bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical reactivity at high pressure: the ordered polymerization of oxalic acid
Authors: Casati Nicola , Jephcoat Andrew , Wilhelm Heribert , Macchi Piero
Published: November 2015

Pressure is known to trigger unusual chemical reactivity in molecular solids. In particular, small molecules containing unsaturated bonds are subject to oligo- or polymerization, effectively synthesizing new compounds. These are tipically energetic materials which can be amorphous, as in the case of carbon monoxide,[1] or crystalline, as for carbon dioxide phase V.[2] In more complex molecular systems, where unsaturated bonds can be only one of the present moieties, stereo-controlled reactivity can be exploited to synthesize topo-tactic structures. We performed a synchrotron single crystal experiment on oxalic acid dihydrate up to 54.7 GPa, using He as pressure transmitting medium to ensure hydrostatic behavior. This is, to the best of our knowledge, the highest pressure ever achieved in a single crystal study on an organic molecule. It had been reported that the species undergoes a proton transfer at mild pressures,[3] and further compression confirms the major role played by hydrogen bonds. After the proton transfer, the species undergoes two phase transitions, caused mainly by a rearrangement of hydrogen bonding patterns, that does not demage the singly crystal nature of the sample. At ~40 GPa an initial bending of the flat oxalic molecule is observed, sign of an enhanced nucleophilic interaction between one oxygen and the carbon of a neighbor molecule. At the highest pressure achieved, a further phase transition is observed. Although the crystallinity is decreased, the new unit cell shows a drastic shrinking in one specific direction. Periodic DFT calculations reveal this metric is compatible with an ordered polymerization of the oxalic acid created by a nucleophilic addition: a monodimensional covalent organic framework is the resulting material (figure). This observation, unique up to now in its kind, is of high relevance for crystal engineering and highlights the potential of high pressure to stimulate new chemistry.
Simple Binary Molecular Mixtures at High Density: the Methane-Nitrogen System
Authors: Gagné-Dumais Laurent , Aldous Catherine , Desgreniers Serge
Published: November 2015

Mixing different molecular species at high density may yield weakly bound compounds or van der Waals solids. These novel solids are stabilized by the application of high pressure and differ in physical properties from solids formed by pure molecular species at comparable thermodynamic conditions. In this contribution, we address the importance in studying the miscibility in dense molecular mixtures and present results of the formation of binary methane-nitrogen compounds at low temperature and high pressure. Methane and nitrogen, with similar potentials and molecular sizes, are expected to be partly miscible in the condensed state. Indeed, binary van der Waals solid phases of methane and nitrogen do occur with the application of pressure. Using single crystal and powder X-ray diffraction with synchrotron radiation, and vibrational spectroscopy, the pressure-concentration phase diagram for this system has been explored from 1 to 16 GPa at room temperature. The existence of novel van der Waals solid phases for samples with concentrations above 10% (methane per volume) is demonstrated. For example, at 7.6 GPa and at room temperature, whereas pure nitrogen and methane exist in a cubic (Pm3n) and in a rhombohedral structure (R-3/m), respectively, our study indicates that a methane-nitrogen sample with ~ 40% methane by volume exhibits, under the same conditions, a novel phase with a tetragonal symmetry with lattice parameters a ~ 11.9 Å and c ~ 6.2 Å. Other novel structures in methane-nitrogen samples with different concentrations under varying pressure conditions have also been observed and will be discussed.
Explosives at Extreme Conditions: Polymorphism of 2,4-Dinitroanisole
Authors: Coster Paul , Henderson Craig , Hunter Steven , Marshall William , Pulham Colin
Published: November 2015

2,4-dinitroanisole (DNAN) is an energetic material, developed as an insensitive replacement for TNT in melt-cast explosive formulations. While DNAN-based formulations demonstrate greatly reduced sensitivity to accidental initiation compared to those using TNT, issues remain with the replacement of TNT with DNAN. For instance, DNAN based formulations have demonstrated catastrophic levels of irreversible growth during heat-cycling, with volume increases of up to 15% reported. [1] In order to investigate the role of polymorphism in the irreversible growth of DNAN, high-pressure and variable-temperature neutron and x-ray diffraction studies have been performed. Two polymorphs of DNAN have been found to exist at ambient temperature and pressure, the thermodynamic form, DNAN-I, and the kinetic form, DNAN-II.[2,3] The phase diagrams of both form-I and -II of DNAN have been explored for the first time. In the case of DNAN-II, two high-pressure phase transitions were found. DNAN-II initially transformed to DNAN-III, which at higher pressures transformed to DNAN-IV. In addition, variable temperature studies demonstrated that the DNAN-II to DNAN-III transition also occurs when DNAN-II is cooled below room temperature. The thermal expansion of the DNAN-II/III lattice was investigated from 150K to 363K, demonstrating that an abrupt change in the thermal behaviour of lattice parameters occurs at the DNAN-II/III transition. From these combined crystallographic studies, the structure of DNAN-III has been solved, showing it is closely related to DNAN-II. In the case of DNAN-I, high-pressure neutron powder diffraction studies demonstrated that it transforms to a new form (DNAN-V) that is distinct from DNAN-II,-III or -IV. Rietveld refinement of the high-pressure DNAN-I data also determined that the material exhibits negative linear compressibility, which is of interest given the use of DNAN as a shock-insensitive energetic material. Comparison of the behaviour of DNAN-I and –II under variable temperature and high-pressure conditions indicates that the kinetic form, DNAN-II, is the denser phase under all conditions studied. This work highlights the importance of crystallographic techniques in order to understand the polymorphism of energetic materials.
Neutron diffraction in diamond anvil cells
Authors: Guthrie Malcolm , Boehler Reinhard , Molaison Jamie , Kothapalli Karunakar , dos Santos Antonio , Tulk Christopher
Published: November 2015

