identified using a "Tri-Unity" system. New bandgap engineering diagrams are provided for each class of combination, based on determination of hybrid lattice constants for the constituent materials in accordance with lattice-matching equations. Using known bandgap figures for previously tested materials, new materials with lattice constants that match desired substrates and have the desired bandgap properties may be formulated by reference to the diagrams and lattice matching equations. In one embodiment, this analysis makes it possible to formulate new super-hetero-epitaxial semiconductor systems, such as systems based on group IV alloys on c-plane LaF.sub.3; group IV alloys on c-plane langasite; Group III-V alloys on c-plane langasite; and group II-VI alloys on c-plane sapphire.

The Role of Connectivity on Electronic Properties of Lead Iodide Perovskite-Derived Compounds

PubMed Central

2017-01-01

We use a layered solution crystal growth method to synthesize high-quality single crystals of two different benzylammonium lead iodide perovskite-like organic/inorganic hybrids. The well-known (C6H5CH2NH3)2PbI4 phase is obtained in the form of bright orange platelets, with a structure comprised of single ⟨100⟩-terminated sheets of corner-sharing PbI6 octahedra separated by bilayers of the organic cations. The presence of water during synthesis leads to formation of a novel minority phase that crystallizes in the form of nearly transparent, light yellow bar-shaped crystals. This phase adopts the monoclinic space group P21/n and incorporates water molecules, with structural formula (C6H5CH2NH3)4Pb5I14·2H2O. The crystal structure consists of ribbons of edge-sharing PbI6 octahedra separated by the organic cations. Density functional theory calculations including spin–orbit coupling show that these edge-sharing PbI6 octahedra cause the band gap to increase with respect to corner-sharing PbI6 octahedra in (C6H5CH2NH3)2PbI4. To gain systematic insight, we model the effect of the connectivity of PbI6 octahedra on the band gap in idealized lead iodide perovskite-derived compounds. We find that increasing the connectivity from corner-, via edge-, to face-sharing causes a significant increase in the band gap. This provides a new mechanism to tailor the optical properties in organic/inorganic hybrid compounds. PMID:28677956

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G

PubMed Central

Stewart-Jones, Guillaume B. E.; Soto, Cinque; Lemmin, Thomas; Chuang, Gwo-Yu; Druz, Aliaksandr; Kong, Rui; Thomas, Paul V.; Wagh, Kshitij; Zhou, Tongqing; Behrens, Anna-Janina; Bylund, Tatsiana; Choi, Chang W.; Davison, Jack R.; Georgiev, Ivelin S.; Joyce, M. Gordon; Do Kwon, Young; Pancera, Marie; Taft, Justin; Yang, Yongping; Zhang, Baoshan; Shivatare, Sachin S.; Shivatare, Vidya S.; Lee, Chang-Chun D.; Wu, Chung-Yi; Bewley, Carole A.; Burton, Dennis R.; Koff, Wayne C.; Connors, Mark; Crispin, Max; Baxa, Ulrich; Korber, Bette T.; Wong, Chi-Huey; Mascola, John R.; Kwong, Peter D.

2017-01-01

The HIV-1-envelope (Env) trimer is covered by a glycan shield of ~90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers imposed by the glycan shield, we crystallized fully glycosylated Env trimers from clades A, B and G, visualizing the shield at 3.4-3.7 Å resolution. These structures reveal the HIV-1-glycan shield to comprise a network of interlocking oligosaccharides, substantially ordered by glycan crowding, which encase the protein component of Env and enable HIV-1 to avoid most antibody-mediated neutralization. The revealed features delineate a taxonomy of N-linked glycan-glycan interactions. Crowded and dispersed glycans are differently ordered, conserved, processed and recognized by antibody. The structures, along with glycan-array binding and molecular dynamics, reveal a diversity in oligosaccharide affinity and a requirement for accommodating glycans amongst known broadly neutralizing antibodies that target the glycan-shielded trimer. PMID:27114034

Quasicrystalline structures and uses thereof

DOEpatents

Steinhardt, Paul Joseph; Chaikin, Paul Michael; Man, Weining

2013-08-13

This invention relates generally to devices constructed from quasicrystalline heterostructures. In preferred embodiments, two or more dielectric materials are arranged in a two- or three-dimensional space in a lattice pattern having at least a five-fold symmetry axis and not a six-fold symmetry axis, such that the quasicrystalline heterostructure exhibits an energy band structure in the space, the band structure having corresponding symmetry, which symmetry is forbidden in crystals, and which band structure comprises a complete band gap. The constructed devices are adapted for manipulating, controlling, modulating, trapping, reflecting and otherwise directing waves including electromagnetic, sound, spin, and surface waves, for a pre-selected range of wavelengths propagating within or through the heterostructure in multiple directions.

Multiple wavelength X-ray monochromators

DOEpatents

Steinmeyer, P.A.

1992-11-17

An improved apparatus and method is provided for separating input x-ray radiation containing first and second x-ray wavelengths into spatially separate first and second output radiation which contain the first and second x-ray wavelengths, respectively. The apparatus includes a crystalline diffractor which includes a first set of parallel crystal planes, where each of the planes is spaced a predetermined first distance from one another. The crystalline diffractor also includes a second set of parallel crystal planes inclined at an angle with respect to the first set of crystal planes where each of the planes of the second set of parallel crystal planes is spaced a predetermined second distance from one another. In one embodiment, the crystalline diffractor is comprised of a single crystal. In a second embodiment, the crystalline diffractor is comprised of a stack of two crystals. In a third embodiment, the crystalline diffractor includes a single crystal that is bent for focusing the separate first and second output x-ray radiation wavelengths into separate focal points. 3 figs.

Multiple wavelength X-ray monochromators

DOEpatents

Steinmeyer, Peter A.

1992-11-17

An improved apparatus and method is provided for separating input x-ray radiation containing first and second x-ray wavelengths into spatially separate first and second output radiation which contain the first and second x-ray wavelengths, respectively. The apparatus includes a crystalline diffractor which includes a first set of parallel crystal planes, where each of the planes is spaced a predetermined first distance from one another. The crystalline diffractor also includes a second set of parallel crystal planes inclined at an angle with respect to the first set of crystal planes where each of the planes of the second set of parallel crystal planes is spaced a predetermined second distance from one another. In one embodiment, the crystalline diffractor is comprised of a single crystal. In a second embodiment, the crystalline diffractor is comprised of a stack of two crystals. In a third embodiment, the crystalline diffractor includes a single crystal that is bent for focussing the separate first and second output x-ray radiation wavelengths into separate focal points.

Nanoamorphous carbon-based photonic crystal infrared emitters

DOEpatents

Norwood, Robert A [Tucson, AZ; Skotheim, Terje [Tucson, AZ

2011-12-13

Provided is a tunable radiation emitting structure comprising: a nanoamorphous carbon structure having a plurality of relief features provided in a periodic spatial configuration, wherein the relief features are separated from each other by adjacent recessed features, and wherein the nanoamorphous carbon comprises a total of from 0 to 60 atomic percent of one or more dopants of the dopant group consisting of: transition metals, lanthanoids, electro-conductive carbides, silicides and nitrides. In one embodiment, a dopant is selected from the group consisting of: Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, La and other lanthanides, Hf, Ta, W, Rh, Os, Ir, Pt, Au, and Hg. In one embodiment, a dopant is selected from the group consisting of: electro-conductive carbides (like Mo.sub.2C), silicides (like MoSi.sub.2) and nitrides (like TiN).

Synthesis and crystal structure of an oxovanadium(IV) complex with a pyrazolone ligand and its use as a heterogeneous catalyst for the oxidation of styrene under mild conditions.

PubMed

Parihar, Sanjay; Pathan, Soyeb; Jadeja, R N; Patel, Anjali; Gupta, Vivek K

2012-01-16

1-Phenyl-3-methyl-4-touloyl-5-pyrazolone (ligand) was synthesized and used to prepare an oxovanadium(IV) complex. The complex was characterized by single-crystal X-ray analysis and various spectroscopic techniques. The single-crystal X-ray analysis of the complex shows that the ligands are coordinated in a syn configuration to each other and create a distorted octahedral environment around the metal ion. A heterogeneous catalyst comprising an oxovanadium(IV) complex and hydrous zirconia was synthesized, characterized by various physicochemical techniques, and successfully used for the solvent-free oxidation of styrene. The influence of the reaction parameters (percent loading, molar ratio of the substrate to H(2)O(2), amount of catalyst, and reaction time) was studied. The catalyst was reused three times without any significant loss in the catalytic activity.

Two tautomeric forms of 2-amino-5,6-dimethylpyrimidin-4-one.

PubMed

Hall, Victoria M; Bertke, Jeffery A; Swift, Jennifer A

2016-06-01

Derivatives of 4-hydroxypyrimidine are an important class of biomolecules. These compounds can undergo keto-enol tautomerization in solution, though a search of the Cambridge Structural Database shows a strong bias toward the 3H-keto tautomer in the solid state. Recrystallization of 2-amino-5,6-dimethyl-4-hydroxypyrimidine, C6H9N3O, from aqueous solution yielded triclinic crystals of the 1H-keto tautomer, denoted form (I). Though not apparent in the X-ray data, the IR spectrum suggests that small amounts of the 4-hydroxy tautomer are also present in the crystal. Monoclinic crystals of form (II), comprised of a 1:1 ratio of both the 1H-keto and the 3H-keto tautomers, were obtained from aqueous solutions containing uric acid. Forms (I) and (II) exhibit one-dimensional and three-dimensional hydrogen-bonding motifs, respectively.

Coarsening Dynamics of Inclusions and Thermocapillary Phenomena in Smectic Liquid Crystal Bubbles

NASA Astrophysics Data System (ADS)

Park, Cheol; Maclennan, Joseph; Glaser, Matthew; Clark, Noel; Trittel, Torsten; Eremin, Alexey; Stannarius, Ralf; Tin, Padetha; Hall, Nancy

The Observation and Analysis of Smectic Islands in Space (OASIS) project comprises a series of experiments that probe interfacial and hydrodynamic behavior of thin spherical-bubbles of smectic liquid crystal in microgravity. Smectic films are the thinnest known stable condensed phase structures, making them ideal for studies of two-dimensional (2D) coarsening dynamics and thermocapillary phenomena in microgravity. The OASIS flight hardware was launched on SpaceX-6 in April 2015 and experiments were carried out on the International Space Station using four different smectic A and C liquid crystal materials in separate sample chambers. We will describe the behavior of collective island dynamics on the bubbles, including temperature gradient-induced themomigration, and the diffusion and coalescence-driven coarsening dynamics of island emulsions in microgravity. This work was supported by NASA Grant No. NNX-13AQ81G, and NSF MRSEC Grants No. DMR-0820579 and DMR-1420736.

Continuum Multiscale Modeling of Finite Deformation Plasticity and Anisotropic Damage in Polycrystals

DTIC Science & Technology

2006-09-01

also been applied to describe degraded composite materials exhibiting a nominally elastic or viscoelastic response [7]. In brittle ceramics, scalar...assumptions regarding the composition of the material (e.g., crystal structure). 2.2. Stresses and balance relations Let s denote the local nominal...nickel (50 wt.%), iron (25 wt.%), and tungsten (25 wt.%). The composite microstructure nominally is comprised of 90% pure W and 10% matrix alloy, and

Materials and methods for the preparation of nanocomposites

DOEpatents

Nag, Angshuman; Talapin, Dmitri V.

2018-01-30

Disclosed herein is an isolable colloidal particle comprising a nanoparticle and an inorganic capping agent bound to the surface of the nanoparticle, a method for making the same in a biphasic solvent mixture, and the formation of structures and solids from the isolable colloidal particle. The process can yield photovoltaic cells, piezoelectric crystals, thermoelectric layers, optoelectronic layers, light emitting diodes, ferroelectric layers, thin film transistors, floating gate memory devices, phase change layers, and sensor devices.

Direct evidence of a multicentre halogen bond: unexpected contraction of the P-XXX-P fragment in triphenylphosphine dihalides.

PubMed

Nikitin, Kirill; Müller-Bunz, Helge; Gilheany, Declan

2013-02-18

Triphenylhalophosphonium halides, Ph(3)PX(2), form crystals comprising bridged linear cations [Ph(3)P-X-X-X-PPh(3)](+) where the X(3) bridge is shortened from 6.56 Å in Cl-Cl-Cl to 6.37 Å in the Br-Br-Br system. It is proposed that this structure is stabilised by five-centre/six-electron (5c-6e) hypervalent interactions.

The Crystal Structure of the Intact E. coli RelBE Toxin-Antitoxin Complex Provides the Structural Basis for Conditional Cooperativity

PubMed Central

Bøggild, Andreas; Sofos, Nicholas; Andersen, Kasper R.; Feddersen, Ane; Easter, Ashley D.; Passmore, Lori A.; Brodersen, Ditlev E.

2012-01-01

Summary The bacterial relBE locus encodes a toxin-antitoxin complex in which the toxin, RelE, is capable of cleaving mRNA in the ribosomal A site cotranslationally. The antitoxin, RelB, both binds and inhibits RelE, and regulates transcription through operator binding and conditional cooperativity controlled by RelE. Here, we present the crystal structure of the intact Escherichia coli RelB2E2 complex at 2.8 Å resolution, comprising both the RelB-inhibited RelE and the RelB dimerization domain that binds DNA. RelE and RelB associate into a V-shaped heterotetrameric complex with the ribbon-helix-helix (RHH) dimerization domain at the apex. Our structure supports a model in which relO is optimally bound by two adjacent RelB2E heterotrimeric units, and is not compatible with concomitant binding of two RelB2E2 heterotetramers. The results thus provide a firm basis for understanding the model of conditional cooperativity at the molecular level. PMID:22981948

Bioactive Glass-Ceramic Scaffolds from Novel ‘Inorganic Gel Casting’ and Sinter-Crystallization

PubMed Central

Elsayed, Hamada; Rincón Romero, Acacio; Ferroni, Letizia; Gardin, Chiara; Zavan, Barbara; Bernardo, Enrico

2017-01-01

Highly porous wollastonite-diopside glass-ceramics have been successfully obtained by a new gel-casting technique. The gelation of an aqueous slurry of glass powders was not achieved according to the polymerization of an organic monomer, but as the result of alkali activation. The alkali activation of a Ca-Mg silicate glass (with a composition close to 50 mol % wollastonite—50 mol % diopside, with minor amounts of Na2O and P2O5) allowed for the obtainment of well-dispersed concentrated suspensions, undergoing progressive hardening by curing at low temperature (40 °C), owing to the formation of a C–S–H (calcium silicate hydrate) gel. An extensive direct foaming was achieved by vigorous mechanical stirring of partially gelified suspensions, comprising also a surfactant. The open-celled structure resulting from mechanical foaming could be ‘frozen’ by the subsequent sintering treatment, at 900–1000 °C, causing substantial crystallization. A total porosity exceeding 80%, comprising both well-interconnected macro-pores and micro-pores on cell walls, was accompanied by an excellent compressive strength, even above 5 MPa. PMID:28772531

Partial oxidation catalyst

DOEpatents

Krumpelt, Michael; Ahmed, Shabbir; Kumar, Romesh; Doshi, Rajiv

2000-01-01

A two-part catalyst comprising a dehydrogenation portion and an oxide-ion conducting portion. The dehydrogenation portion is a group VIII metal and the oxide-ion conducting portion is selected from a ceramic oxide crystallizing in the fluorite or perovskite structure. There is also disclosed a method of forming a hydrogen rich gas from a source of hydrocarbon fuel in which the hydrocarbon fuel contacts a two-part catalyst comprising a dehydrogenation portion and an oxide-ion conducting portion at a temperature not less than about 400.degree. C. for a time sufficient to generate the hydrogen rich gas while maintaining CO content less than about 5 volume percent. There is also disclosed a method of forming partially oxidized hydrocarbons from ethanes in which ethane gas contacts a two-part catalyst comprising a dehydrogenation portion and an oxide-ion conducting portion for a time and at a temperature sufficient to form an oxide.

Conformational Changes and Substrate Recognition in Pseudomonas aeruginosa d-Arginine Dehydrogenase

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

Fu, Guoxing; Yuan, Hongling; Li, Congran

2010-11-15

DADH catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding {alpha}-keto acids and ammonia. Here we report the first X-ray crystal structures of DADH at 1.06 {angstrom} resolution and its complexes with iminoarginine (DADH{sub red}/iminoarginine) and iminohistidine (DADH{sub red}/iminohistidine) at 1.30 {angstrom} resolution. The DADH crystal structure comprises an unliganded conformation and a product-bound conformation, which is almost identical to the DADH{sub red}/iminoarginine crystal structure. The active site of DADH was partially occupied with iminoarginine product (30% occupancy) that interacts with Tyr53 in the minor conformation of a surface loop. This flexible loop forms an 'active site lid',more » similar to those seen in other enzymes, and may play an essential role in substrate recognition. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In the structure of DADH in complex with iminohistidine, two alternate conformations were observed for iminohistidine where the imidazole groups formed hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000-fold difference in k{sub cat}/K{sub m} values for D-arginine and D-histidine. Comparison of the kinetic data for the activity of DADH on different D-amino acids and the crystal structures in complex with iminoarginine and iminohistidine establishes that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity.« less

Method for reducing energy losses in laser crystals

DOEpatents

Atherton, L.J.; DeYoreo, J.J.; Roberts, D.H.

1992-03-24

A process for reducing energy losses in crystals is disclosed which comprises: a. heating a crystal to a temperature sufficiently high as to cause dissolution of microscopic inclusions into the crystal, thereby converting said inclusions into point-defects, and b. maintaining said crystal at a given temperature for a period of time sufficient to cause said point-defects to diffuse out of said crystal. Also disclosed are crystals treated by the process, and lasers utilizing the crystals as a source of light. 12 figs.

Method for reducing energy losses in laser crystals

DOEpatents

Atherton, L. Jeffrey; DeYoreo, James J.; Roberts, David H.

1992-01-01

A process for reducing energy losses in crystals is disclosed which comprises: a. heating a crystal to a temperature sufficiently high as to cause dissolution of microscopic inclusions into the crystal, thereby converting said inclusions into point-defects, and b. maintaining said crystal at a given temperature for a period of time sufficient to cause said point-defects to diffuse out of said crystal. Also disclosed are crystals treated by the process, and lasers utilizing the crystals as a source of light.

Crystal growth and annealing for minimized residual stress

DOEpatents

Gianoulakis, Steven E.

2002-01-01

A method and apparatus for producing crystals that minimizes birefringence even at large crystal sizes, and is suitable for production of CaF.sub.2 crystals. The method of the present invention comprises annealing a crystal by maintaining a minimal temperature gradient in the crystal while slowly reducing the bulk temperature of the crystal. An apparatus according to the present invention includes a thermal control system added to a crystal growth and annealing apparatus, wherein the thermal control system allows a temperature gradient during crystal growth but minimizes the temperature gradient during crystal annealing.

Extruded ceramic honeycomb and method

DOEpatents

Day, J. Paul

1995-04-04

Extruded low-expansion ceramic honeycombs comprising beta-spodumene solid solution as the principal crystal phase and with less than 7 weight percent of included mullite are produced by compounding an extrusion batch comprising a lithium aluminosilicate glass powder and a clay additive, extruding a green honeycomb body from the batch, and drying and firing the green extruded cellular honeycomb to crystallize the glass and clay into a low-expansion spodumene ceramic honeycomb body.

Compact programmable photonic variable delay devices

NASA Technical Reports Server (NTRS)

Yao, X. Steve (Inventor)

1999-01-01

Optical variable delay devices for providing variable true time delay to multiple optical beams simultaneously. A ladder-structured variable delay device comprises multiple basic building blocks stacked on top of each other resembling a ladder. Each basic building block has two polarization beamsplitters and a polarization rotator array arranged to form a trihedron; Controlling an array element of the polarization rotator array causes a beam passing through the array element either going up to a basic building block above it or reflect back towards a block below it. The beams going higher on the ladder experience longer optical path delay. An index-switched optical variable delay device comprises of many birefringent crystal segments connected with one another, with a polarization rotator array sandwiched between any two adjacent crystal segments. An array element in the polarization rotator array controls the polarization state of a beam passing through the element, causing the beam experience different refractive indices or path delays in the following crystal segment. By independently control each element in each polarization rotator array, variable optical path delays of each beam can be achieved. Finally, an index-switched variable delay device and a ladder-structured variable device are cascaded to form a new device which combines the advantages of the two individual devices. This programmable optic device has the properties of high packing density, low loss, easy fabrication, and virtually infinite bandwidth. The device is inherently two dimensional and has a packing density exceeding 25 lines/cm.sup.2. The delay resolution of the device is on the order of a femtosecond (one micron in space) and the total delay exceeds 10 nanosecond. In addition, the delay is reversible so that the same delay device can be used for both antenna transmitting and receiving.

Photonic variable delay devices based on optical birefringence

NASA Technical Reports Server (NTRS)

Yao, X. Steve (Inventor)

2005-01-01

Optical variable delay devices for providing variable true time delay to multiple optical beams simultaneously. A ladder-structured variable delay device comprises multiple basic building blocks stacked on top of each other resembling a ladder. Each basic building block has two polarization beamsplitters and a polarization rotator array arranged to form a trihedron; Controlling an array element of the polarization rotator array causes a beam passing through the array element either going up to a basic building block above it or reflect back towards a block below it. The beams going higher on the ladder experience longer optical path delay. An index-switched optical variable delay device comprises of many birefringent crystal segments connected with one another, with a polarization rotator array sandwiched between any two adjacent crystal segments. An array element in the polarization rotator array controls the polarization state of a beam passing through the element, causing the beam experience different refractive indices or path delays in the following crystal segment. By independently control each element in each polarization rotator array, variable optical path delays of each beam can be achieved. Finally, an index-switched variable delay device and a ladder-structured variable device are cascaded to form a new device which combines the advantages of the two individual devices. This programmable optic device has the properties of high packing density, low loss, easy fabrication, and virtually infinite bandwidth. The device is inherently two dimensional and has a packing density exceeding 25 lines/cm2. The delay resolution of the device is on the order of a femtosecond (one micron in space) and the total delay exceeds 10 nanosecond. In addition, the delay is reversible so that the same delay device can be used for both antenna transmitting and receiving.

The image-forming mirror in the eye of the scallop

NASA Astrophysics Data System (ADS)

Palmer, Benjamin A.; Taylor, Gavin J.; Brumfeld, Vlad; Gur, Dvir; Shemesh, Michal; Elad, Nadav; Osherov, Aya; Oron, Dan; Weiner, Steve; Addadi, Lia

2017-12-01

Scallops possess a visual system comprising up to 200 eyes, each containing a concave mirror rather than a lens to focus light. The hierarchical organization of the multilayered mirror is controlled for image formation, from the component guanine crystals at the nanoscale to the complex three-dimensional morphology at the millimeter level. The layered structure of the mirror is tuned to reflect the wavelengths of light penetrating the scallop’s habitat and is tiled with a mosaic of square guanine crystals, which reduces optical aberrations. The mirror forms images on a double-layered retina used for separately imaging the peripheral and central fields of view. The tiled, off-axis mirror of the scallop eye bears a striking resemblance to the segmented mirrors of reflecting telescopes.

Apparatus for mounting crystal

DOEpatents

Longeway, Paul A.

1985-01-01

A thickness monitor useful in deposition or etching reactor systems comprising a crystal-controlled oscillator in which the crystal is deposited or etched to change the frequency of the oscillator. The crystal rests within a thermally conductive metallic housing and arranged to be temperature controlled. Electrode contacts are made to the surface primarily by gravity force such that the crystal is substantially free of stress otherwise induced by high temperature.

Methods for synthesizing microporous crystals and microporous crystal membranes

DOEpatents

Dutta, Prabir; Severance, Michael; Sun, Chenhu

2017-02-07

A method of making a microporous crystal material, comprising: a. forming a mixture comprising NaOH, water, and one or more of an aluminum source, a silicon source, and a phosphate source, whereupon the mixture forms a gel; b. heating the gel for a first time period, whereupon a first volume of water is removed from the gel and micoroporous crystal nuclei form, the nuclei having a framework; and c.(if a membrane is to be formed) applying the gel to a solid support seeded with microporous crystals having a framework that is the same as the framework of the nuclei; d. heating the gel for a second time period. during which a second volume of water is added to the gel; wherein the rate of addition of the second volume of water is between about 0.5 and about 2.0 fold the rate of removal of the first volume of water.

Means of determining extrusion temperatures

DOEpatents

McDonald, Robert E.; Canonico, Domenic A.

1977-01-01

In an extrusion process comprising the steps of fabricating a metal billet, heating said billet for a predetermined time and at a selected temperature to increase its plasticity and then forcing said heated billet through a small orifice to produce a desired extruded object, the improvement comprising the steps of randomly inserting a plurality of small metallic thermal tabs at different cross sectional depths in said billet as a part of said fabricating step, and examining said extruded object at each thermal tab location for determining the crystal structure at each extruded thermal tab thus revealing the maximum temperature reached during extrusion in each respective tab location section of the extruded object, whereby the thermal profile of said extruded object during extrusion may be determined.

Hollow nanoparticle cathode materials for sodium electrochemical cells and batteries

DOEpatents

Shevchenko, Elena; Rajh, Tijana; Johnson, Christopher S.; Koo, Bonil

2016-07-12

A cathode comprises, in its discharged state, a layer of hollow .gamma.-Fe.sub.2O.sub.3 nanoparticles disposed between two layers of carbon nanotubes, and preferably including a metallic current collector in contact with one of the layers of carbon nanotubes. Individual particles of the hollow .gamma.-Fe.sub.2O.sub.3 nanoparticles comprise a crystalline shell of .gamma.-Fe.sub.2O.sub.3 including cation vacancies within the crystal structure of the shell (i.e., iron vacancies of anywhere between 3% to 90%, and preferably 44 to 77% of available octahedral iron sites). Sodium ions are intercalated within at least some of the cation vacancies within the crystalline shell of the hollow .gamma.-Fe.sub.2O.sub.3 nanoparticles.

An Overview of NASA Biotechnology

NASA Technical Reports Server (NTRS)

Pusey, Marc L.

1997-01-01

Biotechnology research at NASA has comprised three separate areas; cell science and tissue culture, separations methods, and macromolecular crystal growth. This presentation will primarily focus on the macromolecular crystal growth.

SEPARATION OF TIN FROM ALLOYS

DOEpatents

Kattner, W.T.

1959-08-11

A process is described for recovering tin from bronze comprising melting the bronze; slowly cooling the melted metal to from 280 to 240 deg C whereby eta- phase bronze crystallizes; separating the eta-bronze crystals from the liquid metal by mechanical means; melting the separated crystals; slowly cooling the melted eta-crystals to a temperature from 520 to 420 deg C whereby crystals of epsilonbronze precipitate; removing said epsilon-crystals from the remaining molten metal; and reintroducing the remaining molten metal into the process for eta-crystallization.

Empirically testing vaterite structural models using neutron diffraction and thermal analysis

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

Chakoumakos, Bryan C.; Pracheil, Brenda M.; Koenigs, Ryan

Otoliths, calcium carbonate (CaCO 3) ear bones, are among the most commonly used age and growth structures of fishes. Most fish otoliths are comprised of the most dense CaCO 3 polymorph, aragonite. Sturgeon otoliths, in contrast, have been characterized as the rare and structurally enigmatic polymorph, vaterite a metastable polymorph of CaCO 3. Vaterite is an important material ranging from biomedical to personal care applications although its crystal structure is highly debated. We characterized the structure of sturgeon otoliths using thermal analysis and neutron powder diffraction, which is used non-destructively. We confirmed that while sturgeon otoliths are primarily composed ofmore » vaterite, they also contain the denser CaCO 3 polymorph, calcite. For the vaterite fraction, neutron diffraction data provide enhanced discrimination of the carbonate group compared to x-ray diffraction data, owing to the different relative neutron scattering lengths, and thus offer the opportunity to uniquely test the more than one dozen crystal structural models that have been proposed for vaterite. Of those, space group P6 522 model, a = 7.1443(4)Å , c = 25.350(4)Å , V = 1121.5(2)Å 3 provides the best fit to the neutron powder diffraction data, and allows for a structure refinement using rigid carbonate groups.« less

Empirically testing vaterite structural models using neutron diffraction and thermal analysis

DOE PAGES

Chakoumakos, Bryan C.; Pracheil, Brenda M.; Koenigs, Ryan; ...

2016-11-18

Otoliths, calcium carbonate (CaCO 3) ear bones, are among the most commonly used age and growth structures of fishes. Most fish otoliths are comprised of the most dense CaCO 3 polymorph, aragonite. Sturgeon otoliths, in contrast, have been characterized as the rare and structurally enigmatic polymorph, vaterite a metastable polymorph of CaCO 3. Vaterite is an important material ranging from biomedical to personal care applications although its crystal structure is highly debated. We characterized the structure of sturgeon otoliths using thermal analysis and neutron powder diffraction, which is used non-destructively. We confirmed that while sturgeon otoliths are primarily composed ofmore » vaterite, they also contain the denser CaCO 3 polymorph, calcite. For the vaterite fraction, neutron diffraction data provide enhanced discrimination of the carbonate group compared to x-ray diffraction data, owing to the different relative neutron scattering lengths, and thus offer the opportunity to uniquely test the more than one dozen crystal structural models that have been proposed for vaterite. Of those, space group P6 522 model, a = 7.1443(4)Å , c = 25.350(4)Å , V = 1121.5(2)Å 3 provides the best fit to the neutron powder diffraction data, and allows for a structure refinement using rigid carbonate groups.« less

Crystal structure of N-de­acetyl­lappa­coni­tine

PubMed Central

Shi, Xin-Wei; Lu, Qiang-Qiang; Zhou, Jun-Hui; Cui, Xin-Ai

2015-01-01

The title compound, C30H42N2O7 [systematic name: (1S,4S,5S,7S,8S,9S,10S,11S,13R,14S,16S,17R)-20-ethyl-4,8,9-trihy­droxy-1,14,16-tri­meth­oxy­aconitan-4-yl 2-amino­benzoate], isolated from roots of Aconitum sinomontanum Nakai, is a typical aconitane-type C19-diterpenoid alkaloid, which crystallizes with two independent mol­ecules in the asymmetric unit. The conformations of the two independent mol­ecules are closely similar. Each mol­ecule comprises four six-membered rings (A, B, D and E) including one six-membered N-containing heterocyclic ring (E), and two five-membered rings (C and F). Rings A, B and E adopt chair conformations, while ring D displays a boat conformation. Five-membered rings C and F exhibit envelope conformations. IntramolecularN—H⋯O hydrogen bonds between the amino group and carbonyl O atom help to stabilize molecular structure. In the crystal, O—H⋯O hydrogen bonds link the mol­ecules into zigzag chains propagating in [010]. PMID:26396805

Purification, crystallization and preliminary X-ray analysis of Enterococcus faecium aminoglycoside-2′′-phosphotransferase-Ib [APH(2′′)-Ib

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

Walanj, Rupa; Young, Paul; Baker, Heather M.

2005-04-01

APH(2′′)-Ib is an enzyme responsible for high-level gentamicin resistance in E. faecium isolates. Native crystals of this enzyme have been prepared and preliminary X-ray diffraction experiments have been undertaken. Bacterial resistance to the aminoglycoside antibiotics is primarily the result of deactivation of the drugs. Three families of enzymes are responsible for this activity, with one such family being the aminoglycoside phosphotransferases (APHs). The gene encoding one of these enzymes, APH(2′′)-Ib, has been cloned and the protein (comprising 299 amino-acid residues) expressed in Escherichia coli, purified and crystallized in the presence of 16%(w/v) PEG 3350 and gentamicin. The crystals belong tomore » the monoclinic space group P2{sub 1}, with approximate unit-cell parameters a = 79.7, b = 58.8, c = 81.4 Å, β = 98.4°, and preliminary X-ray diffraction analysis is consistent with the presence of two molecules in the asymmetric unit. Synchrotron diffraction data to approximately 2.65 Å resolution were collected from a native APH(2′′)-Ib crystal at beamline BL9-2 at SSRL (Stanford, CA, USA). Selenium-substituted crystals have also been produced and structure determination is proceeding.« less

Realization of atomistic transitions with colloidal nanoparticles using an ultrafast laser

NASA Astrophysics Data System (ADS)

Akguc, Gursoy; Ilday, Serim; Ilday, Omer; Gulseren, Oguz; Makey, Ghaith; Yavuz, Koray

We report on realization of rapid atomistic transitions with colloidal nanoparticles in a setting that constitutes a dissipative far-from-equilibrium system subject to stochastic forces. Large colloidal crystals (comprising hundreds of particles) can be formed and transitions between solid-liquid-gas phases can be observed effortlessly and within seconds. Furthermore, this system allows us to form and dynamically arrest metastable phases such as glassy structures and to controllably transform a crystal pattern from square to hexagonal lattices and vice versa as well as to observe formation and propagation of crystal defects (i.e. line defects, point defects, planar defects). The mechanism largely relies on an interplay between convective forces induced by femtosecond pulses and strong Brownian motion; the former drags the colloids to form and reinforce the crystal and the latter is analogous to lattice vibrations, which makes it possible to observe phase transitions, defect formation and propagation and lattice transformation. This unique system can help us get insight into the mechanisms underlying various solid state phenomena that were previously studied under slowly evolving (within hours/days), near-equilibrium colloidal systems.

Structural Studies of the Tandem Tudor Domains of Fragile X Mental Retardation Related Proteins FXR1 and FXR2

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

Adams-Cioaba, Melanie A.; Guo, Yahong; Bian, ChuanBing

Expansion of the CGG trinucleotide repeat in the 5'-untranslated region of the FMR1, fragile X mental retardation 1, gene results in suppression of protein expression for this gene and is the underlying cause of Fragile X syndrome. In unaffected individuals, the FMRP protein, together with two additional paralogues (Fragile X Mental Retardation Syndrome-related Protein 1 and 2), associates with mRNA to form a ribonucleoprotein complex in the nucleus that is transported to dendrites and spines of neuronal cells. It is thought that the fragile X family of proteins contributes to the regulation of protein synthesis at sites where mRNAs aremore » locally translated in response to stimuli. Here, we report the X-ray crystal structures of the non-canonical nuclear localization signals of the FXR1 and FXR2 autosomal paralogues of FMRP, which were determined at 2.50 and 1.92 {angstrom}, respectively. The nuclear localization signals of the FXR1 and FXR2 comprise tandem Tudor domain architectures, closely resembling that of UHRF1, which is proposed to bind methylated histone H3K9. The FMRP, FXR1 and FXR2 proteins comprise a small family of highly conserved proteins that appear to be important in translational regulation, particularly in neuronal cells. The crystal structures of the N-terminal tandem Tudor domains of FXR1 and FXR2 revealed a conserved architecture with that of FMRP. Biochemical analysis of the tandem Tudor doamins reveals their ability to preferentially recognize trimethylated peptides in a sequence-specific manner.« less

Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p

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

Miller, Matthew T.; Higgin, Joshua J.; Hall, Traci M.Tanaka

2008-06-06

Pumilio/FBF (PUF) family proteins are found in eukaryotic organisms and regulate gene expression post-transcriptionally by binding to sequences in the 3' untranslated region of target transcripts. PUF proteins contain an RNA binding domain that typically comprises eight {alpha}-helical repeats, each of which recognizes one RNA base. Some PUF proteins, including yeast Puf4p, have altered RNA binding specificity and use their eight repeats to bind to RNA sequences with nine or ten bases. Here we report the crystal structures of Puf4p alone and in complex with a 9-nucleotide (nt) target RNA sequence, revealing that Puf4p accommodates an 'extra' nucleotide by modestmore » adaptations allowing one base to be turned away from the RNA binding surface. Using structural information and sequence comparisons, we created a mutant Puf4p protein that preferentially binds to an 8-nt target RNA sequence over a 9-nt sequence and restores binding of each protein repeat to one RNA base.« less

Highly Luminescent 2D-Type Slab Crystals Based on a Molecular Charge-Transfer Complex as Promising Organic Light-Emitting Transistor Materials.

PubMed

Park, Sang Kyu; Kim, Jin Hong; Ohto, Tatsuhiko; Yamada, Ryo; Jones, Andrew O F; Whang, Dong Ryeol; Cho, Illhun; Oh, Sangyoon; Hong, Seung Hwa; Kwon, Ji Eon; Kim, Jong H; Olivier, Yoann; Fischer, Roland; Resel, Roland; Gierschner, Johannes; Tada, Hirokazu; Park, Soo Young

2017-09-01

A new 2:1 donor (D):acceptor (A) mixed-stacked charge-transfer (CT) cocrystal comprising isometrically structured dicyanodistyrylbenzene-based D and A molecules is designed and synthesized. Uniform 2D-type morphology is manifested by the exquisite interplay of intermolecular interactions. In addition to its appealing structural features, unique optoelectronic properties are unveiled. Exceptionally high photoluminescence quantum yield (Φ F ≈ 60%) is realized by non-negligible oscillator strength of the S 1 transition, and rigidified 2D-type structure. Moreover, this luminescent 2D-type CT crystal exhibits balanced ambipolar transport (µ h and µ e of ≈10 -4 cm 2 V -1 s -1 ). As a consequence of such unique optoelectronic characteristics, the first CT electroluminescence is demonstrated in a single active-layered organic light-emitting transistor (OLET) device. The external quantum efficiency of this OLET is as high as 1.5% to suggest a promising potential of luminescent mixed-stacked CT cocrystals in OLET applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Production of crystalline refractory metal oxides containing colloidal metal precipitates and useful as solar-effective absorbers

DOEpatents

Narayan, Jagdish; Chen, Yok

1983-01-01

This invention is a new process for producing refractory crystalline oxides having improved or unusual properties. The process comprises the steps of forming a doped-metal crystal of the oxide; exposing the doped crystal in a bomb to a reducing atmosphere at superatmospheric pressure and a temperature effecting precipitation of the dopant metal in the crystal lattice of the oxide but insufficient to effect net diffusion of the metal out of the lattice; and then cooling the crystal. Preferably, the cooling step is effected by quenching. The process forms colloidal precipitates of the metal in the oxide lattice. The process may be used, for example, to produce thermally stable black MgO crystalline bodies containing magnetic colloidal precipitates consisting of about 99% Ni. The Ni-containing bodies are solar-selective absorbers, having a room-temperature absorptivity of about 0.96 over virtually all of the solar-energy spectrum and exhibiting an absorption edge in the region of 2 .mu.m. The process parameters can be varied to control the average size of the precipitates. The process can produce a black MgO crystalline body containing colloidal Ni precipitates, some of which have the face-centered-cubic structure and others of which have the body-centered cubic structure. The products of the process are metal-precipitate-containing refractory crystalline oxides which have improved or unique optical, mechanical, magnetic, and/or electronic properties.

Materials and methods for the preparation of nanocomposites

DOEpatents

Talapin, Dmitri V.; Kovalenko, Maksym V.; Lee, Jong-Soo; Jiang, Chengyang

2016-05-24

Disclosed herein is an isolable colloidal particle comprising a nanoparticle and an inorganic capping agent bound to the surface of the nanoparticle, a solution of the same, a method for making the same from a biphasic solvent mixture, and the formation of structures and solids from the isolable colloidal particle. The process can yield photovoltaic cells, piezoelectric crystals, thermoelectric layers, optoelectronic layers, light emitting diodes, ferroelectric layers, thin film transistors, floating gate memory devices, imaging devices, phase change layers, and sensor devices.

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G.

PubMed

Stewart-Jones, Guillaume B E; Soto, Cinque; Lemmin, Thomas; Chuang, Gwo-Yu; Druz, Aliaksandr; Kong, Rui; Thomas, Paul V; Wagh, Kshitij; Zhou, Tongqing; Behrens, Anna-Janina; Bylund, Tatsiana; Choi, Chang W; Davison, Jack R; Georgiev, Ivelin S; Joyce, M Gordon; Kwon, Young Do; Pancera, Marie; Taft, Justin; Yang, Yongping; Zhang, Baoshan; Shivatare, Sachin S; Shivatare, Vidya S; Lee, Chang-Chun D; Wu, Chung-Yi; Bewley, Carole A; Burton, Dennis R; Koff, Wayne C; Connors, Mark; Crispin, Max; Baxa, Ulrich; Korber, Bette T; Wong, Chi-Huey; Mascola, John R; Kwong, Peter D

2016-05-05

The HIV-1-envelope (Env) trimer is covered by a glycan shield of ∼90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers imposed by the glycan shield, we crystallized fully glycosylated Env trimers from clades A, B, and G, visualizing the shield at 3.4-3.7 Å resolution. These structures reveal the HIV-1-glycan shield to comprise a network of interlocking oligosaccharides, substantially ordered by glycan crowding, that encase the protein component of Env and enable HIV-1 to avoid most antibody-mediated neutralization. The revealed features delineate a taxonomy of N-linked glycan-glycan interactions. Crowded and dispersed glycans are differently ordered, conserved, processed, and recognized by antibody. The structures, along with glycan-array binding and molecular dynamics, reveal a diversity in oligosaccharide affinity and a requirement for accommodating glycans among known broadly neutralizing antibodies that target the glycan-shielded trimer. Copyright © 2016 Elsevier Inc. All rights reserved.

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al6Pd

PubMed Central

Pauling, Linus

1989-01-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al6Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 Å, b = 37.6 Å, and c = 33.24 Å, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction. Images PMID:16594092

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al(6)Pd.

PubMed

Pauling, L

1989-12-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al(6)Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 A, b = 37.6 A, and c = 33.24 A, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction.

Tuning polymorphism and orientation in organic semiconductor thin films via post-deposition processing.

PubMed

Hiszpanski, Anna M; Baur, Robin M; Kim, Bumjung; Tremblay, Noah J; Nuckolls, Colin; Woll, Arthur R; Loo, Yueh-Lin

2014-11-05

Though both the crystal structure and molecular orientation of organic semiconductors are known to impact charge transport in thin-film devices, separately accessing different polymorphs and varying the out-of-plane molecular orientation is challenging, typically requiring stringent control over film deposition conditions, film thickness, and substrate chemistry. Here we demonstrate independent tuning of the crystalline polymorph and molecular orientation in thin films of contorted hexabenzocoronene, c-HBC, during post-deposition processing without the need to adjust deposition conditions. Three polymorphs are observed, two of which have not been previously reported. Using our ability to independently tune the crystal structure and out-of-plane molecular orientation in thin films of c-HBC, we have decoupled and evaluated the effects that molecular packing and orientation have on device performance in thin-film transistors (TFTs). In the case of TFTs comprising c-HBC, polymorphism and molecular orientation are equally important; independently changing either one affects the field-effect mobility by an order of magnitude.

Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser

DOE PAGES

Popp, David; Loh, N. Duane; Zorgati, Habiba; ...

2017-06-02

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments ( Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determinemore » that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.« less

Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser

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

Popp, David; Loh, N. Duane; Zorgati, Habiba

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments ( Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determinemore » that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.« less

Crystal structure of di-μ-chlorido-bis-(chlorido-{N1,N1-diethyl-N4-[(pyridin-2-yl-κN)methyl-idene]benzene-1,4-di-amine-κN4}mercury(II)).

PubMed

Faizi, Md Serajul Haque; Dege, Necmi; Goleva, Kateryna

2017-06-01

The title dinuclear mercury(II) complex, [Hg 2 Cl 4 (C 16 H 19 N 3 ) 2 ], synthesized from the pyridine-derived Schiff base ( E )- N 1 , N 1 -diethyl- N 4 -[(pyridin-2-yl)methyl-idene]benzene-1,4-di-amine (DPMBD), has inversion symmetry. The five-coordinated Hg II atoms have distorted square-pyramidal stereochemistry comprising two N-atom donors from bidentate chelate BPMBD ligands and three Cl-atom donors, two bridging and one monodentate. The dihedral angle between the benzene and the pyridine rings in the BPMBD ligand is 7.55 (4)°. In the crystal, the dinuclear mol-ecules are linked by weak C-H⋯Cl hydrogen bonds, forming zigzag ribbons lying parallel to [001]. Also present in the structure are π-π inter-actions between benzene and pyridine rings [minimum ring-centroid separation = 3.698 (8) Å].