Neutron diffraction provides many unique advantages for structural studies of materials under extremes of pressure. In addition to the famous sensitivity to light atom positions, neutrons are sensitive to long-range magnetic order and have an extremely high spatial resolution. However, a major downside of neutron techniques, that is keenly felt in high pressure studies, is the comparative weakness of available sources. Some of these limitations have been recently overcome at the Spallation Neutron Source, ORNL, using a newly developed supported diamond-anvil device. For the first time, this new capability allows the possibility of conducting neutron diffraction measurements at pressures approaching 100 GPa. These new developments will be discussed with a look towards the prospects for advances in neutron scattering at high pressure in the near future.
Nanocrystallization and Electronic-Conductivity Enhancement in PEDOT:PSS films
Authors: Fujiwara Akihiko , Masunaga Hiroyasu , Okuzaki Hidenori , Honma Yuta , Sasaki Takahiko
Published: November 2015

The conductive organic polymer, poly(3,4-ethylenedioxythiophene):poly(4-styrenesulfonate), abbreviated as PEDOT:PSS, is widely used in capacitors, antistatic coating etc. and one of the potential materials for the next-generation printable electronics. It is because of its excellent dispersibility in water and high electronic conductivity of more than 1,000 S/cm. Although many preceding studies have provided a variety of possible mechanisms of high conductivity, such as charge transfer between PEDOT and residual solvents, there has been no conclusive explanation for the origin of the high conductivity. Here, we report the nanometer-size crystallization of PEDOT inside the hydrophobic core region of PEDOT:PSS in a solid film and enhancement of electronic conductivity caused by the nanometer-size crystal growth of PEDOT. The structure of PEDOT:PSS has been investigated by means of small- and wide-angle X-ray scatterings (SAXS and WAXS) using high brilliance synchrotron radiation light source in SPring-8, Japan. We have obtained the microscopic structural model of PEDOT:PSS micelle in the water dispersion and the solid polymer film (Fig. 1(a)). Nanometer-size crystals of PEDOT were grown during the course of film fabrication in the wet process from the water dispersion. Furthermore, we found that the better crystallinity of the PEDOT crystal in the films prepared in the different conditions resulted in the higher electrical conductivity (Fig. 1(b)). The result suggests that the size of the crystallite is one of the key parameters for the enhancement of the electronic conductivity in PEDOT:PSS films. These findings shed light on the further improvement of the electrical conductivity of PEDOT:PSS polymer films by controlling the evaporation to dryness in the wet fabrication process.
Aperiodic Crystals at the Mesoscale
Authors: Sakamoto Yasuhiro
Published: November 2015

Materials with mesoscale structural characteristics have attracted great attention across the fields of chemistry, physics, and materials science. A typical example is mesoporous silica, which are synthesized in water/surfactant/silica systems, and has well-defined mesopores resulting in high surface area. Mesoporous silicas have two defining structural characteristics: (i) disorder at the atomic scale, i.e. only short-range order; and (ii) distinct order at the mesoscale, i.e. long-range order. Atomic-scale structural characterization by common diffraction techniques, such as X-ray single crystal diffraction, is challenging for these partially ordered materials. This is because of the difficulty in obtaining large (> 10 µm) single crystals, and because large-distance periodic features cause diffraction intensities to fall off rapidly with scattering angle, so that only limited small-angle data are available. On the other hand, transmission electron microscopy (TEM) is a powerful tool for structural characterization at the mesoscale level due to the stronger interaction of electrons with matter compared to X-rays, enabling the use of very small crystals. In particular, high-resolution TEM (HRTEM) images give the phase and the amplitude of the crystal structure factors experimentally, leading to a 3D structural model by electron crystallography. Cage-type anionic-surfactant-templated mesoporous silicas display rich structural diversity. Among them, cage-type mesoporous silica with tetrahedrally close-packed (TCP) structures can be described by four types of polyhedra, 5^12, 5^12 6^2, 5^12 6^3, and 5^12 6^4.[1] A variety of structural polymorph have been observed and characterized by TEM. Their structures show a close resemblance to the Frank-Kasper phases, which are well known in intermetallic compounds. We found mesoporous silica with dodecagonal quasicrystalline ordering as one of the TCP structures (Figure).[2] In this presentation, I will discuss structural characterization of aperiodic crystals at the mesoscale, such as mesoporous silicas and binary colloidal crystals, by electron microscopy.
Self-Assembly of Block Copolymers - from Periodic to Aperiodic Structures
Authors: Matsushita Yushu
Published: November 2015