Square array photonic crystal fiber-based surface plasmon resonance refractive index sensor

NASA Astrophysics Data System (ADS)

Liu, Min; Yang, Xu; Zhao, Bingyue; Hou, Jingyun; Shum, Ping

2017-12-01

Based on surface plasmon resonance (SPR), a novel refractive index (RI) sensor comprising a square photonic crystal fiber (PCF) is proposed to realize the detection of the annular analyte. Instead of hexagon structure, four large air-holes in a square array are introduced to enhance the sensitivity by allowing two polarization directions of the core mode to be more sensitive. The gold is used as the only plasmonic material. The design purpose is to reduce the difficulty in gold deposition and enhance the RI sensitivity. The guiding properties and the effects of the parameters on the performance of the sensor are numerically investigated by the Finite Element Method (FEM). By optimizing the structure, the sensor can exhibit remarkable sensitivity up to 7250 nm/RIU and resolution of 1.0638 × 10-5 RIU with only one plasmonic material, which is very competitive compared with the other reported externally coated and single-layer coated PCF-based SPR (PCF-SPR) sensors, to our best knowledge.

Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold.

PubMed

Feliciano, Patricia R; Drennan, Catherine L; Nonato, M Cristina

2016-08-30

Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster. Our 2.05 Å resolution data further reveal a dimeric architecture for this FH that resembles a heart, with each lobe comprised of two domains that are arranged around the active site. Besides the active site, where the substrate S-malate is bound bidentate to the unique iron of the [4Fe-4S] cluster, other binding pockets are found near the dimeric enzyme interface, some of which are occupied by malonate, shown here to be a weak inhibitor of this enzyme. Taken together, these data provide a framework both for investigations of the class I FH catalytic mechanism and for drug design aimed at fighting neglected tropical diseases.

OASIS Observation and Analysis of Smectic Islands in Space

NASA Technical Reports Server (NTRS)

Tin, Padetha

2014-01-01

The Observation and Analysis of Smectic Islands in Space (OASIS) project comprises a series of experiments that will probe the interfacial and hydrodynamic behavior of freely suspended liquid crystal films in space. These are the thinnest known stable condensed phase structures, making them ideal for studies of fluctuation and interface phenomena. The experiments seek to verify theories of coarsening dynamics, hydrodynamic flow, relaxation of hydrodynamic perturbations, and hydrodynamic interactions of a near two-dimensional structure. The effects of introducing islands or droplets on a very thin bubble will be studied, both as controllable inclusions that modify the flow and as markers of flow.

Structure of the buffalo secretory signalling glycoprotein at 2.8 Å resolution

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

Ethayathulla, Abdul S.; Srivastava, Devendra B.; Kumar, Janesh

2007-04-01

The crystal structure of a signalling glycoprotein isolated from buffalo dry secretions (SPB-40) has been determined at 2.8 Å resolution. Two unique residues, Tyr120 and Glu269, found in SPB-40 distort the shape of the sugar-binding groove considerably. The water structure in the groove is also different. The conformations of three flexible loops, His188–His197, Phe202–Arg212 and Tyr244–Pro260, also differ from those found in other structurally similar proteins. The crystal structure of a 40 kDa signalling glycoprotein from buffalo (SPB-40) has been determined at 2.8 Å resolution. SPB-40 acts as a protective signalling factor by binding to viable cells during the earlymore » phase of involution, during which extensive tissue remodelling occurs. It was isolated from the dry secretions of Murrah buffalo. It was purified and crystallized using the hanging-drop vapour-diffusion method with 19% ethanol as the precipitant. The protein was also cloned and its complete nucleotide and amino-acid sequences were determined. When compared with the sequences of other members of the family, the sequence of SPB-40 revealed two very important mutations in the sugar-binding region, in which Tyr120 changed to Trp120 and Glu269 changed to Trp269. The structure showed a significant distortion in the shape of the sugar-binding groove. The water structure in the groove is also drastically altered. The folding of the protein chain in the flexible region comprising segments His188–His197, Phe202–Arg212 and Tyr244–Pro260 shows large variations when compared with other proteins of the family.« less

Crystal structure of octa-kis-(4-meth-oxy-pyridinium) bis-(4-meth-oxy-pyridine-κN)tetra-kis-(thio-cyanato-κN)ferrate(III) bis-[(4-meth-oxypyri-dine-κN)pentakis-(thio-cyanato-κN)ferrate(III)] hexa-kis-(thio-cyanato-κN)ferrate(III) with iron in three different octa-hedral coordination environments.

PubMed

Jochim, Aleksej; Jess, Inke; Näther, Christian

2018-03-01

The crystal structure of the title salt, (C 6 H 8 NO) 8 [Fe(NCS) 4 (C 6 H 7 NO) 2 ][Fe(NCS) 5 (C 6 H 7 NO)] 2 [Fe(NCS) 6 ], comprises three negatively charged octa-hedral Fe III complexes with different coordination environments in which the Fe III atoms are coordinated by a different number of thio-cyanate anions and 4-meth-oxy-pyridine ligands. Charge balance is achieved by 4-meth-oxy-pyridinium cations. The asymmetric unit consists of three Fe III cations, one of which is located on a centre of inversion, one on a twofold rotation axis and one in a general position, and ten thio-cyanate anions, two 4-meth-oxy-pyridine ligands and 4-meth-oxy-pyridinium cations (one of which is disordered over two sets of sites). Beside to Coulombic inter-actions between organic cations and the ferrate(III) anions, weak N-H⋯S hydrogen-bonding inter-actions involving the pyridinium N-H groups of the cations and the thio-cyanate S atoms of the complex anions are mainly responsible for the cohesion of the crystal structure.

Efficient dermal delivery of retinyl palmitate: Progressive polarimetry and Raman spectroscopy to evaluate the structure and efficacy.

PubMed

Lee, Jun Bae; Lee, Dong Ryeol; Choi, Nak Cho; Jang, Jihui; Park, Chun Ho; Yoon, Moung Seok; Lee, Miyoung; Won, Kyoungae; Hwang, Jae Sung; Kim, B Moon

2015-10-12

Over the past decades, there has been a growing interest in dermal drug delivery. Although various novel delivery devices and methods have been developed, dermal delivery is still challenging because of problems such as poor drug permeation, instability of vesicles and drug leakage from vesicles induced by fusion of vesicles. To solve the vesicle instability problems in current dermal delivery systems, we developed materials comprised of liquid crystals as a new delivery vehicle of retinyl palmitate and report the characterization of the liquid crystals using a Mueller matrix polarimetry. The stability of the liquid-crystal materials was evaluated using the polarimeter as a novel evaluation tool along with other conventional methods. The dermal delivery of retinyl palmitate was investigated through the use of confocal Raman spectroscopy. The results indicate that the permeation of retinyl palmitate was enhanced by up to 106% compared to that using an ordinary emulsion with retinyl palmitate. Copyright © 2015 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

PubMed Central

Rodríguez Guilbe, María M.; Alfaro Malavé, Elisa C.; Akerboom, Jasper; Marvin, Jonathan S.; Looger, Loren L.; Schreiter, Eric R.

2008-01-01

Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, this protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way. PMID:18607093

Structural Snapshots of Heparin Depolymerization by Heparin Lyase I

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

Han, Young-Hyun; Garron, Marie-Line; Kim, Hye-Yeon

2010-01-12

Heparin lyase I (heparinase I) specifically depolymerizes heparin, cleaving the glycosidic linkage next to iduronic acid. Here, we show the crystal structures of heparinase I from Bacteroides thetaiotaomicron at various stages of the reaction with heparin oligosaccharides before and just after cleavage and product disaccharide. The heparinase I structure is comprised of a {beta}-jellyroll domain harboring a long and deep substrate binding groove and an unusual thumb-resembling extension. This thumb, decorated with many basic residues, is of particular importance in activity especially on short heparin oligosaccharides. Unexpected structural similarity of the active site to that of heparinase II with anmore » ({alpha}/{alpha}){sub 6} fold is observed. Mutational studies and kinetic analysis of this enzyme provide insights into the catalytic mechanism, the substrate recognition, and processivity.« less

Petrology and geochemistry of the orbicular granitoid of Caldera, northern Chile. Models and hypotheses on the formation of radial orbicular textures

NASA Astrophysics Data System (ADS)

Díaz-Alvarado, Juan; Rodríguez, Natalia; Rodríguez, Carmen; Fernández, Carlos; Constanzo, Ítalo

2017-07-01

The orbicular granitoid of Caldera, located at the northern part of the Chilean Coastal Range, is a spectacular example of radial textures in orbicular structures. The orbicular body crops out as a 375 m2 tabular to lensoidal intrusive sheet emplaced in the Lower Jurassic Relincho pluton. The orbicular structures are 3-7 cm in diameter ellipsoids hosted in a porphyritic matrix. The orbicules are comprised by a Qtz-dioritic core (3-5 cm in diameter) composed by Pl + Hbl + Qtz + Bt ± Kfs with equiaxial textures and a gabbroic shell (2-3 cm in diameter) characterized by feathery and radiate textures with a plagioclase + hornblende paragenesis. The radial shell crystals are rooted and orthogonally disposed in the irregular contact with the core. The radial shell, called here inner shell, is in contact with the granodioritic equiaxial interorbicular matrix through a 2-3 mm wide poikilitic band around the orbicule (outer shell). The outer shell and the matrix surrounding the orbicules are characterized by the presence of large hornblende and biotite oikocrystals that include fine-grained rounded plagioclase and magnetite. The oikocrystals of both the outer shell and the matrix have a circumferential arrangement around the orbicule, i.e. orthogonal to the radial inner shell. The coarse-grained granodioritic interorbicular matrix present pegmatitic domains with large acicular hornblende and K-feldspar megacrysts. This work presents a review of the textural characteristics of the orbicules and a complete new mineral and whole-rock geochemical study of the different parts of the orbicular granitoid, together with thermobarometric and crystallographic data, and theoretical modeling of the crystallization and element partitioning processes. We propose a model for the formation of the orbicular radial textures consisting of several processes that are suggested to occur fast and consecutively: superheating, volatile exsolution, undercooling, geochemical fractionation and columnar and equiaxial crystallization. According to the obtained results, the formation of the orbicular granitoid of Caldera may have initiated 1) during the generation of a magmatic fracture in the crystallization front of the Relincho pluton, where the water released by the host crystal mush was dissolved in the new batch of dioritic magma. 2) The high influx of water-rich liquids induced superheating conditions in the newly intruding magma that became a depolymerized liquid, where the only solid particules were the small irregular fragments of the host mush dragged from the fracture walls. 3) Volatile exsolution promoted crystallization under undercooling conditions. 4) Undercooling and nucleation around the core (cold germs) involved the physical and geochemical fractionation between two sub-systems: a gabbroic sub-system that comprises the solid paragénesis with a residual water-rich liquid and a granodioritic sub-system. 5) The orbicules, including core and inner shell, behaved as viscous bodies (crystals + residual liquid) floating in the granodioritic magma. 6) Higher undercooling rates occurred at the starting stage, close to the liquidus, promoting columnar crystallization around the cores and formation of the shells. Conversely, in the granodioritic matrix sub-system, equiaxial crystallization was promoted by low relative crystallization rates. 7) The rest of the crystallization process evolved later in the outer shell and the matrix, as suggested by the poikilitic textures observed in both sides of the orbicule contact, and under conditions close to the solidus of both sub-systems (shell and matrix). The water-rich residual liquid expelled during the orbicular shell crystallization was mingled with the partially crystallized matrix magma, generating the pegmatitic domains with large Kfs megacrysts.

Novel submicronized rebamipide liquid with moderate viscosity: significant effects on oral mucositis in animal models.

PubMed

Nakashima, Takako; Sako, Nobutomo; Matsuda, Takakuni; Uematsu, Naoya; Sakurai, Kazushi; Ishida, Tatsuhiro

2014-01-01

This study aimed at developing a novel rebamipide liquid for an effective treatment of oral mucositis. The healing effects of a variety of liquids comprising submicronized rebamipide crystals were investigated using a rat cauterization-induced oral ulcer model. Whereas 2% rebamipide liquid comprising micro-crystals did not exhibit significant curative effect, 2% rebamipide liquids comprising submicronized crystals with moderate viscosities exhibited healing effects following intra-oral administration. The 2% and 4% optimized rebamipide liquids showed significant healing effects in the rat oral ulcer model (p<0.01). In addition, in the rat radiation-induced glossitis model, whereby the injury was caused to the tongue by exposing only around the rat's snout to a 15 Gy of X-irradiation, the 2% optimized rebamipide liquid significantly reduced the percent area of ulcerated injury (p<0.05). In conclusion, the submicronized rebamipide liquid with moderate viscosity following intra-oral administration showed better both healing effect in the rat oral ulcer model and preventive effect in the rat irradiation-induced glossitis model.

Crystal structure of a mixed-ligand dinuclear Ba-Zn complex with 2-meth-oxy-ethanol having tri-phenyl-acetate and chloride bridges.

PubMed

Utko, Józef; Sobocińska, Maria; Dobrzyńska, Danuta; Lis, Tadeusz

2015-07-01

The dinuclear barium-zinc complex, μ-chlorido-1:2κ(2) Cl:Cl-chlorido-2κCl-bis-(2-meth-oxy-ethanol-1κO)bis-(2-meth-oxy-ethanol-1κ(2) O,O')bis-(μ-tri-phenyl-acetato-1:2κ(2) O:O')bariumzinc, [BaZn(C20H15O2)2Cl2(C3H8O2)4], has been synthesized by the reaction of barium tri-phenyl-acetate, anhydrous zinc chloride and 2-meth-oxy-ethanol in the presence of toluene. The barium and zinc metal cations in the dinuclear complex are linked via one chloride anion and carboxyl-ate O atoms of the tri-phenyl-acetate ligands, giving a Ba⋯Zn separation of 3.9335 (11) Å. The irregular nine-coordinate BaO8Cl coordination centres comprise eight O-atom donors, six of them from 2-meth-oxy-ethanol ligands (four from two bidentate O,O'-chelate inter-actions and two from monodentate inter-actions), two from bridging tri-phenyl-acetate ligands and one from a bridging Cl donor. The distorted tetra-hedral coordination sphere of zinc comprises two O-atom donors from the tri-phenyl-acetate ligands and two Cl donors (one bridging and one terminal). In the crystal, O-H⋯Cl, O-H⋯O and C-H⋯Cl inter-molecular inter-actions form a layered structure, lying parallel to (001).

The structure of amylosucrase from Deinococcus radiodurans has an unusual open active-site topology.

PubMed

Skov, Lars K; Pizzut-Serin, Sandra; Remaud-Simeon, Magali; Ernst, Heidi A; Gajhede, Michael; Mirza, Osman

2013-09-01

Amylosucrases (ASes) catalyze the formation of an α-1,4-glucosidic linkage by transferring a glucosyl unit from sucrose onto an acceptor α-1,4-glucan. To date, several ligand-bound crystal structures of wild-type and mutant ASes from Neisseria polysaccharea and Deinococcus geothermalis have been solved. These structures all display a very similar overall conformation with a deep pocket leading to the site for transglucosylation, subsite -1. This has led to speculation on how sucrose enters the active site during glucan elongation. In contrast to previous studies, the AS structure from D. radiodurans presented here has a completely empty -1 subsite. This structure is strikingly different from other AS structures, as an active-site-lining loop comprising residues Leu214-Asn225 is found in a previously unobserved conformation. In addition, a large loop harbouring the conserved active-site residues Asp133 and Tyr136 is disordered. The result of the changed loop conformations is that the active-site topology is radically changed, leaving subsite -1 exposed and partially dismantled. This structure provides novel insights into the dynamics of ASes and comprises the first structural support for an elongation mechanism that involves considerable conformational changes to modulate accessibility to the sucrose-binding site and thereby allows successive cycles of glucosyl-moiety transfer to a growing glucan chain.

The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture.

PubMed

Merckel, Michael C; Huiskonen, Juha T; Bamford, Dennis H; Goldman, Adrian; Tuma, Roman

2005-04-15

Comparisons of bacteriophage PRD1 and adenovirus protein structures and virion architectures have been instrumental in unraveling an evolutionary relationship and have led to a proposal of a phylogeny-based virus classification. The structure of the PRD1 spike protein P5 provides further insight into the evolution of viral proteins. The crystallized P5 fragment comprises two structural domains: a globular knob and a fibrous shaft. The head folds into a ten-stranded jelly roll beta barrel, which is structurally related to the tumor necrosis factor (TNF) and the PRD1 coat protein domains. The shaft domain is a structural counterpart to the adenovirus spike shaft. The structural relationships between PRD1, TNF, and adenovirus proteins suggest that the vertex proteins may have originated from an ancestral TNF-like jelly roll coat protein via a combination of gene duplication and deletion.

Octacalcium phosphate: osteoconductivity and crystal chemistry.

PubMed

Suzuki, O

2010-09-01

Octacalcium phosphate (OCP), which is structurally similar to hydroxyapatite (HA), is a possible precursor of bone apatite crystals. Although disagreement remains as to whether OCP comprises the initial mineral crystals in the early stage of bone mineralization, the results of recent biomaterial studies using synthetic OCP indicate the potential role of OCP as a bone substitute material, owing to its highly osteoconductive and biodegradable characteristics. OCP tends to convert to HA not only in an in vitro environment, but also as an implant in bone defects. Several lines of evidence from both in vivo and in vitro studies suggest that the conversion process could be involved in the stimulatory capacity of OCP for osteoblastic differentiation and osteoclast formation. However, the osteoconductivity of OCP cannot always be secured if an OCP with distinct crystal characteristics is used, because the stoichiometry and microstructure of OCP crystals greatly affect bone-regenerative properties. Osteoconductivity and stimulatory capabilities may be caused by the chemical characteristics of OCP, which allows the release or exchange of calcium and phosphate ions with the surrounding of this salt, and its tendency to grow towards specific crystal faces, which could be a variable of the synthesis condition. This paper reviews the effect of calcium phosphates on osteoblastic activity and bone regeneration, with a special emphasis on OCP, since OCP seems to be performing better than other calcium phosphates in vivo. 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Crystal Structure of the N-terminal Domain of the Group B Streptococcus Alpha C Protein

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

Auperin,T.; Bolduc, G.; Baron, M.

Group B Streptococcus (GBS) is the leading cause of bacterial pneumonia, sepsis, and meningitis among neonates and an important cause of morbidity among pregnant women and immunocompromised adults. Invasive diseases due to GBS are attributed to the ability of the pathogen to translocate across human epithelial surfaces. The alpha C protein (ACP) has been identified as an invasin that plays a role in internalization and translocation of GBS across epithelial cells. The soluble N-terminal domain of ACP (NtACP) blocks the internalization of GBS. We determined the 1.86-{angstrom} resolution crystal structure of NtACP comprising residues Ser{sup 52} through Leu{sup 225} ofmore » the full-length ACP. NtACP has two domains, an N-terminal {beta}-sandwich and a C-terminal three-helix bundle. Structural and topological alignments reveal that the {beta}-sandwich shares structural elements with the type III fibronectin fold (FnIII), but includes structural elaborations that make it unique. We have identified a potential integrin-binding motif consisting of Lys-Thr-Asp{sup 146}, Arg{sup 110}, and Asp{sup 118}. A similar arrangement of charged residues has been described in other invasins. ACP shows a heparin binding activity that requires NtACP. We propose a possible heparin-binding site, including one surface of the three-helix bundle, and nearby portions of the sandwich and repeat domains. We have validated this prediction using assays of the heparin binding and cell-adhesion properties of engineered fragments of ACP. This is the first crystal structure of a member of the highly conserved Gram-positive surface alpha-like protein family, and it will enable the internalization mechanism of GBS to be dissected at the atomic level.« less

Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection

PubMed Central

Valkov, Eugene; Stamp, Anna; DiMaio, Frank; Baker, David; Verstak, Brett; Roversi, Pietro; Kellie, Stuart; Sweet, Matthew J.; Mansell, Ashley; Gay, Nicholas J.; Martin, Jennifer L.; Kobe, Bostjan

2011-01-01

Initiation of the innate immune response requires agonist recognition by pathogen-recognition receptors such as the Toll-like receptors (TLRs). Toll/interleukin-1 receptor (TIR) domain-containing adaptors are critical in orchestrating the signal transduction pathways after TLR and interleukin-1 receptor activation. Myeloid differentiation primary response gene 88 (MyD88) adaptor-like (MAL)/TIR domain-containing adaptor protein (TIRAP) is involved in bridging MyD88 to TLR2 and TLR4 in response to bacterial infection. Genetic studies have associated a number of unique single-nucleotide polymorphisms in MAL with protection against invasive microbial infection, but a molecular understanding has been hampered by a lack of structural information. The present study describes the crystal structure of MAL TIR domain. Significant structural differences exist in the overall fold of MAL compared with other TIR domain structures: A sequence motif comprising a β-strand in other TIR domains instead corresponds to a long loop, placing the functionally important “BB loop” proline motif in a unique surface position in MAL. The structure suggests possible dimerization and MyD88-interacting interfaces, and we confirm the key interface residues by coimmunoprecipitation using site-directed mutants. Jointly, our results provide a molecular and structural basis for the role of MAL in TLR signaling and disease protection. PMID:21873236

Structural evidence for the role of polar core residue Arg175 in arrestin activation

PubMed Central

Granzin, Joachim; Stadler, Andreas; Cousin, Anneliese; Schlesinger, Ramona; Batra-Safferling, Renu

2015-01-01

Binding mechanism of arrestin requires photoactivation and phosphorylation of the receptor protein rhodopsin, where the receptor bound phosphate groups cause displacement of the long C-tail ‘activating’ arrestin. Mutation of arginine 175 to glutamic acid (R175E), a central residue in the polar core and previously predicted as the ‘phosphosensor’ leads to a pre-active arrestin that is able to terminate phototransduction by binding to non-phosphorylated, light-activated rhodopsin. Here, we report the first crystal structure of a R175E mutant arrestin at 2.7 Å resolution that reveals significant differences compared to the basal state reported in full-length arrestin structures. These differences comprise disruption of hydrogen bond network in the polar core, and three-element interaction including disordering of several residues in the receptor-binding finger loop and the C-terminus (residues 361–404). Additionally, R175E structure shows a 7.5° rotation of the amino and carboxy-terminal domains relative to each other. Consistent to the biochemical data, our structure suggests an important role of R29 in the initial activation step of C-tail release. Comparison of the crystal structures of basal arrestin and R175E mutant provide insights into the mechanism of arrestin activation, where binding of the receptor likely induces structural changes mimicked as in R175E. PMID:26510463

Structural evidence for the role of polar core residue Arg175 in arrestin activation.

PubMed

Granzin, Joachim; Stadler, Andreas; Cousin, Anneliese; Schlesinger, Ramona; Batra-Safferling, Renu

2015-10-29

Binding mechanism of arrestin requires photoactivation and phosphorylation of the receptor protein rhodopsin, where the receptor bound phosphate groups cause displacement of the long C-tail 'activating' arrestin. Mutation of arginine 175 to glutamic acid (R175E), a central residue in the polar core and previously predicted as the 'phosphosensor' leads to a pre-active arrestin that is able to terminate phototransduction by binding to non-phosphorylated, light-activated rhodopsin. Here, we report the first crystal structure of a R175E mutant arrestin at 2.7 Å resolution that reveals significant differences compared to the basal state reported in full-length arrestin structures. These differences comprise disruption of hydrogen bond network in the polar core, and three-element interaction including disordering of several residues in the receptor-binding finger loop and the C-terminus (residues 361-404). Additionally, R175E structure shows a 7.5° rotation of the amino and carboxy-terminal domains relative to each other. Consistent to the biochemical data, our structure suggests an important role of R29 in the initial activation step of C-tail release. Comparison of the crystal structures of basal arrestin and R175E mutant provide insights into the mechanism of arrestin activation, where binding of the receptor likely induces structural changes mimicked as in R175E.

Slovenian Pre-Service Teachers' Conceptions about Liquid Crystals

ERIC Educational Resources Information Center

Pavlin, Jerneja; Vaupotic, Natasa; Glazar, Sasa A.; Cepic, Mojca; Devetak, Iztok

2011-01-01

A total of 448 first-year university students participated in the study at the beginning of the academic year 2009/10. A paper-pencil liquid crystal questionnaire (LCQ) comprising 20 items was used to evaluate students' general conceptions related to liquid crystals, their properties and to the state of matter in general. The results show that 2/3…

Structure of a Burkholderia pseudomallei Trimeric Autotransporter Adhesin Head

PubMed Central

Edwards, Thomas E.; Phan, Isabelle; Abendroth, Jan; Dieterich, Shellie H.; Masoudi, Amir; Guo, Wenjin; Hewitt, Stephen N.; Kelley, Angela; Leibly, David; Brittnacher, Mitch J.; Staker, Bart L.; Miller, Samuel I.; Van Voorhis, Wesley C.; Myler, Peter J.; Stewart, Lance J.

2010-01-01

Background Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region. Methodology/Principal Findings Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 Å resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs. Conclusions/Significance The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics. PMID:20862217

Superlattice strain gage

DOEpatents

Noel, B.W.; Smith, D.L.; Sinha, D.N.

1988-06-28

A strain gage comprising a strained-layer superlattice crystal exhibiting piezoelectric properties is described. A substrate upon which such a strained-layer superlattice crystal has been deposited is attached to an element to be monitored for strain. A light source is focused on the superlattice crystal and the light reflected from, passed through, or emitted from the crystal is gathered and compared with previously obtained optical property data to determine the strain in the element. 8 figs.

Effects of physiological environments on the hydration behavior of mineral trioxide aggregate.

PubMed

Lee, Yuan-Ling; Lee, Bor-Shiunn; Lin, Feng-Huei; Yun Lin, Ava; Lan, Wan-Hong; Lin, Chun-Pin

2004-02-01

Utilizing scanning electron microscope, X-ray diffraction (XRD) and microhardness tests, we evaluated how various physiological environments affect the hydration behavior and physical properties of mineral trioxide aggregate (MTA). We found that the microstructure of hydrated MTA consists of cubic and needle-like crystals. The former comprised the principal structure of MTA, whereas the later were less prominent and formed in the inter-grain spaces between the cubic crystals. MTA samples were hydrated in distilled water, normal saline, pH 7, and pH 5. However, no needle-like crystals were observed in the pH 5 specimens, and erosion of the cubic crystal surfaces was noted. XRD indicated a peak corresponding to Portlandite, a hydration product of MTA, and the peak decreased noticeably in the pH 5 group. The pH 5 specimens' microhardness was also significantly weaker compared to the other three groups (p<0.0001). These findings suggest that physiological environmental effects on MTA formation are determined, in part, by environmental pH and the presence of ions. In particular, an acidic environment of pH 5 adversely affects both the physical properties and the hydration behavior of MTA.

Crystal structure of the Msx-1 homeodomain/DNA complex.

PubMed

Hovde, S; Abate-Shen, C; Geiger, J H

2001-10-09

The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

Growth and characterization of ammonium nickel-cobalt sulfate Tutton's salt for UV light applications

NASA Astrophysics Data System (ADS)

Ghosh, Santunu; Oliveira, Michelle; Pacheco, Tiago S.; Perpétuo, Genivaldo J.; Franco, Carlos J.

2018-04-01

We have obtained a set of sample crystals of the family of Tutton's salt comprise in the isomorphic series with general chemical formula (NH4)2NixCo(1-x) (SO4)2·6H2O, by employing growth from solutions by slow evaporation technique. The samples crystals were characterized by ICP-AES, X-ray powder diffraction analysis, thermogravimetric analysis, UV-Vis-NIR, Raman and FTIR spectroscopy. This type of material has been studied because of its physical and chemical properties not yet understood and they have potential technological applications. Chemical analysis of the samples by ICP-AES method allowed us to investigate the efficiency of the method of growth used. Thermogravimetric analysis provides the information about the thermal stability of the obtained crystals for high temperature applications, and powder X-ray diffraction analysis at ambient and high temperature reveals the structural quality and structural change of the samples respectively. We have used Raman spectroscopy in the range 100-4000 cm-1 and FTIR spectroscopy in the range 400-4000 cm-1 to understand the internal vibrational mode of the octahedral complexes [Ni(H2O)6]2+ and [Co(H2O)6]2+, SO42- and NH4+ tetrahedra. The transmittance of our mixed ammonium nickel cobalt sulfate hexahydrate (ACNSH) crystals is 75% in the UV region, which indicates that they are ideal to use in UV light filters and UV sensors.

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

Evans, III, Boyd Mccutchen; Kisner, Roger A.; Ludtka, Gail Mackiewicz

A method of making a single crystal comprises heating a material comprising magnetic anisotropy to a temperature T sufficient to form a melt of the material. A magnetic field of at least about 1 Tesla is applied to the melt at the temperature T, where a magnetic free energy difference .DELTA.G.sub.m between different crystallographic axes is greater than a thermal energy kT. While applying the magnetic field, the melt is cooled at a rate of about 30.degree. C./min or higher, and the melt solidifies to form a single crystal of the material.

Crystal structure of (2,4-di-tert-butyl-6-{[(6,6'-dimethyl-2'-oxido-1,1'-biphenyl-2-yl)imino]methyl}phenolato-κ(3) O,N,O')bis(propan-2-olato-κO)titanium(IV).

PubMed

Chen, Liang; Wang, Huiran; Deng, Xuebin

2014-09-01

In the mononuclear Ti(IV) title complex, [Ti(C29H33NO2)(C3H6O)2], the TiNO4 coordination polyhedron comprises an N-atom and two O-atom donors from the dianionic Schiff base ligand and two O-atom donors from monodentate isopropoxide anions. The stereochemistry is distorted trigonal-bipyramidal with the N-donor in an elongated axial site [Ti-N = 2.2540 (17) Å], the O-donors having normal Ti-O bond lengths [1.7937 (14) Å (axial)-1.8690 (14) Å]. In the crystal, C-H⋯π inter-actions link mol-ecules into centrosymmetric dimers.

Wide-field-of-view nanoscale Bragg liquid crystal polarization gratings

NASA Astrophysics Data System (ADS)

Xiang, Xiao; Kim, Jihwan; Escuti, Michael J.

2018-02-01

Here, we demonstrate a liquid crystal (LC) polymer Bragg polarization grating (PG) with large angular band- width and high efficiency in transmission-mode for 532 nm wavelength and 400 nm period. The field-of-view (FOV ) is increased significantly while preserving high diffraction efficiency by realizing a monolithic grating comprising two different slants. Using rigorous coupled-wave analysis simulation, we identified a structure with 48° FOV and 70% average first-order efficiency. We then experimentally fabricated and characterized the grating with a photo-aligned LC polymer network, also known as reactive mesogens. We measured 40° FOV and nearly 80% average diffraction efficiency. With this broadened and fairly uniform angular response, this wide FOV Bragg PG is a compelling option for large deflection-angle applications, including near-eye display in augmented reality systems, waveguide based illumination, and beam steering.

Mineral resource of the month: Vermiculite

USGS Publications Warehouse

Tanner, Arnold O.

2014-01-01

Vermiculite comprises a group of hydrated, laminar magnesium-aluminum-iron silicate minerals resembling mica. They are secondary minerals, typically altered biotite, iron-rich phlogopite or other micas or clay-like minerals that are themselves sometimes alteration products of amphibole, chlorite, olivine and pyroxene. Vermiculite deposits are associated with volcanic ultramafic rocks rich in magnesium silicate minerals, and flakes of the mineral range in color from black to shades of brown and yellow. The crystal structure of vermiculite contains water molecules, a property that is critical to its processing for common uses.

Rapid self-assembly of block copolymers to photonic crystals

DOEpatents

Xia, Yan; Sveinbjornsson, Benjamin R; Grubbs, Robert H; Weitekamp, Raymond; Miyake, Garret M; Atwater, Harry A; Piunova, Victoria; Daeffler, Christopher Scot; Hong, Sung Woo; Gu, Weiyin; Russell, Thomas P.

2016-07-05

The invention provides a class of copolymers having useful properties, including brush block copolymers, wedge-type block copolymers and hybrid wedge and polymer block copolymers. In an embodiment, for example, block copolymers of the invention incorporate chemically different blocks comprising polymer size chain groups and/or wedge groups that significantly inhibit chain entanglement, thereby enhancing molecular self-assembly processes for generating a range of supramolecular structures, such as periodic nanostructures and microstructures. The present invention also provides useful methods of making and using copolymers, including block copolymers.

Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase: DAWIDZIAK et al.

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

Dawidziak, Daria M.; Sanchez, Jacint G.; Wagner, Jonathan M.

Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2–ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.

Nanoparticle Superlattice Engineering with DNA

NASA Astrophysics Data System (ADS)

Macfarlane, Robert J.; Lee, Byeongdu; Jones, Matthew R.; Harris, Nadine; Schatz, George C.; Mirkin, Chad A.

2011-10-01

A current limitation in nanoparticle superlattice engineering is that the identities of the particles being assembled often determine the structures that can be synthesized. Therefore, specific crystallographic symmetries or lattice parameters can only be achieved using specific nanoparticles as building blocks (and vice versa). We present six design rules that can be used to deliberately prepare nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nanometer length scale. These design rules outline a strategy to independently adjust each of the relevant crystallographic parameters, including particle size (5 to 60 nanometers), periodicity, and interparticle distance. As such, this work represents an advance in synthesizing tailorable macroscale architectures comprising nanoscale materials in a predictable fashion.

Structure of ATP-Bound Human ATP:Cobalamin Adenosyltransferase

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

Schubert,H.; Hill, C.

Mutations in the gene encoding human ATP:cobalamin adenosyltransferase (hATR) can result in the metabolic disorder known as methylmalonic aciduria (MMA). This enzyme catalyzes the final step in the conversion of cyanocobalamin (vitamin B{sub 12}) to the essential human cofactor adenosylcobalamin. Here we present the 2.5 {angstrom} crystal structure of ATP bound to hATR refined to an R{sub free} value of 25.2%. The enzyme forms a tightly associated trimer, where the monomer comprises a five-helix bundle and the active sites lie on the subunit interfaces. Only two of the three active sites within the trimer contain the bound ATP substrate, therebymore » providing examples of apo- and substrate-bound-active sites within the same crystal structure. Comparison of the empty and occupied sites indicates that twenty residues at the enzyme's N-terminus become ordered upon binding of ATP to form a novel ATP-binding site and an extended cleft that likely binds cobalamin. The structure explains the role of 20 invariant residues; six are involved in ATP binding, including Arg190, which hydrogen bonds to ATP atoms on both sides of the scissile bond. Ten of the hydrogen bonds are required for structural stability, and four are in positions to interact with cobalamin. The structure also reveals how the point mutations that cause MMA are deficient in these functions.« less

High resolution scintillation detector with semiconductor readout

DOEpatents

Levin, Craig S.; Hoffman, Edward J.

2000-01-01

A novel high resolution scintillation detector array for use in radiation imaging such as high resolution Positron Emission Tomography (PET) which comprises one or more parallelepiped crystals with at least one long surface of each crystal being in intimate contact with a semiconductor photodetector such that photons generated within each crystal by gamma radiation passing therethrough is detected by the photodetector paired therewith.

Crystallization and preliminary X-ray diffraction analysis of the Bacillus subtilis replication termination protein in complex with the 37-base-pair TerI-binding site

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

Vivian, J. P.; Porter, C.; Wilce, J. A.

2006-11-01

A preparation of replication terminator protein (RTP) of B. subtilis and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. The replication terminator protein (RTP) of Bacillus subtilis binds to specific DNA sequences that halt the progression of the replisome in a polar manner. These terminator complexes flank a defined region of the chromosome into which they allow replication forks to enter but not exit. Forcing the fusion of replication forks in a specific zone is thought to allow the coordination of post-replicative processes. The functional terminator complex comprises two homodimers each of 29more » kDa bound to overlapping binding sites. A preparation of RTP and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. A data set to 3.9 Å resolution with 97.0% completeness and an R{sub sym} of 12% was collected from a single flash-cooled crystal using synchrotron radiation. The diffraction data are consistent with space group P622, with unit-cell parameters a = b = 118.8, c = 142.6 Å.« less

Crystal structures of 4-meth-oxy-benzoic acid-1,3-bis-(pyridin-4-yl)propane (2/1) and biphenyl-4,4'-di-carb-oxy-lic acid-4-meth-oxy-pyridine (1/2).

PubMed

Gotoh, Kazuma; Ishida, Hiroyuki

2017-07-01

The crystal structures of two hydrogen-bonded compounds, namely 4-meth-oxy-benzoic acid-1,3-bis-(pyridin-4-yl)propane (2/1), C 13 H 14.59 N 2 ·C 8 H 7.67 O 3 ·C 8 H 7.74 O 3 , (I), and biphenyl-4,4'-di-carb-oxy-lic acid-4-meth-oxy-pyridine (1/2), C 14 H 9.43 O 4 ·C 6 H 7.32 NO·C 6 H 7.25 NO, (II), have been determined at 93 K. In (I), the asymmetric unit consists of two crystallographically independent 4-meth-oxy-benzoic acid mol-ecules and one 1,3-bis-(pyridin-4-yl)propane mol-ecule. The asymmetric unit of (II) comprises one biphenyl-4,4'-di-carb-oxy-lic acid mol-ecule and two independent 4-meth-oxy-pyridine mol-ecules. In each crystal, the acid and base mol-ecules are linked by short O-H⋯N/N-H⋯O hydrogen bonds, in which H atoms are disordered over the acid O-atom and base N-atom sites, forming a linear hydrogen-bonded 2:1 or 1:2 unit of the acid and the base. The 2:1 units of (I) are linked via C-H⋯π, π-π and C-H⋯O inter-actions into a tape structure along [101], while the 1:2 units of (II) form a double-chain structure along [-101] through π-π and C-H⋯O inter-actions.

Synthesis and Physical Properties of the Oxofluoride Cu2(SeO3)F2.

PubMed

Mitoudi-Vagourdi, Eleni; Papawassiliou, Wassilios; Müllner, Silvia; Jaworski, Aleksander; Pell, Andrew J; Lemmens, Peter; Kremer, Reinhard K; Johnsson, Mats

2018-04-16

Single crystals of the new compound Cu 2 (SeO 3 )F 2 were successfully synthesized via a hydrothermal method, and the crystal structure was determined from single-crystal X-ray diffraction data. The compound crystallizes in the orthorhombic space group Pnma with the unit cell parameters a = 7.066(4) Å, b = 9.590(4) Å, and c = 5.563(3) Å. Cu 2 (SeO 3 )F 2 is isostructural with the previously described compounds Co 2 TeO 3 F 2 and CoSeO 3 F 2 . The crystal structure comprises a framework of corner- and edge-sharing distorted [CuO 3 F 3 ] octahedra, within which [SeO 3 ] trigonal pyramids are present in voids and are connected to [CuO 3 F 3 ] octahedra by corner sharing. The presence of a single local environment in both the 19 F and 77 Se solid-state MAS NMR spectra supports the hypothesis that O and F do not mix at the same crystallographic positions. Also the specific phonon modes observed with Raman scattering support the coordination around the cations. At high temperatures the magnetic susceptibility follows the Curie-Weiss law with Curie temperature of Θ = -173(2) K and an effective magnetic moment of μ eff ∼ 2.2 μ B . Antiferromagnetic ordering below ∼44 K is indicated by a peak in the magnetic susceptibility. A second though smaller peak at ∼16 K is tentatively ascribed to a magnetic reorientation transition. Both transitions are also confirmed by heat capacity measurements. Raman scattering experiments propose a structural phase instability in the temperature range 6-50 K based on phonon anomalies. Further changes in the Raman shift of modes at ∼46 K and ∼16 K arise from transitions of the magnetic lattice in accordance with the susceptibility and heat capacity measurements.

Bottom-up construction of a superstructure in a porous uranium-organic crystal

NASA Astrophysics Data System (ADS)

Li, Peng; Vermeulen, Nicolaas A.; Malliakas, Christos D.; Gómez-Gualdrón, Diego A.; Howarth, Ashlee J.; Mehdi, B. Layla; Dohnalkova, Alice; Browning, Nigel D.; O'Keeffe, Michael; Farha, Omar K.

2017-05-01

Bottom-up construction of highly intricate structures from simple building blocks remains one of the most difficult challenges in chemistry. We report a structurally complex, mesoporous uranium-based metal-organic framework (MOF) made from simple starting components. The structure comprises 10 uranium nodes and seven tricarboxylate ligands (both crystallographically nonequivalent), resulting in a 173.3-angstrom cubic unit cell enclosing 816 uranium nodes and 816 organic linkers—the largest unit cell found to date for any nonbiological material. The cuboctahedra organize into pentagonal and hexagonal prismatic secondary structures, which then form tetrahedral and diamond quaternary topologies with unprecedented complexity. This packing results in the formation of colossal icosidodecahedral and rectified hexakaidecahedral cavities with internal diameters of 5.0 nanometers and 6.2 nanometers, respectively—ultimately giving rise to the lowest-density MOF reported to date.

Method of fabricating a scalable nanoporous membrane filter

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

Tringe, Joseph W; Balhorn, Rodney L; Zaidi, Saleem

A method of fabricating a nanoporous membrane filter having a uniform array of nanopores etch-formed in a thin film structure (e.g. (100)-oriented single crystal silicon) having a predetermined thickness, by (a) using interferometric lithography to create an etch pattern comprising a plurality array of unit patterns having a predetermined width/diameter, (b) using the etch pattern to etch frustum-shaped cavities or pits in the thin film structure such that the dimension of the frustum floors of the cavities are substantially equal to a desired pore size based on the predetermined thickness of the thin film structure and the predetermined width/diameter ofmore » the unit patterns, and (c) removing the frustum floors at a boundary plane of the thin film structure to expose, open, and thereby create the nanopores substantially having the desired pore size.« less

Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria

PubMed Central

Kim, Youngchang; Joachimiak, Grazyna; Ye, Zi; Binkowski, T. Andrew; Zhang, Rongguang; Gornicki, Piotr; Callahan, Sean M.; Hess, Wolfgang R.; Haselkorn, Robert; Joachimiak, Andrzej

2011-01-01

HetR is an essential regulator of heterocyst development in cyanobacteria. HetR binds to a DNA palindrome upstream of the hetP gene. We report the crystal structure of HetR from Fischerella at 3.0 Å. The protein is a dimer comprised of a central DNA-binding unit containing the N-terminal regions of the two subunits organized with two helix-turn-helix motifs; two globular flaps extending in opposite directions; and a hood over the central core formed from the C-terminal subdomains. The flaps and hood have no structural precedent in the protein database, therefore representing new folds. The structural assignments are supported by site-directed mutagenesis and DNA-binding studies. We suggest that HetR serves as a scaffold for assembly of transcription components critical for heterocyst development. PMID:21628585

Changes in Quaternary Structure in the Signaling Mechanisms of PAS Domains

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

Ayers, Rebecca A.; Moffat, Keith

2008-12-15

FixL from Bradyrhizobium japonicum is a PAS sensor protein in which two PAS domains covalently linked to a histidine kinase domain are responsible for regulating nitrogen fixation in an oxygen-dependent manner. The more C-terminal PAS domain, denoted bjFixLH, contains a heme cofactor that binds diatomic molecules such as carbon monoxide and oxygen and regulates the activity of the FixL histidine kinase as part of a two-component signaling system. We present the structures of ferric, deoxy, and carbon monoxide-bound bjFixLH in a new space group (P1) and at resolutions (1.5--1.8 {angstrom}) higher than the resolutions of those previously obtained. Interestingly, bjFixLHmore » can form two different dimers (in P1 and R32 crystal forms) in the same crystallization solution, where the monomers in one dimer are rotated {approx}175 deg. relative to the second. This suggests that PAS monomers are plastic and that two quite distinct quaternary structures are closely similar in free energy. We use screw rotation analysis to carry out a quantitative pairwise comparison of PAS quaternary structures, which identifies five different relative orientations adopted by isolated PAS monomers. We conclude that PAS monomer arrangement is context-dependent and could differ depending on whether the PAS domains are isolated or are part of a full-length protein. Structurally homologous residues comprise a conserved dimer interface. Using network analysis, we find that the architecture of the PAS dimer interface is continuous rather than modular; the network of residues comprising the interface is strongly connected. A continuous dimer interface is consistent with the low dimer-monomer dissociation equilibrium constant. Finally, we quantitate quaternary structural changes induced by carbon monoxide binding to a bjFixLH dimer, in which monomers rotate by up to 2 deg. relative to each other. We relate these changes to those in other dimeric PAS domains and discuss the role of quaternary structural changes in the signaling mechanisms of PAS sensor proteins.« less

Diffraction crystal for sagittally focusing x-rays

DOEpatents

Ice, Gene E.; Sparks, Jr., Cullie J.

1984-01-01

The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

Diffraction crystals for sagittally focusing x-rays

DOEpatents

Ice, G.E.; Sparks, C.J. Jr.

1982-06-07

The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

Tunable plasmonic crystal

DOEpatents

Dyer, Gregory Conrad; Shaner, Eric A.; Reno, John L.; Aizin, Gregory

2015-08-11

A tunable plasmonic crystal comprises several periods in a two-dimensional electron or hole gas plasmonic medium that is both extremely subwavelength (.about..lamda./100) and tunable through the application of voltages to metal electrodes. Tuning of the plasmonic crystal band edges can be realized in materials such as semiconductors and graphene to actively control the plasmonic crystal dispersion in the terahertz and infrared spectral regions. The tunable plasmonic crystal provides a useful degree of freedom for applications in slow light devices, voltage-tunable waveguides, filters, ultra-sensitive direct and heterodyne THz detectors, and THz oscillators.

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

Li, Yue; Zhao, Yuting; Su, Minfei

Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267–284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1–GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide. A model of a peptide comprising Beclin 1 residues 267–284 docked onto GAPR-1, built using theCABS-dockserver, indicates that this peptide binds to this GAPR-1more » groove. Mutation of the five conserved residues lining this groove, H54A/E86A/G102K/H103A/N138G, abrogates Beclin 1 binding. The 1.27 Å resolution X-ray crystal structure of this pentad mutant GAPR-1 was determined. Comparison with the wild-type (WT) GAPR-1 structure shows that the equatorial groove of the pentad mutant is shallower and more positively charged, and therefore may not efficiently bind Beclin 1 residues 267–284, which include many hydrophobic residues. Both WT and pentad mutant GAPR-1 crystallize as dimers, and in each case the equatorial groove of one subunit is partially occluded by the other subunit, indicating that dimeric GAPR-1 is unlikely to bind Beclin 1. SAXS analysis of WT and pentad mutant GAPR-1 indicates that in solution the WT forms monomers, while the pentad mutant is primarily dimeric. Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1.« less

Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions

PubMed Central

Maréchal, J-D; Kemp, C A; Roberts, G C K; Paine, M J I; Wolf, C R; Sutcliffe, M J

2008-01-01

The cytochromes P450 (CYPs) comprise a vast superfamily of enzymes found in virtually all life forms. In mammals, xenobiotic metabolizing CYPs provide crucial protection from the effects of exposure to a wide variety of chemicals, including environmental toxins and therapeutic drugs. Ideally, the information on the possible metabolism by CYPs required during drug development would be obtained from crystal structures of all the CYPs of interest. For some years only crystal structures of distantly related bacterial CYPs were available and homology modelling techniques were used to bridge the gap and produce structural models of human CYPs, and thereby obtain useful functional information. A significant step forward in the reliability of these models came seven years ago with the first crystal structure of a mammalian CYP, rabbit CYP2C5, followed by the structures of six human enzymes, CYP1A2, CYP2A6, CYP2C8, CYP2C9, CYP2D6 and CYP3A4, and a second rabbit enzyme, CYP2B4. In this review we describe as a case study the evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism. This work has led directly to the successful design of CYP2D6 mutants with novel activity—including creating a testosterone hydroxylase, converting quinidine from inhibitor to substrate, creating a diclofenac hydroxylase and creating a dextromethorphan O-demethylase. Our modelling-derived hypothesis-driven integrated interdisciplinary studies have given key insight into the molecular determinants of CYP2D6 and other important drug metabolizing enzymes. PMID:18026129

Deterministic composite nanophotonic lattices in large area for broadband applications

NASA Astrophysics Data System (ADS)

Xavier, Jolly; Probst, Jürgen; Becker, Christiane

2016-12-01

Exotic manipulation of the flow of photons in nanoengineered materials with an aperiodic distribution of nanostructures plays a key role in efficiency-enhanced broadband photonic and plasmonic technologies for spectrally tailorable integrated biosensing, nanostructured thin film solarcells, white light emitting diodes, novel plasmonic ensembles etc. Through a generic deterministic nanotechnological route here we show subwavelength-scale silicon (Si) nanostructures on nanoimprinted glass substrate in large area (4 cm2) with advanced functional features of aperiodic composite nanophotonic lattices. These nanophotonic aperiodic lattices have easily tailorable supercell tiles with well-defined and discrete lattice basis elements and they show rich Fourier spectra. The presented nanophotonic lattices are designed functionally akin to two-dimensional aperiodic composite lattices with unconventional flexibility- comprising periodic photonic crystals and/or in-plane photonic quasicrystals as pattern design subsystems. The fabricated composite lattice-structured Si nanostructures are comparatively analyzed with a range of nanophotonic structures with conventional lattice geometries of periodic, disordered random as well as in-plane quasicrystalline photonic lattices with comparable lattice parameters. As a proof of concept of compatibility with advanced bottom-up liquid phase crystallized (LPC) Si thin film fabrication, the experimental structural analysis is further extended to double-side-textured deterministic aperiodic lattice-structured 10 μm thick large area LPC Si film on nanoimprinted substrates.

Crystal Structures of Beta- and Gammaretrovirus Fusion Proteins Reveal a Role for Electrostatic Stapling in Viral Entry

PubMed Central

Aydin, Halil; Cook, Jonathan D.

2014-01-01

Membrane fusion is a key step in the life cycle of all envelope viruses, but this process is energetically unfavorable; the transmembrane fusion subunit (TM) of the virion-attached glycoprotein actively catalyzes the membrane merger process. Retroviral glycoproteins are the prototypical system to study pH-independent viral entry. In this study, we determined crystal structures of extramembrane regions of the TMs from Mason-Pfizer monkey virus (MPMV) and xenotropic murine leukemia virus-related virus (XMRV) at 1.7-Å and 2.2-Å resolution, respectively. The structures are comprised of a trimer of hairpins that is characteristic of class I viral fusion proteins and now completes a structural library of retroviral fusion proteins. Our results allowed us to identify a series of intra- and interchain electrostatic interactions in the heptad repeat and chain reversal regions. Mutagenesis reveals that charge-neutralizing salt bridge mutations significantly destabilize the postfusion six-helix bundle and abrogate retroviral infection, demonstrating that electrostatic stapling of the fusion subunit is essential for viral entry. Our data indicate that salt bridges are a major stabilizing force on the MPMV and XMRV retroviral TMs and likely provide the key energetics for viral and host membrane fusion. PMID:24131724

Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation.

PubMed

Ducka, Anna M; Joel, Peteranne; Popowicz, Grzegorz M; Trybus, Kathleen M; Schleicher, Michael; Noegel, Angelika A; Huber, Robert; Holak, Tad A; Sitar, Tomasz

2010-06-29

Three classes of proteins are known to nucleate new filaments: the Arp2/3 complex, formins, and the third group of proteins that contain ca. 25 amino acid long actin-binding Wiskott-Aldrich syndrome protein homology 2 domains, called the WH2 repeats. Crystal structures of the complexes between the actin-binding WH2 repeats of the Spire protein and actin were determined for the Spire single WH2 domain D, the double (SpirCD), triple (SpirBCD), quadruple (SpirABCD) domains, and an artificial Spire WH2 construct comprising three identical D repeats (SpirDDD). SpirCD represents the minimal functional core of Spire that can nucleate actin filaments. Packing in the crystals of the actin complexes with SpirCD, SpirBCD, SpirABCD, and SpirDDD shows the presence of two types of assemblies, "side-to-side" and "straight-longitudinal," which can serve as actin filament nuclei. The principal feature of these structures is their loose, open conformations, in which the sides of actins that normally constitute the inner interface core of a filament are flipped inside out. These Spire structures are distant from those seen in the filamentous nuclei of Arp2/3, formins, and in the F-actin filament.

Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation

PubMed Central

Ducka, Anna M.; Joel, Peteranne; Popowicz, Grzegorz M.; Trybus, Kathleen M.; Schleicher, Michael; Noegel, Angelika A.; Huber, Robert; Holak, Tad A.; Sitar, Tomasz

2010-01-01

Three classes of proteins are known to nucleate new filaments: the Arp2/3 complex, formins, and the third group of proteins that contain ca. 25 amino acid long actin-binding Wiskott-Aldrich syndrome protein homology 2 domains, called the WH2 repeats. Crystal structures of the complexes between the actin-binding WH2 repeats of the Spire protein and actin were determined for the Spire single WH2 domain D, the double (SpirCD), triple (SpirBCD), quadruple (SpirABCD) domains, and an artificial Spire WH2 construct comprising three identical D repeats (SpirDDD). SpirCD represents the minimal functional core of Spire that can nucleate actin filaments. Packing in the crystals of the actin complexes with SpirCD, SpirBCD, SpirABCD, and SpirDDD shows the presence of two types of assemblies, “side-to-side” and “straight-longitudinal,” which can serve as actin filament nuclei. The principal feature of these structures is their loose, open conformations, in which the sides of actins that normally constitute the inner interface core of a filament are flipped inside out. These Spire structures are distant from those seen in the filamentous nuclei of Arp2/3, formins, and in the F-actin filament. PMID:20538977

Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus

DOE PAGES

Laino, Aldana; Lopez-Zavala, Alonso A.; Garcia-Orozco, Karina D.; ...

2017-09-11

Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus ( PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, andmore » it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant ( K m) was 1.7 mM with a k cat of 75 s –1. Two crystal structures are presented, the apo PvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Lastly, these results contribute to knowledge of mechanistic details of the function of arginine kinase.« less

Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus

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

Laino, Aldana; Lopez-Zavala, Alonso A.; Garcia-Orozco, Karina D.

Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus ( PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, andmore » it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant ( K m) was 1.7 mM with a k cat of 75 s –1. Two crystal structures are presented, the apo PvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Lastly, these results contribute to knowledge of mechanistic details of the function of arginine kinase.« less

Deterministic composite nanophotonic lattices in large area for broadband applications

PubMed Central

Xavier, Jolly; Probst, Jürgen; Becker, Christiane

2016-01-01

Exotic manipulation of the flow of photons in nanoengineered materials with an aperiodic distribution of nanostructures plays a key role in efficiency-enhanced broadband photonic and plasmonic technologies for spectrally tailorable integrated biosensing, nanostructured thin film solarcells, white light emitting diodes, novel plasmonic ensembles etc. Through a generic deterministic nanotechnological route here we show subwavelength-scale silicon (Si) nanostructures on nanoimprinted glass substrate in large area (4 cm2) with advanced functional features of aperiodic composite nanophotonic lattices. These nanophotonic aperiodic lattices have easily tailorable supercell tiles with well-defined and discrete lattice basis elements and they show rich Fourier spectra. The presented nanophotonic lattices are designed functionally akin to two-dimensional aperiodic composite lattices with unconventional flexibility- comprising periodic photonic crystals and/or in-plane photonic quasicrystals as pattern design subsystems. The fabricated composite lattice-structured Si nanostructures are comparatively analyzed with a range of nanophotonic structures with conventional lattice geometries of periodic, disordered random as well as in-plane quasicrystalline photonic lattices with comparable lattice parameters. As a proof of concept of compatibility with advanced bottom-up liquid phase crystallized (LPC) Si thin film fabrication, the experimental structural analysis is further extended to double-side-textured deterministic aperiodic lattice-structured 10 μm thick large area LPC Si film on nanoimprinted substrates. PMID:27941869

Characterization of two distinctly different mineral-related proteins from the teeth of the Camarodont sea urchin Lytechinus variegatus: Specificity of function with relation to mineralization

NASA Astrophysics Data System (ADS)

Veis, A.; Alvares, K.; Dixit, S. N.; Robach, J. S.; Stock, S. R.

2009-06-01

The majority of the mineral phase of the Lytechinus variegatus tooth is comprised of magnesium containing calcite crystal elements, collectively arranged so that they appear as a single crystal under polarized light, as well as under X-ray or electron irradiation. However, the crystal elements are small, and in spite of the common alignment of their crystal axes, are not the same size or shape in different parts of the tooth. The toughness of the tooth structure arises from the fact that it is a composite in which the crystals are coated with surface layers of organic matter that probably act to inhibit crack formation and elongation. In the growth region the organic components represent a greater part of the tooth structure. In the most heavily mineralized adoral region the primary plates fuse with inter-plate pillars. Using Scanning Electron Microscopy; TOF-SIMS mapping of the characteristic amino acids of the mineral related proteins; and isolation and characterization of the mineral-protected protein we report that the late-forming inter-plate pillars had more than a three-fold greater Mg content than the primary plates. Furthermore, the aspartic acid content of the mineralrelated protein was highest in the high Mg pillars whereas the mineral-protected protein of the primary plates was richer in glutamic acid content.These results suggest that the Asp-rich protein(s) is important for formation of the late developing inter-plate pillars that fuse the primary plates and increase the stiffness of the most mature tooth segment. Supported by NIDCR Grant DE R01-01374 to AV.

Design and Performance of a 1 mm3 Resolution Clinical PET System Comprising 3-D Position Sensitive Scintillation Detectors.

PubMed

Hsu, David F C; Freese, David L; Reynolds, Paul D; Innes, Derek R; Levin, Craig S

2018-04-01

We are developing a 1-mm 3 resolution, high-sensitivity positron emission tomography (PET) system for loco-regional cancer imaging. The completed system will comprise two cm detector panels and contain 4 608 position sensitive avalanche photodiodes (PSAPDs) coupled to arrays of mm 3 LYSO crystal elements for a total of 294 912 crystal elements. For the first time, this paper summarizes the design and reports the performance of a significant portion of the final clinical PET system, comprising 1 536 PSAPDs, 98 304 crystal elements, and an active field-of-view (FOV) of cm. The sub-system performance parameters, such as energy, time, and spatial resolutions are predictive of the performance of the final system due to the modular design. Analysis of the multiplexed crystal flood histograms shows 84% of the crystal elements have>99% crystal identification accuracy. The 511 keV photopeak energy resolution was 11.34±0.06% full-width half maximum (FWHM), and coincidence timing resolution was 13.92 ± 0.01 ns FWHM at 511 keV. The spatial resolution was measured using maximum likelihood expectation maximization reconstruction of a grid of point sources suspended in warm background. The averaged resolution over the central 6 cm of the FOV is 1.01 ± 0.13 mm in the X-direction, 1.84 ± 0.20 mm in the Y-direction, and 0.84 ± 0.11 mm in the Z-direction. Quantitative analysis of acquired micro-Derenzo phantom images shows better than 1.2 mm resolution at the center of the FOV, with subsequent resolution degradation in the y-direction toward the edge of the FOV caused by limited angle tomography effects.

An NMR Study of Biomimetic Fluorapatite – Gelatine Mesocrystals

PubMed Central

Vyalikh, Anastasia; Simon, Paul; Rosseeva, Elena; Buder, Jana; Scheler, Ulrich; Kniep, Rüdiger

2015-01-01

The mesocrystal system fluoroapatite—gelatine grown by double-diffusion is characterized by hierarchical composite structure on a mesoscale. In the present work we apply solid state NMR to characterize its structure on the molecular level and provide a link between the structural organisation on the mesoscale and atomistic computer simulations. Thus, we find that the individual nanocrystals are composed of crystalline fluorapatite domains covered by a thin boundary apatite-like layer. The latter is in contact with an amorphous layer, which fills the interparticle space. The amorphous layer is comprised of the organic matrix impregnated by isolated phosphate groups, Ca3F motifs and water molecules. Our NMR data provide clear evidence for the existence of precursor complexes in the gelatine phase, which were not involved in the formation of apatite crystals, proving hence theoretical predictions on the structural pre-treatment of gelatine by ion impregnation. The interfacial interactions, which may be described as the glue holding the composite materials together, comprise hydrogen bond interactions with the apatite PO43− groups. The reported results are in a good agreement with molecular dynamics simulations, which address the mechanisms of a growth control by collagen fibers, and with experimental observations of an amorphous cover layer in biominerals. PMID:26515127

Development of modal layering in granites: a case study from the Carna Pluton, Connemara, Ireland

NASA Astrophysics Data System (ADS)

McKenzie, Kirsty; McCarthy, William; Hunt, Emma

2016-04-01

Modal layering in igneous rocks uniquely record dynamic processes operating in magma chambers and also host a large proportion of Earth's strategic mineral deposits. This research investigates the origin of biotite modal layering and primary pseudo-sedimentary structures in felsic magmas, by using a combination of Crystal Size Distribution (CSD) analysis and Electron Probe Microanalysis (EPMA) to determine the mechanisms responsible for the development of these structures in the Carna Pluton, Connemara, Ireland. The Carna Pluton is a composite granodiorite intrusion and is one of five plutons comprising the Galway Granite Complex (425 - 380 Ma). Prominent 30 cm thick modal layers are defined by sharp basal contacts to a biotite-rich (20%) granite, which grades upward over 10 cm into biotite-poor, alkali-feldspar megacrystic granite. The layering strikes parallel to, and dips 30-60° N toward the external pluton contact. Pseudo-sedimentary structures (cross-bedding, flame structures, slumping and crystal graded bedding) are observed within these layers. Petrographic observations indicate the layers contain euhedral biotite and fresh undeformed quartz and feldspar. Throughout the pluton, alkali-feldspar phenocrysts define a foliation that is sub-parallel to the strike of biotite modal layers. Together these observations indicate that the intrusion's concentric foliation, biotite layers and associated structures formed in the magmatic state and due to a complex interaction between magma flow and crystallisation processes. Biotite CSDs (>250 crystals per sample) were determined for nine samples across three biotite-rich layers in a single unit. Preliminary CSD results suggest biotite within basal contacts accumulated via fractional crystallisation within an upward-growing crystal pile, likely reflecting the yield strength of the magma as a limiting factor to gravitational settling of biotite. This is supported by the abrupt decrease in mean biotite crystal size across the contact, compared to the biotite crystals in the megacrystic granite below. CSD results provide additional evidence for in-situ textural coarsening of biotite. This study proposes a new model for the crystallisation dynamics of the Carna Pluton. During emplacement, 2 - 5 cm alkali-feldspar megacrysts were aligned and fractional crystallisation was the primary mechanism driving the formation of biotite modal layers. Pseudo-sedimentary structures are interpreted to have formed due to the entrainment of biotite crystals within a necessarily highly fluid magma chamber. However, this interpretation is difficult to reconcile with the high viscosities commonly associated with granitic melts. To test this hypothesis, ongoing EPMA analysis on biotite F content and Fe/(Fe+Mg) ratios will assess whether the magma viscosity could have been low enough to produce these features via flow processes; or whether expansion of the pluton and tilting of planar primary magmatic layers, prior to solidification, could be responsible.

Structural Studies of Bacterioferritin B (BfrB) from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center¥

PubMed Central

Weeratunga, Saroja K.; Lovell, Scott; Yao, Huili; Battaile, Kevin P.; Fischer, Christopher J.; Gee, Casey E.; Rivera, Mario

2010-01-01

The structure of recombinant P. aeruginosa bacterioferritin B (Pa BfrB) has been solved from crystals grown from protein devoid of core mineral iron (as-isolated) and from protein mineralized with ~ 600 iron atoms (mineralized). Structures were also obtained from crystals grown from mineralized BfrB after soaking them in FeSO4 solution (Fe soak) and in separate experiments after soaking them in FeSO4 solution followed by soaking in crystallization solution (double soak). Although the structures consist of a typical bacterioferritin fold comprised of a nearly spherical 24-mer assembly that binds 12 heme molecules, comparison of microenvironments observed in the distinct structures provided interesting insights: The ferroxidase center in the as-isolated, mineralized and double soak structures is empty. The ferroxidase ligands (except His130) are poised to bind iron with minimal conformational changes. The His130 side chain, on the other hand, must rotate toward the ferroxidase center to coordinate iron. In comparison, the structure obtained from crystals soaked in an FeSO4 solution display a fully occupied ferroxidase center and iron bound to the internal, Fe(in), and external, Fe(out), surfaces of Pa BfrB. The conformation of His130 in this structure is rotated toward the ferroxidase center and coordinates an iron ion. The structures also revealed a pore on the surface of Pa BfrB that likely serves as an entry port for Fe2+ to the ferroxidase center. On its opposite end the pore is capped by the side chain of His130 when it adopts its “gate closed” conformation that enables coordination to a ferroxidase iron. A change to its “gate-open”, non-coordinative conformation, creates a path for the translocation of iron from the ferroxidase center to the interior cavity. These structural observations, together with findings obtained from iron incorporation measurements in solution suggest that the ferroxidase pore is the dominant entry route for the uptake of iron by Pa BfrB. These findings, which are clearly distinct from those made with E. coli Bfr (Crow, A. C., Lawson, T. L., Lewin, A., Moore, G. R., and Le Brun, N. E. (2009) J. Am. Chem. Soc. 131, 6808–6813) indicate that not all bacterioferritins operate in the same manner. PMID:20067302

A Non-Linear Model for Elastic Dielectric Crystals with Mobile Vacancies

DTIC Science & Technology

2009-07-01

crystals, vacancies typically carry an electric charge [18,37]. Such charged vacancies notably influence dielectric properties and elec- trical loss...characteristics of capacitors, oscillators, and tunable fil- ters [19], for example those comprised of perovskite ceramic crystals such as barium titanate...thermomechanical and thermoelectrical couplings, respectively, and the final term capturing non-mechanical sources of heat energy. 3.3. Representative free energy

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

Zhou, Chen; Pinkerton, Frederick E.; Herbst, Jan F.

New magnetic materials containing cerium, iron, and small additions of a third element are disclosed. These materials comprise compounds Ce(Fe.sub.12-xM.sub.x) where x=1-4, having the ThMn.sub.12 tetragonal crystal structure (space group I4/mmm, #139). Compounds with M=B, Al, Si, P, S, Sc, Co, Ni, Zn, Ga, Ge, Zr, Nb, Hf, Ta, and W are identified theoretically, and one class of compounds based on M=Si has been synthesized. The Si cognates are characterized by large magnetic moments (4.pi.M.sub.s greater than 1.27 Tesla) and high Curie temperatures (264.ltoreq.T.sub.c.ltoreq.305.degree. C.). The Ce(Fe.sub.12-xM.sub.x) compound may contain one or more of Ti, V, Cr, and Mo inmore » combination with an M element. Further enhancement in T.sub.c is obtained by nitriding the Ce compounds through heat treatment in N.sub.2 gas while retaining the ThMn.sub.12 tetragonal crystal structure; for example CeFe.sub.10Si.sub.2N.sub.1.29 has T.sub.c=426.degree. C.« less

A Highly Sensitive Resistive Pressure Sensor Based on a Carbon Nanotube-Liquid Crystal-PDMS Composite.

PubMed

Pan, Jin; Liu, Shiyu; Yang, Yicheng; Lu, Jiangang

2018-06-08

Resistive pressure sensors generally employ microstructures such as pores and pyramids in the active layer or on the electrodes to reduce the Young’s modulus and improve the sensitivity. However, such pressure sensors always exhibit complex fabrication process and have difficulties in controlling the uniformity of microstructures. In this paper, we demonstrated a highly sensitive resistive pressure sensor based on a composite comprising of low-polarity liquid crystal (LPLC), multi-walled carbon nanotube (MWCNT), and polydimethylsiloxane (PDMS) elastomer. The LPLC in the PDMS forms a polymer-dispersed liquid crystal (PDLC) structure which can not only reduce the Young’s modulus but also contribute to the construction of conductive paths in the active layer. By optimizing the concentration of LC in PDMS elastomer, the resistive pressure sensor shows a high sensitivity of 5.35 kPa −1 , fast response (<150 ms), and great durability. Fabrication process is also facile and the uniformity of the microstructures can be readily controlled. The pressure sensor offers great potential for applications in emerging wearable devices and electronic skins.

Crystalline ricin D, a toxic anti-tumor lectin from seeds of Ricinus communis

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

Wei, C.H.; Koh, C.

1978-03-25

A toxic lectin, ricin D, present in the seeds of Ricinus communis has been purified and crystallized in a form suitable for high resolution crystallographic structure studies. This protein is different from a previously found form of ricin (also present in the same seeds), the only ricin for which a preliminary x-ray investigation has been reported so far. Ricin D crystallizes from an aqueous solution in an orthorhombic unit cell of symmetry P2/sub 1/2/sub 1/2/sub 1/ and a = 79.0, b = 114.7, and c = 72.8 A. The asymmetric unit contains one molecule with an average molecular weight ofmore » 62,400. The crystal is fairly stable to x-radiation and has a water content of approximately 54% by volume. It appears to comprise two closely related species of proteins, the major species corresponding to ricin D and the other presumably corresponding to a deamidation product of ricin D. The two species have nearly identical molecular size and amino acid compositions, but different charges.« less

Fabrication and Analysis of Photonic Crystals

ERIC Educational Resources Information Center

Campbell, Dean J.; Korte, Kylee E.; Xia, Younan

2007-01-01

These laboratory experiments are designed to explore aspects of nanoscale chemistry by constructing and spectroscopically analyzing thin films of photonic crystals. Films comprised of colloidal spheres and polydimethylsiloxane exhibit diffraction-based stop bands that shift reversibly upon exposure to some common solvents. Topics covered in these…

Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.

PubMed

Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

2015-11-13

ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.

Multimode theory of plasmon excitation at a metal - photonic crystal interface

NASA Astrophysics Data System (ADS)

Kuznetsova, T. I.; Raspopov, N. A.

2017-12-01

Surface plasmon excitation at a photonic crystal - metal interface is studied taking into account multiple scattering of an initial light wave on a periodical crystal structure. The analysis is focused on calculating characteristics of the eigenwaves in a one-dimensional crystal, which comprise a set of harmonics with the wavevectors separated from each other by the value of the crystal lattice wavevector. Reflection from the crystal - metal interface binds the amplitudes of propagating and evanescent modes. Calculations show that for the dielectric characteristics of a synthetic opal and a substrate made of a real metal with a ruby laser radiation used as the initial wave, the fulfilment of plasmon resonance conditions leads to a local increase in the surface plasmon amplitude by a factor of 6.4 - 9 as compared to the average amplitude of the initial wave. As a rule, the effect can only be obtained for a single surface wave, all other waves being substantially weaker than the main plasmon. There is a specific case where the resonance condition holds for two modes simultaneously. In this case, two oppositely directed fluxes of equal intensity are generated at the interface. The resonance condition breaks at a small deviation of the incident angle of the initial wave θ from the normal direction (|θ| ⩾ 10-4 rad). In the latter case, the picture is asymmetric: at angles |θ| ⩾ 5 × 10-3 rad, only one plasmon remains intensive. The local density of electromagnetic energy at the photonic crystal - metal interface may exceed the corresponding value of the initial wave by a factor of 40 - 80.

Laser furnace and method for zone refining of semiconductor wafers

NASA Technical Reports Server (NTRS)

Griner, Donald B. (Inventor); zur Burg, Frederick W. (Inventor); Penn, Wayne M. (Inventor)

1988-01-01

A method of zone refining a crystal wafer (116 FIG. 1) comprising the steps of focusing a laser beam to a small spot (120) of selectable size on the surface of the crystal wafer (116) to melt a spot on the crystal wafer, scanning the small laser beam spot back and forth across the surface of the crystal wafer (116) at a constant velocity, and moving the scanning laser beam across a predetermined zone of the surface of the crystal wafer (116) in a direction normal to the laser beam scanning direction and at a selectible velocity to melt and refine the entire crystal wafer (116).

Crystal structure of 3-hy-droxy-methyl-1,2,3,4-tetra-hydro-isoquinolin-1-one.

PubMed

Caracelli, Ignez; Hino, Camila Lury; Zukerman-Schpector, Julio; Biaggio, Francisco Carlos; Tiekink, Edward R T

2015-08-01

In the title compound, C10H11NO2, two independent but virtually superimposable mol-ecules, A and B, comprise the asymmetric unit. The heterocyclic ring in each mol-ecule has a screw-boat conformation, and the methyl-hydroxyl group occupies a position to one side of this ring with N-C-C-O torsion angles of -55.30 (15) (mol-ecule A) and -55.94 (16)° (mol-ecule B). In the crystal, O-H⋯O and N-H⋯O hydrogen bonding leads to 11-membered {⋯HNCO⋯HO⋯HNC2O} heterosynthons, involving three different mol-ecules, which are edge-shared to generate a supra-molecular chain along the a axis. Inter-actions of the type C-H⋯O provide additional stability to the chains, and link these into a three-dimensional architecture.

Band transition and topological interface modes in 1D elastic phononic crystals.

PubMed

Yin, Jianfei; Ruzzene, Massimo; Wen, Jihong; Yu, Dianlong; Cai, Li; Yue, Linfeng

2018-05-01

In this report, we design a one-dimensional elastic phononic crystal (PC) comprised of an Aluminum beam with periodically arranged cross-sections to study the inversion of bulk bands due to the change of topological phases. As the geometric parameters of the unit cell varies, the second bulk band closes and reopens forming a topological transition point. This phenomenon is confirmed for both longitudinal waves and bending waves. By constructing a structural system formed by two PCs with different topological phases, for the first time, we experimentally demonstrate the existence of interface mode within the bulk band gap as a result of topological transition for both longitudinal and bending modes in elastic systems, although for bending modes, additional conditions have to be met in order to have the interface mode due to the dispersive nature of the bending waves in uniform media compared to the longitudinal waves.

Crystal Structure and Biochemical Characterization of a Mycobacterium smegmatis AAA-Type Nucleoside Triphosphatase Phosphohydrolase (Msm0858).

PubMed

Unciuleac, Mihaela-Carmen; Smith, Paul C; Shuman, Stewart

2016-05-15

AAA proteins (ATPases associated with various cellular activities) use the energy of ATP hydrolysis to drive conformational changes in diverse macromolecular targets. Here, we report the biochemical characterization and 2.5-Å crystal structure of a Mycobacterium smegmatis AAA protein Msm0858, the ortholog of Mycobacterium tuberculosis Rv0435c. Msm0858 is a magnesium-dependent ATPase and is active with all nucleoside triphosphates (NTPs) and deoxynucleoside triphosphates (dNTPs) as substrates. The Msm0858 structure comprises (i) an N-terminal domain (amino acids [aa] 17 to 201) composed of two β-barrel modules and (ii) two AAA domains, D1 (aa 212 to 473) and D2 (aa 476 to 744), each of which has ADP in the active site. Msm0858-ADP is a monomer in solution and in crystallized form. Msm0858 domains are structurally homologous to the corresponding modules of mammalian p97. However, the position of the N-domain modules relative to the AAA domains in the Msm0858-ADP tertiary structure is different and would impede the formation of a p97-like hexameric quaternary structure. Mutational analysis of the A-box and B-box motifs indicated that the D1 and D2 AAA domains are both capable of ATP hydrolysis. Simultaneous mutations of the D1 and D2 active-site motifs were required to abolish ATPase activity. ATPase activity was effaced by mutation of the putative D2 arginine finger, suggesting that Msm0858 might oligomerize during the ATPase reaction cycle. A truncated variant Msm0858 (aa 212 to 745) that lacks the N domain was characterized as a catalytically active homodimer. Recent studies have underscored the importance of AAA proteins (ATPases associated with various cellular activities) in the physiology of mycobacteria. This study reports the ATPase activity and crystal structure of a previously uncharacterized mycobacterial AAA protein, Msm0858. Msm0858 consists of an N-terminal β-barrel domain and two AAA domains, each with ADP bound in the active site. Msm0858 is a structural homolog of mammalian p97, with respect to the linear order and tertiary structures of their domains. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Lanthanum manganite-based air electrode for solid oxide fuel cells

DOEpatents

Ruka, Roswell J.; Kuo, Lewis; Li, Baozhen

1999-01-01

An air electrode material for a solid oxide fuel cell is disclosed. The electrode material is based on lanthanum manganite having a perovskite-like crystal structure ABO.sub.3. The A-site of the air electrode material preferably comprises La, Ca, Ce and at least one lanthanide selected from Sm, Gd, Dy, Er, Y and Nd. The B-site of the electrode material comprises Mn with substantially no dopants. The ratio of A:B is preferably slightly above 1. A preferred air electrode composition is of the formula La.sub.w Ca.sub.x Ln.sub.y Ce.sub.z MnO.sub.3, wherein Ln comprises at least one lanthanide selected from Sm, Gd, Dy, Er, Y and Nd, w is from about 0.55 to about 0.56, x is from about 0.255 to about 0.265, y is from about 0.175 to about 0.185, and z is from about 0.005 to about 0.02. The air electrode material possesses advantageous chemical and electrical properties as well as favorable thermal expansion and thermal cycle shrinkage characteristics.

Lanthanum manganite-based air electrode for solid oxide fuel cells

DOEpatents

Ruka, R.J.; Kuo, L.; Li, B.

1999-06-29

An air electrode material for a solid oxide fuel cell is disclosed. The electrode material is based on lanthanum manganite having a perovskite-like crystal structure ABO[sub 3]. The A-site of the air electrode material preferably comprises La, Ca, Ce and at least one lanthanide selected from Sm, Gd, Dy, Er, Y and Nd. The B-site of the electrode material comprises Mn with substantially no dopants. The ratio of A:B is preferably slightly above 1. A preferred air electrode composition is of the formula La[sub w]Ca[sub x]Ln[sub y]Ce[sub z]MnO[sub 3], wherein Ln comprises at least one lanthanide selected from Sm, Gd, Dy, Er, Y and Nd, w is from about 0.55 to about 0.56, x is from about 0.255 to about 0.265, y is from about 0.175 to about 0.185, and z is from about 0.005 to about 0.02. The air electrode material possesses advantageous chemical and electrical properties as well as favorable thermal expansion and thermal cycle shrinkage characteristics. 10 figs.

Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates.

PubMed

Moche, Martin; Shanklin, John; Ghoshal, Alokesh; Lindqvist, Ylva

2003-07-04

Delta9 stearoyl-acyl carrier protein (ACP) desaturase is a mu-oxo-bridged di-iron enzyme, which belongs to the structural class I of large helix bundle proteins and that catalyzes the NADPH and O2-dependent formation of a cis-double bond in stearoyl-ACP. The crystal structures of complexes with azide and acetate, respectively, as well as the apoand single-iron forms of Delta9 stearoyl-ACP desaturase from Ricinus communis have been determined. In the azide complex, the ligand forms a mu-1,3-bridge between the two iron ions in the active site, replacing a loosely bound water molecule. The structure of the acetate complex is similar, with acetate bridging the di-iron center in the same orientation with respect to the di-iron center. However, in this complex, the iron ligand Glu196 has changed its coordination mode from bidentate to monodentate, the first crystallographic observation of a carboxylate shift in Delta9 stearoyl-ACP desaturase. The two complexes are proposed to mimic a mu-1,2 peroxo intermediate present during catalytic turnover. There are striking structural similarities between the di-iron center in the Delta9 stearoyl-ACP desaturase-azide complex and in the reduced rubrerythrin-azide complex. This suggests that Delta9 stearoyl-ACP desaturase might catalyze the formation of water from exogenous hydrogen peroxide at a low rate. From the similarity in iron center structure, we propose that the mu-oxo-bridge in oxidized desaturase is bound to the di-iron center as in rubrerythrin and not as reported for the R2 subunit of ribonucleotide reductase and the hydroxylase subunit of methane monooxygenase. The crystal structure of the one-iron depleted desaturase species demonstrates that the affinities for the two iron ions comprising the di-iron center are not equivalent, Fe1 being the higher affinity site and Fe2 being the lower affinity site.

Chromatic X-ray magnifying method and apparatus by Bragg reflective planes on the surface of Abbe sphere

DOEpatents

Thoe, Robert S.

1991-01-01

Method and apparatus for producing sharp, chromatic, magnified images of X-ray emitting objects, are provided. The apparatus, which constitutes an X-ray microscope or telescope, comprises a connected collection of Bragg reflecting planes, comprised of either a bent crystal or a synthetic multilayer structure, disposed on and adjacent to a locus determined by a spherical surface. The individual Bragg planes are spatially oriented to Bragg reflect radiation from the object location toward the image location. This is accomplished by making the Bragg planes spatially coincident with the surfaces of either a nested series of prolate ellipsoids of revolution, or a nested series of spheres. The spacing between the Bragg reflecting planes can be tailored to control the wavelengths and the amount of the X-radiation that is Bragg reflected to form the X-ray image.

Structure, function, and self-assembly of single network gyroid (I4132) photonic crystals in butterfly wing scales.

PubMed

Saranathan, Vinodkumar; Osuji, Chinedum O; Mochrie, Simon G J; Noh, Heeso; Narayanan, Suresh; Sandy, Alec; Dufresne, Eric R; Prum, Richard O

2010-06-29

Complex three-dimensional biophotonic nanostructures produce the vivid structural colors of many butterfly wing scales, but their exact nanoscale organization is uncertain. We used small angle X-ray scattering (SAXS) on single scales to characterize the 3D photonic nanostructures of five butterfly species from two families (Papilionidae, Lycaenidae). We identify these chitin and air nanostructures as single network gyroid (I4(1)32) photonic crystals. We describe their optical function from SAXS data and photonic band-gap modeling. Butterflies apparently grow these gyroid nanostructures by exploiting the self-organizing physical dynamics of biological lipid-bilayer membranes. These butterfly photonic nanostructures initially develop within scale cells as a core-shell double gyroid (Ia3d), as seen in block-copolymer systems, with a pentacontinuous volume comprised of extracellular space, cell plasma membrane, cellular cytoplasm, smooth endoplasmic reticulum (SER) membrane, and intra-SER lumen. This double gyroid nanostructure is subsequently transformed into a single gyroid network through the deposition of chitin in the extracellular space and the degeneration of the rest of the cell. The butterflies develop the thermodynamically favored double gyroid precursors as a route to the optically more efficient single gyroid nanostructures. Current approaches to photonic crystal engineering also aim to produce single gyroid motifs. The biologically derived photonic nanostructures characterized here may offer a convenient template for producing optical devices based on biomimicry or direct dielectric infiltration.

Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii

PubMed Central

Sutton, Kristin A.; Breen, Jennifer; Russo, Thomas A.; Schultz, L. Wayne; Umland, Timothy C.

2016-01-01

The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the sixth step of the seven-step shikimate pathway. Chorismate, the product of the pathway, is a precursor for the biosynthesis of aromatic amino acids, siderophores and metabolites such as folate, ubiquinone and vitamin K. The shikimate pathway is present in bacteria, fungi, algae, plants and apicomplexan parasites, but is absent in humans. The EPSP synthase enzyme produces 5-enolpyruvylshikimate 3-phosphate and phosphate from phosphoenolpyruvate and shikimate 3-phosphate via a transferase reaction, and is the target of the herbicide glyphosate. The Acinetobacter baumannii gene encoding EPSP synthase, aroA, has previously been demonstrated to be essential during host infection for the growth and survival of this clinically important drug-resistant ESKAPE pathogen. Prephenate dehydrogenase is also encoded by the bifunctional A. baumannii aroA gene, but its activity is dependent upon EPSP synthase since it operates downstream of the shikimate pathway. As part of an effort to evaluate new antimicrobial targets, recombinant A. baumannii EPSP (AbEPSP) synthase, comprising residues Ala301–Gln756 of the aroA gene product, was overexpressed in Escherichia coli, purified and crystallized. The crystal structure, determined to 2.37 Å resolution, is described in the context of a potential antimicrobial target and in comparison to EPSP synthases that are resistant or sensitive to the herbicide glyphosate. PMID:26919521

Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii.

PubMed

Sutton, Kristin A; Breen, Jennifer; Russo, Thomas A; Schultz, L Wayne; Umland, Timothy C

2016-03-01

The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the sixth step of the seven-step shikimate pathway. Chorismate, the product of the pathway, is a precursor for the biosynthesis of aromatic amino acids, siderophores and metabolites such as folate, ubiquinone and vitamin K. The shikimate pathway is present in bacteria, fungi, algae, plants and apicomplexan parasites, but is absent in humans. The EPSP synthase enzyme produces 5-enolpyruvylshikimate 3-phosphate and phosphate from phosphoenolpyruvate and shikimate 3-phosphate via a transferase reaction, and is the target of the herbicide glyphosate. The Acinetobacter baumannii gene encoding EPSP synthase, aroA, has previously been demonstrated to be essential during host infection for the growth and survival of this clinically important drug-resistant ESKAPE pathogen. Prephenate dehydrogenase is also encoded by the bifunctional A. baumannii aroA gene, but its activity is dependent upon EPSP synthase since it operates downstream of the shikimate pathway. As part of an effort to evaluate new antimicrobial targets, recombinant A. baumannii EPSP (AbEPSP) synthase, comprising residues Ala301-Gln756 of the aroA gene product, was overexpressed in Escherichia coli, purified and crystallized. The crystal structure, determined to 2.37 Å resolution, is described in the context of a potential antimicrobial target and in comparison to EPSP synthases that are resistant or sensitive to the herbicide glyphosate.

Structure, function, and self-assembly of single network gyroid (I4132) photonic crystals in butterfly wing scales

PubMed Central

Saranathan, Vinodkumar; Osuji, Chinedum O.; Mochrie, Simon G. J.; Noh, Heeso; Narayanan, Suresh; Sandy, Alec; Dufresne, Eric R.; Prum, Richard O.

2010-01-01

Complex three-dimensional biophotonic nanostructures produce the vivid structural colors of many butterfly wing scales, but their exact nanoscale organization is uncertain. We used small angle X-ray scattering (SAXS) on single scales to characterize the 3D photonic nanostructures of five butterfly species from two families (Papilionidae, Lycaenidae). We identify these chitin and air nanostructures as single network gyroid (I4132) photonic crystals. We describe their optical function from SAXS data and photonic band-gap modeling. Butterflies apparently grow these gyroid nanostructures by exploiting the self-organizing physical dynamics of biological lipid-bilayer membranes. These butterfly photonic nanostructures initially develop within scale cells as a core-shell double gyroid (Ia3d), as seen in block-copolymer systems, with a pentacontinuous volume comprised of extracellular space, cell plasma membrane, cellular cytoplasm, smooth endoplasmic reticulum (SER) membrane, and intra-SER lumen. This double gyroid nanostructure is subsequently transformed into a single gyroid network through the deposition of chitin in the extracellular space and the degeneration of the rest of the cell. The butterflies develop the thermodynamically favored double gyroid precursors as a route to the optically more efficient single gyroid nanostructures. Current approaches to photonic crystal engineering also aim to produce single gyroid motifs. The biologically derived photonic nanostructures characterized here may offer a convenient template for producing optical devices based on biomimicry or direct dielectric infiltration. PMID:20547870

One-step synthesis and structural features of CdS/montmorillonite nanocomposites.