Block copolymers with incompatible components are known to self-assemble into regular structures with mesoscopic length scales. This paper introduces periodic and aperiodic tiling structures from two kinds of three component terpolymer systems. One includes binary blends of linear poly(isoprene-styrene-2-vinylpyridine)(ISP) triblock terpolymers with cylindrical structures. When average composition of a blend is a little off from symmetry, i.e., composition ratio of three components are 0.24/0.59/0.17 for I/S/P, the system show unusual cylindrical array, where gray P domain has 5 black I domain neighbors, however it has found this structure is a periodic one with hexagonal symmetry. The other system is star-shaped terpolymers from the same polymer species, that is polyisoprene(I), polystyrene(S) and poly(2-vinylpyridine)(P). It was clarified that if composition ratio is in the vicinity of 1/1/1 for I/S/P, terpolymers tend to exhibit cylindrical structures whose cross sections possess the feature of regular two-dimensional tilings, that is, Archimedean tilings. However, when the ratio is varied to some extent, the structure formed deviates from regular tiling, and finally the sample, I1S2.7P2.5, was confirmed to show quasicrystalline tiling with dodecagonal symmetry as also verified by X-ray diffraction experiments.[1]
X-ray reflectivity study of the glass transition temperature of thin films
Authors: Stoev Krassimir , Sakurai Kenji
Published: November 2015

The glass transition takes place in amorphous materials (like polymers) during heating or cooling, and can be described as reversible transition from a hard and brittle state into a rubber-like state. Although physical properties of the material change significantly during the glass transition, this is not a phase transition of the material. The temperature at which the transition between the glassy and rubbery state occurs is called the glass transition temperature, and this temperature is always lower than the melting temperature. Thermodynamically, the glass transition is associated with transfer of heat between the system and its surrounding and with an abrupt volume change. Previously it was shown that the glass transition temperature of nano-films is different from that of bulk materials [1], which signifies the importance of determining this parameter for such systems. In the current work, we use quick X-ray reflectivity (qXRR) measurements to determine the glass transition temperature of polyvinyl acetate (PVAc). PVAc is rubbery synthetic polymer with the formula (C4H6O2), a density of 1.18 g/cm3, and a glass transition temperature for bulk material of 30oC [2]. Regular X-ray reflectivity measurements are based on θ/2θ scans at grazing incidence and typically require 0.5-1.5 h for a single scan. The qXRR technique is based on simultaneous measurement of the whole angular x-ray reflectivity profile and is suitable for in-situ measurement without moving the sample and/or the x-ray optics. Thus, the qXRR technique allows for very fast measurement of the x-ray reflectivity curves (duration of each scan is typically 0.1–20 sec [3]), which permits studying the time evolution of chemical, thermal, and mechanical changes at the surface and interface of different materials. X-ray reflectivity measurements give information about both density and thickness of thin films, and are suitable for studying glass transition phenomena. Nano-thickness PVAc layers on a Si substrate were examined with the qXRR technique, with x-ray reflectivity scans (each 10-seconds in duration) being recorded while temperature was changed from 20 to 50oC (total of 331 scans over 7 hours and 46 minutes). In the current paper, the experimental setup, the data-processing, and the analysis of the results from the qXRR measurements will be presented.
Synchrotron radiation study of the surface impurities at Naica gypsum crystals
Authors: Castillo Isai , Fuentes-Cobas Luis , Montero-Cabrera Maria , Fuentes-Montero Maria , Esparza-Ponce Hilda , Carreno-Márquez Jalil , Reyes-Cortes Manuel
Published: November 2015