PubMed

Han, Zhaohui; Zhu, Huaiyong; Bulcock, Shaun R; Ringer, Simon P

2005-02-24

A novel synthesis method was introduced for the nanocomposites of cadmium sulfide and montmorillonite. This method features the combination of an ion exchange process and an in situ hydrothermal decomposition process of a complex precursor, which is simple in contrast to the conventional synthesis methods that comprise two separate steps for similar nanocomposite materials. Cadmium sulfide species in the composites exist in the forms of pillars and nanoparticles, the crystallized sulfide particles are in the hexagonal phase, and the sizes change when the amount of the complex for the synthesis is varied. Structural features of the nanocomposites are similar to those of the clay host but changed because of the introduction of the sulfide into the clay.

Recent advance in the design of small molecular modulators of estrogen-related receptors.

PubMed

Lu, Xiaoyun; Peng, Lijie; Lv, Man; ding, Ke

2012-01-01

The estrogen-related receptors (ERRs), comprising ERRα, ERRβ and ERRγ, are the members of the nuclear receptor superfamily, which have been functionally implicated in estrogen signal pathway in various patterns. However, no natural ligand of ERRs has been identified to data, so identification of the synthetic modulators (inverse agonist and agonist) of ERRs would be highly effective in the treatment of estrogen-related pathologies, such as diabetes, breast cancer and osteoporosis. This review summarizes the structures and biological functions of ERR subtypes, and the progress in designing the small molecular modulators of ERRs as well as the detailed description of available co-crystal structures of the LBD of ERRs in three distinct states: unligand, inverse agonist bound, and agonist bound.

Self-Assembly in Systems Containing Silicone Compounds

NASA Astrophysics Data System (ADS)

Ferreira, Maira Silva; Loh, Watson

2009-01-01

Chemical systems formed by silicone solvents and surfactants have potential applications in a variety of industrial products. In spite of their technological relevance, there are few reports on the scientific literature that focus on characterizing such ternary systems. In this work, we have aimed to develop a general, structural investigation on the phase diagram of one system that typically comprises silicone-based chemicals, by means of the SAXS (small-angle X-ray scattering) technique. Important features such as the presence of diverse aggregation states in the overall system, either on their own or in equilibrium with other structures, have been detected. As a result, optically isotropic chemical systems (direct and/or reversed microemulsions) and liquid crystals with lamellar or hexagonal packing have been identified and characterized.

Predicting the structural and electronic properties of two-dimensional single layer boron nitride sheets

NASA Astrophysics Data System (ADS)

Li, Xiao-Dong; Cheng, Xin-Lu

2018-02-01

Three two-dimensional (2D) single layer boron nitride sheets have been predicted based on the first-principles calculations. These 2D boron nitride sheets are comprised of equivalent boron atoms and nitride atoms with sp2 and sp bond hybridization. The geometry optimization reflects that they all possess stable planar crystal structures with the space group P 6 bar 2 m (D3h3) symmetry. The charge density distribution manifests that the B-N bonds in these boron nitride sheets are covalent in nature but with ionic characteristics. The tunable band gaps indicate their potential applications in nanoscale electronic and optoelectronic devices by changing the length of sp-bonded Bsbnd N linkages.

Cluster Tool for In Situ Processing and Comprehensive Characterization of Thin Films at High Temperatures.

PubMed

Wenisch, Robert; Lungwitz, Frank; Hanf, Daniel; Heller, René; Zscharschuch, Jens; Hübner, René; von Borany, Johannes; Abrasonis, Gintautas; Gemming, Sibylle; Escobar-Galindo, Ramon; Krause, Matthias

2018-06-13

A new cluster tool for in situ real-time processing and depth-resolved compositional, structural and optical characterization of thin films at temperatures from -100 to 800 °C is described. The implemented techniques comprise magnetron sputtering, ion irradiation, Rutherford backscattering spectrometry, Raman spectroscopy, and spectroscopic ellipsometry. The capability of the cluster tool is demonstrated for a layer stack MgO/amorphous Si (∼60 nm)/Ag (∼30 nm), deposited at room temperature and crystallized with partial layer exchange by heating up to 650 °C. Its initial and final composition, stacking order, and structure were monitored in situ in real time and a reaction progress was defined as a function of time and temperature.

Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers

PubMed Central

Feld, Geoffrey K.; Thoren, Katie L.; Kintzer, Alexander F.; Sterling, Harry J.; Tang, Iok I.; Greenberg, Shoshana G.; Williams, Evan R.; Krantz, Bryan A.

2011-01-01

The protein transporter, anthrax lethal toxin, is comprised of protective antigen (PA), a transmembrane translocase, and lethal factor (LF), a cytotoxic enzyme. Following assembly into holotoxin complexes, PA forms an oligomeric channel that unfolds LF and translocates it into the host cell. We report the crystal structure of the core of a lethal toxin complex to 3.1-Å resolution; the structure contains a PA octamer bound to four LF PA-binding domains (LFN). The first α helix and β strand of each LFN unfold and dock into a deep amphipathic cleft on the surface of the PA octamer, which we call the α clamp. The α clamp possesses nonspecific polypeptide binding activity and is functionally relevant to efficient holotoxin assembly, PA octamer formation, and LF unfolding and translocation. This structure provides insight on the mechanism of translocation-coupled protein unfolding. PMID:21037566

Bottom-up construction of a superstructure in a porous uranium-organic crystal

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

Li, Peng; Vermeulen, Nicolaas A.; Malliakas, Christos D.

Bottom-up construction of highly intricate structures from simple building blocks remains one of the most difficult challenges in chemistry. We report a structurally complex, mesoporous uranium-based metal-organic framework (MOF) made from simple starting components. The structure comprises 10 uranium nodes and seven tricarboxylate ligands (both crystallographically nonequivalent), resulting in a 173.3-angstrom cubic unit cell enclosing 816 uranium nodes and 816 organic linkers—the largest unit cell found to date for any nonbiological material. The cuboctahedra organize into pentagonal and hexagonal prismatic secondary structures, which then form tetrahedral and diamond quaternary topologies with unprecedented complexity. This packing results in the formation ofmore » colossal icosidodecahedral and rectified hexakaidecahedral cavities with internal diameters of 5.0 nanometers and 6.2 nanometers, respectively—ultimately giving rise to the lowest-density MOF reported to date.« less

SCINTILLATION EXPOSURE RATE DETECTOR

DOEpatents

Spears, W.G.

1960-11-01

A radiation detector for gamma and x rays is described. The detector comprises a scintillation crystal disposed between a tantalum shield and the input of a photomultiplier tube, the crystal and the shield cooperating so that their combined response to a given quantity of radiation at various energy levels is substantially constant.

Chalcogenide nanocrystal assembly: Controlling heterogeneity and modulating heterointerfaces

NASA Astrophysics Data System (ADS)

Davis, Jessica

This dissertation work is focused on developing methods to facilitate charge transport in heterostructured materials that comprise a nanoscale component. Multicomponent semiconductor materials were prepared by (1) spin coating of discrete nanomaterials onto porous silicon (pSi) or (2) self-assembly. Spin-coating of colloidal quantum dot (QD) PbS solutions was employed to create prototype PbS QD based radiation detection devices using porous silicon (pSi) as an n-type support and charge transport material. These devices were initially tested as a photodetector to ascertain the possibility of their use in high energy radiation detection. Short chain thiolate ligands (4-fluorothiophenolate) and anion passivation at the particle interface were evaluated to augment interparticle transport. However, the samples showed minimum interaction with the light source possibly due to poor infiltration into the pSi. The second project was also driven by the potential synergistic properties that can be achieved in multicomponent metal chalcogenide nanostructures, potentially useful in optoelectronic devices. Working with well-established methods for single component metal chalcogenide (MQ) particle gels this dissertation research sought to develop practical methods for co-gelation of different component particles with complimentary functionalities. By monitoring the kinetics of aggregation using time resolved dynamic light scattering and NMR spectroscopy the kinetics of aggregation of the two most common crystal structures for CdQ nanocrystals was studied and it was determined that the hexagonal (wurtzite) crystal structure aggregated faster than the cubic (zinc blende) crystal structure. For gel coupling of nanoparticles with differing Q (Q=S, Se and Te), once we accounted for the crystal structure effects, it was determined that the relative redox characteristics of Q govern the reaction rate. The oxidative sol-gel assembly routes were also employed to fabricate metal chalcogenide NC gels with different NC components with control over the degree of mixing. In order to control the degree of mixing, the factors that underscore sol-gel oxidative assembly were elucidated and the aggregation and gelation kinetics of metal chalcogenide QDs were monitored through time-resolved dynamic light scattering (TR-DLS), and nuclear magnetic resonance spectroscopy (NMR). Through these kinetic studies of the surface speciation of metal chalcogenides, control over heterogeneity in dual component CdSe-ZnS system, was achieved through adjustment of the capping ligand, the native crystal structure and the chalcogenide, thereby changing the relative rates of assembly for each component independently.

Reusable fast opening switch

DOEpatents

Van Devender, J.P.; Emin, D.

1983-12-21

A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and metallic states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.

Reusable fast opening switch

DOEpatents

Van Devender, John P.; Emin, David

1986-01-01

A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and insulating states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.

Loading rate effect on nanohardness of human enamel

NASA Astrophysics Data System (ADS)

Biswas, Nilormi; Dey, Arjun; Mukhopadhyay, Anoop K.

2012-07-01

In the present work, nanoindentation technique has been utilised to study the physics of deformation at the scale of micro/nano-structure of tooth enamel which is basically the hardest natural biomaterial in the human body comprising of a hybrid combination of hydroxypatite ceramic nano-crystal and organic-protein matrix. We have observed about 8 % increase in the nanohardness of human enamel with the increase in loading rate from 1 × 103 μN s-1 to 3 × 105 μN s-1. The results have been explained in terms of the maximum shear stress generated underneath the nanoindenter.

Crystal Structure of Menin Reveals Binding Site for Mixed Lineage Leukemia (MLL) Protein

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

Murai, Marcelo J.; Chruszcz, Maksymilian; Reddy, Gireesh

2014-10-02

Menin is a tumor suppressor protein that is encoded by the MEN1 (multiple endocrine neoplasia 1) gene and controls cell growth in endocrine tissues. Importantly, menin also serves as a critical oncogenic cofactor of MLL (mixed lineage leukemia) fusion proteins in acute leukemias. Direct association of menin with MLL fusion proteins is required for MLL fusion protein-mediated leukemogenesis in vivo, and this interaction has been validated as a new potential therapeutic target for development of novel anti-leukemia agents. Here, we report the first crystal structure of menin homolog from Nematostella vectensis. Due to a very high sequence similarity, the Nematostellamore » menin is a close homolog of human menin, and these two proteins likely have very similar structures. Menin is predominantly an {alpha}-helical protein with the protein core comprising three tetratricopeptide motifs that are flanked by two {alpha}-helical bundles and covered by a {beta}-sheet motif. A very interesting feature of menin structure is the presence of a large central cavity that is highly conserved between Nematostella and human menin. By employing site-directed mutagenesis, we have demonstrated that this cavity constitutes the binding site for MLL. Our data provide a structural basis for understanding the role of menin as a tumor suppressor protein and as an oncogenic co-factor of MLL fusion proteins. It also provides essential structural information for development of inhibitors targeting the menin-MLL interaction as a novel therapeutic strategy in MLL-related leukemias.« less

Crystal Structure of the Escherichia coli 23S rRNA: m{5}C Methyltransferase RlmI (YccW) Reveals Evolutionary Links Between RNA Modification Enzymes

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

Sunita, S.; Tkaczuk, K; Purta, E

2008-01-01

Methylation is the most common RNA modification in the three domains of life. Transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to specific atoms of RNA nucleotides is catalyzed by methyltransferase (MTase) enzymes. The rRNA MTase RlmI (rRNA large subunit methyltransferase gene I; previously known as YccW) specifically modifies Escherichia coli 23S rRNA at nucleotide C1962 to form 5-methylcytosine. Here, we report the crystal structure of RlmI refined at 2 {angstrom} to a final R-factor of 0.194 (R{sub free} = 0.242). The RlmI molecule comprises three domains: the N-terminal PUA domain; the central domain, which resembles a domain previously foundmore » in RNA:5-methyluridine MTases; and the C-terminal catalytic domain, which contains the AdoMet-binding site. The central and C-terminal domains are linked by a {Beta}-hairpin structure that has previously been observed in several MTases acting on nucleic acids or proteins. Based on bioinformatics analyses, we propose a model for the RlmI-AdoMet-RNA complex. Comparative structural analyses of RlmI and its homologs provide insight into the potential function of several structures that have been solved by structural genomics groups and furthermore indicate that the evolutionary paths of RNA and DNA 5-methyluridine and 5-methylcytosine MTases have been closely intertwined.« less

Structural Basis of Interdomain Communication in the Hsc70 Chaperone

PubMed Central

Jiang, Jianwen; Prasad, Kondury; Lafer, Eileen M.; Sousa, Rui

2015-01-01

Summary Hsp70 family proteins are highly conserved chaperones involved in protein folding, degradation, targeting and translocation, and protein complex remodeling. They are comprised of an N-terminal nucleotide binding domain (NBD) and a C-terminal protein substrate binding domain (SBD). ATP binding to the NBD alters SBD conformation and substrate binding kinetics, but an understanding of the mechanism of interdomain communication has been hampered by the lack of a crystal structure of an intact chaperone. Were-port here the 2.6 Å structure of a functionally intact bovine Hsc70 (bHsc70) and a mutational analysis of the observed interdomain interface and the immediately adjacent interdomain linker. This analysis identifies interdomain interactions critical for chaperone function and supports an allosteric mechanism in which the interdomain linker invades and disrupts the interdomain interface when ATP binds. PMID:16307916

Direct-patterned optical waveguides on amorphous silicon films

DOEpatents

Vernon, Steve; Bond, Tiziana C.; Bond, Steven W.; Pocha, Michael D.; Hau-Riege, Stefan

2005-08-02

An optical waveguide structure is formed by embedding a core material within a medium of lower refractive index, i.e. the cladding. The optical index of refraction of amorphous silicon (a-Si) and polycrystalline silicon (p-Si), in the wavelength range between about 1.2 and about 1.6 micrometers, differ by up to about 20%, with the amorphous phase having the larger index. Spatially selective laser crystallization of amorphous silicon provides a mechanism for controlling the spatial variation of the refractive index and for surrounding the amorphous regions with crystalline material. In cases where an amorphous silicon film is interposed between layers of low refractive index, for example, a structure comprised of a SiO.sub.2 substrate, a Si film and an SiO.sub.2 film, the formation of guided wave structures is particularly simple.

Electro-optical tunable birefringent filter

DOEpatents

Levinton, Fred M [Princeton, NJ

2012-01-31

An electrically tunable Lyot type filter is a Lyot that include one or more filter elements. Each filter element may have a planar, solid crystal comprised of a material that exhibits birefringence and is electro-optically active. Transparent electrodes may be coated on each face of the crystal. An input linear light polarizer may be located on one side of the crystal and oriented at 45 degrees to the optical axis of the birefringent crystal. An output linear light polarizer may be located on the other side of the crystal and oriented at -45 degrees with respect to the optical axis of the birefringent crystal. When an electric voltage is applied between the electrodes, the retardation of the crystal changes and so does the spectral transmission of the optical filter.

Modular supramolecular approach for co-crystallization of donors and acceptors into ordered networks

DOEpatents

Stupp, Samuel I.; Stoddart, J. Fraser; Shveyd, Alex K.; Tayi, Alok S.; Sue, Andrew C. H.; Narayanan, Ashwin

2016-09-20

Organic charge-transfer (CT) co-crystals in a mixed stack system are disclosed, wherein a donor molecule (D) and an acceptor molecule (A) occupy alternating positions (DADADA) along the CT axis. A platform is provided which amplifies the molecular recognition of donors and acceptors and produces co-crystals at ambient conditions, wherein the platform comprises (i) a molecular design of the first constituent (.alpha.-complement), (ii) a molecular design of the second compound (.beta.-complement), and (iii) a solvent system that promotes co-crystallization.

Lithium niobate single-crystal and photo-functional device

DOEpatents

Gopalan, Venkatraman; Mitchell, Terrence E.; Kitamura, Kenji; Furukawa, Yasunori

2001-01-01

Provided are lithium niobate single-crystal that requires a low voltage of not larger than 10 kV/nm for its ferroelectric polarization inversion and of which the polarization can be periodically inverted with accuracy even at such a low voltage, and a photo-functional device comprising the crystal. The crystal has a molar fraction of Li.sub.2 O/(Nb.sub.2 O.sub.5 +Li.sub.2 O) of falling between 0.49 and 0.52. The photo-functional device can convert a laser ray being incident thereon.

Modular supramolecular approach for co-crystallization of donors and acceptors into ordered networks

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

Stupp, Samuel I.; Stoddart, J. Fraser; Shveyd, Alexander K.

Organic charge-transfer (CT) co-crystals in a mixed stack system are disclosed, wherein a donor molecule (D) and an acceptor molecule (A) occupy alternating positions (DADADA) along the CT axis. A platform is provided which amplifies the molecular recognition of donors and acceptors and produces co-crystals at ambient conditions, wherein the platform comprises (i) a molecular design of the first constituent (.alpha.-complement), (ii) a molecular design of the second compound (.beta.-complement), and (iii) a solvent system that promotes co-crystallization.

Electroluminescent devices formed using semiconductor nanocrystals as an electron transport media and method of making such electroluminescent devices

DOEpatents

Alivisatos, A. Paul; Colvin, Vickie

1996-01-01

An electroluminescent device is described, as well as a method of making same, wherein the device is characterized by a semiconductor nanocrystal electron transport layer capable of emitting visible light in response to a voltage applied to the device. The wavelength of the light emitted by the device may be changed by changing either the size or the type of semiconductor nanocrystals used in forming the electron transport layer. In a preferred embodiment the device is further characterized by the capability of emitting visible light of varying wavelengths in response to changes in the voltage applied to the device. The device comprises a hole processing structure capable of injecting and transporting holes, and usually comprising a hole injecting layer and a hole transporting layer; an electron transport layer in contact with the hole processing structure and comprising one or more layers of semiconductor nanocrystals; and an electron injecting layer in contact with the electron transport layer for injecting electrons into the electron transport layer. The capability of emitting visible light of various wavelengths is principally based on the variations in voltage applied thereto, but the type of semiconductor nanocrystals used and the size of the semiconductor nanocrystals in the layers of semiconductor nanometer crystals may also play a role in color change, in combination with the change in voltage.

Single crystal EPR study at 95 GHz of a large Fe based molecular nanomagnet: toward the structuring of magnetic nanoparticle properties.

PubMed

Castelli, L; Fittipaldi, M; Powell, A K; Gatteschi, D; Sorace, L

2011-08-28

A W-band single-crystal EPR study has been performed on a molecular cluster comprising 19 iron(III) ions bridged by oxo- hydroxide ions, Fe(19), in order to investigate magnetic nanosystems with a behavior in between the one of Magnetic NanoParticles (MNP) and that of Single Molecule Magnets (SMM). The Fe(19) has a disk-like shape: a planar Fe(7) core with a brucite (Mg(OH)(2)) structure enclosed in a "shell" of 12 Fe(III) ions. EPR and magnetic measurements revealed an S = 35/2 ground state with an S = 33/2 excited state lying ∼ 8 K above. The presence of other low-lying excited states was also envisaged. Rhombic Zero Field Splitting (ZFS) tensors were determined, the easy axes lying in the Fe(19) plane for both the multiplets. At particular temperatures and orientations, a partially resolved fine structure could be observed which could not be distinguished in powder spectra, due to orientation disorder. The similarities of the EPR behavior of Fe(19) and MNP, together with the accuracy of single crystal analysis, helped to shed light on spectral features observed in MNP spectra, that is a sharp line at g = 2 and a low intensity transition at g = 4. Moreover, a theoretical analysis has been used to estimate the contribution to the total magnetic anisotropy of core and surface; this latter is crucial in determining the easy axis-type anisotropy, alike that of MNP surface. This journal is © The Royal Society of Chemistry 2011

Crystal structure of octa­kis­(4-meth­oxy­pyridinium) bis­(4-meth­oxy­pyridine-κN)tetra­kis­(thio­cyanato-κN)ferrate(III) bis­[(4-meth­oxypyri­dine-κN)pentakis­(thio­cyanato-κN)ferrate(III)] hexa­kis­(thio­cyanato-κN)ferrate(III) with iron in three different octa­hedral coordination environments

PubMed Central

Jochim, Aleksej; Jess, Inke; Näther, Christian

2018-01-01

The crystal structure of the title salt, (C6H8NO)8[Fe(NCS)4(C6H7NO)2][Fe(NCS)5(C6H7NO)]2[Fe(NCS)6], comprises three negatively charged octa­hedral FeIII complexes with different coordination environments in which the FeIII atoms are coordinated by a different number of thio­cyanate anions and 4-meth­oxy­pyridine ligands. Charge balance is achieved by 4-meth­oxy­pyridinium cations. The asymmetric unit consists of three FeIII cations, one of which is located on a centre of inversion, one on a twofold rotation axis and one in a general position, and ten thio­cyanate anions, two 4-meth­oxy­pyridine ligands and 4-meth­oxy­pyridinium cations (one of which is disordered over two sets of sites). Beside to Coulombic inter­actions between organic cations and the ferrate(III) anions, weak N—H⋯S hydrogen-bonding inter­actions involving the pyridinium N—H groups of the cations and the thio­cyanate S atoms of the complex anions are mainly responsible for the cohesion of the crystal structure. PMID:29765708

Programmable growth of branched silicon nanowires using a focused ion beam.

PubMed

Jun, Kimin; Jacobson, Joseph M

2010-08-11

Although significant progress has been made in being able to spatially define the position of material layers in vapor-liquid-solid (VLS) grown nanowires, less work has been carried out in deterministically defining the positions of nanowire branching points to facilitate more complicated structures beyond simple 1D wires. Work to date has focused on the growth of randomly branched nanowire structures. Here we develop a means for programmably designating nanowire branching points by means of focused ion beam-defined VLS catalytic points. This technique is repeatable without losing fidelity allowing multiple rounds of branching point definition followed by branch growth resulting in complex structures. The single crystal nature of this approach allows us to describe resulting structures with linear combinations of base vectors in three-dimensional (3D) space. Finally, by etching the resulting 3D defined wire structures branched nanotubes were fabricated with interconnected nanochannels inside. We believe that the techniques developed here should comprise a useful tool for extending linear VLS nanowire growth to generalized 3D wire structures.

RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn

PubMed Central

Schroeder, Kersten T.; Daldrop, Peter; Lilley, David M.J.

2011-01-01

Summary The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure. PMID:21893284

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

PubMed

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-12-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

PubMed Central

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-01-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit. PMID:12515387

Crystal structure of an SH2-kinase construct of c-Abl and effect of the SH2 domain on kinase activity

PubMed Central

Lorenz, Sonja; Deng, Patricia; Hantschel, Oliver; Superti-Furga, Giulio; Kuriyan, John

2018-01-01

Constitutive activation of the non-receptor tyrosine kinase c-Abl (Abl1) in the Bcr-Abl1 fusion oncoprotein is the molecular cause of chronic myeloid leukemia. Recent studies have indicated that an interaction between the SH2 domain and the N-lobe of the c-Abl kinase domain has a critical role in leukemogenesis. To dissect the structural basis of this phenomenon we studied c-Abl constructs comprising the SH2 and kinase domains in vitro. We present a crystal structure of an SH2-kinase domain construct bound to dasatinib, which contains the relevant interface between the SH2 domain and the N-lobe of the kinase domain. We show that the presence of the SH2 domain enhances kinase activity moderately and that this effect depends on contacts in the SH2-N-lobe interface and is abrogated by specific mutations. Consistently, formation of the interface decreases slightly the association rate of imatinib with the kinase domain. That the effects are small compared to the dramatic in vivo consequences suggests an important function of the SH2-N-lobe interaction might be to help disassemble the autoinhibited conformation of c-Abl and promote processive phosphorylation, rather than substantially stimulate kinase activity. PMID:25779001

Exposure to space radiation of high-performance infrared multilayer filters

NASA Technical Reports Server (NTRS)

Seeley, J. S.; Hawkins, G. J.; Hunneman, R.

1991-01-01

The University of Reading experiment exposed IR interference filters and crystal substrates on identical earth facing and leading-edge sites of the Long Duration Exposure Facility (LDEF). Filters mostly comprised multilayer coatings of lead telluride (PbTe)/II-IV on germanium (Ge) and other substrates: crystals comprised CdTe, MgF2, sapphire, quartz, silicon, and some softer materials. Identical control samples were maintained in the laboratory throughout the experiment. The filters were novel in their design, construction and manufacture, and categorized high-performance because of their ability to resolve emission spectra of the important atmospheric gases for various purposes in remote sensing. No significant changes were found in the spectra of the hard-coated filters or in the harder crystals (the softer materials were degraded to an extent). By virtue of this well-documented and long exposure in LDEF, the qualification of the filter type is significantly improved for its future requirements.

Influence of a mineral insecticide particle size on bait efficacy against Reticulitermes flavipes (Isoptera: Rhinotermitidae)

Treesearch

Thomas g. Shelton; Laurent Cartier; Terence L. Wagner; Christian Becker

2007-01-01

We examined the efficacy of termiticidal baits comprised of powdered acellulose and a mineral insecticide, cryolite crystals, in laboratory bioassays against pseudergates of Eastern subterranean termites [Reticulitermes flavipes (Kollar)]. The influence of cryolite crystal size [0 (control), 0.2, and 20 pm diameter particles] on the overall mortality...

"Bettering Her Education and Widening Her Sphere": Betwixt and between Coeducational Experiences

ERIC Educational Resources Information Center

Snowden, Monique L.

2011-01-01

This article is a focused response to the call for a "conscious use of crystallization," in qualitative research. To this end, the author brings into play a full-bodied textual metaphor, the "palimpsest," to stimulate the expansion of an integrated crystallization typology--comprised of woven and patched approaches.…

Pyritized mudstone and associated facies in the Permian-Triassic boundary of the Çürük Daǧ section, Southern Turkey

NASA Astrophysics Data System (ADS)

Varol, Baki; Koşun, Erdal; Ünal Pinar, Neslihan; Ayranci, Korhan

2011-03-01

This paper is the first study of pyritized mudstones (PM) in the Permian-Triassic (P-T) boundary section of the Çürük Dağ (Taurus, Antalya Nappes, Turkey). The mudstones were generally formed as lensoidal-shaped layers or infill materials within nodular platform limestones (hardground). Normal marine fauna is diminished in the pyritized limestones, whereas tube-like microorganisms are apparently increased with the association of pyrite crystals consisting of both framboidal and cubic crystals. The total rock volumes are up to 50-60% clay minerals and are mainly made up of in situ kaolinite and subordinate mixed layer clays (illite-vermiculite). Kaolinite preferentially developed on feldspar crystals, sometimes covering ostracoda bivalves together with gypsum micronodules composed of fan-shaped gypsum crystals. The origin of the kaolinite is, in situ, directly related to feldspar dissolution via heterotrophic bacteria. Thus, kaolinite is found along with bacterial structures. Other mineralogical compositions include established quartz (mostly β-quartz), gypsum crystals (100-200 μm) glauconite and magnetite. Magnetite grains comprise a minor amount (1-2%) and show some bacterial-induced crystal orientations. Glauconite is formed as an accessory mineral that occurs as infill material in biogenic grains. On the other hand, some microspheres represented by a silica-dominated composition are only observed in scanning electron microscopes (SEM) studies under high magnification. Isotope values (d34S) obtained from the pyritized mudstones show an isotopic heterogeneity that suggests that the pyritized mudstone consists of at least two components, with different sulphur-concentrations and d34S values.

Predictive Structure-Based Toxicology Approaches To Assess the Androgenic Potential of Chemicals.

PubMed

Trisciuzzi, Daniela; Alberga, Domenico; Mansouri, Kamel; Judson, Richard; Novellino, Ettore; Mangiatordi, Giuseppe Felice; Nicolotti, Orazio

2017-11-27

We present a practical and easy-to-run in silico workflow exploiting a structure-based strategy making use of docking simulations to derive highly predictive classification models of the androgenic potential of chemicals. Models were trained on a high-quality chemical collection comprising 1689 curated compounds made available within the CoMPARA consortium from the US Environmental Protection Agency and were integrated with a two-step applicability domain whose implementation had the effect of improving both the confidence in prediction and statistics by reducing the number of false negatives. Among the nine androgen receptor X-ray solved structures, the crystal 2PNU (entry code from the Protein Data Bank) was associated with the best performing structure-based classification model. Three validation sets comprising each 2590 compounds extracted by the DUD-E collection were used to challenge model performance and the effectiveness of Applicability Domain implementation. Next, the 2PNU model was applied to screen and prioritize two collections of chemicals. The first is a small pool of 12 representative androgenic compounds that were accurately classified based on outstanding rationale at the molecular level. The second is a large external blind set of 55450 chemicals with potential for human exposure. We show how the use of molecular docking provides highly interpretable models and can represent a real-life option as an alternative nontesting method for predictive toxicology.

Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form

PubMed Central

Zheng, Heping; Mandal, Arabinda; Shumilin, Igor A.; Chordia, Mahendra D.; Panneerdoss, Subbarayalu; Herr, John C.; Minor, Wladek

2016-01-01

Sperm Lysozyme-Like Protein 1 (SLLP1) is one of the lysozyme-like proteins predominantly expressed in mammalian testes that lacks bacteriolytic activity, localizes in the sperm acrosome, and exhibits high affinity for an oolemmal receptor, SAS1B. The crystal structure of mouse SLLP1 (mSLLP1) was determined at 2.15Å resolution. mSLLP1 monomer adopts a structural fold similar to that of chicken/mouse lysozymes retaining all four canonical disulfide bonds. mSLLP1 is distinct from c-lysozyme by substituting two essential catalytic residues (E35T/D52N), exhibiting different surface charge distribution, and by forming helical filaments approximately 75Å in diameter with a 25Å central pore comprised of six monomers per helix turn repeating every 33Å. Cross-species alignment of all reported SLLP1 sequences revealed a set of invariant surface regions comprising a characteristic fingerprint uniquely identifying SLLP1 from other c-lysozyme family members. The fingerprint surface regions reside around the lips of the putative glycan binding groove including three polar residues (Y33/E46/H113). A flexible salt bridge (E46-R61) was observed covering the glycan binding groove. The conservation of these regions may be linked to their involvement in oolemmal protein binding. Interaction between SLLP1 monomer and its oolemmal receptor SAS1B was modeled using protein-protein docking algorithms, utilizing the SLLP1 fingerprint regions along with the SAS1B conserved surface regions. This computational model revealed complementarity between the conserved SLLP1/SAS1B interacting surfaces supporting the experimentally-observed SLLP1/SAS1B interaction involved in fertilization. PMID:26198801

Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form.

PubMed

Zheng, H; Mandal, A; Shumilin, I A; Chordia, M D; Panneerdoss, S; Herr, J C; Minor, W

2015-07-01

Sperm lysozyme-like protein 1 (SLLP1) is one of the lysozyme-like proteins predominantly expressed in mammalian testes that lacks bacteriolytic activity, localizes in the sperm acrosome, and exhibits high affinity for an oolemmal receptor, SAS1B. The crystal structure of mouse SLLP1 (mSLLP1) was determined at 2.15 Å resolution. mSLLP1 monomer adopts a structural fold similar to that of chicken/mouse lysozymes retaining all four canonical disulfide bonds. mSLLP1 is distinct from c-lysozyme by substituting two essential catalytic residues (E35T/D52N), exhibiting different surface charge distribution, and by forming helical filaments approximately 75 Å in diameter with a 25 Å central pore comprised of six monomers per helix turn repeating every 33 Å. Cross-species alignment of all reported SLLP1 sequences revealed a set of invariant surface regions comprising a characteristic fingerprint uniquely identifying SLLP1 from other c-lysozyme family members. The fingerprint surface regions reside around the lips of the putative glycan-binding groove including three polar residues (Y33/E46/H113). A flexible salt bridge (E46-R61) was observed covering the glycan-binding groove. The conservation of these regions may be linked to their involvement in oolemmal protein binding. Interaction between SLLP1 monomer and its oolemmal receptor SAS1B was modeled using protein-protein docking algorithms, utilizing the SLLP1 fingerprint regions along with the SAS1B conserved surface regions. This computational model revealed complementarity between the conserved SLLP1/SAS1B interacting surfaces supporting the experimentally observed SLLP1/SAS1B interaction involved in fertilization. © 2015 American Society of Andrology and European Academy of Andrology.

Free-standing nanomechanical and nanophotonic structures in single-crystal diamond

NASA Astrophysics Data System (ADS)

Burek, Michael John

Realizing complex three-dimensional structures in a range of material systems is critical to a variety of emerging nanotechnologies. This is particularly true of nanomechanical and nanophotonic systems, both relying on free-standing small-scale components. In the case of nanomechanics, necessary mechanical degrees of freedom require physically isolated structures, such as suspended beams, cantilevers, and membranes. For nanophotonics, elements like waveguides and photonic crystal cavities rely on light confinement provided by total internal reflection or distributed Bragg reflection, both of which require refractive index contrast between the device and surrounding medium (often air). Such suspended nanostructures are typically fabricated in a heterolayer structure, comprising of device (top) and sacrificial (middle) layers supported by a substrate (bottom), using standard surface nanomachining techniques. A selective, isotropic etch is then used to remove the sacrificial layer, resulting in free-standing devices. While high-quality, crystalline, thin film heterolayer structures are readily available for silicon (as silicon-on-insulator (SOI)) or III-V semiconductors (i.e. GaAs/AlGaAs), there remains an extensive list of materials with attractive electro-optic, piezoelectric, quantum optical, and other properties for which high quality single-crystal thin film heterolayer structures are not available. These include complex metal oxides like lithium niobate (LiNbO3), silicon-based compounds such as silicon carbide (SiC), III-V nitrides including gallium nitride (GaN), and inert single-crystals such as diamond. Diamond is especially attractive for a variety of nanoscale technologies due to its exceptional physical and chemical properties, including high mechanical hardness, stiffness, and thermal conductivity. Optically, it is transparent over a wide wavelength range (from 220 nm to the far infrared), has a high refractive index (n ~ 2.4), and is host to a vast inventory of luminescent defect centers (many with direct optical access to highly coherent electron and nuclear spins). Diamond has many potential applications ranging from radio frequency nanoelectromechanical systems (RF-NEMS), to all-optical signal processing and quantum optics. Despite the commercial availability of wafer-scale nanocrystalline diamond thin films on foreign substrates (namely SiO2), this diamond-on-insulator (DOI) platform typically exhibits inferior material properties due to friction, scattering, and absorption losses at grain boundaries, significant surface roughness, and large interfacial stresses. In the absence of suitable heteroepitaxial diamond growth, substantial research and development efforts have focused on novel processing techniques to yield nanoscale single-crystal diamond mechanical and optical elements. In this thesis, we demonstrate a scalable 'angled-etching' nanofabrication method for realizing nanomechanical systems and nanophotonic networks starting from bulk single-crystal diamond substrates. Angled-etching employs anisotropic oxygen-based plasma etching at an oblique angle to the substrate surface, resulting in suspended optical structures with triangular cross-sections. Using this approach, we first realize single-crystal diamond nanomechanical resonant structures. These nanoscale diamond resonators exhibit high mechanical quality-factors (approaching Q ~ 105) with mechanical resonances up to 10 MHz. Next, we demonstrate engineered nanophotonic structures, specifically racetrack resonators and photonic crystal cavities, in bulk single-crystal diamond. Our devices feature large optical Q-factors, in excess of 10 5, and operate over a wide wavelength range, spanning visible and telecom. These newly developed high-Q diamond optical nanocavities open the door for a wealth of applications, ranging from nonlinear optics and chemical sensing, to quantum information processing and cavity optomechanics. Beyond isolated nanophotonic devices, we also developed free-standing angled-etched diamond waveguides which efficiently route photons between optical nanocavities, realizing true on-chip diamond nanophotonic networks. A high efficiency fiber-optical interface with aforementioned on-chip diamond nanophotonic networks, achieving > 90% power coupling, is also demonstrated. Lastly, we demonstrate a cavity-optomechanical system in single-crystal diamond, which builds upon previously realized diamond nanobeam photonic crystal cavities fabricated by angled-etching. Specifically, we demonstrate diamond optomechanical crystals (OMCs), where the engineered co-localization of photons and phonons in a quasi-periodic diamond nanostructure leads to coupling of an optical cavity field to a mechanical mode via the radiation pressure of light. In contrast to other material systems, diamond OMCs possess large intracavity photon capacity and sufficient optomechanical coupling rates to exceed a cooperativity of ~ 1 at room temperature and realize large amplitude optomechanical self-oscillations.

Crystal structure of a feruloyl esterase belonging to the tannase family: a disulfide bond near a catalytic triad.

PubMed

Suzuki, Kentaro; Hori, Akane; Kawamoto, Kazusa; Thangudu, Ratna Rajesh; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Yamada, Chihaya; Arakawa, Takatoshi; Wakagi, Takayoshi; Koseki, Takuya; Fushinobu, Shinya

2014-10-01

Feruloyl esterase (FAE) catalyzes the hydrolysis of the ferulic and diferulic acids present in plant cell wall polysaccharides, and tannase catalyzes the hydrolysis of tannins to release gallic acid. The fungal tannase family in the ESTHER database contains various enzymes, including FAEs and tannases. Despite the importance of FAEs and tannases in bioindustrial applications, three-dimensional structures of the fungal tannase family members have been unknown. Here, we determined the crystal structure of FAE B from Aspergillus oryzae (AoFaeB), which belongs to the fungal tannase family, at 1.5 Å resolution. AoFaeB consists of a catalytic α/β-hydrolase fold domain and a large lid domain, and the latter has a novel fold. To estimate probable binding models of substrates in AoFaeB, an automated docking analysis was performed. In the active site pocket of AoFaeB, residues responsible for the substrate specificity of the FAE activity were identified. The catalytic triad of AoFaeB comprises Ser203, Asp417, and His457, and the serine and histidine residues are directly connected by a disulfide bond of the neighboring cysteine residues, Cys202 and Cys458. This structural feature, the "CS-D-HC motif," is unprecedented in serine hydrolases. A mutational analysis indicated that the novel structural motif plays essential roles in the function of the active site. © 2014 Wiley Periodicals, Inc.

Crystal structure and activity studies of the C11 cysteine peptidase from Parabacteroides merdae in the human gut microbiome

DOE PAGES

McLuskey, Karen; Grewal, Jaspreet S.; Das, Debanu; ...

2016-03-03

Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms. However, for the clostripain family (denoted C11), little is currently known. Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution. PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain. It shares core structural elements with clan CD cysteine peptidases but otherwise structurally differs from the other familiesmore » in the clan. These studies also revealed a well ordered break in the polypeptide chain at Lys 147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed Lys 147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca 2+ for activity. Altogether, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.« less

Structural Basis of HCV Neutralization by Human Monoclonal Antibodies Resistant to Viral Neutralization Escape

PubMed Central

Krey, Thomas; Meola, Annalisa; Keck, Zhen-yong; Damier-Piolle, Laurence; Foung, Steven K. H.; Rey, Felix A.

2013-01-01

The high mutation rate of hepatitis C virus allows it to rapidly evade the humoral immune response. However, certain epitopes in the envelope glycoproteins cannot vary without compromising virus viability. Antibodies targeting these epitopes are resistant to viral escape from neutralization and understanding their binding-mode is important for vaccine design. Human monoclonal antibodies HC84-1 and HC84-27 target conformational epitopes overlapping the CD81 receptor-binding site, formed by segments aa434–446 and aa610–619 within the major HCV glycoprotein E2. No neutralization escape was yet observed for these antibodies. We report here the crystal structures of their Fab fragments in complex with a synthetic peptide comprising aa434–446. The structures show that the peptide adopts an α-helical conformation with the main contact residues F442 and Y443 forming a hydrophobic protrusion. The peptide retained its conformation in both complexes, independently of crystal packing, indicating that it reflects a surface feature of the folded glycoprotein that is exposed similarly on the virion. The same residues of E2 are also involved in interaction with CD81, suggesting that the cellular receptor binds the same surface feature and potential escape mutants critically compromise receptor binding. In summary, our results identify a critical structural motif at the E2 surface, which is essential for virus propagation and therefore represents an ideal candidate for structure-based immunogen design for vaccine development. PMID:23696737

Lead magnesium niobate actuator for micropositioning

DOEpatents

Swift, Charles D.; Bergum, John W.

1994-01-01

An improved lead magnesium niobate actuator is disclosed comprising a cylindrical lead magnesium niobate crystal stack mounted in a cylindrical casing wherein a bias means, such as one or more belleville washers, is located between one end of the crystal stack and a partially closed end of the casing; and adjustment means are provided which bear against the opposite end of the crystal stack, whereby an adjustable compressive force is constantly applied against the crystal stack, whether the crystal stack is actuated in an extended position, or is in an unactuated contracted position. In a preferred embodiment, cooling ports are provided for the circulation of coolant in the actuator to cool the crystal stack, and provision is made for removal and replacement of the crystal stack without disconnecting the actuator from the external device being actuated.

Structural Studies of Bacterioferritin B from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center

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

Weeratunga, Saroja K.; Lovell, Scott; Yao, Huili

2010-03-16

The structure of recombinant Pseudomonas aeruginosa bacterioferritin B (Pa BfrB) has been determined from crystals grown from protein devoid of core mineral iron (as-isolated) and from protein mineralized with {approx}600 iron atoms (mineralized). Structures were also obtained from crystals grown from mineralized BfrB after they had been soaked in an FeSO{sub 4} solution (Fe soak) and in separate experiments after they had been soaked in an FeSO{sub 4} solution followed by a soak in a crystallization solution (double soak). Although the structures consist of a typical bacterioferritin fold comprised of a nearly spherical 24-mer assembly that binds 12 heme molecules,more » comparison of microenvironments observed in the distinct structures provided interesting insights. The ferroxidase center in the as-isolated, mineralized, and double-soak structures is empty. The ferroxidase ligands (except His130) are poised to bind iron with minimal conformational changes. The His130 side chain, on the other hand, must rotate toward the ferroxidase center to coordinate iron. In comparison, the structure obtained from crystals soaked in an FeSO{sub 4} solution displays a fully occupied ferroxidase center and iron bound to the internal, Fe{sub (in)}, and external, Fe{sub (out)}, surfaces of Pa BfrB. The conformation of His130 in this structure is rotated toward the ferroxidase center and coordinates an iron ion. The structures also revealed a pore on the surface of Pa BfrB that likely serves as a port of entry for Fe{sup 2+} to the ferroxidase center. On its opposite end, the pore is capped by the side chain of His130 when it adopts its 'gate-closed' conformation that enables coordination to a ferroxidase iron. A change to its 'gate-open', noncoordinative conformation creates a path for the translocation of iron from the ferroxidase center to the interior cavity. These structural observations, together with findings obtained from iron incorporation measurements in solution, suggest that the ferroxidase pore is the dominant entry route for the uptake of iron by Pa BfrB. These findings, which are clearly distinct from those made with Escherichia coli Bfr [Crow, A. C., Lawson, T. L., Lewin, A., Moore, G. R., and Le Brun, N. E. (2009) J. Am. Chem. Soc. 131, 6808-6813], indicate that not all bacterioferritins operate in the same manner.« less

Novel alkaline earth copper germanates with ferro and antiferromagnetic S=1/2 chains

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

Brandao, Paula; Reis, Mario S; Gai, Zheng

Two new alkaline earth copper(II) germanates were hydrothermally synthesized: CaCuGeO4 center dot H2O (1) and BaCu2Ge3O9 center dot H2O (2), and their structures determined by single crystal X-ray diffraction. Compound (1) crystallizes in space group P2(1)/c with a=5.1320(2) angstrom, b=16.1637(5) angstrom, c=5.4818(2) angstrom, beta=102.609(2)degrees, V=443.76(3) angstrom(3) and Z=4. This copper germanate contains layers of composition [CuGeO4](infinity)(2-) comprising CuO4 square planes and GeO4 tetrahedra with calcium and water molecules in the inter-layer space. Compound (2) crystallizes in the Cmcm space group with a=5.5593(3) angstrom, b=10.8606(9) angstrom, c=13.5409(8) angstrom, V=817.56(9) angstrom(3) and Z=4. This structure contains GeO6 and CuO6 octahedra as wellmore » as GeO4 tetrahedra, forming a three-dimensional network of interconnecting six-membered ring channels. The magnetic susceptibility for both samples can be interpreted as S=1/2 chains, in agreement with the copper topology observed in the crystal structure. The susceptibility of (1) exhibits a Bonner-Fisher type behavior, resulting from antiferromagnetic intra-chain interactions without three-dimensional ordering down to 5 K-the lowest measured temperature. This observation, together with the absence of super-exchange paths between the copper chains, make this system particularly promising for the study of low dimensional magnetism. The magnetic properties of (2) show a very weak ferromagnetic near-neighbor interaction along the chain. In this compound a peak the chi T plot seems to indicate the onset of interchain antiferromagentic correlations. However, no ordering temperature is detected in the susceptibility data.« less

Current advances in synchrotron radiation instrumentation for MX experiments

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

Owen, Robin L.; Juanhuix, Jordi; Fuchs, Martin

2016-07-01

Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choicemore » for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.« less

Current advances in synchrotron radiation instrumentation for MX experiments.