The Cave of Swords was discovered in 1910 at Naica mine, Chihuahua, Mexico. Its crystals now are 0.1-0.3m long and their surface is opaque and ocher. For over 100 years these crystals continue to amaze and give us clues about their formation [1]. This work refers to the use of synchrotron radiation for phase identification on gypsum single crystals surfaces (GSCS). The experiments were performed at beamlines (BL) 11-3 and 2-3 of the Stanford Synchrotron Radiation Lightsource (SSRL). Synchrotron X-Ray micro-Fluorescence (μ-SXRF) and micro-X-ray absorption (μ-XANES) at BL 2-3, as well as Grazing Incidence X-ray Diffraction (GI-XRD) and Transmission X-ray Microscope (TXM) at BL 11-3, were employed for elemental and phase identification. For µ-SXRF spectroscopy at the Pb LIII absorption edge some region of interests were selected on each sample. In some samples Fe K-edge μ-XANES spectra were obtained. Spectra from BL 2-3 were analyzed by standard procedures of in-house software tools and using SMAK [2]. Ni, Cu, Co, V, K, Ti, Fe, Mn, Pb, Zn, Ca and S elements were identified. Hematite phase was identified by μ-XANES. All GI-XRD and TXM 2D X-ray diffraction patterns (2D-XRD) were calibrated using standard procedures developed at BL 11-3. 2D-XRD data were analyzed by ANAELU [3], Wfdiff [2] and FindIt codes. Figure shows above a TXM image, mapping where 2D-XRD patterns were recorded. Impurities in the sample increase from left to right, as was observed by direct inspection. Below, 2D-XRD patterns show at left the single crystal spots and at right the mosaic tracks of gypsum crystals. It was concluded that the crystal structure is affected by impurities. Hematite, chalcopyrite, sphalerite, cuprite, galena, and alabandite phases were determined by GI-XRD at GSCS. Acknowledgment: Stanford Synchrotron Radiation Lightsource, Harvard Museum of Natural History and CONACYT CB-183706.
Local order in wüstite. Fe1-xO, using a PDF approach
Authors: Welberry Richard , Goossens Darren
Published: November 2015

Many minerals (and materials more widely) show evidence of strong and complex local structural ordering. This local ordering can affect a material's mechanical properties, its transport properties (for example, how vacancies relate to oxygen transport through the structure) and its thermodynamics, and so is clearly of prime importance. For crystalline materials the analysis of single crystal diffuse scattering (SCDS) is the most definitive way of determining local structure but for many minerals (and materials more widely) single crystals of a sufficient size for such studies are often not readily obtainable and powder diffraction data must suffice. While conventional powder XRD (e.g. using Rietveld refinement) can provide information about the average crystal structure, total scattering (TS) – which includes both Bragg peaks and diffuse scattering – is needed if information about the local structure and short-range order is to be gained. The pair distribution function (PDF) analysis of such total scattering data has become a widely used technique for extracting such local structural information from a wide variety of materials including crystalline powders, nano-materials, amorphous materials, glasses and liquids. The aim of the present work is to explore the sensitivity of the PDF methodology to various aspects of disorder and short-range order for a mineral system for which the local structure has been characterised previously using SCDS. The system chosen for this study is the non-stoichiometric iron oxide wüstite, (Fe1–xO, x = 0.057). The X-ray diffraction patterns obtained from a single crystal of wüstite show strong and richly structured diffuse scattering (see Fig. 1). This has enabled a detailed model of the defect structure to be established. The aim is to assess to what extent this defect structure model could have been established using PDF analysis of powder diffraction data.
Pair distribution function analysis at the Brazilian synchrotron light source
Authors: Saleta Martín , Mastelaro Valmor , Granado Eduardo
Published: November 2015

The XDS beamline of the Synchrotron Light National Laboratory (LNLS), was designed to take advantage of the 4T superconducting multipole wiggler inserted in the storage ring. This multipurpose beam line is employed for X-ray diffraction and X-ray absorption spectroscopy in the energy range between 5 and 30 keV. The X-ray diffraction patterns can be acquired in two different arrangements: a) Bragg-Brentano configuration, using a scintillation detector with an analyzer and b) Debye-Scherrer configuration, where the sample is mounted into capillaries and the diffraction pattern is acquired with an arrangement of 6 Mythen detectors or a scintillator. The sample can be measured at different atmospheres and temperatures. The viability of the beamline for pair distribution function analysis (PDF) was tested measuring two different standards: 1) Al2O3 and 2) BaTiO3. The patterns were acquired at room temperature using the two detection setups at an energy of 20 keV. The samples were mounted inside 0.3 mm boron-rich glass capillaries. In addition to the sample pattern, we also measured the empty capillary (background) to subtract it to the sample data. The acquired and normalized patterns were converted into total scattering PDF (G(r)) with the PDFgetX3.[1] The experimental G(r) was fitted with the PDFgui.[2] Both data sets were fitted in the corresponding structural phase with cell parameters close to the ones reported in the literature. In the special case of the BaTiO3 sample, it was very carefully modeled. We particularly focused in evaluating if we can discriminate the correct structural phase, as this sample presents different phases (orthorhombic, tetragonal and cubic). We could identify that the sample, at room temperature, was at the expected tetragonal phase. Finally, we will present a preliminary analysis of the following systems: Pb1-xRxZr1-yTiyO3 (R=La&Ba) and Ba1-xRxZr1-yTiyO3 (R=La&Ca) at the ferro- and paraelectric states by PDF.
In situ total X-ray scattering study of WO3nanoparticle formation
Authors: Saha Dipankar , Jensen Kirsten , Tyrsted Christoffer , Bøjesen Espen , Mamakhel Aref , Dippel Ann-Christin , Christensen Mogens , Iversen Bo
Published: November 2015