PubMed

Owen, Robin L; Juanhuix, Jordi; Fuchs, Martin

2016-07-15

Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing. Copyright © 2016. Published by Elsevier Inc.

Current advances in synchrotron radiation instrumentation for MX experiments

PubMed Central

Owen, Robin L.; Juanhuix, Jordi; Fuchs, Martin

2017-01-01

Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualization and positioning, the sample environment, beam shaping, detectors and data acquisition and processing. PMID:27046341

Structure refinement of the δ1p phase in the Fe-Zn system by single-crystal X-ray diffraction combined with scanning transmission electron microscopy.

PubMed

Okamoto, Norihiko L; Tanaka, Katsushi; Yasuhara, Akira; Inui, Haruyuki

2014-04-01

The structure of the δ1p phase in the iron-zinc system has been refined by single-crystal synchrotron X-ray diffraction combined with scanning transmission electron microscopy. The large hexagonal unit cell of the δ1p phase with the space group of P63/mmc comprises more or less regular (normal) Zn12 icosahedra, disordered Zn12 icosahedra, Zn16 icosioctahedra and dangling Zn atoms that do not constitute any polyhedra. The unit cell contains 52 Fe and 504 Zn atoms so that the compound is expressed with the chemical formula of Fe13Zn126. All Fe atoms exclusively occupy the centre of normal and disordered icosahedra. Iron-centred normal icosahedra are linked to one another by face- and vertex-sharing forming two types of basal slabs, which are bridged with each other by face-sharing with icosioctahedra, whereas disordered icosahedra with positional disorder at their vertex sites are isolated from other polyhedra. The bonding features in the δ1p phase are discussed in comparison with those in the Γ and ζ phases in the iron-zinc system.

Crystal structure of BaMn2(AsO4)2 containing discrete [Mn4O18]28- units.

PubMed

Alcantar, Salvador; Ledbetter, Hollis R; Ranmohotti, Kulugammana G S

2017-12-01

In our attempt to search for mixed alkaline-earth and transition metal arsenates, the title compound, barium dimanganese(II) bis-(arsenate), has been synthesized by employing a high-temperature RbCl flux. The crystal structure of BaMn 2 (AsO 4 ) 2 is made up of MnO 6 octa-hedra and AsO 4 tetra-hedra assembled by sharing corners and edges into infinite slabs with composition [Mn 2 (AsO 4 ) 2 ] 2- that extend parallel to the ab plane. The barium cations reside between parallel slabs maintaining the inter-slab connectivity through coordination to eight oxygen anions. The layered anionic framework comprises weakly inter-acting [Mn 4 O 18 ] 28- tetra-meric units. In each tetra-mer, the manganese(II) cations are in a planar arrangement related by a center of inversion. Within the slabs, the tetra-meric units are separated from each other by 6.614 (2) Å (Mn⋯Mn distances). The title compound has isostructural analogues amongst synthetic Sr M 2 ( X O 4 ) 2 compounds with M = Ni, Co, and X = As, P.

Current advances in synchrotron radiation instrumentation for MX experiments

DOE PAGES

Owen, Robin L.; Juanhuix, Jordi; Fuchs, Martin

2016-04-01

Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Moreover, it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choicemore » for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. One main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. Furthermore, we discuss the most critical optical components, aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.« less

Crystal and Solution Structures of a Prokaryotic M16B Peptidase: an Open and Shut Case

PubMed Central

Aleshin, Alexander E.; Gramatikova, Svetlana; Hura, Gregory L.; Bobkov, Andrey; Strongin, Alex Y.; Stec, Boguslaw; Tainer, John A.; Liddington, Robert C.; Smith, Jeffrey W.

2013-01-01

SUMMARY The M16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a ‘‘clam-shell’’ surrounding the active site. The M16A and M16C subfamilies form one class (‘‘peptidasomes’’): they degrade 30–70 residue peptides, and adopt both open and closed conformations. The eukaryotic M16B subfamily forms a second class (‘‘processing proteases’’): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. Here, we report the solution and crystal structures of a prokaryotic M16B peptidase, and demonstrate that it has features of both classes: thus, it forms stable ‘‘open’’ homodimers in solution that resemble the processing proteases; but the clam-shell closes upon binding substrate, a feature of the M16A/C peptidasomes. Moreover, clam-shell closure is required for proteolytic activity. We predict that other prokaryotic M16B family members will form dimeric peptidasomes, and propose a model for the evolution of the M16 family. PMID:19913481

Synthesis, crystal structures and spectroscopic properties of triazine-based hydrazone derivatives; a comparative experimental-theoretical study.

PubMed

Arshad, Muhammad Nadeem; Bibi, Aisha; Mahmood, Tariq; Asiri, Abdullah M; Ayub, Khurshid

2015-04-03

We report here a comparative theoretical and experimental study of four triazine-based hydrazone derivatives. The hydrazones are synthesized by a three step process from commercially available benzil and thiosemicarbazide. The structures of all compounds were determined by using the UV-Vis., FT-IR, NMR (1H and 13C) spectroscopic techniques and finally confirmed unequivocally by single crystal X-ray diffraction analysis. Experimental geometric parameters and spectroscopic properties of the triazine based hydrazones are compared with those obtained from density functional theory (DFT) studies. The model developed here comprises of geometry optimization at B3LYP/6-31G (d, p) level of DFT. Optimized geometric parameters of all four compounds showed excellent correlations with the results obtained from X-ray diffraction studies. The vibrational spectra show nice correlations with the experimental IR spectra. Moreover, the simulated absorption spectra also agree well with experimental results (within 10-20 nm). The molecular electrostatic potential (MEP) mapped over the entire stabilized geometries of the compounds indicated their chemical reactivates. Furthermore, frontier molecular orbital (electronic properties) and first hyperpolarizability (nonlinear optical response) were also computed at the B3LYP/6-31G (d, p) level of theory.

Gamma ray camera

DOEpatents

Perez-Mendez, V.

1997-01-21

A gamma ray camera is disclosed for detecting rays emanating from a radiation source such as an isotope. The gamma ray camera includes a sensor array formed of a visible light crystal for converting incident gamma rays to a plurality of corresponding visible light photons, and a photosensor array responsive to the visible light photons in order to form an electronic image of the radiation therefrom. The photosensor array is adapted to record an integrated amount of charge proportional to the incident gamma rays closest to it, and includes a transparent metallic layer, photodiode consisting of a p-i-n structure formed on one side of the transparent metallic layer, and comprising an upper p-type layer, an intermediate layer and a lower n-type layer. In the preferred mode, the scintillator crystal is composed essentially of a cesium iodide (CsI) crystal preferably doped with a predetermined amount impurity, and the p-type upper intermediate layers and said n-type layer are essentially composed of hydrogenated amorphous silicon (a-Si:H). The gamma ray camera further includes a collimator interposed between the radiation source and the sensor array, and a readout circuit formed on one side of the photosensor array. 6 figs.

Gamma ray camera

DOEpatents

Perez-Mendez, Victor

1997-01-01

A gamma ray camera for detecting rays emanating from a radiation source such as an isotope. The gamma ray camera includes a sensor array formed of a visible light crystal for converting incident gamma rays to a plurality of corresponding visible light photons, and a photosensor array responsive to the visible light photons in order to form an electronic image of the radiation therefrom. The photosensor array is adapted to record an integrated amount of charge proportional to the incident gamma rays closest to it, and includes a transparent metallic layer, photodiode consisting of a p-i-n structure formed on one side of the transparent metallic layer, and comprising an upper p-type layer, an intermediate layer and a lower n-type layer. In the preferred mode, the scintillator crystal is composed essentially of a cesium iodide (CsI) crystal preferably doped with a predetermined amount impurity, and the p-type upper intermediate layers and said n-type layer are essentially composed of hydrogenated amorphous silicon (a-Si:H). The gamma ray camera further includes a collimator interposed between the radiation source and the sensor array, and a readout circuit formed on one side of the photosensor array.

Crystallization and preliminary crystallographic studies of a novel noncatalytic carbohydrate-binding module from the Ruminococcus flavefaciens cellulosome.

PubMed

Venditto, Immacolata; Goyal, Arun; Thompson, Andrew; Ferreira, Luis M A; Fontes, Carlos M G A; Najmudin, Shabir

2015-01-01

Microbial degradation of the plant cell wall is a fundamental biological process with considerable industrial importance. Hydrolysis of recalcitrant polysaccharides is orchestrated by a large repertoire of carbohydrate-active enzymes that display a modular architecture in which a catalytic domain is connected via linker sequences to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs direct the appended catalytic modules to their target substrates, thus potentiating catalysis. The genome of the most abundant ruminal cellulolytic bacterium, Ruminococcus flavefaciens strain FD-1, provides an opportunity to discover novel cellulosomal proteins involved in plant cell-wall deconstruction. It encodes a modular protein comprising a glycoside hydrolase family 9 catalytic module (GH9) linked to two unclassified tandemly repeated CBMs (termed CBM-Rf6A and CBM-Rf6B) and a C-terminal dockerin. The novel CBM-Rf6A from this protein has been crystallized and data were processed for the native and a selenomethionine derivative to 1.75 and 1.5 Å resolution, respectively. The crystals belonged to orthorhombic and cubic space groups, respectively. The structure was solved by a single-wavelength anomalous dispersion experiment using the CCP4 program suite and SHELXC/D/E.

Structure and Function of Thermostable Direct Hemolysin (TDH) from Vibrio Parahaemolyticus

NASA Astrophysics Data System (ADS)

Hashimoto, Hiroshi; Yamane, Tsutomu; Ikeguchi, Mitsunori; Nakahira, Kumiko; Yanagihara, Itaru

Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic food-borne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside the pore. Molecular dynamics (MD) simulations suggested that water molecules permeate freely through the central and side channel pores. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin.

Screening and Crystallization Plates for Manual and High-throughput Protein Crystal Growth

NASA Technical Reports Server (NTRS)

Thorne, Robert E. (Inventor); Berejnov, Viatcheslav (Inventor); Kalinin, Yevgeniy (Inventor)

2010-01-01

In one embodiment, a crystallization and screening plate comprises a plurality of cells open at a top and a bottom, a frame that defines the cells in the plate, and at least two films. The first film seals a top of the plate and the second film seals a bottom of the plate. At least one of the films is patterned to strongly pin the contact lines of drops dispensed onto it, fixing their position and shape. The present invention also includes methods and other devices for manual and high-throughput protein crystal growth.

Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.

PubMed

Yarbrough, D; Wachter, R M; Kallio, K; Matz, M V; Remington, S J

2001-01-16

The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-A resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P2(1) and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low ( approximately 23%) amino acid sequence homology. The monomer consists of an 11-stranded beta barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a approximately 27 x 34-A rectangular array in two approximately antiparallel pairs. The geometry at the alpha carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp(2) hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90 degrees out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.

Thermally induced gelling of oil-in-water emulsions comprising partially crystallized droplets: the impact of interfacial crystals.

PubMed

Thivilliers, Florence; Laurichesse, Eric; Saadaoui, Hassan; Leal-Calderon, Fernando; Schmitt, Véronique

2008-12-02

We produced triglyceride-in-water emulsions comprising partially crystallized droplets, stabilized by a mixture of protein and low molecular weight surfactant. The emulsions were emulsified in the melted state of the oil phase and stored at low temperature (4 degrees C) right after fabrication to induce oil crystallization. The systems were then warmed to room temperature for a short period of time and cooled again to 4 degrees C. Owing to this treatment referred to as temperature cycling or "tempering", the initially fluid emulsions turned into hard gels. We followed the bulk rheological properties of the materials during and after tempering. The storage modulus, G', exhibited a dramatic increase when tempering was applied. We showed that the systems evolved following two distinct regimes that depend on the average droplet size and on the surfactant-to-protein molar ratio. Gelling may involve partial coalescence of the droplets, i.e., film rupturing with no further shape relaxation because of the solid nature of the droplets. Alternatively, gelling may occur without film rupturing, and is reminiscent of a jamming transition induced by surface roughness. We discussed the origin of these two mechanisms in terms of the properties (size and protuberance) of the interfacial oil crystals.

Structure of the extracellular domains of the human interleukin-6 receptor α-chain

PubMed Central

Varghese, J. N.; Moritz, R. L.; Lou, M.-Z.; van Donkelaar, A.; Ji, H.; Ivancic, N.; Branson, K. M.; Hall, N. E.; Simpson, R. J.

2002-01-01

Dysregulated production of IL-6 and its receptor (IL-6R) are implicated in the pathogenesis of multiple myeloma, autoimmune diseases and prostate cancer. The IL-6R complex comprises two molecules each of IL-6, IL-6R, and the signaling molecule, gp130. Here, we report the x-ray structure (2.4 Å) of the IL-6R ectodomains. The N-terminal strand of the Ig-like domain (D1) is disulfide-bonded to domain D2, and domains D2 and D3, the cytokine-binding domain, are structurally similar to known cytokine-binding domains. The head-to-tail packing of two closely associated IL-6R molecules observed in the crystal may be representative of the configuration of the physiological dimer of IL-6R and provides new insight into the architecture of the IL-6R complex. PMID:12461182

Water oxidation chemistry of photosystem II.

PubMed

Brudvig, Gary W

2008-03-27

Photosystem II (PSII) uses light energy to split water into protons, electrons and O2. In this reaction, nature has solved the difficult chemical problem of efficient four-electron oxidation of water to yield O2 without significant amounts of reactive intermediate species such as superoxide, hydrogen peroxide and hydroxyl radicals. In order to use nature's solution for the design of artificial catalysts that split water, it is important to understand the mechanism of the reaction. The recently published X-ray crystal structures of cyanobacterial PSII complexes provide information on the structure of the Mn and Ca ions, the redox-active tyrosine called YZ and the surrounding amino acids that comprise the O2-evolving complex (OEC). The emerging structure of the OEC provides constraints on the different hypothesized mechanisms for O2 evolution. The water oxidation mechanism of PSII is discussed in the light of biophysical and computational studies, inorganic chemistry and X-ray crystallographic information.

Consistent Application of the Boltzmann Distribution to Residual Entropy in Crystals

ERIC Educational Resources Information Center

Kozliak, Evguenii I.

2007-01-01

Four different approaches to residual entropy (the entropy remaining in crystals comprised of nonsymmetric molecules like CO, N[subscript 2]O, FClO[subscript 3], and H[subscript 2]O as temperatures approach 0 K) are analyzed and a new method of its calculation is developed based on application of the Boltzmann distribution. The inherent connection…

Efficient room-temperature source of polarized single photons

DOEpatents

Lukishova, Svetlana G.; Boyd, Robert W.; Stroud, Carlos R.

2007-08-07

An efficient technique for producing deterministically polarized single photons uses liquid-crystal hosts of either monomeric or oligomeric/polymeric form to preferentially align the single emitters for maximum excitation efficiency. Deterministic molecular alignment also provides deterministically polarized output photons; using planar-aligned cholesteric liquid crystal hosts as 1-D photonic-band-gap microcavities tunable to the emitter fluorescence band to increase source efficiency, using liquid crystal technology to prevent emitter bleaching. Emitters comprise soluble dyes, inorganic nanocrystals or trivalent rare-earth chelates.

Optical control of graphene plasmon using liquid crystal layer 29K New One

DTIC Science & Technology

2017-03-01

AFRL-AFOSR-UK-TR-2017-0014 Optical control of graphene plasmon using liquid crystal layer 29K New One Viktor Yuriyovych Reshetnyak SCIENCE AND... plasmon using liquid crystal layer 29K New One 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER STCU-P652 5c.  PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) Viktor...the basic research and establishes possible optical ways to control the surface plasmon polariton in graphene layer. A system comprises the graphene

Crystal structure and biochemical characterization of beta-keto thiolase B from polyhydroxyalkanoate-producing bacterium Ralstonia eutropha H16

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

Kim, Eun-Jung; Son, Hyeoncheol Francis; Kim, Sangwoo

Highlights: • We determined a crystal structure of β-keto thiolase from Ralstonia eutropha H16 (ReBktB). • Distinct substrate binding mode ReBktB was elucidated. • Enzymatic kinetic parameters of ReBktB were revealed. - Abstract: ReBktB is a β-keto thiolase from Ralstonia eutropha H16 that catalyzes condensation reactions between acetyl-CoA with acyl-CoA molecules that contains different numbers of carbon atoms, such as acetyl-CoA, propionyl-CoA, and butyryl-CoA, to produce valuable bioproducts, such as polyhydroxybutyrate, polyhydroxybutyrate-hydroxyvalerate, and hexanoate. We solved a crystal structure of ReBktB at 2.3 Å, and the overall structure has a similar fold to that of type II biosynthetic thiolases, suchmore » as PhbA from Zoogloea ramigera (ZrPhbA). The superposition of this structure with that of ZrPhbA complexed with CoA revealed the residues that comprise the catalytic and substrate binding sites of ReBktB. The catalytic site of ReBktB contains three conserved residues, Cys90, His350, and Cys380, which may function as a covalent nucleophile, a general base, and second nucleophile, respectively. For substrate binding, ReBktB stabilized the ADP moiety of CoA in a distinct way compared to ZrPhbA with His219, Arg221, and Asp228 residues, whereas the stabilization of β-mercaptoethyamine and pantothenic acid moieties of CoA was quite similar between these two enzymes. Kinetic study of ReBktB revealed that K{sub m}, V{sub max}, and K{sub cat} values of 11.58 μM, 1.5 μmol/min, and 102.18 s{sup −1}, respectively, and the catalytic and substrate binding sites of ReBktB were further confirmed by site-directed mutagenesis experiments.« less

Apparatus and methods for using achromatic phase matching at high orders of dispersion

DOEpatents

Richman, Bruce; Trebino, Rick; Bisson, Scott; Sidick, Erkin

2001-01-01

Achromatic phase-matching (APM) is used for efficiently multiplying the frequency of broad bandwidth light by using a nonlinear optical medium comprising a second-harmonic generation (SHG) crystal. Stationary optical elements whose configuration, properties, and arrangement have been optimized to match the dispersion characteristics of the SHG crystal to at least the second order. These elements include a plurality of prismatic elements for directing an input light beam onto the SHG crystal such that each ray wavelength is aligned to match the phase-matching angle for the crystal at each wavelength of light to at least the second order and such that every ray wavelength overlap within the crystal.

Photoconductivity in the chalcohalide semiconductor, SbSeI: a new candidate for hard radiation detection.

PubMed

Wibowo, Arief C; Malliakas, Christos D; Liu, Zhifu; Peters, John A; Sebastian, Maria; Chung, Duck Young; Wessels, Bruce W; Kanatzidis, Mercouri G

2013-06-17

We investigated an antimony chalcohalide compound, SbSeI, as a potential semiconductor material for X-ray and γ-ray detection. SbSeI has a wide band gap of 1.70 eV with a density of 5.80 g/cm(3), and it crystallizes in the orthorhombic Pnma space group with a one-dimensional chain structure comprised of infinite zigzag chains of dimers [Sb2Se4I8]n running along the crystallographic b axis. In this study, we investigate conditions for vertical Bridgman crystal growth using combinations of the peak temperature and temperature gradients as well as translation rate set in a three-zone furnace. SbSeI samples grown at 495 °C peak temperature and 19 °C/cm temperature gradient with 2.5 mm/h translation rate produced a single phase of columnar needlelike crystals aligned along the translational direction of the growth. The ingot sample exhibited an n-type semiconductor with resistivity of ∼10(8) Ω·cm. Photoconductivity measurements on these specimens allowed us to determine mobility-lifetime (μτ) products for electron and hole carriers that were found to be of similar order of magnitude (∼10(-4) cm(2)/V). Further, the SbSeI ingot with well-aligned, one-dimensional columnar needlelike crystals shows an appreciable response of Ag Kα X-ray.

Structural and mutational analyses of Aes, an inhibitor of MalT in Escherichia coli.

PubMed

Schiefner, André; Gerber, Kinga; Brosig, Alexander; Boos, Winfried

2014-02-01

The acyl esterase Aes effectively inhibits the transcriptional activity of MalT-the central activator of maltose and maltodextrin utilizing genes in Escherichia coli. To provide better insight into the nature of the interaction between Aes and MalT, we determined two different crystal structures of Aes-in its native form and covalently modified by a phenylmethylsulfonyl moiety at its active site serine. Both structures show distinct space groups and were refined to a resolution of 1.8 Å and 2.3 Å, respectively. The overall structure of Aes resembles a canonical α/β-hydrolase fold, which is extended by a funnel-like cap structure that forms the substrate-binding site. The catalytic triad of Aes, comprising residues Ser165, His292, and Asp262, is located at the bottom of this funnel. Analysis of the crystal-packing contacts of the two different space groups as well as analytical size-exclusion chromatography revealed a homodimeric arrangement of Aes. The Aes dimer adopts an antiparallel contact involving both the hydrolase core and the cap, with its twofold axis perpendicular to the largest dimension of Aes. To identify the surface area of Aes that is responsible for the interaction with MalT, we performed a structure-based alanine-scanning mutagenesis to pinpoint Aes residues that are significantly impaired in MalT inhibition, but still exhibit wild-type expression and enzymatic activity. These residues map to a shallow slightly concave surface patch of Aes at the opposite site of the dimerization interface and indicate the surface area that interacts with MalT. Copyright © 2013 Wiley Periodicals, Inc.

Crystal structures of Mmm1 and Mdm12–Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites

PubMed Central

Jeong, Hanbin; Park, Jumi; Jun, Youngsoo; Lee, Changwook

2017-01-01

The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) comprises mitochondrial distribution and morphology 12 (Mdm12), maintenance of mitochondrial morphology 1 (Mmm1), Mdm34, and Mdm10 and mediates physical membrane contact sites and nonvesicular lipid trafficking between the ER and mitochondria in yeast. Herein, we report two crystal structures of the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain of Mmm1 and the Mdm12–Mmm1 complex at 2.8 Å and 3.8 Å resolution, respectively. Mmm1 adopts a dimeric SMP structure augmented with two extra structural elements at the N and C termini that are involved in tight self-association and phospholipid coordination. Mmm1 binds two phospholipids inside the hydrophobic cavity, and the phosphate ion of the distal phospholipid is specifically recognized through extensive H-bonds. A positively charged concave surface on the SMP domain not only mediates ER membrane docking but also results in preferential binding to glycerophospholipids such as phosphatidylcholine (PC), phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylserine (PS), some of which are substrates for lipid-modifying enzymes in mitochondria. The Mdm12–Mmm1 structure reveals two Mdm12s binding to the SMP domains of the Mmm1 dimer in a pairwise head-to-tail manner. Direct association of Mmm1 and Mdm12 generates a 210-Å-long continuous hydrophobic tunnel that facilitates phospholipid transport. The Mdm12–Mmm1 complex binds all glycerophospholipids except for phosphatidylethanolamine (PE) in vitro. PMID:29078410

Lead magnesium niobate actuator for micropositioning

DOEpatents

Swift, C.D.; Bergum, J.W.

1994-10-25

An improved lead magnesium niobate actuator is disclosed comprising a cylindrical lead magnesium niobate crystal stack mounted in a cylindrical casing wherein a bias means, such as one or more belleville washers, is located between one end of the crystal stack and a partially closed end of the casing; and adjustment means are provided which bear against the opposite end of the crystal stack, whereby an adjustable compressive force is constantly applied against the crystal stack, whether the crystal stack is actuated in an extended position, or is in an unactuated contracted position. In a preferred embodiment, cooling ports are provided for the circulation of coolant in the actuator to cool the crystal stack, and provision is made for removal and replacement of the crystal stack without disconnecting the actuator from the external device being actuated. 3 figs.

New vanadium tellurites: Syntheses, structures, optical properties of noncentrosymmetric VTeO{sub 4}(OH), centrosymmetric Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})

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

Liang, Ming-Li; State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002; Marsh, Matthew

Two new vanadium tellurites, VTeO{sub 4}(OH) (1) and Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2), have been synthesized successfully with the use of hydrothermal reactions. The crystal structures of the two compounds were determined by single-crystal X-ray diffraction. Compound 1 crystallizes in the polar space group Pca2{sub 1} (No. 29) while compound 2 crystallizes in the centrosymmetric space group C2/c (No. 15). The topography of compound 1 reveals a two-dimensional, layered structure comprised of VO{sub 6} octahedral chains and TeO{sub 3}(OH) zig-zag chains. Compound 2, on the contrary, features a three-dimensional [V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})]{sup 4-} anionic framework withmore » Ba{sup 2+} ions filled into the 10-member ring helical tunnels. The [V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})]{sup 4-} anionic network is the first 3D vanadium tellurite framework to be discovered in the alkaline-earth vanadium tellurite system. Powder second harmonic generation (SHG) measurements indicate that compound 1 shows a weak SHG response of about 0.3×KDP (KH{sub 2}PO{sub 4}) under 1064 nm laser radiation. Infrared spectroscopy, elemental analysis, thermal analysis, and dipole moment calculations have also been carried out. - Graphical abstract: VTeO{sub 4}(OH) (1) crystallizes in the noncentrosymmetric space group Pca2{sub 1} (No. 29) while Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2) crystallizes in the centrosymmetric space group C2/c (No. 15). - Highlights: • VTeO{sub 4}(OH) (1) and Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2) have been synthesized successfully with the use of hydrothermal reactions. • VTeO{sub 4}(OH) (1) crystallizes in the noncentrosymmetric space group Pca2{sub 1} and displays a weak SHG response. • VTeO{sub 4}(OH) (1) represents only the fourth SHG-active material found in vanadium tellurite systems. • Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2) exhibits a novel three-dimensional [V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})]{sup 4-} anionic framework.« less

Thin transparent conducting films of cadmium stannate

DOEpatents

Wu, Xuanzhi; Coutts, Timothy J.

2001-01-01

A process for preparing thin Cd.sub.2 SnO.sub.4 films. The process comprises the steps of RF sputter coating a Cd.sub.2 SnO.sub.4 layer onto a first substrate; coating a second substrate with a CdS layer; contacting the Cd.sub.2 SnO.sub.4 layer with the CdS layer in a water- and oxygen-free environment and heating the first and second substrates and the Cd.sub.2 SnO.sub.4 and CdS layers to a temperature sufficient to induce crystallization of the Cd.sub.2 SnO.sub.4 layer into a uniform single-phase spinel-type structure, for a time sufficient to allow full crystallization of the Cd.sub.2 SnO.sub.4 layer at that temperature; cooling the first and second substrates to room temperature; and separating the first and second substrates and layers from each other. The process can be conducted at temperatures less than 600.degree. C., allowing the use of inexpensive soda lime glass substrates.

Ultrastructural and elemental analysis of sialoliths and their comparison with nephroliths.

PubMed

Rakesh, Nagaraju; Bhoomareddy Kantharaj, Yashoda Devi; Agarwal, Manjushree; Agarwal, Kunal

2014-02-01

Sialoliths are common in the submandibular gland and its duct system, although their exact cause of formation is still a matter of debate. The aims of this study were to: (a) analyze sialoliths ultrastructurally, and to determine the role of foreign bodies or organic materials in the formation of sialolith nuclei; and (b) compare nephroliths with sialoliths ultrastructurally. Three sialoliths and two nephroliths were analyzed ultrastructurally by a scanning electron microscope and X-ray diffractometer. The main structures of the sialoliths were found to be hydroxyapatite crystals. No organic cores were observed in the central parts of the sialoliths. In nephroliths, calcium oxalate, calcium phosphate, and struvite crystals were found. The energy-dispersive X-ray microanalysis found that sialoliths and nephroliths were predominantly composed of elements comprising calcium, phosphorous, magnesium, sodium, chloride, silicon, iron, and potassium. Sialoliths in the submandibular salivary glands might form secondary to sialadenitis, but not via a luminal organic nidus. © 2014 Wiley Publishing Asia Pty Ltd.

Probing the limit of magnesium uptake by β-tricalcium phosphate in biphasic mixtures formed from calcium deficient apatites

NASA Astrophysics Data System (ADS)

Kumar, P. Nandha; Mishra, Sandeep K.; Kannan, S.

2015-11-01

A series of magnesium doped non-stoichiometric calcium deficient apatites were synthesized through an aqueous precipitation route. The resultant structural changes during heat treatment were investigated by X-ray diffraction, Raman and FT-IR spectroscopy and Rietveld refinement. The results confirmed the formation of biphasic mixtures comprising Ca10(PO4)6(OH)2 and β-Ca3(PO4)2 after heat treatment at 1000 °C with the preferential occupancy of Mg2+ at the crystal lattice of β-Ca3(PO4)2. The concentration of Mg2+ uptake in β-Ca3(PO4)2 is limited till reaching the stoichiometric ratio of (Ca+Mg)/P=1.67 and beyond this stoichiometric value [(Ca+Mg)/P>1.67], Mg2+ precipitates as Mg(OH)2 and thereafter gets converted to MgO during heat treatment. Any kind of Mg2+ uptake in the crystal lattice of Ca10(PO4)6(OH)2 is discarded from the investigation.

Crystal structure of 3-hy­droxy­methyl-1,2,3,4-tetra­hydro­isoquinolin-1-one

PubMed Central

Caracelli, Ignez; Hino, Camila Lury; Zukerman-Schpector, Julio; Biaggio, Francisco Carlos; Tiekink, Edward R. T.

2015-01-01

In the title compound, C10H11NO2, two independent but virtually superimposable mol­ecules, A and B, comprise the asymmetric unit. The heterocyclic ring in each mol­ecule has a screw-boat conformation, and the methyl­hydroxyl group occupies a position to one side of this ring with N—C—C—O torsion angles of −55.30 (15) (mol­ecule A) and −55.94 (16)° (mol­ecule B). In the crystal, O—H⋯O and N—H⋯O hydrogen bonding leads to 11-membered {⋯HNCO⋯HO⋯HNC2O} heterosynthons, involving three different mol­ecules, which are edge-shared to generate a supra­molecular chain along the a axis. Inter­actions of the type C—H⋯O provide additional stability to the chains, and link these into a three-dimensional architecture. PMID:26396795

A neutron-X-ray, NMR and calorimetric study of glassy Probucol synthesized using containerless techniques

NASA Astrophysics Data System (ADS)

Weber, J. K. R.; Benmore, C. J.; Tailor, A. N.; Tumber, S. K.; Neuefeind, J.; Cherry, B.; Yarger, J. L.; Mou, Q.; Weber, W.; Byrn, S. R.

2013-10-01

Acoustic levitation was used to trap 1-3 mm diameter drops of Probucol and other pharmaceutical materials in containerless conditions. Samples were studied in situ using X-ray diffraction and ex situ using neutron diffraction, NMR and DSC techniques. The materials were brought into non-equilibrium states by supersaturating solutions or by supercooling melts. The glass transition and crystallization temperatures of glassy Probucol were 29 ± 1 and 71 ± 1 °C respectively. The glassy form was stable with a shelf life of at least 8 months. A neutron/X-ray difference function of the glass showed that while molecular sub-groups remain rigid, many of the hydrogen correlations observed in the crystal become smeared out in the disordered material. The glass is principally comprised of slightly distorted Form I Probucol molecules with disordered packing rather than large changes in the individual molecular structure. Avoiding surface contact-induced nucleation provided access to highly non-equilibrium phases and enabled synthesis of phase-pure glasses.

Thermal oxidation of single crystal aluminum antimonide and materials having the same

DOEpatents

Sherohman, John William; Yee, Jick Hong; Coombs, III, Arthur William; Wu, Kuang Jen J.

2012-12-25

In one embodiment, a method for forming a non-conductive crystalline oxide layer on an AlSb crystal includes heat treating an AlSb crystal in a partial vacuum atmosphere at a temperature conducive for air adsorbed molecules to desorb, surface molecule groups to decompose, and elemental Sb to evaporate from a surface of the AlSb crystal and exposing the AlSb crystal to an atmosphere comprising oxygen to form a crystalline oxide layer on the surface of the AlSb crystal. In another embodiment, a method for forming a non-conductive crystalline oxide layer on an AlSb crystal includes heat treating an AlSb crystal in a non-oxidizing atmosphere at a temperature conducive for decomposition of an amorphous oxidized surface layer and evaporation of elemental Sb from the AlSb crystal surface and forming stable oxides of Al and Sb from residual surface oxygen to form a crystalline oxide layer on the surface of the AlSb crystal.

The role of group index engineering in series-connected photonic crystal microcavities for high density sensor microarrays

PubMed Central

Zou, Yi; Chakravarty, Swapnajit; Zhu, Liang; Chen, Ray T.

2014-01-01

We experimentally demonstrate an efficient and robust method for series connection of photonic crystal microcavities that are coupled to photonic crystal waveguides in the slow light transmission regime. We demonstrate that group index taper engineering provides excellent optical impedance matching between the input and output strip waveguides and the photonic crystal waveguide, a nearly flat transmission over the entire guided mode spectrum and clear multi-resonance peaks corresponding to individual microcavities that are connected in series. Series connected photonic crystal microcavities are further multiplexed in parallel using cascaded multimode interference power splitters to generate a high density silicon nanophotonic microarray comprising 64 photonic crystal microcavity sensors, all of which are interrogated simultaneously at the same instant of time. PMID:25316921

Group III-nitride thin films grown using MBE and bismuth

DOEpatents

Kisielowski, Christian K.; Rubin, Michael

2002-01-01

The present invention comprises growing gallium nitride films in the presence of bismuth using MBE at temperatures of about 1000 K or less. The present invention further comprises the gallium nitride films fabricated using the inventive fabrication method. The inventive films may be doped with magnesium or other dopants. The gallium nitride films were grown on sapphire substrates using a hollow anode Constricted Glow Discharge nitrogen plasma source. When bismuth was used as a surfactant, two-dimensional gallium nitride crystal sizes ranging between 10 .mu.m and 20 .mu.m were observed. This is 20 to 40 times larger than crystal sizes observed when GaN films were grown under similar circumstances but without bismuth. It is thought that the observed increase in crystal size is due bismuth inducing an increased surface diffusion coefficient for gallium. The calculated value of 4.7.times.10.sup.-7 cm.sup.2 /sec. reveals a virtual substrate temperature of 1258 K which is 260 degrees higher than the actual one.

Group III-nitride thin films grown using MBE and bismuth

DOEpatents

Kisielowski, Christian K.; Rubin, Michael

2000-01-01

The present invention comprises growing gallium nitride films in the presence of bismuth using MBE at temperatures of about 1000 K or less. The present invention further comprises the gallium nitride films fabricated using the inventive fabrication method. The inventive films may be doped with magnesium or other dopants. The gallium nitride films were grown on sapphire substrates using a hollow anode Constricted Glow Discharge nitrogen plasma source. When bismuth was used as a surfactant, two-dimensional gallium nitride crystal sizes ranging between 10 .mu.m and 20 .mu.m were observed. This is 20 to 40 times larger than crystal sizes observed when GaN films were grown under similar circumstances but without bismuth. It is thought that the observed increase in crystal size is due bismuth inducing an increased surface diffusion coefficient for gallium. The calculated value of 4.7.times.10.sup.-7 cm.sup.2 /sec. reveals a virtual substrate temperature of 1258 K which is 260 degrees higher than the actual one.

Thermal barrier coating having high phase stability

DOEpatents

Subramanian, Ramesh

2002-01-01

A device (10) comprising a substrate (22) having a deposited ceramic thermal barrier coating characterized by a microstructure having gaps (28) where the thermal barrier coating comprises a first thermal barrier layer (40), and a second thermal barrier layer (30) with a pyrochlore crystal structure having a chemical formula of A.sup.n+.sub.2-x B.sup.m+.sub.2+x O.sub.7-y, where A is selected from the group of elements consisting of La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and mixtures thereof, where B is selected from the group of elements consisting of Zr, Hf, Ti and mixtures thereof, where n and m are the valence of A and B respectively, and for -0.5.ltoreq.x.ltoreq.0.5, ##EQU1## and excluding the following combinations for x=0, y=0: A=La and B=Zr; A=La and B=Hf; A=Gd and B=Hf; and A=Yb and B=Ti.

Novel Hybrid Virtual Screening Protocol Based on Molecular Docking and Structure-Based Pharmacophore for Discovery of Methionyl-tRNA Synthetase Inhibitors as Antibacterial Agents

PubMed Central

Liu, Chi; He, Gu; Jiang, Qinglin; Han, Bo; Peng, Cheng

2013-01-01

Methione tRNA synthetase (MetRS) is an essential enzyme involved in protein biosynthesis in all living organisms and is a potential antibacterial target. In the current study, the structure-based pharmacophore (SBP)-guided method has been suggested to generate a comprehensive pharmacophore of MetRS based on fourteen crystal structures of MetRS-inhibitor complexes. In this investigation, a hybrid protocol of a virtual screening method, comprised of pharmacophore model-based virtual screening (PBVS), rigid and flexible docking-based virtual screenings (DBVS), is used for retrieving new MetRS inhibitors from commercially available chemical databases. This hybrid virtual screening approach was then applied to screen the Specs (202,408 compounds) database, a structurally diverse chemical database. Fifteen hit compounds were selected from the final hits and shifted to experimental studies. These results may provide important information for further research of novel MetRS inhibitors as antibacterial agents. PMID:23839093

Functional and Structural Impact of Target Uridine Substitutions on the H/ACA Ribonucleoprotein Particle Pseudouridine Synthase

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

Zhou, Jing; Liang, Bo; Li, Hong

2010-09-17

Box H/ACA ribonucleoprotein protein particles catalyze the majority of pseudouridylation in functional RNA. Different from stand alone pseudouridine synthases, the RNP pseudouridine synthase comprises multiple protein subunits and an RNA subunit. Previous studies showed that each subunit, regardless its location, is sensitive to the step of subunit placement at the catalytic center and potentially to the reaction status of the substrate. Here we describe the impact of chemical substitutions of target uridine on enzyme activity and structure. We found that 3-methyluridine in place of uridine inhibited its isomerization while 2{prime}-deoxyuridine or 4-thiouridine did not. Significantly, crystal structures of an archaealmore » box H/ACA RNP bound with the nonreactive and the two postreactive substrate analogues showed only subtle structural changes throughout the assembly except for a conserved tyrosine and a substrate anchoring loop of Cbf5. Our results suggest a potential role of these elements and the subunit that contacts them in substrate binding and product release.« less

A bifacial quantum dot-sensitized solar cell with all-cadmium sulfide photoanode

NASA Astrophysics Data System (ADS)

Ma, Chunqing; Tang, Qunwei; Liu, Danyang; Zhao, Zhiyuan; He, Benlin; Chen, Haiyan; Yu, Liangmin

2015-02-01

Pursuit of a high power conversion efficiency and reduction of electricity-generation cost has been a persistent objective for quantum dot-sensitized solar cells (QDSSCs). We present here the fabrication of a QDSSC comprising a nanoflower-structured CdS anode, a liquid electrolyte having S2-/Sn2- redox couples, and a transparent CoSe counter electrode. Nanoflower-structured CdS anodes are prepared by a successive ionic layer adsorption and reaction (SILAR) method and subsequently hydrothermal strategy free of any surfactant or template. The CdS nanoparticles synthesized by a SILAR method act as "seed crystal" for growth of CdS nanoflowers. The average electron lifetime is markedly elevated in nanoflower-structured CdS anode in comparison with CdS nanoparticle or nanoporous CdS microsphere anode. Herein, we study the effect of synthesis method on CdS morphology and solar cell's photovoltaic performance, showing a power conversion efficiency of 1.67% and 1.17% for nanoflower-structured CdS QDSSC under front and rear irradiations, respectively.

Process for growing a film epitaxially upon an oxide surface and structures formed with the process

DOEpatents

McKee, Rodney Allen; Walker, Frederick Joseph

1998-01-01

A process and structure wherein a film comprised of a perovskite or a spinel is built epitaxially upon a surface, such as an alkaline earth oxide surface, involves the epitaxial build up of alternating constituent metal oxide planes of the perovskite or spinel. The first layer of metal oxide built upon the surface includes a metal element which provides a small cation in the crystalline structure of the perovskite or spinel, and the second layer of metal oxide built upon the surface includes a metal element which provides a large cation in the crystalline structure of the perovskite or spinel. The layering sequence involved in the film build up reduces problems which would otherwise result from the interfacial electrostatics at the first atomic layers, and these oxides can be stabilized as commensurate thin films at a unit cell thickness or grown with high crystal quality to thicknesses of 0.5-0.7 .mu.m for optical device applications.

Process for growing a film epitaxially upon an oxide surface and structures formed with the process

DOEpatents

McKee, Rodney A.; Walker, Frederick J.

1995-01-01

A process and structure wherein a film comprised of a perovskite or a spinel is built epitaxially upon a surface, such as an alkaline earth oxide surface, involves the epitaxial build up of alternating constituent metal oxide planes of the perovskite or spinel. The first layer of metal oxide built upon the surface includes a metal element which provides a small cation in the crystalline structure of the perovskite or spinel, and the second layer of metal oxide built upon the surface includes a metal element which provides a large cation in the crystalline structure of the perovskite or spinel. The layering sequence involved in the film build up reduces problems which would otherwise result from the interfacial electrostatics at the first atomic layers, and these oxides can be stabilized as commensurate thin films at a unit cell thickness or grown with high crystal quality to thicknesses of 0.5-0.7 .mu.m for optical device applications.

A bacterial Argonaute with noncanonical guide RNA specificity

PubMed Central

Kaya, Emine; Doxzen, Kevin W.; Knoll, Kilian R.; Wilson, Ross C.; Strutt, Steven C.; Kranzusch, Philip J.; Doudna, Jennifer A.

2016-01-01

Eukaryotic Argonaute proteins induce gene silencing by small RNA-guided recognition and cleavage of mRNA targets. Although structural similarities between human and prokaryotic Argonautes are consistent with shared mechanistic properties, sequence and structure-based alignments suggested that Argonautes encoded within CRISPR-cas [clustered regularly interspaced short palindromic repeats (CRISPR)-associated] bacterial immunity operons have divergent activities. We show here that the CRISPR-associated Marinitoga piezophila Argonaute (MpAgo) protein cleaves single-stranded target sequences using 5′-hydroxylated guide RNAs rather than the 5′-phosphorylated guides used by all known Argonautes. The 2.0-Å resolution crystal structure of an MpAgo–RNA complex reveals a guide strand binding site comprising residues that block 5′ phosphate interactions. Using structure-based sequence alignment, we were able to identify other putative MpAgo-like proteins, all of which are encoded within CRISPR-cas loci. Taken together, our data suggest the evolution of an Argonaute subclass with noncanonical specificity for a 5′-hydroxylated guide. PMID:27035975

UTa 2O(S 2) 3Cl 6: A ribbon structure containing a heterobimetallic 5 d-5 f M 3 cluster

NASA Astrophysics Data System (ADS)

Wells, Daniel M.; Chan, George H.; Ellis, Donald E.; Ibers, James A.

2010-02-01

A new solid-state compound containing a heterobimetallic cluster of U and Ta, UTa 2O(S 2) 3Cl 6, has been synthesized and its structure has been characterized by single-crystal X-ray diffraction methods. UTa 2O(S 2) 3Cl 6 was synthesized from UCl 4 and Ta 1.2S 2 at 883 K. The O is believed to have originated in the Ta 1.2S 2 reactant. The compound crystallizes in the space group P1¯ of the triclinic system. The structure comprises a UTa 2 unit bridged by μ 2-S 2 and μ 3-O groups. Each Ta atom bonds to two μ 2-S 2, the μ 3-O, and two terminal Cl atoms. Each U atom bonds to two μ 2-S 2, the μ 3-O, and four Cl atoms. The Cl atoms bridge in pairs to neighboring U atoms to form a ribbon structure. The bond distances are normal and are consistent with formal oxidation states of +IV/+V/-II/-I/-I for U/Ta/O/S/Cl, respectively. The optical absorbance spectrum displays characteristic transition peaks near the absorption edge. Density functional theory was used to assign these peaks to transitions between S 1- valence-band states and empty U 5 f-6 d hybrid bands. Density-of-states analysis shows overlap between Ta 5 d and U bands, consistent with metal-metal interactions.

Constitutive Modeling of Superalloy Single Crystals and Directionally Solidified Materials

NASA Technical Reports Server (NTRS)

Walker, K. P.; Jordan, E. H.

1985-01-01

A unified viscoplastic constitutive relation based on crystallographic slip theory was developed for the deformation analysis of nickel base face centered cubic superalloy single crystals at elevated temperature. The single crystal theory is embedded in a self consistent method to derive a constitutive relation for a directionally solidified material comprised of a polycrystalline aggregate of columnar cylindrical grains. One of the crystallographic axes of the cylindrical crystals points in the columnar direction while the remaining crystallographic axes are oriented at random in the basal plane perpendicular to the columnar direction. These constitutive formulations are coded in FORTRAN for use in nonlinear finite element and boundary element programs.

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling.

PubMed

D'Cruz, Akshay A; Kershaw, Nadia J; Chiang, Jessica J; Wang, May K; Nicola, Nicos A; Babon, Jeffrey J; Gack, Michaela U; Nicholson, Sandra E

2013-12-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp(488) and Trp(621)) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs.

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling

PubMed Central

D'Cruz, Akshay A.; Kershaw, Nadia J.; Chiang, Jessica J.; Wang, May K.; Nicola, Nicos A.; Babon, Jeffrey J.; Gack, Michaela U.; Nicholson, Sandra E.

2014-01-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp488 and Trp621) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs. PMID:24015671

Simple liquid crystal display backlight unit comprising only a single-sheet micropatterned polydimethylsiloxane (PDMS) light-guide plate.

PubMed

Lee, Joo-Hyung; Lee, Hong-Seok; Lee, Byung-Kee; Choi, Won-Seok; Choi, Hwan-Young; Yoon, Jun-Bo

2007-09-15

A simple liquid crystal display (LCD) backlight unit (BLU) comprising only a single-sheet polydimethylsiloxane (PDMS) light-guide plate (LGP) has been developed. The PDMS LGP, having micropatterns with an inverse-trapezoidal cross section, was fabricated by backside 3-D diffuser lithography followed by PDMS-to-PDMS replication. The fabricated BLU showed an average luminance of 2878 cd/m(2) with 73.3% uniformity when mounted in a 5.08 cm backlight module with four side view 0.85cd LEDs. The developed BLU can greatly reduce the cost and thickness of LCDs, and it can be applied to flexible displays as a flexible light source due to the flexible characteristic of the PDMS itself.

Nondestructive method for chemically machining crucibles or molds from their enclosed ingots and castings

DOEpatents

Stout, Norman D.; Newkirk, Herbert W.

1991-01-01

An inventive method is described for chemically machining rhenium, rhenium and tungsten alloy, and group 5b and 6b crucibles or molds from included ingots and castings comprised of oxide crystals including YAG and YAG based crystals, garnets, corundum crystals, and ceramic oxides. A mixture of potassium hydroxide and 15 to 90 weight percent of potassium nitrate is prepared and maintained at a temperature above melting and below the lower of 500 degrees centigrade or the temperature of decomposition of the mixture. The enveloping metal container together with its included oxide crystal object is rotated within the heated KOH-KNO.sub.3 mixture, until the container is safely chemically machined away from the included oxide crystal object.

Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly.

PubMed

Chernyatina, Anastasia A; Nicolet, Stefan; Aebi, Ueli; Herrmann, Harald; Strelkov, Sergei V

2012-08-21

Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) "rod" domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

Anisotropic Energy Transport Properties of 1,3,5-Triamino-2,4,6-Trinitrobenzene (TATB)

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew P.

Anisotropic energy transport properties were determined theoretically for crystals of the insensitive explosive 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) using molecular dynamics simulations. Determination of these properties is necessary for the analysis and interpretation of molecular dynamics predictions of transient processes such as shock response and hot spot formation/relaxation and is similarly important for the accurate parameterization of meso- and continuum-scale engineering models aimed at understanding complex processes such as ignition and growth leading to detonation. TATB crystal exhibits a graphitic-like layered packing structure with a two-dimensional hydrogen-bonding network that forms within, but not between, the molecule-thick layers that comprise the crystal. This structure is thought to be the primary factor behind the significant anisotropy in many physical properties of TATB crystals. Anisotropic thermal conductivity coefficients were determined for initially defect-free and defective TATB crystals and isotropic values were determined for the liquid at temperatures and pressures up to (1800 K, 2.0 GPa). The room temperature, atmospheric pressure thermal conductivity for TATB is predicted to be generally greater and more anisotropic than the thermal conductivities of other molecular explosives; conduction within the layers is approximately 70% greater than conduction between the layers. The conductivity is predicted to decrease with temperature approximately as λ ∝ 1/T over the interval 200 K ≤ T ≤ 700 K and to linearly increase with pressure up to 2.5 GPa. Direction-dependent relaxation of idealized one-dimensional hot spots was studied. Results from hot spot relaxation simulations were compared with and fit to solutions for the one-dimensional diffusive heat equation by treating the thermal di.usivity as a parameter to assess the validity of using continuum models to describe heat transport in TATB on length scales below 10 nm. A dissipative particle dynamics (DPD) at constant energy (DPDE) coarsegrained model is developed for TATB and applied to micron-scale shock simulations wherein the predicted shock response is shown to be highly sensitive to a model parameter controlling kinetics of energy transport between inter- and intramolecular degrees of freedom. A generalized crystal-cutting method is developed that enables facile construction of three-dimensionally periodic simulation cells containing arbitrarily oriented single crystals and crystal-crystal interfaces for materials of arbitrary symmetry class. Strategies for non-uniform sampling of molecular dynamics simulations of transient phenomena are proposed that have the potential to drastically reduce data storage costs.

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

SH3-like motif-containing C-terminal domain of staphylococcal teichoic acid transporter suggests possible function.

PubMed

Ko, Tzu-Ping; Tseng, Shih-Ting; Lai, Shu-Jung; Chen, Sheng-Chia; Guan, Hong-Hsiang; Shin Yang, Chia; Jung Chen, Chun; Chen, Yeh

2016-09-01

The negatively charged bacterial polysaccharides-wall teichoic acids (WTAs) are synthesized intracellularly and exported by a two-component transporter, TagGH, comprising a transmembrane subunit TagG and an ATPase subunit TagH. We determined the crystal structure of the C-terminal domain of TagH (TagH-C) to investigate its function. The structure shows an N-terminal SH3-like subdomain wrapped by a C-terminal subdomain with an anti-parallel β-sheet and an outer shell of α-helices. A stretch of positively charged surface across the subdomain interface is flanked by two negatively charged regions, suggesting a potential binding site for negatively charged polymers, such as WTAs or acidic peptide chains. Proteins 2016; 84:1328-1332. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Phase Transformations and Metallization of Magnesium Oxide at High Pressure and Temperature

NASA Astrophysics Data System (ADS)

McWilliams, R. Stewart; Spaulding, Dylan K.; Eggert, Jon H.; Celliers, Peter M.; Hicks, Damien G.; Smith, Raymond F.; Collins, Gilbert W.; Jeanloz, Raymond

2012-12-01

Magnesium oxide (MgO) is representative of the rocky materials comprising the mantles of terrestrial planets, such that its properties at high temperatures and pressures reflect the nature of planetary interiors. Shock-compression experiments on MgO to pressures of 1.4 terapascals (TPa) reveal a sequence of two phase transformations: from B1 (sodium chloride) to B2 (cesium chloride) crystal structures above 0.36 TPa, and from electrically insulating solid to metallic liquid above 0.60 TPa. The transitions exhibit large latent heats that are likely to affect the structure and evolution of super-Earths. Together with data on other oxide liquids, we conclude that magmas deep inside terrestrial planets can be electrically conductive, enabling magnetic field-producing dynamo action within oxide-rich regions and blurring the distinction between planetary mantles and cores.

Doping of germanium and silicon crystals with non-hydrogenic acceptors for far infrared lasers

DOEpatents

Haller, Eugene E.; Brundermann, Erik

2000-01-01

A method for doping semiconductors used for far infrared lasers with non-hydrogenic acceptors having binding energies larger than the energy of the laser photons. Doping of germanium or silicon crystals with beryllium, zinc or copper. A far infrared laser comprising germanium crystals doped with double or triple acceptor dopants permitting the doped laser to be tuned continuously from 1 to 4 terahertz and to operate in continuous mode. A method for operating semiconductor hole population inversion lasers with a closed cycle refrigerator.

Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication.

PubMed

Assenberg, René; Mastrangelo, Eloise; Walter, Thomas S; Verma, Anil; Milani, Mario; Owens, Raymond J; Stuart, David I; Grimes, Jonathan M; Mancini, Erika J

2009-12-01

The flavivirus genome comprises a single strand of positive-sense RNA, which is translated into a polyprotein and cleaved by a combination of viral and host proteases to yield functional proteins. One of these, nonstructural protein 3 (NS3), is an enzyme with both serine protease and NTPase/helicase activities. NS3 plays a central role in the flavivirus life cycle: the NS3 N-terminal serine protease together with its essential cofactor NS2B is involved in the processing of the polyprotein, whereas the NS3 C-terminal NTPase/helicase is responsible for ATP-dependent RNA strand separation during replication. An unresolved question remains regarding why NS3 appears to encode two apparently disconnected functionalities within one protein. Here we report the 2.75-A-resolution crystal structure of full-length Murray Valley encephalitis virus NS3 fused with the protease activation peptide of NS2B. The biochemical characterization of this construct suggests that the protease has little influence on the helicase activity and vice versa. This finding is in agreement with the structural data, revealing a single protein with two essentially segregated globular domains. Comparison of the structure with that of dengue virus type 4 NS2B-NS3 reveals a relative orientation of the two domains that is radically different between the two structures. Our analysis suggests that the relative domain-domain orientation in NS3 is highly variable and dictated by a flexible interdomain linker. The possible implications of this conformational flexibility for the function of NS3 are discussed.

Rare-earth transition-metal gallium chalcogenides RE3MGaCh7 (M=Fe, Co, Ni; Ch=S, Se)

NASA Astrophysics Data System (ADS)

Rudyk, Brent W.; Stoyko, Stanislav S.; Oliynyk, Anton O.; Mar, Arthur

2014-02-01

Six series of quaternary rare-earth transition-metal chalcogenides RE3MGaCh7 (M=Fe, Co, Ni; Ch=S, Se), comprising 33 compounds in total, have been prepared by reactions of the elements at 1050 °C (for the sulphides) or 900 °C (for the selenides). They adopt noncentrosymmetric hexagonal structures (ordered Ce3Al1.67S7-type, space group P63, Z=2) with cell parameters in the ranges of a=9.5-10.2 Å and c=6.0-6.1 Å for the sulphides and a=10.0-10.5 Å and c=6.3-6.4 Å for the selenides as refined from powder X-ray diffraction data. Single-crystal structures were determined for five members of the sulphide series RE3FeGaS7 (RE=La, Pr, Tb) and RE3CoGaS7 (RE=La, Tb). The highly anisotropic crystal structures consist of one-dimensional chains of M-centred face-sharing octahedra and stacks of Ga-centred tetrahedra all pointing in the same direction. Magnetic measurements on the sulphides reveal paramagnetic behaviour in some cases and long-range antiferromagnetic behaviour with low Néel temperatures (15 K or lower) in others. Ga L-edge XANES spectra support the presence of highly cationic Ga tetrahedral centres with a tendency towards more covalent Ga-Ch character on proceeding from the sulphides to the selenides. Band structure calculations on La3FeGaS7 indicate that the electronic structure is dominated by Fe 3d-based states near the Fermi level.

Crystal structure and mutational analysis of aminoacylhistidine dipeptidase from Vibrio alginolyticus reveal a new architecture of M20 metallopeptidases.

PubMed

Chang, Chin-Yuan; Hsieh, Yin-Cheng; Wang, Ting-Yi; Chen, Yi-Chin; Wang, Yu-Kuo; Chiang, Ting-Wei; Chen, Yi-Ju; Chang, Cheng-Hsiang; Chen, Chun-Jung; Wu, Tung-Kung

2010-12-10

Aminoacylhistidine dipeptidases (PepD, EC 3.4.13.3) belong to the family of M20 metallopeptidases from the metallopeptidase H clan that catalyze a broad range of dipeptide and tripeptide substrates, including L-carnosine and L-homocarnosine. Homocarnosine has been suggested as a precursor for the neurotransmitter γ-aminobutyric acid (GABA) and may mediate the antiseizure effects of GABAergic therapies. Here, we report the crystal structure of PepD from Vibrio alginolyticus and the results of mutational analysis of substrate-binding residues in the C-terminal as well as substrate specificity of the PepD catalytic domain-alone truncated protein PepD(CAT). The structure of PepD was found to exist as a homodimer, in which each monomer comprises a catalytic domain containing two zinc ions at the active site center for its hydrolytic function and a lid domain utilizing hydrogen bonds between helices to form the dimer interface. Although the PepD is structurally similar to PepV, which exists as a monomer, putative substrate-binding residues reside in different topological regions of the polypeptide chain. In addition, the lid domain of the PepD contains an "extra" domain not observed in related M20 family metallopeptidases with a dimeric structure. Mutational assays confirmed both the putative di-zinc allocations and the architecture of substrate recognition. In addition, the catalytic domain-alone truncated PepD(CAT) exhibited substrate specificity to l-homocarnosine compared with that of the wild-type PepD, indicating a potential value in applications of PepD(CAT) for GABAergic therapies or neuroprotection.

Luminescent MOFs comprising mixed tritopic linkers and Cd(II)/Zn(II) nodes for selective detection of organic nitro compounds and iodine capture

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

Rachuri, Yadagiri; Bisht, Kamal Kumar; Academy of Scientific and Innovative Research

2015-03-15

Two CPs ([Cd{sub 3}(BTC){sub 2}(TIB){sub 2}(H{sub 2}O){sub 4}].(H{sub 2}O){sub 2}){sub n} (1) and ([Zn{sub 3}(BTC){sub 2}(TIB){sub 2}].(H{sub 2}O){sub 6}){sub n} (2) composed of tripodal linkers BTC (1,3,5-benzenetricarboxylate) and TIB (1,3,5-tris(imidazol-1-ylmethyl)benzene) were synthesized via solvothermal route and structurally characterized. Single crystal structural analysis reveals 1 possesses a novel 3D framework structure, whereas 2 represents a previously established compound. Owing to the d{sup 10} configuration of metal nodes and robust 3D frameworks, 1 and 2 exhibit excellent fluorescence properties which have been exploited to sense organic nitro compounds in vapor phase. Compound 1 demonstrates selective sensing of nitromethane over structurally similar methanolmore » with ca. 70 and 43% fluorescence quenching in case of former and later. Similarly, 58% fluorescence quenching was observed in case of nitrobenzene over the structurally resembling toluene for which 30% quenching was observed. Compound 2 did not show any preference for nitro compounds and exhibited comparable fluorescence quenching when exposed to the vapors of nitro or other geometrically resembling organic molecules. Furthermore, adsorption experiments revealed that 1 and 2 can uptake 2.74 and 14.14 wt% molecular iodine respectively in vapor phase which can be released in organic solvents such as hexane and acetonitrile. The maximal iodine uptake in case of 1 and 2 corresponds to 0.15 and 0.80 molecules of iodine per formula unit of respective frameworks. Comprehensive structural description, thermal stability and luminescence behavior for both CPs has also been presented. - Graphical abstract: Two 3D luminescent CPs comprising mixed tripodal ligands have been hydrothermally synthesized and structurally characterized. Iodine encapsulation capacity of synthesized CPs is evaluated and their fluorescence quenching in presence of small organic molecules is exploited for sensing of nitro organics. - Highlights: • Two 3D mixed ligand coordination polymers containing Cd and Zn center are prepared. • Crystal structure and thermal stability of synthesized CPs has been described. • Photoluminescence intensity of CPs was observed to vary in presence of organic vapors. • Photoluminescence quenching in case of Cd CP is exploited to selectively sense nitro organics. • These thermally stable robust CPs are also used for iodine adsorption.« less

Crystal structures of 4-meth­oxy­benzoic acid–1,3-bis­(pyridin-4-yl)propane (2/1) and biphenyl-4,4′-di­carb­oxy­lic acid–4-meth­oxy­pyridine (1/2)

PubMed Central

Gotoh, Kazuma; Ishida, Hiroyuki

2017-01-01

The crystal structures of two hydrogen-bonded compounds, namely 4-meth­oxy­benzoic acid–1,3-bis­(pyridin-4-yl)propane (2/1), C13H14.59N2·C8H7.67O3·C8H7.74O3, (I), and biphenyl-4,4′-di­carb­oxy­lic acid–4-meth­oxy­pyridine (1/2), C14H9.43O4·C6H7.32NO·C6H7.25NO, (II), have been determined at 93 K. In (I), the asymmetric unit consists of two crystallographically independent 4-meth­oxy­benzoic acid mol­ecules and one 1,3-bis­(pyridin-4-yl)propane mol­ecule. The asymmetric unit of (II) comprises one biphenyl-4,4′-di­carb­oxy­lic acid mol­ecule and two independent 4-meth­oxy­pyridine mol­ecules. In each crystal, the acid and base mol­ecules are linked by short O—H⋯N/N—H⋯O hydrogen bonds, in which H atoms are disordered over the acid O-atom and base N-atom sites, forming a linear hydrogen-bonded 2:1 or 1:2 unit of the acid and the base. The 2:1 units of (I) are linked via C—H⋯π, π–π and C—H⋯O inter­actions into a tape structure along [101], while the 1:2 units of (II) form a double-chain structure along [-101] through π–π and C—H⋯O inter­actions. PMID:28932435

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

Volume-scalable high-brightness three-dimensional visible light source

DOEpatents

Subramania, Ganapathi; Fischer, Arthur J; Wang, George T; Li, Qiming

2014-02-18

A volume-scalable, high-brightness, electrically driven visible light source comprises a three-dimensional photonic crystal (3DPC) comprising one or more direct bandgap semiconductors. The improved light emission performance of the invention is achieved based on the enhancement of radiative emission of light emitters placed inside a 3DPC due to the strong modification of the photonic density-of-states engendered by the 3DPC.

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

PubMed

Allen, Frank H; Motherwell, W D Samuel

2002-06-01

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

Recovering and recycling uranium used for production of molybdenum-99

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

Reilly, Sean Douglas; May, Iain; Copping, Roy

A processes for recycling uranium that has been used for the production of molybdenum-99 involves irradiating a solution of uranium suitable for forming fission products including molybdenum-99, conditioning the irradiated solution to one suitable for inducing the formation of crystals of uranyl nitrate hydrates, then forming the crystals and a supernatant and then separating the crystals from the supernatant, thus using the crystals as a source of uranium for recycle. Molybdenum-99 is recovered from the supernatant using an adsorbent such as alumina. Another process involves irradiation of a solid target comprising uranium, forming an acidic solution from the irradiated targetmore » suitable for inducing the formation of crystals of uranyl nitrate hydrates, then forming the crystals and a supernatant and then separating the crystals from the supernatant, thus using the crystals as a source of uranium for recycle. Molybdenum-99 is recovered from the supernatant using an adsorbent such as alumina.« less

Bacterially induced mineralization of calcium carbonate: the role of exopolysaccharides and capsular polysaccharides.

PubMed

Ercole, Claudia; Cacchio, Paola; Botta, Anna Lucia; Centi, Valeria; Lepidi, Aldo

2007-02-01

Bacterially induced carbonate mineralization has been proposed as a new method for the restoration of limestones in historic buildings and monuments. We describe here the formation of calcite crystals by extracellular polymeric substances isolated from Bacillus firmus and Bacillus sphaericus. We isolated bacterial outer structures (glycocalix and parietal polymers), such as exopolysaccharides (EPS) and capsular polysaccharides (CPS) and checked for their influence on calcite precipitation. CPS and EPS extracted from both B. firmus and B. sphaericus were able to mediate CaCO3 precipitation in vitro. X-ray microanalysis showed that in all cases the formed crystals were calcite. Scanning electron microscopy showed that the shape of the crystals depended on the fractions utilized. These results suggest the possibility that biochemical composition of CPS or EPS influences the resulting morphology of CaCO3. There were no precipitates in the blank samples. CPS and EPS comprised of proteins and glycoproteins. Positive alcian blue staining also reveals acidic polysaccharides in CPS and EPS fractions. Proteins with molecular masses of 25-40 kDa and 70 kDa in the CPS fraction were highly expressed in the presence of calcium oxalate. This high level of synthesis could be related to the binding of calcium ions and carbonate deposition.

Nonlinear Optics and Solitons in Photonic Crystal Fibres

NASA Astrophysics Data System (ADS)

Skryabin, Dmitry V.; Wadsworth, William J.

The fibre optics revolution in communication technologies followed the 1950's demonstration of the glass fibres with dielectric cladding [1]. Transmission applications of fibre optics have become a dominant modern day technology not least because nonlinearities present in - or introduced into - glass and enhanced by the tight focusing of the fibre modes allow for numerous light processing techniques, such as amplification, frequency conversion, pulse shaping, and many others. For these reasons, and because of the rich fundamental physics behind it, nonlinear fibre optics has become a blossoming discipline in its own right [1]. The 1990's witnessed another important development in fibre optics. Once again it came from a new approach to the fibre cladding, comprising a periodic pattern of air holes separated by glass membranes forming a photonic crystal structure [2, 3]. This prompted the name Photonic Crystal Fibres (PCFs). The fascinating story behind the invention of PCF and research into various fibre designs can be found, e.g., in [4]. Our aim here is to review the role played by PCFs in nonlinear and quantum optics, which is becoming the mainstream of the PCF related research and applications. Our focus will be on the areas where PCFs have brought to life effects and applications which were previously difficult, impossible to observe or simply not thought about.

Coarsening Dynamics and Marangoni Effects in Thin Liquid Crystal Bubbles in Microgravity

NASA Technical Reports Server (NTRS)

Clark, Noel; Glaser, Matthew; Maclennan, Joseph; Park, Cheol; Tin, Padetha; Hall, Nancy R.; Sheehan, Christopher; Storck, Jennifer

2015-01-01

The Observation and Analysis of Smectic Islands in Space (OASIS) flight hardware was successfully launched on SpaceX-6 on April 15, 2015 and was operated in the Microgravity Science Glovebox (MSG) on board the International Space Station (ISS). The OASIS project comprises a series of experiments that probe the interfacial and hydrodynamic behavior of spherical-bubble freely suspended liquid crystal (FSLC) membranes in space. These are the thinnest known stable condensed phase structures, making them ideal for studies of two-dimensional (2D) coarsening dynamics and thermocapillary phenomena in microgravity. The OASIS experimental investigation was carried out using four different smectic A and C liquid crystal materials in four separate sample chambers housed inside the MSG. In this report, we present the behavior of collective dynamics on 2D bubble surface, including the equilibrium spatial organization and interaction of islands in electric fields and temperature gradients, and the diffusion and coalescence-driven coarsening dynamics of island emulsions in microgravity. We have observed spontaneous bubble thickening behavior caused by gradients between the bubble-blowing needle and ambient air temperatures. A uniform, thicker band forms during coarsening as a result of non-uniform heating by the LED illumination panels. These are proposed to be a result of Marangoni convection on the bubble surface.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

PubMed

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Synthesis, crystal structure, optical and thermal properties of lanthanide hydrogen-polyphosphates Ln[H(PO3)4] (Ln = Tb, Dy, Ho).

PubMed

Förg, Katharina; Höppe, Henning A

2015-11-28

Lanthanide hydrogen-polyphosphates Ln[H(PO3)4] (Ln = Tb, Dy, Ho) were synthesised as colourless (Ln = Tb, Dy) and light pink (Ln = Ho) crystalline powders by reaction of Tb4O7/Dy2O3/Ho2O3 with H3PO3 at 380 °C. All compounds crystallise isotypically (P2(1)/c (no. 14), Z = 4, a(Tb) = 1368.24(4) pm, b(Tb) = 710.42(2) pm, c(Tb) = 965.79(3) pm, β(Tb) = 101.200(1)°, 3112 data, 160 parameters, wR2 = 0.062, a(Ho) = 1363.34(5) pm, b(Ho) = 709.24(3) pm, c(Ho) = 959.07(4) pm, β(Ho) = 101.055(1)°, 1607 data, 158 parameters, wR2 = 0.058). The crystal structure comprises two different infinite helical chains of corner-sharing phosphate tetrahedra. In-between these chains the lanthanide ions are located, coordinated by seven oxygen atoms belonging to four different polyphosphate chains. Vibrational, UV/Vis and fluorescence spectra of Ln[H(PO3)4] (Ln = Tb, Dy, Ho) as well as Dy[H(PO3)4]:Ln (Ln = Ce, Eu) and the magnetic and thermal behaviour of Tb[H(PO3)4] are reported.

Large negative magnetoresistance of a nearly Dirac material: Layered antimonide EuMnS b2

NASA Astrophysics Data System (ADS)

Yi, Changjiang; Yang, Shuai; Yang, Meng; Wang, Le; Matsushita, Yoshitaka; Miao, Shanshan; Jiao, Yuanyuan; Cheng, Jinguang; Li, Yongqing; Yamaura, Kazunari; Shi, Youguo; Luo, Jianlin

2017-11-01

Single crystals of EuMnS b2 were successfully grown and their structural and electronic properties were investigated systematically. The material crystallizes in an orthorhombic-layered structure (space group: Pnma, No. 62) comprising a periodic sequence of -MnSb/Eu/Sb/Eu/- layers (˜1 nm in thickness), and massless fermions are expected to emerge in the Sb layer, by analogy of the candidate Dirac materials EuMnB i2 and A Mn P n2 (A =Ca or Sr or Ba, P n =Sb or Bi). The magnetic and specific heat measurements of EuMnS b2 suggest an antiferromagnetic ordering of Eu moments near 20 K. A characteristic hump appears in the temperature-dependent electrical resistivity curve at ˜25 K . A spin-flop transition of Eu moments with an onset magnetic field of ˜15 kOe (at 2 K) was observed. Interestingly, EuMnS b2 shows a negative magnetoresistance (up to -95 % ) in contrast to the positive magnetoresistances observed for EuMnB i2 and A Mn P n2 (A =Ca or Sr or Ba, P n =Sb or Bi), providing a unique opportunity to study the correlation between electronic and magnetic properties in this class of materials.

Crystal Structure of the Eukaryotic Origin Recognition Complex

PubMed Central

Bleichert, Franziska; Botchan, Michael R.; Berger, James M.

2015-01-01

Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset. The 3.5 Å resolution crystal structure of Drosophila ORC reveals that the 270 kDa initiator core complex comprises a two-layered notched ring in which a collar of winged-helix domains from the Orc1-5 subunits sits atop a layer of AAA+ ATPase folds. Although canonical inter-AAA+ domain interactions exist between four of the six ORC subunits, unanticipated features are also evident, including highly interdigitated domain-swapping interactions between the winged-helix folds and AAA+ modules of neighboring protomers, and a quasi-spiral arrangement of DNA binding elements that circumnavigate a ~20 Å wide channel in the center of the complex. Comparative analyses indicate that ORC encircles DNA, using its winged-helix domain face to engage the MCM2-7 complex during replicative helicase loading; however, an observed >90° out-of-plane rotation for the Orc1 AAA+ domain disrupts interactions with catalytic amino acids in Orc4, narrowing and sealing off entry into the central channel. Prima facie, our data indicate that Drosophila ORC can switch between active and autoinhibited conformations, suggesting a novel means for cell cycle and/or developmental control of ORC functions. PMID:25762138

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

Mezo, Adam R.; Sridhar, Vandana; Badger, John

The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A. R., McDonnell, K. A., Tan Hehir, C. A., Low, S. C., Palombella, V. J., Stattel, J. M., Kamphaus, G. D., Fraley, C., Zhang, Y., Dumont, J. A., and Bitonti, A. J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 2337-2342). Herein, the x-raymore » crystal structure of a representative monomeric peptide in complex with human FcRn was solved to 2.6 {angstrom} resolution. The structure shows that the peptide binds to human FcRn at the same general binding site as does the Fc domain of IgG. The data correlate well with structure-activity relationship data relating to how the peptide family binds to human FcRn. In addition, the x-ray crystal structure of a representative dimeric peptide in complex with human FcRn shows how the bivalent ligand can bridge two FcRn molecules, which may be relevant to the mechanism by which the dimeric peptides inhibit FcRn and increase IgG catabolism in vivo. Modeling of the peptide:FcRn structure as compared with available structural data on Fc and FcRn suggest that the His-6 and Phe-7 (peptide) partially mimic the interaction of His-310 and Ile-253 (Fc) in binding to FcRn, but using a different backbone topology.« less

DETECTOR FOR MODULATED AND UNMODULATED SIGNALS

DOEpatents

Patterson, H.H.; Webber, G.H.

1959-08-25

An r-f signal-detecting device is described, which is embodied in a compact coaxial circuit principally comprising a detecting crystal diode and a modulating crystal diode connected in parallel. Incoming modulated r-f signals are demodulated by the detecting crystal diode to furnish an audio input to an audio amplifier. The detecting diode will not, however, produce an audio signal from an unmodulated r-f signal. In order that unmodulated signals may be detected, such incoming signals have a locally produced audio signal superimposed on them at the modulating crystal diode and then the"induced or artificially modulated" signal is reflected toward the detecting diode which in the process of demodulation produces an audio signal for the audio amplifier.

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

PubMed

Nakamura, Akira; Ohtsuka, Jun; Kashiwagi, Tatsuki; Numoto, Nobutaka; Hirota, Noriyuki; Ode, Takahiro; Okada, Hidehiko; Nagata, Koji; Kiyohara, Motosuke; Suzuki, Ei-Ichiro; Kita, Akiko; Wada, Hitoshi; Tanokura, Masaru

2016-02-26

Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. In addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. In this paper, we also report results of crystallization experiments for two protein samples. Crystals grown in the system exhibited magnetic orientation and showed higher and more homogeneous quality compared with the control crystals. The structural analysis reveals that making use of the magnetic microgravity during the crystallization process helps us to build a well-refined protein structure model, which has no significant structural differences with a control structure. Therefore, the system contributes to improvement in efficiency of structural analysis for "difficult" proteins, such as membrane proteins and supermolecular complexes.

Insight into the core-shell structures of Cu-In-S microspheres

NASA Astrophysics Data System (ADS)

Wochnik, Angela S.; Frank, Anna; Heinzl, Christoph; Häusler, Jonas; Schneider, Julian; Hoffmann, Ramona; Matich, Sonja; Scheu, Christina

2013-12-01

In this study we report about the inner and outer structure of CuInS2 microspheres which might be used e.g. in pastes for simple, low-cost solar cell preparation, as well as in electrodes for light-driven water splitting. The microspheres are synthesized via a mild, template-free solvothermal synthesis route and characterised by electron and focused ion beam microscopy, X-ray diffraction, inductively coupled plasma atomic emission and energy dispersive X-ray spectroscopy. The investigations of cross sections prepared by focused ion beam showed that the spheres consist of compact cores and flaky surface structures. Depending on the reaction time, the core possesses a stoichiometric or Cu-rich chemical composition surrounded by an In-rich shell. The flaky surface always comprises a stoichiometric composition in tetragonal chalcopyrite crystal structure, whereas the other areas additionally show minor contributions of CuS, and CuInS2 in hexagonal wurtzite structure. The presence of different phases can be beneficial for future applications since they offer different absorption behaviour in the visible range.

Structural Basis for the Acyltransferase Activity of Lecithin:Retinol Acyltransferase-like Proteins*

PubMed Central

Golczak, Marcin; Kiser, Philip D.; Sears, Avery E.; Lodowski, David T.; Blaner, William S.; Palczewski, Krzysztof

2012-01-01

Lecithin:retinol acyltransferase-like proteins, also referred to as HRAS-like tumor suppressors, comprise a vertebrate subfamily of papain-like or NlpC/P60 thiol proteases that function as phospholipid-metabolizing enzymes. HRAS-like tumor suppressor 3, a representative member of this group, plays a key role in regulating triglyceride accumulation and energy expenditure in adipocytes and therefore constitutes a novel pharmacological target for treatment of metabolic disorders causing obesity. Here, we delineate a catalytic mechanism common to lecithin:retinol acyltransferase-like proteins and provide evidence for their alternative robust lipid-dependent acyltransferase enzymatic activity. We also determined high resolution crystal structures of HRAS-like tumor suppressor 2 and 3 to gain insight into their active site architecture. Based on this structural analysis, two conformational states of the catalytic Cys-113 were identified that differ in reactivity and thus could define the catalytic properties of these two proteins. Finally, these structures provide a model for the topology of these enzymes and allow identification of the protein-lipid bilayer interface. This study contributes to the enzymatic and structural understanding of HRAS-like tumor suppressor enzymes. PMID:22605381

Method for fabrication of ceramic dielectric films on copper foils

DOEpatents

Ma, Beihai; Narayanan, Manoj; Dorris, Stephen E.; Balachandran, Uthamalingam

2017-06-14

The present invention provides copper substrate coated with a lead-lanthanum-zirconium-titanium (PLZT) ceramic film, which is prepared by a method comprising applying a layer of a sol-gel composition onto a copper foil. The sol-gel composition comprises a precursor of a ceramic material suspended in 2-methoxyethanol. The layer of sol-gel is then dried at a temperature up to about 250.degree. C. The dried layer is then pyrolyzed at a temperature in the range of about 300 to about 450.degree. C. to form a ceramic film from the ceramic precursor. The ceramic film is then crystallized at a temperature in the range of about 600 to about 750.degree. C. The drying, pyrolyzing and crystallizing are performed under a flowing stream of an inert gas.

Frequency mixing crystal

DOEpatents

Ebbers, Christopher A.; Davis, Laura E.; Webb, Mark

1992-01-01

In a laser system for converting infrared laser light waves to visible light comprising a source of infrared laser light waves and means of harmoic generation associated therewith for production of light waves at integral multiples of the frequency of the original wave, the improvement of said means of harmonic generation comprising a crystal having the chemical formula X.sub.2 Y(NO.sub.3).sub.5 .multidot.2 nZ.sub.2 o wherein X is selected from the group consisting of Li, Na, K, Rb, Cs, and Tl; Y is selected from the group consisting of Sc, Y, La, Ce, Nd, Pr, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Al, Ga, and In; Z is selected from the group consisting of H and D; and n ranges from 0 to 4.

High-speed prediction of crystal structures for organic molecules

NASA Astrophysics Data System (ADS)

Obata, Shigeaki; Goto, Hitoshi

2015-02-01

We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order to improve a performance of simulations for crystal structure predictions. The performance experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). The experimental results show that our parallel algorithm could achieve speed-ups of 214 and 179 times using 256 processor cores on crystal structure optimizations in predictions of crystal structures for 3-aza-bicyclo(3.3.1)nonane-2,4-dione and 2-diazo-3,5-cyclohexadiene-1-one, respectively. We expect that this parallel algorithm is always possible to reduce computational costs of any crystal structure predictions.

THE STRUCTURES OF COILED-COIL DOMAINS FROM TYPE THREE SECRETION SYSTEM TRANSLOCATORS REVEAL HOMOLOGY TO PORE-FORMING TOXINS

PubMed Central

Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V.

2012-01-01

Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SS) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) which is responsible for over one million deaths per year. The Shigella type III secretion apparatus (T3SA) is comprised of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 Å and 2.8 Å limiting resolution, respectively. These newly identified domains are comprised of extended length (114 Å in IpaB and 71 Å in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably colicin Ia. This suggests that these mechanistically-separate and functionally-distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events. PMID:22321794

Photovoltaic Cell Having A P-Type Polycrystalline Layer With Large Crystals

DOEpatents

Albright, Scot P.; Chamberlin, Rhodes R.

1996-03-26

A photovoltaic cell has an n-type polycrystalline layer and a p-type polycrystalline layer adjoining the n-type polycrystalline layer to form a photovoltaic junction. The p-type polycrystalline layer comprises a substantially planar layer portion having relatively large crystals adjoining the n-type polycrystalline layer. The planar layer portion includes oxidized impurities which contribute to obtainment of p-type electrical properties in the planar layer portion.

Telescoping low vibration pulling mechanism for Czochralski crystal growth

NASA Astrophysics Data System (ADS)

Iseler, G. W.

1985-02-01

A telescoping low vibration pulling mechanism is described for use in Czochralski crystal growth apparatus, comprising a broached brushing which defines an internal circumference of teeth on the circumference of a splined shaft. The brushing is coupled to the means for rotation via a hollow tube and the splined shaft, couplable to a seed shaft, and an elevation means telescopes through said brushing within said hollow tube.

Utilization of High-Temperature Slags From Metallurgy Based on Crystallization Behaviors

NASA Astrophysics Data System (ADS)

Sun, Yongqi; Zhang, Zuotai

2018-05-01

Here, following the principle of modifying crystallization behaviors, including avoidance and optimization, we review recent research on the utilization of hot slags. Because of the high-temperature property (1450-1650°C), the utilization of hot slags are much different from that of other wastes. We approach this issue from two main directions, namely, material recycling and heat utilization. From the respect of material recycling, the utilization of slags mainly follows total utilization and partial utilization, whereas the heat recovery from slags follows two main paths, namely, physical granulation and chemical reaction. The effective disposal of hot slags greatly depends on clarifying the crystallization behaviors, and thus, we discuss some optical techniques and their applicable scientific insights. For the purpose of crystallization avoidance, characterizing the glass-forming ability of slags is of great significance, whereas for crystallization modification, the selection of chemical additives and control of crystallization conditions comprise the central routes.

A review on the synthesis, crystal growth, structure and physical properties of rare earth based quaternary intermetallic compounds

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

Mumbaraddi, Dundappa; Sarkar, Sumanta; Peter, Sebastian C., E-mail: sebastiancp@jncasr.ac.in

2016-04-15

This review highlights the synthesis and crystal growth of quaternary intermetallic compounds based on rare earth metals. In the first part of this review, we highlight briefly about intermetallics and their versatile properties in comparison to the constituent elements. In the next part, we have discussed about various synthesis techniques with more focus on the metal flux technique towards the well shaped crystal growth of novel compounds. In the subsequent parts, several disordered quaternary compounds have been reviewed and then outlined most known ordered quaternary compounds with their complex structure. A special attention has been given to the ordered compoundsmore » with structural description and relation to the parent binary and ternary compounds. The importance of electronic and structural feature is highlighted as the key roles in designing these materials for emerging applications. - Graphical abstract: Rare earth based quaternary intermetallic compounds crystallize in complex novel crystal structures. The diversity in the crystal structure may induce unique properties and can be considered them as future materials. - Highlights: • Crystal growth and crystal structure of quaternary rare earth based intermetallics. • Structural complexity of quaternary compounds in comparison to the parent compounds. • Novel quaternary compounds display unique crystal structure.« less

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Method for fabrication of ceramic dielectric films on copper foils

DOEpatents

Ma, Beihai; Narayanan, Manoj; Dorris, Stephen E.; Balachandran, Uthamalingam

2015-03-10

The present invention provides a method for fabricating a ceramic film on a copper foil. The method comprises applying a layer of a sol-gel composition onto a copper foil. The sol-gel composition comprises a precursor of a ceramic material suspended in 2-methoxyethanol. The layer of sol-gel is then dried at a temperature up to about 250.degree. C. The dried layer is then pyrolyzed at a temperature in the range of about 300 to about 450.degree. C. to form a ceramic film from the ceramic precursor. The ceramic film is then crystallized at a temperature in the range of about 600 to about 750.degree. C. The drying, pyrolyzing and crystallizing are performed under a flowing stream of an inert gas. In some embodiments an additional layer of the sol-gel composition is applied onto the ceramic film and the drying, pyrolyzing and crystallizing steps are repeated for the additional layer to build up a thicker ceramic layer on the copper foil. The process can be repeated one or more times if desired.

Method of treating alkali metal sulfide and carbonate mixtures

DOEpatents

Kohl, Arthur L.; Rennick, Robert D.; Savinsky, Martin W.

1978-01-01

A method of removing and preferably recovering sulfur values from an alkali metal sulfide and carbonate mixture comprising the steps of (1) introducing the mixture in an aqueous medium into a first carbonation zone and reacting the mixture with a gas containing a major amount of CO.sub.2 and a minor amount of H.sub.2 S; (2) introducing the resultant product from step 1 into a stripping zone maintained at subatmospheric pressure, and contacting this product with steam to produce a gaseous mixture, comprising H.sub.2 S and water vapor, and a liquor of reduced sulfide content; (3) introducing the liquor of reduced sulfide content into a second carbonation zone, and reacting the liquor with substantially pure gaseous CO.sub.2 in an amount sufficient to precipitate bicarbonate crystals and produce an offgas containing CO.sub.2 and H.sub.2 S for use in step 1; (4) recovering the bicarbonate crystals from step 3, and thermally decomposing the crystals to produce an alkaline metal carbonate product and a substantially pure CO.sub.2 offgas for use in step 3.

Spin Hamiltonian Analysis of the SMM V15 Using High Field ESR

NASA Astrophysics Data System (ADS)

Martens, Mathew; van Tol, Hans; Bertaina, Sylvain; Barbara, Bernard; Muller, Achim; Chiorescu, Irinel

2014-03-01

We have studied molecular magnets using high field / high frequency Electron Spin Resonance. Such molecular structures contain many quantum spins linked by exchange interactions and consequently their energy structure is often complex and require a good understanding of the molecular spin Hamiltonian. In particular, we studied the V15 molecule, comprised of 15 spins 1/2 and a total spin 1/2, which is a system that recently showed quantum Rabi oscillations of its total quantum spin. This type of molecule is an essential system for advancing molecular structures into quantum computing. We used high frequency characterization techniques (of hundreds of GHz) to gain insight into the exchange anisotropy interactions, crystal field, and anti-symmetric interactions present in this system. We analyzed the data using a detailed numerical analysis of spin interactions and our findings regarding the V15 spin Hamiltonian will be discussed. Supported by the NSF Cooperative Agreement Grant No. DMR-0654118 and No. NHMFL UCGP 5059, NSF grant No. DMR-0645408.