In situ total scattering in combination with pair distribution function (PDF) and powder X-ray diffraction (PXRD) methods have been used to unravel the mechanism of WO3nanoparticle formation from aqueous precursor solution of ammonium metatungstate [(NH4)6H2W12O40.xH2O (AMT)] under hydrothermal condition. Total scattering studies can extract precise atomic scale structural information from solutions, amorphous solids, nanosized structures as well as from crystals [1]. The reaction mechanism was followed in an in situ reactor at synchrotron [2]. The study reveals that a complex precursor structure exists in the solution. It consists of edge and corner sharing WO6octahedra. While heating the solution, the precursor structure undergoes a reorientation with time converting the edge sharing octahedra to corner sharing octahedra before forming the nanoparticles. While the octahedra locally become reoriented there is no evidence of long range order. After 10 min. of heating, the nuclei in the solution abruptly cluster together and form crystalline particles. The sudden formation of nano crystals is also confirmed by in situ PXRD measurement. Further PDF analysis also reveals that local structure in hexagonal WO3is different than the average structure and it also rationalizes the formation of two different hexagonal phase of WO3in two different syhtesis procedure [3].
In-situ hydrogen gas loading setup for synchrotron X-ray total scattering
Authors: Kim Hyunjeong , Sakaki Kouji , Asano Kohta , Yamauchi Miho , Machida Akihiko , Watanuki Tetsu , Nakamura Yumiko
Published: November 2015

Hydrogen has been considered as a promising alternative fuel for transportation, provided we can find a way to store a large amount of hydrogen in a compact way. The realization of such a storage system can be achieved by developing materials that can easily absorb, safely store, and rapidly release hydrogen repeatedly. However, there is currently no material to meet all the requirements for on board storage. Great efforts have been made to understand hydrogenation properties of currently available materials to look for a way to improve properties or to prepare new materials. However, investigating the structure of some of these materials is challenging since their hydrides are only available under hydrogen gas pressure. Furthermore, many novel materials with improved properties often show heavily disordered or nanoscale structural features which are difficult to characterize using conventional crystallographic technique alone (crystallographically challenged hydrogen storage materials). In order to investigate the structural change in crystallographically challenged hydrogen storage materials during hydrogenation or dehydrogenation processes we have developed in-situ hydrogen gas loading setup for synchrotron X-ray total scattering experiments at the Japan Atomic Energy Agency (JAEA) beamline of BL22XU [1] at SPring-8. Coupled to an area detector [1,2], this setup allows us to obtain the atomic pair distribution function (PDF) [3] of metal hydrides either in equilibrium or in non-equilibrium state with hydrogen. In this poster, we will introduce our in-situ setup and present some preliminary results on AB5-type intermetallic compounds and Pd nanoparticles.
Size-dependent non-space filling atomic packing in metallic nanoparticles
Authors: Doan-Nguyen Vicky , Kimber Simon , Pontoni Diego , Reifsnyder Danielle , Diroll Benjamin , Yang Xiaohao , Miglierini Marcel , Murray Christopher , Billinge Simon
Published: November 2015

Ni-Pd nanoparticles synthesized for CO catalysis are characterized by transmission electron microscopy and total X-ray scattering. The sizes of these nanoparticles can be tuned to size with great control over the monodispersity of the samples. The pair distribution functions of the reveal a local ordering within the highly disordered atomic structure within the nanoparticles. The PDFs show a size-dependent deviation from typical bulk face centered cubic (fcc) structure for these materials. The long-range isotropic disorder within these non-fcc nanoparticles can be fitted using an exponentially damped single-mode sine wave. Below a diameter of 5 nm, the Ni-Pd nanoparticles exhibit local ordering of atoms as found in typical icosahedral clusters. The transition from fcc to non-space filling atomic packing of icosahedral clusters in a nanoparticle is modeled to show the structural origin of the observed PDFs. Understanding this type of disorder can give insight into structure-property relations for applications in heterogeneous catalysis.
Structure analysis for Fe-based and Ni-based metal-metalloid amorphous alloys
Authors: Arima Hiroshi , Kawamata Toru , Yokoyama Yoshihiko , Sugiyama Kazumasa , Otomo Toshiya
Published: November 2015

Transition metal-metalloid amorphous systems such as Fe-B and Ni-B are usually applied for the soft magnetic metallic glassy alloys and are counted as one of prominent categories in the field of amorphous alloy technology. Since glass forming ability of these systems correlates closely with the atomic level structure depending on chemical species of metal and metalloid, the local structure analysis for these glassy alloys is strongly required. In order to obtain the reliable structural model for these metal (Fe, Ni)-metalloid (B) amorphous samples, we determined the partial structural functions by combinational use of neutron diffraction (ND) and anomalous X-ray scattering (AXS). The amorphous ribbon samples were produced by the single-roller melt-spinning technique. The AXS measurements at Fe and Ni absorption edges were carried out at BL-7C of Photon Factory, KEK. The ND experiment was performed by using the time-of-flight technique and high intensity total diffractometer, NOVA at MLF, J-PARC. The figure shows the g(r)s for Fe80B20, Ni81B19, and Ni60B40calculated by the interference functions obtained by ND measurements. The dashed lines in the figure indicate the interatomic distances estimated from Goldschmidt atomic radii (Fe: 1.28 Å, Ni: 1.25 Å, B: 0.97 Å). At the nearest neighbor region up to about 3 Å, the first peak could be accounted for a harmony of metal (M)–B and B–B pair correlations and the second peak is mainly contributed by the M-M pair correlation. As for the three dimensional structural modeling of the amorphous samples, reverse Monte Carlo simulation has been performed starting from an initial model of 2,000 atoms with the b.c.c. structure. The present simulation results are found to reproduce the experimental interference functions obtained by the ND, ordinary X-ray diffraction, and AXS measurements. We will present the obtained structural model and local structural units around B including their arrangement.
Understanding the properties of energy materials from their local structure
Authors: Kim Hyunjeong
Published: November 2015