Structural and optical characterization of ZnO/Mg(x)Zn(1-x)O multiple quantum wells based random laser diodes.

PubMed

Jiang, Qike; Zheng, He; Wang, Jianbo; Long, Hao; Fang, Guojia

2012-12-01

Two kinds of laser diodes (LDs) comprised of ZnO/Mg(x)Zn(1-x)O (ZnO/MZO) multiple quantum wells (MQWs) grown on GaN (MQWs/GaN) and Si (MQWs/Si) substrates, respectively, have been constructed. The LD with MQWs/GaN exhibits ultraviolet random lasing under electrical excitation, while that with MQWs/Si does not. In the MQWs/Si, ZnO/MZO MQWs consist of nanoscaled crystallites, and the MZO layers undergo a phase separation of cubic MgO and hexagonal ZnO. Moreover, the Mg atom predominantly locates in the MZO layers along with a significant aggregation at the ZnO/MZO interfaces; in sharp contrast, the ZnO/MZO MQWs in the MQWs/GaN show a well-crystallized structure with epitaxial relationships among GaN, MZO, and ZnO. Notably, Mg is observed to diffuse into the ZnO well layers. The structure-optical property relationship of these two LDs is further discussed.

OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites.

PubMed

Shazman, Shula; Lee, Hunjoong; Socol, Yakov; Mann, Richard S; Honig, Barry

2014-01-01

We present OnTheFly (http://bhapp.c2b2.columbia.edu/OnTheFly/index.php), a database comprising a systematic collection of transcription factors (TFs) of Drosophila melanogaster and their DNA-binding sites. TFs predicted in the Drosophila melanogaster genome are annotated and classified and their structures, obtained via experiment or homology models, are provided. All known preferred TF DNA-binding sites obtained from the B1H, DNase I and SELEX methodologies are presented. DNA shape parameters predicted for these sites are obtained from a high throughput server or from crystal structures of protein-DNA complexes where available. An important feature of the database is that all DNA-binding domains and their binding sites are fully annotated in a eukaryote using structural criteria and evolutionary homology. OnTheFly thus provides a comprehensive view of TFs and their binding sites that will be a valuable resource for deciphering non-coding regulatory DNA.

Structure of a Protein Phosphatase 2A Holoenzyme: Insights into B55-Mediated Tau Dephosphorylation

PubMed Central

Xu, Yanhui; Chen, Yu; Zhang, Ping; Jeffrey, Philip D.; Shi, Yigong

2009-01-01

Summary Protein phosphatase 2A (PP2A) regulates many essential aspects of cellular physiology. Members of the regulatory B/B55/PR55 family are thought to play a key role in the dephosphorylation of Tau, whose hyperphosphorylation contributes to Alzheimer's disease. The underlying mechanisms of the PP2A-Tau connection remain largely enigmatic. Here, we report the complete reconstitution of a Tau dephosphorylation assay and the crystal structure of a heterotrimeric PP2A holoenzyme involving the regulatory subunit Bα. We show that Bα specifically and markedly facilitates dephosphorylation of the phosphorylated Tau in our reconstituted assay. The Bα subunit comprises a seven-bladed β propeller, with an acidic, substrate-binding groove located in the center of the propeller. The β propeller latches onto the ridge of the PP2A scaffold subunit with the help of a protruding β hairpin arm. Structure-guided mutagenesis studies revealed the underpinnings of PP2A-mediated dephosphorylation of Tau. PMID:18922469

Enhanced photoelectrical performance of dye-sensitized solar cells with double-layer TiO2 on perovskite SrTiO3 substrate

NASA Astrophysics Data System (ADS)

Liu, Qiuhong; Sun, Qiong; Zhang, Min; Li, Yang; Zhao, Mei; Dong, Lifeng

2016-04-01

In this research, perovskite SrTiO3 particles are synthesized by a hydrothermal method, and TiO2 with a double-layer structure is grown on the SrTiO3 surface by a hydrolysis-condensation process. Structural characterizations reveal that TiO2 comprises of two phases: anatase film at the bottom and single-crystal rutile nanorods grown along the [110] direction on top. The TiO2-SrTiO3 composite film is investigated as photoanode material for dye-sensitized solar cells. In comparison with pure TiO2 and SrTiO3, the composite photoanode shows a much better performance in photoelectric conversion efficiency (1.35 %), which is about 2 and 100 times as efficient as pure TiO2 and SrTiO3, respectively. This indicates that the composite structure can facilitate charge carrier transfer and reduce electron-hole recombination to enhance photoelectrical properties of TiO2-based photoanode materials.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein.

PubMed

Rahaman, Siti Nurulnabila A; Mat Yusop, Jastina; Mohamed-Hussein, Zeti-Azura; Ho, Kok Lian; Teh, Aik-Hong; Waterman, Jitka; Ng, Chyan Leong

2016-03-01

C1ORF123 is a human hypothetical protein found in open reading frame 123 of chromosome 1. The protein belongs to the DUF866 protein family comprising eukaryote-conserved proteins with unknown function. Recent proteomic and bioinformatic analyses identified the presence of C1ORF123 in brain, frontal cortex and synapses, as well as its involvement in endocrine function and polycystic ovary syndrome (PCOS), indicating the importance of its biological role. In order to provide a better understanding of the biological function of the human C1ORF123 protein, the characterization and analysis of recombinant C1ORF123 (rC1ORF123), including overexpression and purification, verification by mass spectrometry and a Western blot using anti-C1ORF123 antibodies, crystallization and X-ray diffraction analysis of the protein crystals, are reported here. The rC1ORF123 protein was crystallized by the hanging-drop vapor-diffusion method with a reservoir solution comprised of 20% PEG 3350, 0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate pH 6.5. The crystals diffracted to 1.9 Å resolution and belonged to an orthorhombic space group with unit-cell parameters a = 59.32, b = 65.35, c = 95.05 Å. The calculated Matthews coefficient (VM) value of 2.27 Å(3) Da(-1) suggests that there are two molecules per asymmetric unit, with an estimated solvent content of 45.7%.

Simple, Green, and High-Yield Production of Boron-Based Nanostructures with Diverse Morphologies by Dissolution and Recrystallization of Layered Magnesium Diboride Crystals in Water.

PubMed

Gunda, Harini; Das, Saroj Kumar; Jasuja, Kabeer

2018-04-05

Layered metal diborides that contain metal atoms sandwiched between boron honeycomb planes offer a rich opportunity to access graphenic forms of boron. We recently demonstrated that magnesium diboride (MgB 2 ) could be exfoliated by ultrasonication in water to yield boron-based nanosheets. However, knowledge of the fate of metal boride crystals in aqueous phases is still in its incipient stages. This work presents our preliminary findings on the discovery that MgB 2 crystals can undergo dissolution in water under ambient conditions to result in precursors (prenucleation clusters) that, upon aging, undergo nonclassical crystallization preferentially growing in lateral directions by two-dimensional (2D) oriented attachment. We show that this recrystallization can be utilized as an avenue to obtain a high yield (≈92 %) of boron-based nanostructures, including nanodots, nanograins, nanoflakes, and nanosheets. These nanostructures comprise boron honeycomb planes chemically modified with hydride and oxy functional groups, which results in an overall negative charge on their surfaces. This ability of MgB 2 crystals to yield prenucleation clusters that can self-seed to form nanostructures comprising chemically modified boron honeycomb planes presents a new facet to the physicochemical interaction of MgB 2 with water. These findings also open newer avenues to obtain boron-based nanostructures with tunable morphologies by varying the chemical milieu during recrystallization. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms

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

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalasemore » (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.« less

Understanding Crystal Populations: The Role of Textural Analysis in Determining Magmatic Timescales

NASA Astrophysics Data System (ADS)

Jerram, D. A.

2006-12-01

Crystal populations in igneous rocks that erupt at the Earths surface act as records of magma chamber processes at depth, predominantly recording episodes of growth/nucleation and geochemical changes within the host body. Detailed inspection of such crystal populations, however, reveals a complex crystal cargo that comprises crystals which have grown directly from the host, crystals that have spent one or more protracted periods being isolated from the host magma and crystals that originated from a completely different magma body and/or country rock. To further interrogate this crystal cargo we can use textural analysis techniques to fully quantify the crystal population and gather important information about the population, such as crystal morphology, spatial distribution and size relationships. When quantified, such data can be used to better constrain the different components of the resultant crystal population and how they relate to each other. Additionally, by combining textural analysis information with geochemical analysis, a powerful measure of magma timescales and magma chamber processes results. In this contribution the different types of textural analysis techniques in 2D and 3D are introduced with examples from both plutonic and volcanic systems presented to highlight the roll of this approach to quantifying magma timescales.

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

Jia, Xiaofei; Singh, Rajendra; Homann, Stefanie

The HIV-1 protein Nef inhibits antigen presentation by class I major histocompatibility complex (MHC-I). We determined the mechanism of this activity by solving the crystal structure of a protein complex comprising Nef, the MHC-I cytoplasmic domain (MHC-I CD) and the {mu}1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-{mu}1 interface, which encompasses the cargo-recognition site of {mu}1 and the proline-rich strand of Nef. The Nef C terminus induces a previously unobserved conformational change in {mu}1, whereas the N terminus binds the Nef core tomore » position it optimally for complex formation. Positively charged patches on {mu}1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity.« less

Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin*

PubMed Central

Yanagihara, Itaru; Nakahira, Kumiko; Yamane, Tsutomu; Kaieda, Shuji; Mayanagi, Kouta; Hamada, Daizo; Fukui, Takashi; Ohnishi, Kiyouhisa; Kajiyama, Shin'ichiro; Shimizu, Toshiyuki; Sato, Mamoru; Ikegami, Takahisa; Ikeguchi, Mitsunori; Honda, Takeshi; Hashimoto, Hiroshi

2010-01-01

Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-Cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin. PMID:20335168

Structure of the Get3 targeting factor in complex with its membrane protein cargo

DOE PAGES

Mateja, Agnieszka; Paduch, Marcin; Chang, Hsin-Yang; ...

2015-03-06

Tail-anchored (TA) proteins are a physiologically important class of membrane proteins targeted to the endoplasmic reticulum by the conserved guided-entry of TA proteins (GET) pathway. During transit, their hydrophobic transmembrane domains (TMDs) are chaperoned by the cytosolic targeting factor Get3, but the molecular nature of the functional Get3-TA protein targeting complex remains unknown. In this paper, we reconstituted the physiologic assembly pathway for a functional targeting complex and showed that it comprises a TA protein bound to a Get3 homodimer. Crystal structures of Get3 bound to different TA proteins showed an α-helical TMD occupying a hydrophobic groove that spans themore » Get3 homodimer. Finally, our data elucidate the mechanism of TA protein recognition and shielding by Get3 and suggest general principles of hydrophobic domain chaperoning by cellular targeting factors.« less

Pyrochlore-type catalysts for the reforming of hydrocarbon fuels

DOEpatents

Berry, David A [Morgantown, WV; Shekhawat, Dushyant [Morgantown, WV; Haynes, Daniel [Morgantown, WV; Smith, Mark [Morgantown, WV; Spivey, James J [Baton Rouge, LA

2012-03-13

A method of catalytically reforming a reactant gas mixture using a pyrochlore catalyst material comprised of one or more pyrochlores having the composition A.sub.2-w-xA'.sub.wA''.sub.xB.sub.2-y-zB'.sub.yB''.sub.zO.sub.7-.DELTA.. Distribution of catalytically active metals throughout the structure at the B site creates an active and well dispersed metal locked into place in the crystal structure. This greatly reduces the metal sintering that typically occurs on supported catalysts used in reforming reactions, and reduces deactivation by sulfur and carbon. Further, oxygen mobility may also be enhanced by elemental exchange of promoters at sites in the pyrochlore. The pyrochlore catalyst material may be utilized in catalytic reforming reactions for the conversion of hydrocarbon fuels into synthesis gas (H.sub.2+CO) for fuel cells, among other uses.

Pyrochlore catalysts for hydrocarbon fuel reforming

DOEpatents

Berry, David A.; Shekhawat, Dushyant; Haynes, Daniel; Smith, Mark; Spivey, James J.

2012-08-14

A method of catalytically reforming a reactant gas mixture using a pyrochlore catalyst material comprised of one or more pyrochlores having the composition A₂B_2-y-zB'_yB"_zO_7-.DELTA., where y>0 and z.gtoreq.0. Distribution of catalytically active metals throughout the structure at the B site creates an active and well dispersed metal locked into place in the crystal structure. This greatly reduces the metal sintering that typically occurs on supported catalysts used in reforming reactions, and reduces deactivation by sulfur and carbon. Further, oxygen mobility may also be enhanced by elemental exchange of promoters at sites in the pyrochlore. The pyrochlore catalyst material may be utilized in catalytic reforming reactions for the conversion of hydrocarbon fuels into synthesis gas (H₂+CO) for fuel cells, among other uses.

Synthesis, Crystal Structure, and Magnetic Properties of the Linear-Chain Cobalt Oxide Sr 5Pb 3CoO 12

NASA Astrophysics Data System (ADS)

Yamaura, K.; Huang, Q.; Takayama-Muromachi, E.

2002-02-01

The novel spin-chain cobalt oxide Sr5Pb3CoO12 [Poverline6×2m, a=10.1093(2) Å and c=3.562 51(9) Å at 295 K] is reported. A polycrystalline sample of the compound was studied by neutron diffraction (at 6 and 295 K) and magnetic susceptibility measurements (5 to 390 K). The cobalt oxide was found to be analogous to the copper oxide Sr5Pb3CuO12, which is comprised of magnetic-linear chains at an interchain distance of 10 Å. Although the cobalt oxide chains (μeff of 3.64 μB per Co) are substantially antiferromagnetic (θW=-38.8 K), neither low-dimensional magnetism nor long-range ordering has been found; a local-structure disorder in the chains might have an impact on the magnetism. This compound is highly electrically insulating.

Evolving pharmacology of orphan GPCRs: IUPHAR Commentary.

PubMed

Davenport, Anthony P; Harmar, Anthony J

2013-10-01

The award of the 2012 Nobel Prize in Chemistry to Robert Lefkowitz and Brian Kobilka for their work on the structure and function of GPCRs, spanning a period of more than 20 years from the cloning of the human β2 -adrenoceptor to determining the crystal structure of the same protein, has earned both researchers a much deserved place in the pantheon of major scientific discoveries. GPCRs comprise one of the largest families of proteins, controlling many major physiological processes and have been a major focus of the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR) since its inception in 1987. We report here recent efforts by the British Pharmacological Society and NC-IUPHAR to define the endogenous ligands of 'orphan' GPCRs and to place authoritative and accessible information about these crucial therapeutic targets online. © 2013 The British Pharmacological Society.

Structure and positron annihilation spectra of tin incorporated in mesoporous molecular sieves

NASA Astrophysics Data System (ADS)

Zhang, H. Y.; He, Y. J.; Chen, Y. B.; Wang, H. Y.

2002-12-01

Mesoporous molecular sieves (MCM-41) consist of an ordered array of silica tubules comprised of pores with uniform controllable diameters in the nanometer range. Tin was successfully incorporated into MCM-41 using wet chemical techniques. Detailed structural analysis via x-ray diffraction and high resolution transmission electron microscopy confirm this, and indicate that, after sintering samples in air, SnO2 crystal nanoclusters formed in the channels. These conclusions are further supported by a study of the positron annihilation spectrum. In particular, the insensitivity, after incorporation of tin, of the long-lived component of the positron annihilation spectrum to whether an air or a vacuum annealing atmosphere is used indicates that tin in the MCM-41 channels hinders the entry of quenching oxygen from the air. Furthermore, after sintering, the complete loss of this long-lived component indicates that SnO2 nanoclusters fill the channels.

The structure of an RNAi polymerase links RNA silencing and transcription.

PubMed

Salgado, Paula S; Koivunen, Minni R L; Makeyev, Eugene V; Bamford, Dennis H; Stuart, David I; Grimes, Jonathan M

2006-12-01

RNA silencing refers to a group of RNA-induced gene-silencing mechanisms that developed early in the eukaryotic lineage, probably for defence against pathogens and regulation of gene expression. In plants, protozoa, fungi, and nematodes, but apparently not insects and vertebrates, it involves a cell-encoded RNA-dependent RNA polymerase (cRdRP) that produces double-stranded RNA triggers from aberrant single-stranded RNA. We report the 2.3-A resolution crystal structure of QDE-1, a cRdRP from Neurospora crassa, and find that it forms a relatively compact dimeric molecule, each subunit of which comprises several domains with, at its core, a catalytic apparatus and protein fold strikingly similar to the catalytic core of the DNA-dependent RNA polymerases responsible for transcription. This evolutionary link between the two enzyme types suggests that aspects of RNA silencing in some organisms may recapitulate transcription/replication pathways functioning in the ancient RNA-based world.

Structural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2.

PubMed

Xu, Emma-Ruoqi; Blythe, Emily E; Fischer, Gerhard; Hyvönen, Marko

2017-07-28

Bone morphogenetic proteins (BMPs) are secreted growth factors that promote differentiation processes in embryogenesis and tissue development. Regulation of BMP signaling involves binding to a variety of extracellular proteins, among which are many von Willebrand factor C (vWC) domain-containing proteins. Although the crystal structure of the complex of crossveinless-2 (CV-2) vWC1 and BMP-2 previously revealed one mode of the vWC/BMP-binding mechanism, other vWC domains may bind to BMP differently. Here, using X-ray crystallography, we present for the first time structures of the vWC domains of two proteins thought to interact with BMP-2: collagen IIA and matricellular protein CCN3. We found that these two vWC domains share a similar N-terminal fold that differs greatly from that in CV-2 vWC, which comprises its BMP-2-binding site. We analyzed the ability of these vWC domains to directly bind to BMP-2 and detected an interaction only between the collagen IIa vWC and BMP-2. Guided by the collagen IIa vWC domain crystal structure and conservation of surface residues among orthologous domains, we mapped the BMP-binding epitope on the subdomain 1 of the vWC domain. This binding site is different from that previously observed in the complex between CV-2 vWC and BMP-2, revealing an alternative mode of interaction between vWC domains and BMPs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Physical and Structural Studies on the Cryo-cooling of Insulin Crystals

NASA Technical Reports Server (NTRS)

Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

2003-01-01

Reflection profiles were analyzed from microgravity-(mg) and earth-grown insulin crystals to measure mosaicity (h) and to reveal mosaic domain structure and composition. The effects of cryocooling on single and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were larger, more homogeneous, and more perfect than earth crystals. Several mg crystals contained primarily a single mosaic domain with havg of 0.005deg. The earth crystals varied in quality and all contained multiple domains with havg of 0.031deg. Cryocooling caused a 43-fold increase in h for mg crystals (havg=0.217deg) and an %fold increase for earth crystals (havg=0.246deg). These results indicate that very well-ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryo-cooling. Cryo-cooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryo-cooled single domain crystals relative to cryo-cooled multi-domain crystals. This improved signal, along with the increase in crystal size, facilitated the measurement of the weaker high- resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit cell dimensions which may be linked to cryo-cooling-associated structural changes and disorder.

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

2008-02-01

An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

Partial polarizer filter

NASA Technical Reports Server (NTRS)

Title, A. M. (Inventor)

1978-01-01

A birefringent filter module comprises, in seriatum. (1) an entrance polarizer, (2) a first birefringent crystal responsive to optical energy exiting the entrance polarizer, (3) a partial polarizer responsive to optical energy exiting the first polarizer, (4) a second birefringent crystal responsive to optical energy exiting the partial polarizer, and (5) an exit polarizer. The first and second birefringent crystals have fast axes disposed + or -45 deg from the high transmitivity direction of the partial polarizer. Preferably, the second crystal has a length 1/2 that of the first crystal and the high transmitivity direction of the partial polarizer is nine times as great as the low transmitivity direction. To provide tuning, the polarizations of the energy entering the first crystal and leaving the second crystal are varied by either rotating the entrance and exit polarizers, or by sandwiching the entrance and exit polarizers between pairs of half wave plates that are rotated relative to the polarizers. A plurality of the filter modules may be cascaded.

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

Ozkendir, Osman Murat, E-mail: ozkendir@gmail.com

Highlights: • Crystal and electronic structure properties of Nd{sub x}Ti{sub 1−x}BO{sub 2+d} structure were investigated. • New crystal structures for Nd–Ti complexes are determined. • Distortions in the crystal structure were observed as a result of Boron shortage. • Prominent change in electronic properties of the samples with the increasing Nd amount. - Abstract: Neodymium substituted TiBO{sub 3} samples were investigated according to their crystal, electric and electronic properties. Studies were conducted by X-ray absorption fine structure spectroscopy (XAFS) technique for the samples with different substitutions in the preparation processes. To achieve better crystal structure results during the study, XRDmore » pattern results were supported by extended-XAFS (EXAFS) analysis. The electronic structure analysis were studied by X-ray absorption near-edge structure spectroscopy (XANES) measurements at the room temperatures. Due to the substituted Nd atoms, prominent changes in crystal structure, new crystal geometries for Nd-Ti complexes, phase transitions in the crystals structure were detected according to the increasing Nd substitutions in the samples. In the entire stages of the substitutions, Nd atoms were observed as governing the whole phenomena due to their dominant characteristics in Ti geometries. Besides, electrical resistivity decay was determined in the materials with the increasing amount of Nd substitution.« less

High-throughput crystallization screening.

PubMed

Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

2014-01-01

Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

Crystal structure of metagenomic β-xylosidase/ α-l-arabinofuranosidase activated by calcium.

PubMed

Matsuzawa, Tomohiko; Kaneko, Satoshi; Kishine, Naomi; Fujimoto, Zui; Yaoi, Katsuro

2017-09-01

The crystal structure of metagenomic β-xylosidase/α-l-arabinofuranosidase CoXyl43, activated by calcium ions, was determined in its apo and complexed forms with xylotriose or l-arabinose in the presence and absence of calcium. The presence of calcium ions dramatically increases the kcat of CoXyl43 for p-nitrophenyl β-d-xylopyranoside and reduces the Michaelis constant for p-nitrophenyl α-l-arabinofuranoside. CoXyl43 consists of a single catalytic domain comprised of a five-bladed β-propeller. In the presence of calcium, a single calcium ion was observed at the centre of this catalytic domain, behind the catalytic pocket. In the absence of calcium, the calcium ion was replaced with one sodium ion and one water molecule, and the positions of these cations were shifted by 1.3 Å. The histidine-319 side chain, which coordinates to the 2-hydroxyl oxygen atom of the bound xylose molecule in the catalytic pocket, also coordinates to the calcium ion, but not to the sodium ion. The calcium-dependent increase in activity appears to be caused by the structural change in the catalytic pocket induced by the tightly bound calcium ion and coordinating water molecules, and by the protonation state of glutamic acid-268, the catalytic acid of the enzyme. Our findings further elucidate the complex relationship between metal ions and glycosidases. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase–rhodanese fusion protein functions in sulfur assimilation

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

Motl, Nicole; Skiba, Meredith A.; Kabil, Omer

Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts H2S to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO–rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium Burkholderia phytofirmans. The crystal structures ofmore » wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The B. phytofirmans PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that B. phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the Staphylococcus aureus PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.« less

Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin

DOE PAGES

Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; ...

2015-12-04

Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, wemore » present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.« less

Crystal structure of an SH2-kinase construct of c-Abl and effect of the SH2 domain on kinase activity.

PubMed

Lorenz, Sonja; Deng, Patricia; Hantschel, Oliver; Superti-Furga, Giulio; Kuriyan, John

2015-06-01

Constitutive activation of the non-receptor tyrosine kinase c-Abl (cellular Abelson tyrosine protein kinase 1, Abl1) in the Bcr (breakpoint cluster region)-Abl1 fusion oncoprotein is the molecular cause of chronic myeloid leukaemia (CML). Recent studies have indicated that an interaction between the SH2 (Src-homology 2) domain and the N-lobe (N-terminal lobe) of the c-Abl kinase domain (KD) has a critical role in leukaemogenesis [Grebien et al. (2011) Cell 147, 306-319; Sherbenou et al. (2010) Blood 116, 3278-3285]. To dissect the structural basis of this phenomenon, we studied c-Abl constructs comprising the SH2 and KDs in vitro. We present a crystal structure of an SH2-KD construct bound to dasatinib, which contains the relevant interface between the SH2 domain and the N-lobe of the KD. We show that the presence of the SH2 domain enhances kinase activity moderately and that this effect depends on contacts in the SH2/N-lobe interface and is abrogated by specific mutations. Consistently, formation of the interface decreases slightly the association rate of imatinib with the KD. That the effects are small compared with the dramatic in vivo consequences suggests an important function of the SH2-N-lobe interaction might be to help disassemble the auto-inhibited conformation of c-Abl and promote processive phosphorylation, rather than substantially stimulate kinase activity.

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

PubMed

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

cis-trans Germanium chains in the intermetallic compounds ALi{sub 1-x}In{sub x}Ge{sub 2} and A{sub 2}(Li{sub 1-x}In{sub x}){sub 2}Ge{sub 3} (A=Sr, Ba, Eu)-experimental and theoretical studies

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

You, Tae-Soo; Bobev, Svilen, E-mail: bobev@udel.ed

Two types of strontium-, barium- and europium-containing germanides have been synthesized using high temperature reactions and characterized by single-crystal X-ray diffraction. All reported compounds also contain mixed-occupied Li and In atoms, resulting in quaternary phases with narrow homogeneity ranges. The first type comprises EuLi{sub 0.91(1)}In{sub 0.09}Ge{sub 2}, SrLi{sub 0.95(1)}In{sub 0.05}Ge{sub 2} and BaLi{sub 0.99(1)}In{sub 0.01}Ge{sub 2}, which crystallize in the orthorhombic space group Pnma (BaLi{sub 0.9}Mg{sub 0.1}Si{sub 2} structure type, Pearson code oP16). The lattice parameters are a=7.129(4)-7.405(4) A; b=4.426(3)-4.638(2) A; and c=11.462(7)-11.872(6) A. The second type includes Eu{sub 2}Li{sub 1.36(1)}In{sub 0.64}Ge{sub 3} and Sr{sub 2}Li{sub 1.45(1)}In{sub 0.55}Ge{sub 3}, whichmore » adopt the orthorhombic space group Cmcm (Ce{sub 2}Li{sub 2}Ge{sub 3} structure type, Pearson code oC28) with lattice parameters a=4.534(2)-4.618(2) A; b=19.347(8)-19.685(9) A; and c=7.164(3)-7.260(3) A. The polyanionic sub-structures in both cases feature one-dimensional Ge chains with alternating Ge-Ge bonds in cis- and trans-conformation. Theoretical studies using the tight-binding linear muffin-tin orbital (LMTO) method provide the rationale for optimizing the overall bonding by diminishing the {pi}-p delocalization along the Ge chains, accounting for the experimentally confirmed substitution of Li forIn. -- Graphical abstract: Presented are the single-crystal structures of two types of closely related intermetallics, as well as their band structures, calculated using tight-binding linear muffin-tin orbital (TB-LMTO-ASA) method. Display Omitted« less

Isolation, purification, crystallization and preliminary X-ray studies of two 30 kDa proteins from silkworm haemolymph.

PubMed

Pietrzyk, Agnieszka J; Bujacz, Anna; Łochyńska, Małgorzata; Jaskólski, Mariusz; Bujacz, Grzegorz

2011-03-01

Juvenile hormone-binding protein (JHBP) and the low-molecular-mass lipoprotein PBMHP-12 belong to a group of 30 kDa proteins that comprise the major protein component of the haemolymph specific to the fifth-instar larvae stage of the mulberry silkworm Bombyx mori L. Proteins from this group are often essential for the development of the insect. In a project aimed at crystallographic characterization of B. mori JHBP (BmJHBP), it was copurified together with PBMHP-12. Eventually, the two proteins were isolated and crystallized separately. The BmJHBP crystals were orthorhombic (space group C222(1)) and the PBMHP-12 crystals were triclinic. The crystals diffracted X-rays to 2.9 Å (BmJHBP) and 1.3 Å (PBMHP-12) resolution.

A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

NASA Astrophysics Data System (ADS)

Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

2017-12-01

Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

An unusual crystal growth method of the chalcohalide semiconductor, β-Hg 3S 2Cl 2: A new candidate for hard radiation detection

DOE PAGES

Wibowo, Arief C.; Malliakas, Christos D.; Li, Hao; ...

2016-03-16

Here, we assess the mercury chalcohalide compound, β-Hg 3S 2Cl 2, as a potential semiconductor material for X-ray and γ-ray detection. It has a high density (6.80 g/cm 3) and wide band gap (2.56 eV) and crystallizes in the cubic Pm4more » $$\\bar{3}$$n space group with a three-dimensional structure comprised of [Hg 12S 8] cubes with Cl atoms located within and between the cubes, featuring a trigonal pyramidal SHg3 as the main building block. First-principle electronic structure calculations at the density functional theory level predict that the compound has closely lying indirect and direct band gaps. We have successfully grown transparent, single crystals of β-Hg 3S 2Cl 2 up to 7 mm diameter and 1 cm long using a new approach by the partial decomposition of the quaternary Hg 3Bi 2S 2Cl 8 compound followed by the formation of β-Hg 3S 2Cl 2 and an impermeable top layer, all happening in situ during vertical Bridgman growth. The decomposition process was optimized by varying peak temperatures and temperature gradients using a 2 mm/h translation rate of the Bridgman technique. Formation of the quaternary Hg 3Bi 2S 2Cl 8 followed by its partial decomposition into β-Hg 3S 2Cl 2 was confirmed by in situ temperature-dependent synchrotron powder diffraction studies. The single crystal samples obtained had resistivity of 10 10 Ω·cm and mobility-lifetime products of electron and hole carriers of 1.4(4) × 10 –4 cm 2/V and 7.5(3) × 10 –5 cm 2/V, respectively. Further, an appreciable Ag X-ray photoconductivity response was observed showing the potential of β-Hg 3S 2Cl 2 as a hard radiation detector material.« less

Early stages of carbonate mineralization revealed from molecular simulations: Implications for biomineral formation

NASA Astrophysics Data System (ADS)

Wallace, A. F.; DeYoreo, J.; Banfield, J. F.

2011-12-01

The carbonate mineral constituents of many biomineralized products, formed both in and ex vivo, grow by a multi-stage crystallization process that involves the nucleation and structural reorganization of transient amorphous phases. The existence of transient phases and cluster species has significant implications for carbonate nucleation and growth in natural and engineered environments, both modern and ancient. The structure of these intermediate phases remains elusive, as does the nature of the disorder to order transition, however, these process details may strongly influence the interpretation of elemental and isotopic climate proxy data obtained from authigenic and biogenic carbonates. While molecular simulations have been applied to certain aspects of crystal growth, studies of metal carbonate nucleation are strongly inhibited by the presence of kinetic traps that prevent adequate sampling of the potential landscape upon which the growing clusters reside within timescales accessible by simulation. This research addresses this challenge by marrying the recent Kawska-Zahn (KZ) approach to simulation of crystal nucleation and growth from solution with replica-exchange molecular dynamics (REMD) techniques. REMD has been used previously to enhance sampling of protein conformations that occupy energy wells that are separated by sizable thermodynamic and kinetic barriers, and is used here to probe the initial formation and onset of order within hydrated calcium and iron carbonate cluster species during nucleation. Results to date suggest that growing clusters initiate as short linear ion chains that evolve into two- and three-dimensional structures with continued growth. The planar structures exhibit an obvious 2d lattice, while establishment of a 3d lattice is hindered by incomplete ion desolvation. The formation of a dehydrated core consisting of a single carbonate ion is observed when the clusters are ~0.75 nm. At the same size a distorted, but discernible calcite-type lattice is also apparent. Continued growth results in expansion of the dehydrated core, however, complete desolvation and incorporation of cations into the growing carbonate phase is not achieved until the cluster grows to ~1.2 nm. Exploration of the system free energy along the crystallization path reveals "special" cluster sizes that correlate with ion desolvation milestones. The formation of these species comprise critical bottlenecks on the energy landscape and for the establishment of order within the growing clusters.

Inorganic Crystal Structure Database (ICSD)

National Institute of Standards and Technology Data Gateway

SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery.

PubMed

Catana, Cornel; Stouten, Pieter F W

2007-01-01

The ability to accurately predict biological affinity on the basis of in silico docking to a protein target remains a challenging goal in the CADD arena. Typically, "standard" scoring functions have been employed that use the calculated docking result and a set of empirical parameters to calculate a predicted binding affinity. To improve on this, we are exploring novel strategies for rapidly developing and tuning "customized" scoring functions tailored to a specific need. In the present work, three such customized scoring functions were developed using a set of 129 high-resolution protein-ligand crystal structures with measured Ki values. The functions were parametrized using N-PLS (N-way partial least squares), a multivariate technique well-known in the 3D quantitative structure-activity relationship field. A modest correlation between observed and calculated pKi values using a standard scoring function (r2 = 0.5) could be improved to 0.8 when a customized scoring function was applied. To mimic a more realistic scenario, a second scoring function was developed, not based on crystal structures but exclusively on several binding poses generated with the Flo+ docking program. Finally, a validation study was conducted by generating a third scoring function with 99 randomly selected complexes from the 129 as a training set and predicting pKi values for a test set that comprised the remaining 30 complexes. Training and test set r2 values were 0.77 and 0.78, respectively. These results indicate that, even without direct structural information, predictive customized scoring functions can be developed using N-PLS, and this approach holds significant potential as a general procedure for predicting binding affinity on the basis of in silico docking.

Copper Selenidophosphates Cu4P2Se6, Cu4P3Se4, Cu4P4Se3, and CuP2Se, Featuring Zero-, One-, and Two-Dimensional Anions.

PubMed

Kuhn, Alexander; Schoop, Leslie M; Eger, Roland; Moudrakovski, Igor; Schwarzmüller, Stefan; Duppel, Viola; Kremer, Reinhard K; Oeckler, Oliver; Lotsch, Bettina V

2016-08-15

Five new compounds in the Cu/P/Se phase diagram have been synthesized, and their crystal structures have been determined. The crystal structures of these compounds comprise four previously unreported zero-, one-, and two-dimensional selenidophosphate anions containing low-valent phosphorus. In addition to two new modifications of Cu4P2Se6 featuring the well-known hexaselenidohypodiphosphate(IV) ion, there are three copper selenidophosphates with low-valent P: Cu4P3Se4 contains two different new anions, (i) a monomeric (zero-dimensional) selenidophosphate anion [P2Se4](4-) and (ii) a one-dimensional selenidophosphate anion [Formula: see text], which is related to the well-known gray-Se-like [Formula: see text] Zintl anion. Cu4P4Se3 contains one-dimensional [Formula: see text] polyanions, whereas CuP2Se contains the 2D selenidophosphate [Formula: see text] polyanion. It consists of charge-neutral CuP2Se layers separated by a van der Waals gap which is very rare for a Zintl-type phase. Hence, besides black P, CuP2Se constitutes a new possible source of 2D oxidized phosphorus containing layers for intercalation or exfoliation experiments. Additionally, the electronic structures and some fundamental physical properties of the new compounds are reported. All compounds are semiconducting with indirect band gaps of the orders of around 1 eV. The phases reported here add to the structural diversity of chalcogenido phosphates. The structural variety of this family of compounds may translate into a variety of tunable physical properties.

Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity.

PubMed

Chandra, N R; Ramachandraiah, G; Bachhawat, K; Dam, T K; Surolia, A; Vijayan, M

1999-01-22

A mannose-specific agglutinin, isolated from garlic bulbs, has been crystallized in the presence of a large excess of alpha-d-mannose, in space group C2 and cell dimensions, a=203.24, b=43.78, c=79.27 A, beta=112.4 degrees, with two dimers in the asymmetric unit. X-ray diffraction data were collected up to a nominal resolution of 2.4 A and the structure was solved by molecular replacement. The structure, refined to an R-factor of 22.6 % and an Rfree of 27.8 % reveals a beta-prism II fold, similar to that in the snowdrop lectin, comprising three antiparallel four-stranded beta-sheets arranged as a 12-stranded beta-barrel, with an approximate internal 3-fold symmetry. This agglutinin is, however, a dimer unlike snowdrop lectin which exists as a tetramer, despite a high degree of sequence similarity between them. A comparison of the two structures reveals a few substitutions in the garlic lectin which stabilise it into a dimer and prevent tetramer formation. Three mannose molecules have been identified on each subunit. In addition, electron density is observed for another possible mannose molecule per dimer resulting in a total of seven mannose molecules in each dimer. Although the mannose binding sites and the overall structure are similar in the subunits of snowdrop and garlic lectin, their specificities to glycoproteins such as GP120 vary considerably. These differences appear, in part, to be a direct consequence of the differences in oligomerisation, implying that variation in quaternary association may be a mode of achieving oligosaccharide specificity in bulb lectins. Copyright 1998 Academic Press.

Thermophotovoltaic energy conversion using photonic bandgap selective emitters

DOEpatents

Gee, James M.; Lin, Shawn-Yu; Fleming, James G.; Moreno, James B.

2003-06-24

A method for thermophotovoltaic generation of electricity comprises heating a metallic photonic crystal to provide selective emission of radiation that is matched to the peak spectral response of a photovoltaic cell that converts the radiation to electricity. The use of a refractory metal, such as tungsten, for the photonic crystal enables high temperature operation for high radiant flux and high dielectric contrast for a full 3D photonic bandgap, preferable for efficient thermophotovoltaic energy conversion.

Interfacial dislocations in (111) oriented (Ba 0.7Sr 0.3)TiO 3 films on SrTiO 3 single crystal

DOE PAGES

Shen, Xuan; Yamada, Tomoaki; Lin, Ruoqian; ...

2015-10-08

In this study, we have investigated the interfacial structure of epitaxial (Ba,Sr)TiO 3 films grown on (111)-oriented SrTiO 3 single-crystal substrates using transmission electron microscopy (TEM) techniques. Compared with the (100) epitaxial perovskite films, we observe dominant dislocation half-loop with Burgers vectors of a<110> comprised of a misfit dislocation along <112>, and threading dislocations along <110> or <100>. The misfit dislocation with Burgers vector of a <110> can dissociate into two ½ a <110> partial dislocations and one stacking fault. We found the dislocation reactions occur not only between misfit dislocations, but also between threading dislocations. Via three-dimensional electron tomography,more » we retrieved the configurations of the threading dislocation reactions. The reactions between threading dislocations lead to a more efficient strain relaxation than do the misfit dislocations alone in the near-interface region of the (111)-oriented (Ba 0.7Sr 0.3)TiO 3 films.« less

The quorum-quenching lactonase from Alicyclobacter acidoterrestris : purification, kinetic characterization, crystallization and crystallographic analysis

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

Bergonzi, Celine; Schwab, Michael; Chabriere, Eric

Lactonases comprise a class of enzymes that hydrolyze lactones, including acyl-homoserine lactones (AHLs); the latter are used as chemical signaling molecules by numerous Gram-negative bacteria. Lactonases have therefore been demonstrated to quench AHL-based bacterial communication. In particular, lactonases are capable of inhibiting bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. A novel representative from the metallo-β-lactamase superfamily, named AaL, was isolated from the thermoacidophilic bacteriumAlicyclobacter acidoterrestris. Kinetic characterization proves AaL to be a proficient lactonase, with catalytic efficiencies (k cat/K m) against AHLs in the region of 10 5Mmore » -1s -1. AaL exhibits a very broad substrate specificity. Its structure is expected to reveal the molecular determinants for its substrate binding and specificity, as well as to provide grounds for future protein-engineering projects. Here, the expression, purification, characterization, crystallization and X-ray diffraction data collection of AaL at 1.65Å resolution are reported.« less

Microgravity

NASA Image and Video Library

1992-06-25

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

Zeolites

NASA Technical Reports Server (NTRS)

1992-01-01

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

From molecule to solid: The prediction of organic crystal structures

NASA Astrophysics Data System (ADS)

Dzyabchenko, A. V.

2008-10-01

A method for predicting the structure of a molecular crystal based on the systematic search for a global potential energy minimum is considered. The method takes into account unequal occurrences of the structural classes of organic crystals and symmetry of the multidimensional configuration space. The programs of global minimization PMC, comparison of crystal structures CRYCOM, and approximation to the distributions of the electrostatic potentials of molecules FitMEP are presented as tools for numerically solving the problem. Examples of predicted structures substantiated experimentally and the experience of author’s participation in international tests of crystal structure prediction organized by the Cambridge Crystallographic Data Center (Cambridge, UK) are considered.

Crystals of Janus colloids at various interaction ranges

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

Preisler, Z.; Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht; Vissers, T.

We investigate the effect of interaction range on the phase behaviour of Janus particles with a Kern-Frenkel potential. Specifically, we study interaction ranges Δ = 0.1σ, 0.3σ, 0.4σ, 0.5σ with σ the particle diameter, and use variable box shape simulations to predict crystal structures. We found that changing the interaction range beyond 0.2σ drastically increases the variety of possible crystal structures. In addition to close-packed structures, we find body-centered tetragonal and AA-stacked hexagonal crystals, as well as several lamellar crystals. For long interaction ranges and low temperatures, we also observe an extremely large number of metastable structures which compete withmore » the thermodynamically stable ones. These competing structures hinder the detection of the lowest-energy crystal structures, and are also likely to interfere with the spontaneous formation of the ground-state structure. Finally, we determine the gas-liquid coexistence curves for several interaction ranges, and observe that these are metastable with respect to crystallization.« less

Atoms in Action: Observing Atomic Motion with Dynamic in situ X-ray Diffraction

NASA Astrophysics Data System (ADS)

Cox, Jordan Michael

Metal-organic framework (MOF) materials are rich in both structural diversity and application. These materials are comprised of metal atoms or clusters which are connected in a three-dimensional polymer-like network by bridging organic linker molecules. One of the major attractive features in MOFs is their permanent pore space which can potentially be used to adsorb or exchange foreign molecules from/with the surrounding environment. While MOFs are an active area of scientific interest, MOF materials are still relatively new, only 20 years old. As such, there is still much that needs to be understood about these materials before they can be effectively applied to widespread chemical problems like CO2 sequestration or low-pressure hydrogen fuel storage. One of the most important facets of MOF chemistry to understand in order to rationally design MOF materials with tailor-made properties is the relationship between the structural features in a MOF and the chemical and physical properties of that material. By examining in detail the atomic structure of a MOF with known properties under a variety of conditions, scientists can begin to unravel the guiding principles which govern these relationships. X-ray diffraction remains one of the most effective tools for determining the structure of a crystalline material with atomic resolution, and has been applied to the determination of MOF structures for years. Typically these experiments have been carried out using powder X-ray diffraction, but this technique lacks the high-resolution structural information found in single-crystal methods. Some studies have been reported which use specialized devices, sometimes called Environmental Control Cells, to study single crystalline MOFs under non-ambient chemical conditions in situ . However, these in situ studies are performed under static conditions. Even in cases where the ECC provides continued access to the local chemical environment during diffraction data collections, the environment is left static or data is not collected until after the material has equilibrated to its new environment. First, a unique ECC has been designed and constructed which allows continuous access to the local chemical environment of a single-crystal sample while maintaining ease of use, minimizing size, and which is easily adaptable to a wide variety of gaseous and liquid chemical stimuli. Novel methods have been developed and are herein described for utilizing this ECC and in situ X-ray diffraction methods in a dynamic manner for monitoring the structural responses of single crystals to changes in their local chemical environment. These methods provide the opportunity for the determination of changes in unit cell parameters and even complete crystal structures during adsorption, desorption, and exchange processes in MOF materials. The application of these methods to the determination of the dehydration process of a previously reported cobalt-based MOF have revealed surprising structural and dynamics data. Several new intermediate structures have been determined in this process, including one metastable species and several actively transitioning species during the dehydration process. Applying these methods to the ethanol solvation process in the same material again yielded results which were richer in structural information than the previously reported ex situ structures. A computational study of rotational potential energy surfaces in a family of photochromic MOF linkers revealed the important role rotational stereoisomers can play in maintaining light-activated functionality when these linkers are incorporated into next-generation functional MOF materials. Finally, the application of novel photocrystallography techniques were used in conjunction with spectroscopic methods to determine the nature of the anomalous behavior of a photochromic diarylethene single-crystal.

Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2008-01-01

A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

A top-down approach to crystal engineering of a racemic Δ2-isoxazoline.

PubMed

Lombardo, Giuseppe M; Rescifina, Antonio; Chiacchio, Ugo; Bacchi, Alessia; Punzo, Francesco

2014-02-01

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C13H12N2O7, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top-down approach to be a useful tool for crystal engineering.

Device and method for screening crystallization conditions in solution crystal growth

NASA Technical Reports Server (NTRS)

Carter, Daniel C. (Inventor)

1995-01-01

A device and method for detecting optimum protein crystallization conditions and for growing protein crystals in either 1g or microgravity environments comprising a housing, defining at least one pair of chambers for containing crystallization solutions is presented. The housing further defines an orifice therein for providing fluid communication between the chambers. The orifice is adapted to receive a tube which contains a gelling substance for limiting the rate of diffusive mixing of the crystallization solutions. The solutions are diffusively mixed over a period of time defined by the quantity of gelling substance sufficient to achieve equilibration and to substantially reduce density driven convection disturbances therein. The device further includes endcaps to seal the first and second chambers. One of the endcaps includes a dialysis chamber which contains protein solution in which protein crystals are grown. Once the endcaps are in place, the protein solution is exposed to the crystallization solutions wherein the solubility of the protein solution is reduced at a rate responsive to the rate of diffusive mixing of the crystallization solutions. This allows for a controlled approach to supersaturation and allows for screening of crystal growth conditions at preselected intervals.

Device and Method for Screening Crystallization Conditions in Solution Crystal Growth

NASA Technical Reports Server (NTRS)

Carter, Daniel C. (Inventor)

1997-01-01

A device and method for detecting optimum protein crystallization conditions and for growing protein crystals in either 1 g or microgravity environments comprising a housing defining at least one pair of chambers for containing crystallization solutions. The housing further defines an orifice therein for providing fluid communication between the chambers. The orifice is adapted to receive a tube which contains a gelling substance for limiting the rate of diffusive mixing of the crystallization solutions. The solutions are diffusively mixed over a period of time defined by the quantity of gelling substance sufficient to achieve equilibration and to substantially reduce density driven convection disturbances therein. The device further includes endcaps to seal the first and second chambers. One of the endcaps includes a dialysis chamber which contains protein solution in which protein crystals are grown. Once the endcaps are in place. the protein solution is exposed to the crystallization solutions wherein the solubility of the protein solution is reduced at a rate responsive to the rate of diffusive mixing of the crystallization solutions. This allows for a controlled approach to supersaturation and allows for screening of crystal growth conditions at preselected intervals.

3-{(E)-[4-(4-Hy-droxy-3-meth-oxy-phen-yl)butan-2-yl-idene]amino}-1-phenyl-urea: crystal structure and Hirshfeld surface analysis.

PubMed

Tan, Ming Yueh; Crouse, Karen A; Ravoof, Thahira B S A; Jotani, Mukesh M; Tiekink, Edward R T

2018-01-01

Two independent mol-ecules ( A and B ) comprise the asymmetric unit of the title compound, C 18 H 21 N 3 O 3 . The urea moiety is disubstituted with one amine being linked to a phenyl ring, which is twisted out of the plane of the CN 2 O urea core [dihedral angles = 25.57 (11) ( A ) and 29.13 (10)° ( B )]. The second amine is connected to an imine ( E conformation), which is linked in turn to an ethane bridge that links a disubstituted benzene ring. Intra-molecular amine-N-H⋯N(imine) and hydroxyl-O-H⋯O(meth-oxy) hydrogen bonds close S (5) loops in each case. The mol-ecules have twisted conformations with the dihedral angles between the outer rings being 38.64 (81) ( A ) and 48.55 (7)° ( B ). In the crystal, amide-N-H⋯O(amide) hydrogen bonds link the mol-ecules A and B via an eight-membered {⋯HNCO} 2 synthon. Further associations between mol-ecules, leading to supra-molecular layers in the ac plane, are hydrogen bonds of the type hydroxyl-O-H⋯N(imine) and phenyl-amine-N-H⋯O(meth-oxy). Connections between layers, leading to a three-dimensional architecture, comprise benzene-C-H⋯O(hy-droxy) inter-actions. A detailed analysis of the calculated Hirshfeld surfaces shows mol-ecules A and B participate in very similar inter-molecular inter-actions and that any variations relate to conformational differences between the mol-ecules.

Block Copolymer Directed Biomimetic Mineral Formation for Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Gleeson, Sarah; Yu, Tony; Chen, Xi; Marcolongo, Michele; Li, Christopher

Bone is a hierarchically structured biocomposite comprised of mineralized collagen fibrils. The mechanical properties of bone can be precisely tuned by the structure and morphology of the mineral nanocrystals as well as the organic collagen fibrils. Synthetic materials that can mimic the nanostructure of natural bone show promise to replicate bone's structural function, yet little is known about the mechanism of mineral formation. We previously have shown that hierarchically ordered polymer fibers control the distribution and orientation of hydroxyapatite, enhancing mechanical properties and biocompatibility. We demonstrate a new method for mineralization by forming block copolymer single crystal films of polycaprolactone-block-poly(acrylic acid) (PCL- b-PAA) so that lamellar anionic PAA nanodomains recruit mineral ions and provide one-dimensional confinement to induce orientation. The effect of the anionic domain dimensions on mineral content, orientation, and structure within the polymer matrix is shown. The mechanical properties of the nanocomposite are evaluated to determine the role of mineral orientation and crystallinity in composite strength. These results can be used to tailor the physical mineralization environment to create a more biomimetic bone material.

Structure of the protein phosphatase 2A holoenzyme.

PubMed

Xu, Yanhui; Xing, Yongna; Chen, Yu; Chao, Yang; Lin, Zheng; Fan, Eugene; Yu, Jong W; Strack, Stefan; Jeffrey, Philip D; Shi, Yigong

2006-12-15

Protein Phosphatase 2A (PP2A) plays an essential role in many aspects of cellular physiology. The PP2A holoenzyme consists of a heterodimeric core enzyme, which comprises a scaffolding subunit and a catalytic subunit, and a variable regulatory subunit. Here we report the crystal structure of the heterotrimeric PP2A holoenzyme involving the regulatory subunit B'/B56/PR61. Surprisingly, the B'/PR61 subunit has a HEAT-like (huntingtin-elongation-A subunit-TOR-like) repeat structure, similar to that of the scaffolding subunit. The regulatory B'/B56/PR61 subunit simultaneously interacts with the catalytic subunit as well as the conserved ridge of the scaffolding subunit. The carboxyterminus of the catalytic subunit recognizes a surface groove at the interface between the B'/B56/PR61 subunit and the scaffolding subunit. Compared to the scaffolding subunit in the PP2A core enzyme, formation of the holoenzyme forces the scaffolding subunit to undergo pronounced conformational rearrangements. This structure reveals significant ramifications for understanding the function and regulation of PP2A.

Structural evolution of Halaban Area, Eastern Arabian Shield, Saudi Arabia

NASA Astrophysics Data System (ADS)

Al-Amri, Yousef; Kassem1, Osama M. K.

2017-04-01

Neoproterozoic basement complex comprises a metamorphic/igneous suite (Abt schist and sheared granitoids) with syn-accretionary transpressive structures, unconformably overlain by a post-amalgamation volcanosedimentary sequence. This study aims to attempt to exposed post-accretionary thrusting and thrust-related structures at Halaban area, Eastern Arabian Shield. The Rf/ϕ and Fry methods are utilized on quartz and feldspar porphyroclasts, as well as on mafic crystals, such as hornblende and biotite, in eighteen samples. The X/Z axial ratios range from 1.12 to 4.99 for Rf/ϕ method and from 1.65 to 4.00 for Fry method. The direction of finite strain for the long axes displays clustering along the WNW trend (occasionally N) with slight plunging. Finite strain accumulated without any significant volume change contemporaneously with syn-accretionary transpressive structures. It indicates that the contacts between various lithological units in the Halaban area were formed under brittle to semi-ductile deformation conditions. The penetrative subhorizontal foliation was concurrent with thrusting and shows nearly the same attitudes of tectonic contacts with the overlying nappes. Keywords: Finite strain analysis, volcanosedimentary sequence, Halaban area, Eastern Arabian Shield, Saudi Arabia.

Structural Basis for Telomerase RNA Recognition and RNP Assembly by the Holoenzyme La Family Protein p65

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

Singh, Mahavir; Wang, Zhonghua; Koo, Bon-Kyung

2012-07-01

Telomerase is a ribonucleoprotein complex essential for maintenance of telomere DNA at linear chromosome ends. The catalytic core of Tetrahymena telomerase comprises a ternary complex of telomerase RNA (TER), telomerase reverse transcriptase (TERT), and the essential La family protein p65. NMR and crystal structures of p65 C-terminal domain and its complex with stem IV of TER reveal that RNA recognition is achieved by a combination of single- and double-stranded RNA binding, which induces a 105{sup o} bend in TER. The domain is a cryptic, atypical RNA recognition motif with a disordered C-terminal extension that forms an {alpha} helix in themore » complex necessary for hierarchical assembly of TERT with p65-TER. This work provides the first structural insight into biogenesis and assembly of TER with a telomerase-specific protein. Additionally, our studies define a structurally homologous domain (xRRM) in genuine La and LARP7 proteins and suggest a general mode of RNA binding for biogenesis of their diverse RNA targets.« less

Preparation of novel flame-retardant organoclay and its application to natural rubber composites

NASA Astrophysics Data System (ADS)

Zhang, Guangjian; Wang, Jincheng

2018-04-01

In this study, a novel type of flame-retardant montmorillonite (MMT) was prepared using a new approach to obtain highly branched polymer chains. First, MMT was modified using a small liquid crystal molecule comprising N,N,N tris(2-hydroxyethyl)sbnd N-dodecylammonium bromide and organic MMT (OMMT) was obtained. Next, three generations of dendrimer-modified organoclay comprising DOMMT-1, DOMMT-2, and DOMMT-3 were successfully prepared using OMMT and branching units of ethylenediamine and methyl acrylate. Their chemical structures were characterized and confirmed by different methods. The DOMMT organoclay was used in the preparation of natural rubber (NR) composites. The tensile strength and elongation at breakage for NR/DOMMT-10 were 17.3 MPa and 697%, respectively, which were about 13.8% and 10.8% higher, respectively, compared with that for the pure NR. After the addition of DOMMT, the horizontal burning time increased by about 69% and the thermal stability was also improved. We also propose a possible flame-retardant and reinforcing mechanism for this novel organoclay in an NR matrix.

Method of manufacturing corrosion resistant tubing from welded stock of titanium or titanium base alloy

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

Meredith, S.E.; Benjamin, J.F.

1993-07-13

A method is described of manufacturing corrosion resistant tubing from seam welded stock of a titanium or titanium based alloy, comprising: cold pilgering a seam welded tube hollow of titanium or titanium based alloy in a single pass to a final sized tubing, the tube hollow comprising a strip which has been bent and welded along opposed edges thereof to form the tube hollow, the tube hollow optionally being heat treated prior to the cold pilgering step provided the tube hollow is not heated to a temperature which would transform the titanium or titanium alloy into the beta phase, themore » cold pilgering effecting a reduction in cross sectional area of the tube hollow of at least 50% and a reduction of wall thickness of at least 50%, in order to achieve a radially oriented crystal structure; and annealing the final sized tubing at a temperature and time sufficient to effect complete recrystallization and reform grains in a weld area along the seam into smaller, homogeneous grains.« less

Salvage of failed protein targets by reductive alkylation.

PubMed

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.

Salvage of Failed Protein Targets by Reductive Alkylation

PubMed Central

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins. PMID:24590719

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds

PubMed Central

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C.; Orimo, Shin-ichi

2016-01-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures. PMID:27032978

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds.

PubMed

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C; Orimo, Shin-ichi

2016-04-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures.

From screen to structure with a harvestable microfluidic device.

PubMed

Stojanoff, Vivian; Jakoncic, Jean; Oren, Deena A; Nagarajan, V; Poulsen, Jens-Christian Navarro; Adams-Cioaba, Melanie A; Bergfors, Terese; Sommer, Morten O A

2011-08-01

Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.

Structural and optical properties of WTe2 single crystals synthesized by DVT technique

NASA Astrophysics Data System (ADS)

Dixit, Vijay; Vyas, Chirag; Pathak, V. M.; Soalanki, G. K.; Patel, K. D.

2018-05-01

Layered transition metal di-chalcogenide (LTMDCs) crystals have attracted much attention due to their potential in optoelectronic device applications recently due to realization of their monolayer based structures. In the present investigation we report growth of WTe2 single crystals by direct vapor transport (DVT) technique. These crystals are then characterized by energy dispersive analysis of x-rays (EDAX) to study stoichiometric composition after growth. The structural properties are studied by x-ray diffraction (XRD) and selected area electron diffraction (SAED) is used to confirm orthorhombic structure of grown WTe2 crystal. Surface morphological properties of the crystals are also studied by scanning electron microscope (SEM). The optical properties of the grown crystals are studied by UV-Visible spectroscopy which gives direct band gap of 1.44 eV for grown WTe2 single crystals.

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

PubMed

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

PubMed

Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

2017-10-10

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

Two distinct crystallization processes in supercooled liquid

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

Tane, Masakazu, E-mail: mtane@sanken.osaka-u.ac.jp; Kimizuka, Hajime; Ichitsubo, Tetsu

2016-05-21

Using molecular dynamics simulations we show that two distinct crystallization processes, depending on the temperature at which crystallization occurs, appear in a supercooled liquid. As a model for glass-forming materials, an Al{sub 2}O{sub 3} model system, in which both the glass transition and crystallization from the supercooled liquid can be well reproduced, is employed. Simulations in the framework of an isothermal-isobaric ensemble indicate that the calculated time-temperature-transformation curve for the crystallization to γ(defect spinel)-Al{sub 2}O{sub 3} exhibited a typical nose shape, as experimentally observed in various glass materials. During annealing above the nose temperature, the structure of the supercooled liquidmore » does not change before the crystallization, because of the high atomic mobility (material transport). Thus, the crystallization is governed by the abrupt crystal nucleation, which results in the formation of a stable crystal structure. In contrast, during annealing below the nose temperature, the structure of the supercooled liquid gradually changes before the crystallization, and the formed crystal structure is less stable than that formed above the nose temperature, because of the restricted material transport.« less

Membrane protein separation and analysis by supercritical fluid chromatography-mass spectrometry.

PubMed

Zhang, Xu; Scalf, Mark; Westphall, Michael S; Smith, Lloyd M

2008-04-01

Membrane proteins comprise 25-30% of the human genome and play critical roles in a wide variety of important biological processes. However, their hydrophobic nature has compromised efforts at structural characterization by both X-ray crystallography and mass spectrometry. The detergents that are generally used to solubilize membrane proteins interfere with the crystallization process essential to X-ray studies and cause severe ion suppression effects that hinder mass spectrometric analysis. In this report, the use of supercritical fluid chromatography-mass spectrometry for the separation and analysis of integral membrane proteins and hydrophobic peptides is investigated. It is shown that detergents are rapidly and effectively separated from the proteins and peptides, yielding them in a state suitable for direct mass spectrometric analysis.

Correlation of Intermolecular Acyl Transfer Reactivity with Noncovalent Lattice Interactions in Molecular Crystals: Toward Prediction of Reactivity of Organic Molecules in the Solid State.

PubMed

Krishnaswamy, Shobhana; Shashidhar, Mysore S

2018-04-06

Intermolecular acyl transfer reactivity in several molecular crystals was studied, and the outcome of the reactivity was analyzed in the light of structural information obtained from the crystals of the reactants. Minor changes in the molecular structure resulted in significant variations in the noncovalent interactions and packing of molecules in the crystal lattice, which drastically affected the facility of the intermolecular acyl transfer reactivity in these crystals. Analysis of the reactivity vs crystal structure data revealed dependence of the reactivity on electrophile···nucleophile interactions and C-H···π interactions between the reacting molecules. The presence of these noncovalent interactions augmented the acyl transfer reactivity, while their absence hindered the reactivity of the molecules in the crystal. The validity of these correlations allows the prediction of intermolecular acyl transfer reactivity in crystals and co-crystals of unknown reactivity. This crystal structure-reactivity correlation parallels the molecular structure-reactivity correlation in solution-state reactions, widely accepted as organic functional group transformations, and sets the stage for the development of a similar approach for reactions in the solid state.

Crystal growth, differential gas adsorption, high thermal stability, and reversible coordination of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O)

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

Halake, Shobha; Ok, Kang Min, E-mail: kmok@cau.ac.kr

2015-11-15

Single crystals of two barium-organic framework materials, Ba(SBA)(DMF){sub 4} (CAUMOF-15) and Ba{sub 2}(BTEC)(H{sub 2}O) (CAUMOF-16), have been grown through solvothermal reactions (H{sub 2}SBA=4,4′-sulfonyldibenzoic acid and H{sub 4}BTEC=1,2,4,5-benzenetetracarboxylic acid). The crystal structures of the reported frameworks have been determined by single-crystal X-ray diffraction. The materials have been fully characterized by powder X-ray diffraction (PXRD), elemental analyses, Infrared (IR) spectroscopy, and thermogravimetric analyses (TGA). CAUMOF-15 reveals a three-dimensional open-framework that comprises of an inorganic motif with one-dimensional chains and the SBA linkers. CAUMOF-16 shows another three-dimensional backbone consisting of layers of edge-shared BaO{sub 9} and BaO{sub 10} polyhedra, and BTEC pillars. Bothmore » of the 3D frameworks exhibit relatively high thermal stabilities. The PXRD and IR spectral data confirm that CAUMOF-15 and CAUMOF-16 reveal reversible coordinations of the respective solvent molecules, DMF and H{sub 2}O. Gas adsorption properties towards nitrogen, hydrogen, and carbon dioxide have been also investigated. - Graphical abstract: Crystals of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O), exhibiting a differential gas adsorption, a high thermal stability, and a reversible coordination of solvent molecules have been grown. - Highlights: • Crystals of two new 3D Ba-MOFs are grown. • The two Ba-MOFs reveal very high thermal stabilities up to ca. 400 °C. • Ba(SBA)(DMF){sub 4} exhibits differential gas adsorption properties. • The two Ba-MOFs show reversible coordination of the solvent molecules.« less

Transistor and memory devices based on novel organic and biomaterials

NASA Astrophysics Data System (ADS)

Tseng, Jia-Hung

Organic semiconductor devices have aroused considerable interest because of the enormous potential in many technological applications. Organic electroluminescent devices have been extensively applied in display technology. Rapid progress has also been made in transistor and memory devices. This thesis considers aspects of the transistor based on novel organic single crystals and memory devices using hybrid nanocomposites comprising polymeric/inorganic nanoparticles, and biomolecule/quantum dots. Organic single crystals represent highly ordered structures with much less imperfections compared to amorphous thin films for probing the intrinsic charge transport in transistor devices. We demonstrate that free-standing, thin organic single crystals with natural flexing ability can be fabricated as flexible transistors. We study the surface properties of the organic crystals to determine a nearly perfect surface leading to high performance transistors. The flexible transistors can maintain high performance under reversible bending conditions. Because of the high quality crystal technique, we further develop applications on organic complementary circuits and organic single crystal photovoltaics. In the second part, two aspects of memory devices are studied. We examine the charge transfer process between conjugated polymers and metal nanoparticles. This charge transfer process is essential for the conductance switching in nanoseconds to induce the memory effect. Under the reduction condition, the charge transfer process is eliminated as well as the memory effect, raising the importance of coupling between conjugated systems and nanoparticle accepters. The other aspect of memory devices focuses on the interaction of virus biomolecules with quantum dots or metal nanoparticles in the devices. We investigate the impact of memory function on the hybrid bio-inorganic system. We perform an experimental analysis of the charge storage activation energy in tobacco mosaic virus with platinum nanoparticles. It is established that the effective barrier height in the materials systems needs to be further engineered in order to have sufficiently long retention times. Finally other novel architectures such as negative differential resistance devices and high density memory arrays are investigated for their influence on memory technology.

Zwitterionic and free forms of arylmethyl Meldrum's acids.

PubMed

Mierina, Inese; Mishnev, Anatoly; Jure, Mara

2015-09-01

C-Alkyl (including C-arylmethyl) derivatives of Meldrum's acids are attractive building blocks in organic synthesis, mainly due to the unusually high acidity of the resulting compounds. Three examples, namely 5-[4-(diethylamino)benzyl]-2,2-dimethyl-1,3-dioxane-4,6-dione, C17H23NO4, (I), 2,2-dimethyl-5-(2,4,6-trimethoxybenzyl)-1,3-dioxane-4,6-dione, C16H20O7, (II), and 5-(4-hydroxy-3,5-dimethoxybenzyl)-2,2-dimethyl-1,3-dioxane-4,6-dione, C15H18O7, (III), have been synthesized, characterized by NMR and IR spectroscopy, and studied by single-crystal X-ray structure analysis. The nature of the different substituents resulted in remarkable differences in both the molecular conformations and the crystal packing arrangements. The presence of a substituent with a basic centre in compound (I) leads to the formation of an inner salt accompanied by drastic changes in the conformation of the 1,3-dioxane-4,6-dione fragment. By virtue of strong N-H···O hydrogen bonds, the residues are assembled into infinite chains with the graph-set descriptor C(10). Compound (II) contains methoxy groups in both the ortho- and para-positions of the arylmethyl fragment. Because of the absence of classical hydrogen-bond donors in this structure, the crystal packing is controlled by van der Waals forces and weak C-H···O interactions. Compound (III) contains methoxy groups in both meta-positions and a hydroxy group in the para-position. Supramolecular tetrameric synthons which comprise hydrogen-bonded dimers associated into tetramers through π-π interactions of overlapping benzene rings were observed.

Crystallization of the Zagami Shergottite: An Experimental Study

NASA Technical Reports Server (NTRS)

Lofgren, Gary E.; McCoy, Timothy J.

2000-01-01

Spherulites are usually rounded or spherical objects found in rhyolitic obsidian. They usually comprise acicular crystals of alkali feldspar that radiate from a single point. The radiating array of crystalline fibers typically have a similar crystallographic orientation such that a branch fiber departs slightly but appreciably from that of its parent fiber. Individual fibers range from 1 to several micrometers in diameter. The spherulites most likely form by heterogeneous nucleation on microscopic seed crystals, bubbles, or some other surface at high degrees of supercooling. They grow very rapidly stabilizing their fibrous habit and typically range in size from microscopic to a few cm in diameter.

Large area projection liquid-crystal video display system with inherent grid pattern optically removed

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang (Inventor)

1992-01-01

A relatively small and low-cost system is provided for projecting a large and bright television image onto a screen. A miniature liquid crystal array is driven by video circuitry to produce a pattern of transparencies in the array corresponding to a television image. Light is directed against the rear surface of the array to illuminate it, while a projection lens lies in front of the array to project the image of the array onto a large screen. Grid lines in the liquid crystal array are eliminated by a spacial filter which comprises a negative of the Fourier transform of the grid.

Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli.

PubMed

Cupp-Vickery, Jill R; Silberg, Jonathan J; Ta, Dennis T; Vickery, Larry E

2004-04-16

IscA, an 11 kDa member of the hesB family of proteins, binds iron and [2Fe-2S] clusters, and participates in the biosynthesis of iron-sulfur proteins. We report the crystal structure of the apo-protein form of IscA from Escherichia coli to a resolution of 2.3A. The crystals belong to the space group P3(2)21 and have unit cell dimensions a=b=66.104 A, c=150.167 A (alpha=beta=90 degrees, gamma=120 degrees ). The structure was solved using single-wavelength anomalous dispersion (SAD) phasing of a selenomethionyl derivative, and the IscA model was refined to R=21.4% (Rfree=25.4%). IscA exists as an (alpha1alpha2)2 homotetramer with the (alpha1alpha2) dimer comprising the asymmetric unit. Cys35, implicated in Fe-S cluster assembly, is located in a central cavity formed at the tetramer interface with the gamma-sulfur atoms of residues from the alpha1 and alpha2' monomers (and alpha1'alpha2) positioned close to one another (approximately equal 7 A). C-terminal residues 99-107 are disordered, and the exact positions of Cys99 and Cys101 could not be determined. However, computer modeling of C-terminal residues in the tetramer suggests that Cys99 and Cys101 in the alpha1 monomer and those of the alpha1' monomer (or alpha2 and alpha2') are positioned sufficiently close to coordinate [2Fe-2S] clusters between the two dimers, whereas this is not possible within the (alpha1alpha2) or (alpha1'alpha2') dimer. This symmetrical arrangement allows for binding of two [2Fe-2S] clusters on opposite sides of the tetramer. Modeling further reveals that Cys101 is positioned sufficiently close to Cys35 to allow Cys35 to participate in cluster assembly, formation, or transfer.

Prediction and theoretical characterization of p-type organic semiconductor crystals for field-effect transistor applications.

PubMed

Atahan-Evrenk, Sule; Aspuru-Guzik, Alán

2014-01-01

The theoretical prediction and characterization of the solid-state structure of organic semiconductors has tremendous potential for the discovery of new high performance materials. To date, the theoretical analysis mostly relied on the availability of crystal structures obtained through X-ray diffraction. However, the theoretical prediction of the crystal structures of organic semiconductor molecules remains a challenge. This review highlights some of the recent advances in the determination of structure-property relationships of the known organic semiconductor single-crystals and summarizes a few available studies on the prediction of the crystal structures of p-type organic semiconductors for transistor applications.

METAL PHTHALOCYANINES

DOEpatents

Frigerio, N.A.

1962-03-27

A process is given for preparing heavy metal phthalocyanines, sulfonated or not. The process comprises mixing an inorganic metal salt with dimethyl formamide or methyl sulfoxide; separating the metal complex formed from the solution; mixing the complex with an equimolar amount of sodium, potassium, lithium, magnesium, or beryllium sulfonated or unsulfonated phthalocyanine whereby heavy-metal phthalocyanine crystals are formed; and separating the crystals from the solution. Uranyl, thorium, lead, hafnium, and lanthanide rare earth phthalocyanines can be produced by the process. (AEC)

The potential for the indirect crystal structure verification of methyl glycosides based on acetates' parent structures: GIPAW and solid-state NMR approaches

NASA Astrophysics Data System (ADS)

Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz M.; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

2017-10-01

A convenient method for the indirect crystal structure verification of methyl glycosides was demonstrated. Single-crystal X-ray diffraction structures for methyl glycoside acetates were deacetylated and subsequently subjected to DFT calculations under periodic boundary conditions. Solid-state NMR spectroscopy served as a guide for calculations. A high level of accuracy of the modelled crystal structures of methyl glycosides was confirmed by comparison with published results of neutron diffraction study using RMSD method.

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

NASA Astrophysics Data System (ADS)

Cheung, Eugene Y.; David, Sarah E.; Harris, Kenneth D. M.; Conway, Barbara R.; Timmins, Peter

2007-03-01

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H 2NC(CH 3) 3-n(CH 2OH) n, with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family ( n=0, 1, 2), but significantly contrasting structural properties for the member with n=3.

Unraveling the Driving Forces in the Self-Assembly of Monodisperse Naphthalenediimide-Oligodimethylsiloxane Block Molecules

PubMed Central

2017-01-01

Block molecules belong to a rapidly growing research field in materials chemistry in which discrete macromolecular architectures bridge the gap between block copolymers (BCP) and liquid crystals (LCs). The merging of characteristics from both BCP and LCs is expected to result in exciting breakthroughs, such as the discovery of unexpected morphologies or significant shrinking of domain spacings in materials that possess the high definition of organic molecules and the processability of polymers. Here we report the bulk self-assembly of two families of monodisperse block molecules comprised of naphthalenediimides (NDIs) and oligodimethylsiloxanes (ODMS). These materials are characterized by waxy texture, strong long-range order, and very low mobility, typical properties of conformationally disordered crystals. Our investigation unambiguously reveals that thermodynamic immiscibility and crystallization direct the self-assembly of ODMS-based block molecules. We show that a synergy of high incompatibility between the blocks and crystallization of the NDIs causes nanophase separation, giving access to hexagonally packed columnar (Colh) and lamellar (LAM) morphologies with sub-10 nm periodicities. The domain spacings can be tuned by mixing molecules with different ODMS lengths and the same number of NDIs, introducing an additional layer of control. X-ray scattering experiments reveal macrophase separation whenever this constitutional bias is not observed. Finally, we highlight our “ingredient approach” to obtain perfect order in sub-10 nm structured materials with a simple strategy built on a crystalline “hard” moiety and an incompatible “soft” ODMS partner. Following this simple rule, our recipe can be extended to a number of systems. PMID:28380290

Transparent electrode for optical switch

DOEpatents

Goldhar, Julius; Henesian, Mark A.

1986-01-01

A low pressure gas electrode utilizing ionized gas in a glow discharge regime forms a transparent electrode for electro-optical switches. The transparent electrode comprises a low pressure gas region on both sides of the crystal. When the gas is ionized, e.g., by a glow discharge in the low pressure gas, the plasma formed is a good conductor. The gas electrode acts as a highly uniform conducting electrode. Since the plasma is transparent to a high energy laser beam passing through the crystal, the electrode is a transparent electrode. A crystal exposed from two sides to such a plasma can be charged up uniformly to any desired voltage. The plasma can be created either by the main high voltage pulser used to charge up the crystal or by auxiliary discharges or external sources of ionization. A typical configuration utilizes 10 torr argon in the discharge region adjacent to each crystal face.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein

PubMed Central

Rahaman, Siti Nurulnabila A.; Mat Yusop, Jastina; Mohamed-Hussein, Zeti-Azura; Ho, Kok Lian; Teh, Aik-Hong; Waterman, Jitka; Ng, Chyan Leong

2016-01-01

C1ORF123 is a human hypothetical protein found in open reading frame 123 of chromosome 1. The protein belongs to the DUF866 protein family comprising eukaryote-conserved proteins with unknown function. Recent proteomic and bioinformatic analyses identified the presence of C1ORF123 in brain, frontal cortex and synapses, as well as its involvement in endocrine function and polycystic ovary syndrome (PCOS), indicating the importance of its biological role. In order to provide a better understanding of the biological function of the human C1ORF123 protein, the characterization and analysis of recombinant C1ORF123 (rC1ORF123), including overexpression and purification, verification by mass spectrometry and a Western blot using anti-C1ORF123 antibodies, crystallization and X-ray diffraction analysis of the protein crystals, are reported here. The rC1ORF123 protein was crystallized by the hanging-drop vapor-diffusion method with a reservoir solution comprised of 20% PEG 3350, 0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate pH 6.5. The crystals diffracted to 1.9 Å resolution and belonged to an orthorhombic space group with unit-cell parameters a = 59.32, b = 65.35, c = 95.05 Å. The calculated Matthews coefficient (V M) value of 2.27 Å3 Da−1 suggests that there are two molecules per asymmetric unit, with an estimated solvent content of 45.7%. PMID:26919524

In-situ study on growth units of Ba2Mg(B3O6)2 crystal

NASA Astrophysics Data System (ADS)

Lv, X. S.; Sun, Y. L.; Tang, X. L.; Wan, S. M.; Zhang, Q. L.; You, J. L.; Yin, S. T.

2013-05-01

BMBO (Ba2Mg(B3O6)2 crystal) is an excellent birefringent crystal and a potential stimulated Raman scattering (SRS) crystal. In this paper, high temperature Raman spectroscopy was used to in-situ study the melt structure near a BMBO crystal-melt interface. [B3O6]3- groups were found in this region. The result reveals that both of BaO bonds and MgO bonds are the weak bonds in the BMBO crystal structure. During the melting process, the crystal structure broke into Ba2+ ions, Mg2+ ions and [B3O6]3- groups. Our experimental results confirmed that the well-developed faces of BMBO crystals are the (001), (101) and (012) faces. Based on attachment energy theory, the crystal growth habit was discussed. The (001) (101) and (012) crystal faces linked by the weak BaO bonds and MgO bonds have smaller attachment energies and slower growth rates, and thus present in the final morphology. The (012) crystal face has a multi-terrace structure, which suggests that BMBO crystal grows with a layer-by-layer mode.

Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Mishima, Yumiko; Maeno, Yuka; Ishikawa, Kazuhiko

2014-01-01

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed. PMID:24598756

The Petrogenesis of the Unit 7/8 and 11/12 Chrome-spinel Seams of the Rum Eastern Layered Intrusion (NW Scotland) Re-evaluated

NASA Astrophysics Data System (ADS)

O'Driscoll, B.; Daly, J. S.; Emeleus, C. H.; Donaldson, C. H.

2007-12-01

Laterally extensive (~2 mm thick) chrome-spinel seams in the Rum Layered Suite, NW Scotland, occur at the junctions of several of the coupled peridotite-troctolite macro-rhythmic units that make up the bulk of the eastern part of the intrusion. A detailed petrographic study of the rocks immediately above and below two of these seams suggests that existing models for seam formation involving early crystallisation and gravitational settling of chrome-spinel crystals from a newly emplaced body of picritic magma may be flawed. Instead, the textural relationships between minerals suggest that olivine crystallisation in the peridotite above each of the seams occurred before that of most of the chrome-spinel. Reaction textures between olivine and chrome-spinel crystals are commonly observed, with plagioclase usually occurring as thin rims between both olivine and chrome-spinel where both are in close proximity. The textural evidence suggests a significant degree of olivine crystal-shape change; it seems that many of the olivine crystals immediately above the main seams may initially have had much more complex (harrisitic) crystal shapes before modification to simpler morphologies in a crystal mush. Plagioclase occurs in the peridotite as large oikocrysts up to several cm in size. Additionally, the chrome-spinel seams occur only in those units that display extensive evidence of syn-magmatic deformation of unconsolidated cumulate in the underlying troctolite, and the seams themselves often exhibit small-scale load structures. A model suggesting in-situ crystallisation of the chrome-spinel seams is proposed, whereby mixing of an evolved interstitial liquid with a primitive picritic melt occurred approximately at the crystal mush-magma interface. The former was released from the unconsolidated troctolite mush as a response to re-mobilization and chaotic slumping, possibly triggered by emplacement of some of the hot picrite into the crystal mush pile. Significant undercooling in the picrite due to emplacement-related cooling had already produced a crystal framework comprising complex skeletal olivine crystal morphologies with very fast growth rates. It is envisaged that the significantly modified olivine textures in the peridotite immediately above both seams can be attributed to upward- moving porosity waves of the same 'mixed' interstitial melt that precipitated the chrome-spinel seams. In addition to formation of the seams at the main unit junctions, 'necklace' or 'chain-like' distributions of chrome-spinel crystals around olivine crystals in the peridotite, as well as the large plagioclase oikocrysts, argue for the presence of a mobile interstitial melt with a protracted cooling history.

Shallow melt apparatus for semicontinuous czochralski crystal growth

DOEpatents

Wang, Tihu; Ciszek, Theodore F.

2006-01-10

In a single crystal pulling apparatus for providing a Czochralski crystal growth process, the improvement of a shallow melt In a single crystal pulling apparatus for providing a Czochralski crystal growth process, the improvement of a shallow melt crucible (20) to eliminate the necessity supplying a large quantity of feed stock materials that had to be preloaded in a deep crucible to grow a large ingot, comprising a gas tight container a crucible with a deepened periphery (25) to prevent snapping of a shallow melt and reduce turbulent melt convection; source supply means for adding source material to the semiconductor melt; a double barrier (23) to minimize heat transfer between the deepened periphery (25) and the shallow melt in the growth compartment; offset holes (24) in the double barrier (23) to increase melt travel length between the deepened periphery (25) and the shallow growth compartment; and the interface heater/heat sink (22) to control the interface shape and crystal growth rate.

Electrochemically stable electrolytes

DOEpatents

Angell, Charles Austen; Zhang, Sheng-Shui; Xu, Kang

1999-01-01

This invention relates generally to inorganic ionic liquids which function as electrolytes and do not crystallize at ambient temperature. More specifically, this invention is directed to quasi-salt inorganic ionic liquids which comprise the reaction product of a strong Lewis acid with an inorganic halide-donating molecule. This invention is further directed to quasi-salt inorganic ionic liquid mixtures which comprise combinations of electrolyte additives and quasi-salt inorganic ionic liquids. These quasi-salt inorganic ionic liquid mixtures are useful electrolytes.

Electrochemically stable electrolytes

DOEpatents

Angell, C.A.; Zhang, S.S.; Xu, K.

1999-01-05

This invention relates generally to inorganic ionic liquids which function as electrolytes and do not crystallize at ambient temperature. More specifically, this invention is directed to quasi-salt inorganic ionic liquids which comprise the reaction product of a strong Lewis acid with an inorganic halide-donating molecule. This invention is further directed to quasi-salt inorganic ionic liquid mixtures which comprise combinations of electrolyte additives and quasi-salt inorganic ionic liquids. These quasi-salt inorganic ionic liquid mixtures are useful electrolytes. 16 figs.

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

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

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

Bio-inspired nitrile hydration by peptidic ligands based on L-cysteine, L-methionine or L-penicillamine and pyridine-2,6-dicarboxylic acid.

PubMed

Byrne, Cillian; Houlihan, Kate M; Devi, Prarthana; Jensen, Paul; Rutledge, Peter J

2014-12-12

Nitrile hydratase (NHase, EC 4.2.1.84) is a metalloenzyme which catalyses the conversion of nitriles to amides. The high efficiency and broad substrate range of NHase have led to the successful application of this enzyme as a biocatalyst in the industrial syntheses of acrylamide and nicotinamide and in the bioremediation of nitrile waste. Crystal structures of both cobalt(III)- and iron(III)-dependent NHases reveal an unusual metal binding motif made up from six sequential amino acids and comprising two amide nitrogens from the peptide backbone and three cysteine-derived sulfur ligands, each at a different oxidation state (thiolate, sulfenate and sulfinate). Based on the active site geometry revealed by these crystal structures, we have designed a series of small-molecule ligands which integrate essential features of the NHase metal binding motif into a readily accessible peptide environment. We report the synthesis of ligands based on a pyridine-2,6-dicarboxylic acid scaffold and L-cysteine, L-S-methylcysteine, L-methionine or L-penicillamine. These ligands have been combined with cobalt(III) and iron(III) and tested as catalysts for biomimetic nitrile hydration. The highest levels of activity are observed with the L-penicillamine ligand which, in combination with cobalt(III), converts acetonitrile to acetamide at 1.25 turnovers and benzonitrile to benzamide at 1.20 turnovers.

Diverse oligomeric states of CEACAM IgV domains

PubMed Central

Bonsor, Daniel A.; Günther, Sebastian; Beadenkopf, Robert; Beckett, Dorothy; Sundberg, Eric J.

2015-01-01

Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) comprise a large family of cell surface adhesion molecules that bind to themselves and other family members to carry out numerous cellular functions, including proliferation, signaling, differentiation, tumor suppression, and survival. They also play diverse and significant roles in immunity and infection. The formation of CEACAM oligomers is caused predominantly by interactions between their N-terminal IgV domains. Although X-ray crystal structures of CEACAM IgV domain homodimers have been described, how CEACAMs form heterodimers or remain monomers is poorly understood. To address this key aspect of CEACAM function, we determined the crystal structures of IgV domains that form a homodimeric CEACAM6 complex, monomeric CEACAM8, and a heterodimeric CEACAM6–CEACAM8 complex. To confirm and quantify these interactions in solution, we used analytical ultracentrifugation to measure the dimerization constants of CEACAM homodimers and isothermal titration calorimetry to determine the thermodynamic parameters and binding affinities of CEACAM heterodimers. We found the CEACAM6–CEACAM8 heterodimeric state to be substantially favored energetically relative to the CEACAM6 homodimer. Our data provide a molecular basis for the adoption of the diverse oligomeric states known to exist for CEACAMs and suggest ways in which CEACAM6 and CEACAM8 regulate the biological functions of one another, as well as of additional CEACAMs with which they interact, both in cis and in trans. PMID:26483485

Diverse oligomeric states of CEACAM IgV domains.

PubMed

Bonsor, Daniel A; Günther, Sebastian; Beadenkopf, Robert; Beckett, Dorothy; Sundberg, Eric J

2015-11-03

Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) comprise a large family of cell surface adhesion molecules that bind to themselves and other family members to carry out numerous cellular functions, including proliferation, signaling, differentiation, tumor suppression, and survival. They also play diverse and significant roles in immunity and infection. The formation of CEACAM oligomers is caused predominantly by interactions between their N-terminal IgV domains. Although X-ray crystal structures of CEACAM IgV domain homodimers have been described, how CEACAMs form heterodimers or remain monomers is poorly understood. To address this key aspect of CEACAM function, we determined the crystal structures of IgV domains that form a homodimeric CEACAM6 complex, monomeric CEACAM8, and a heterodimeric CEACAM6-CEACAM8 complex. To confirm and quantify these interactions in solution, we used analytical ultracentrifugation to measure the dimerization constants of CEACAM homodimers and isothermal titration calorimetry to determine the thermodynamic parameters and binding affinities of CEACAM heterodimers. We found the CEACAM6-CEACAM8 heterodimeric state to be substantially favored energetically relative to the CEACAM6 homodimer. Our data provide a molecular basis for the adoption of the diverse oligomeric states known to exist for CEACAMs and suggest ways in which CEACAM6 and CEACAM8 regulate the biological functions of one another, as well as of additional CEACAMs with which they interact, both in cis and in trans.

Giant magneto-optical Kerr rotation, quality factor and figure of merit in cobalt-ferrite magnetic nanoparticles doped in silica matrix as the only defect layer embedded in magnetophotonic crystals

NASA Astrophysics Data System (ADS)

Zamani, Mehdi; Hocini, Abdesselam

2018-03-01

In this work, we report on the theoretical study of one-dimensional magnetophotonic crystals (MPC) comprising of periodic dielectric structure Si/SiO and of silica matrix doped with cobalt-ferrite (CoFe2O4) magnetic nanoparticles as the only magnetic defect layer. Such structure can be prepared by sol-gel dip coating method that controls the thickness of each layer with nanometer level, hence, can overcome the problem of integration of the magneto-optical (MO) devices. We have studied the influence of the volume fraction (concentration of magnetic nanoparticles VF%) on the optical (reflectance, transmittance and absorption) and MO (Kerr rotation) responses in reflection-type one-dimensional MPCs. During investigation of the influence of magnetic nanoparticle's concentration, we found that giant Kerr rotations (even ≈135° for VF = 39%) can be obtained accompanied by large reflectance and low amounts for transmittance and absorption. We report on the demonstration of large MO quality factor and figure of merit in cobalt-ferrite magnetic nanoparticles in the infrared regime. Given the large Kerr rotation, high reflectance accompanied by low absorption and nearly zero transmittance of the 1D MPC containing cobalt-ferrite magnetic nanoparticles, large MO Q factor and figure of merit are obtained.

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

Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.

Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, wemore » present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.« less