Numerous energy materials with improved properties often show nano- or heavily disordered structural features which are hardly characterized by the conventional crystallographic technique alone. By using the atomic pair distribution function (PDF) analysis [1]on X-ray and neutron total scattering data, we have investigated various energy materials to elucidate structural features closely linked to their properties. Some of the examples are heavily disordered V1-xTixH2 for hydrogen storage [2] and layered Li1.2Mn0.567Ni0.166Co0.067O2 cathode material for lithium ion batteries. These materials possess an intricate structure and could easily lead to misleading results if one relies on only one structure probing technique. In this talk, I will show how their structural information was extracted from the x-ray and neutron PDFs obtained at BL22XU at SPring-8 and NOVA at J-PARC, respectively and how it was used with information available from other techniques to understand the properties of these energy materials.
X-ray Scattering Studies of amorphous thin film materials
Authors: Ma Qing
Published: November 2015

In light of advances in detector technology, we revisit wide angle x-ray scattering techniques and their application to amorphous thin films that are of technological importance. For thin film materials the asymmetrical reflection geometry is employed to avoid the substrate signals. Incident x-ray angles are typically set close to the critical angles. There are various complications related to this geometry, in particular, raw scattering patterns being distorted. In addition, because these materials are typically weak scatterers due to disorder, increased data collection efficiency is always desired. Here, we report our activities using a 4-element vortex Si-drift detector for wide angle x-ray scattering experiments and present some experimental data collected on amorphous transparent conducting oxides.
Advancing Single-Particle EM towards Atomic Resolution
Authors: Chen James
Published: November 2015

Recent advances in single-particle electron microscopy (EM) have enabled the structural elucidation of several macromolecular complexes at near-atomic resolution. These achievements have been assisted by both well-ordered molecular specimens and rapid improvements in the direct-electron-detection technology. However, substantial challenges remain as the research field pushes the single-particle EM imaging technique towards even higher resolution, especially on smaller and dynamic molecular assemblies. Facilitated by the state-of-the-art electron microscopes at the OHSU-FEI Living Lab, I have been conducting research on effective approaches to cryo-EM data acquisition and data analysis. For the data acquisition, the central aim is to record TEM images of minimally damaged molecular specimens (due to the high-energy electron beam) on the detector. For the data analysis, my goal is to extract the maximal amount of information from the data images (at very low signal-to-noise ratio) for unbiased particle 2D classification and 3D reconstruction. I will discuss my research effort in these areas in the context of structural biology studies.
Electron microscopy and functional analysis of recombinant innexin gap junctions
Authors: Oshima Atsunori , Matsuzawa Tomohiro , Murata Kazuyoshi , Nishikawa Kouki , Fujiyoshi Yoshinori
Published: November 2015

Innexin is a molecular component of invertebrate gap junctions, which have an important role in neural and muscular electrical activity in invertebrates. Although the structure of vertebrate connexin26 was revealed by X-ray crystallography [1], the structure of innexin channels remains poorly understood. To study the structure of innexin gap junction channels, we expressed and purified Caenorhabditis elegans innexin-6 (INX-6) gap junction channels, and characterized their molecular dimensions and channel permeability using electron microscopy (EM) and a fluorescent dye transfer assay, respectively [2]. Negative-staining and thin-section EM of isolated INX-6 gap junction plaques revealed a loosely packed hexagonal lattice. We performed single particle analysis of purified INX-6 channels with negative-staining and cryo EM. Based on the negative-stain EM images, the class average of the junction form had a longitudinal height of 220 Å, a channel diameter of 110 Å in the absence of detergent micelles, and an extracellular gap space of 60 Å, whereas the class average of the hemichannels had diameters of up to 140 Å in the presence of detergent micelles. Cryo EM images revealed rotational peaks that could be related to the INX-6 subunits. Structural analysis of the reconstituted INX-6 channels with single particle analysis and electron tomography suggested that the oligomeric number of the INX-6 channel was distinct from that of the dodecameric connexin channel. Dye transfer experiments indicated that the INX-6-GFP-His channels were permeable to 3-kDa and 10-kDa dextran-conjugated tracers. These findings indicate that INX-6 channels have a characteristic oligomer component that differs from that in connexin gap junction channels.
Crystal structures of γ-glutamyltranspeptidase in complex with inhibitors
Authors: Hirabayashi Kei , Ida Tomoyo , Li Chunjie , Suzuki Hideyuki , Fukuyama Keiichi , Hiratake Jun , Wada Kei
Published: November 2015

γ-Glutamyltranspeptidase (GGT; EC 2.3.2.2) is involved in the degradation of γ-glutamyl compounds such as glutathione (GSH; γ-glutamyl-cysteinyl-glycine) . A major physiological role of this enzyme is to cleave the extracellular GSH as a source of cysteine for intracellular glutathione biosynthesis. Another crucial role of GGT is to cleave glutathione-S-conjugates as a key step in detoxification of xenobiotics and drug metabolism. In mammals, GGT has been implicated in physiological disorders such as Parkinson's disease, other neurodegenerative diseases including Alzheimer's disease and cardiovascular disease. The indispensable roles played by GGT in GSH-mediated detoxification and cellular response to oxidative stress suggest that GGT is an attractive pharmaceutical target. We here report the binding mode of acivicin, a well-known glutamine antagonist, to B. subtilis GGT at 1.8 Å resolution showing that acivicin is bound to the Oγ atom of Thr403, the catalytic nucleophile of the enzyme, through its C3 atom [1]. The observed electron density around the C3 atom was best fitted to the planar and sp2 hybridized carbon, consistent with a simple nucleophilic substitution of Cl at the imino carbon by Oγ atom of Thr403. Furthermore, comparison of three bacterial enzymes, the GGTs from E. coli, H. pylori and B. subtilis in complex with acivicin, showed significant diversity in the orientation of the dihydroisoxazole ring among three GGTs. The differences are discussed in terms of the recognition of the α-amino and α-carboxy groups in preference to the dihydroisoxazole ring as observed in time-lapse soaking crystal structures of B. subtilis GGT with acivicin.
Malic enzyme is a target for drug design to combat obesity and cancer
Authors: Saha Rinku , Thakkar Shraddha , Al-Dwairi Ahmed , Gokulan Kuppan , Simmen Frank , Varughese Kottayil
Published: November 2015

The cytosolic malic enzyme (ME1) plays an important role in insulin-induced lipogenesis and has profound effects on colon cancer progression. ME1 generates pyruvate, NADPH and carbon dioxide from malate, a Krebs cycle intermediate. NADPH has an important role in de novo synthesis of long-chain fatty acids whereas pyruvate is cycled back into mitochondria. The pyruvate cycle has been hypothesized to be a necessary component of glucose-stimulated insulin secretion. Increased insulin signaling in liver and adipose tissues leads to higher accumulation of fat mass increasing the risk for obesity. NADPH and fatty acids also support cancer cell proliferation and migration. Thus ME1 may be a suitable drug target to counter obesity and prevent cancer progression. In the current work, computer-aided drug design techniques were used to identify possible ME1 inhibitors with therapeutic value. The software package SYBYL was used for defining the binding pocket and virtual screening was performed to mine through large databases (ZINC-UCSF) containing drug-like molecules in order to identify molecules that could form hydrogen bonds to the enzyme and fit into the active site. The molecules so obtained were then used for docking using the software packages SURFLEX DOCK (SYBYL) and AutoDock Vina (Scripps Research Institute). Lead molecules having minimum binding energy score were identified and two in vitro assays were carried out on the top hit molecules. We tested a total of 11 compounds for activity using an enzyme assay and 4 of these compounds were found to diminish NADPH production significantly. Additionally we performed a cell proliferation assay with colorectal cancer cell line (HCT-116) using the above 4 compounds and three of these compounds exhibited strong activity against cancer cell growth. Supported in part by NIH grant CA136493.
Catalysis of ubiquitin transfer by the RBR ubiquitin ligase parkin
Authors: Trempe Jean-François , Krett Jonathan , Sauvé Véronique , Seirafi Marjan , Grenier Karl , Tang Matthew , Gehring kalle , Fon Edward
Published: November 2015

Mutations in the Parkin gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING1-In-Between-RING2 (RBR) E3 ubiquitin ligase, which functions through a two-step mechanism involving a parkin~ubiquitin thioester intermediate [1]. However, compared to other ubiquitin ligases, parkin exhibits low basal activity and requires activation both in vitro and in cells. As parkin is neuroprotective in various models of Parkinson's disease, understanding how it catalyses ubiquitin transfer will be critical. We previously reported the crystal structure of full-length parkin [2]. The structure shows parkin in an auto-inhibited state and provides insight into how it is activated. The RING0 domain occludes the ubiquitin acceptor site Cys431 in RING2 whereas a novel Repressor Element of Parkin (REP) binds RING1 and blocks its E2-binding site. Remarkably, mutations that disrupt these inhibitory interactions activate parkin both in vitro and in cells. The structure also reveals that His433 and Glu444 form a catalytic dyad adjacent to Cys431. Here, we show that His433 catalyses the acyl transfer of ubiquitin carboxy terminus from Cys431 to a target lysine side-chain amino group. Mutation of His433 does not affect UbcH7~ubiquitin discharging or thioester intermediate formation, but prevents formation of polyubiquitin chains on parkin. However, mutation of His433 does not affect significantly parkin's mitochondrial recruitment and substrate ubiquitination, suggesting that other factors might be at play in vivo. We also investigate the catalytic role of other residues located around the Cys431, such as Trp462. The work provides insight into the mechanism of ubiquitination by RBR E3 ligases with important implications for Parkinson's disease.
Structural basis of SOSS1 complex assembly and recognition of ssDNA
Authors: Ren Wendan , Chen Hongxia , Sun Qiangzu , Tang Xuhua , Lim Siew Choo , Huang Jun , Song Hai wei
Published: November 2015

The SOSS1 complex comprising SOSSA, SOSSB1 and SOSSC senses single-stranded DNA (ssDNA) and promotes repair of DNA double-strand breaks (DSBs). But how SOSS1 is assembled and recognizes ssDNA remains elusive. Crystal structure of the N-terminal half of SOSSA (SOSSAN) in complex with SOSSB1 and SOSSC showed that SOSSAN serves as a scaffold to bind both SOSSB1 and SOSSC for assembling the SOSS1 complex. The structures of SOSSAN/B1 in complex with a 12nt ssDNA and SOSSAN/B1/C in complex with a 35nt ssDNA showed that SOSSB1 interacts with both SOSSAN and ssDNA via two distinct surfaces. Recognition of ssDNA with a length up to nine nucleotides is solely mediated by SOSSB1 while neither SOSSC nor SOSSAN are critical for ssDNA binding. These results reveal the structural basis of SOSS1 assembly and provide a framework for further studying the mechanism governing longer ssDNA recognition by the SOSS1 complex during DSB repair.
Structural basis of pharmacological chaperoning for human β-galactosidase
Authors: Suzuki Hironori , Ohto Umeharu , Higaki Katsumi , Mena-Barragán Teresa , Aguilar-Moncayo Matilde , Ortiz Mellet Carmen , Nanba Eiji , García Fernández José Manuel , Suzuki Yoshiyuki , Shimizu Toshiyuki
Published: November 2015

GM1-gangliosidosis and Morquio B are rare lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. These diseases are caused by deficiencies in the lysosomal enzyme human β-Galactosidase (β-Gal), frequently related to misfolding and subsequent endoplasmic reticulum-associated degradation (ERAD) due to mutations in the β-Gal gene. Pharmacological chaperone (PC) therapy is a newly developed molecular therapeutic approach by using small molecule ligands of the mutant enzyme that are able to promote the correct folding, prevent ERAD and promote trafficking to the lysosome. Here, we present the enzymological properties of wild-type human β-Gal and two representative mutations in GM1 gangliosidosis Japanese patients (R201C and I51T). We have also evaluated the PC effect of two competitive inhibitors of β-Gal. Moreover, we determined the crystal structures of β-Gal in complex with these compouds and two structurally related analogues to elucidate the detailed atomic view of the recognition mechanism. All compounds bind to the active site of β-Gal with the sugar moiety making hydrogen bonds to active site residues. Moreover, the binding affinity, the enzyme selectivity and the PC potential are strongly affected by the mono or bicyclic structure of the core as well as the orientation, the nature and the length of the exocyclic substituent. These results provide understanding on the mechanism of action of β-Gal selective chaperoning by newly developed PC compounds.
Structure of parkin reveals the mechanism of autoinhibition
Authors: Seirafi Marjan , Trempe Jean-Francois , Sauve Veronique , Kozlov Guennadi , Menade Marie , Nagar Bhushan , Gehring kalle
Published: November 2015

Mutations in the gene park2 that codes for a RING-In-Between-RING (RBR) E3 ubiquitin ligase are responsible for an autosomal recessive form of Parkinson's disease (PD). Compared to other ubiquitin ligases, the parkin protein exhibits low basal activity and requires activation both in vitro and in cells. Parkin is a 465-residue E3 ubiquitin ligase promoting mitophagy of damaged mitochondria. Parkin has two RING motifs RING1 and RING2 linked by a cysteine- rich in-between-RING (IBR) motif, a recently identified zinc-coordinating motif termed RING0, and an N-terminal ubiquitin-like domain (Ubl). It is believed that parkin may function as a RING/HECT hybrid, where ubiquitin is first transferred by the E2 enzyme onto parkin active cysteine and then to the substrate. Here, we report the crystal structure of full-length parkin at low resolution. This structure shows parkin in an auto-inhibited state and provides insight into how it is activated. In the structure RING0 occludes the ubiquitin acceptor site Cys431 in RING2 whereas a novel repressor element of parkin (REP) binds RING1 and blocks its E2-binding site. The ubiquitin-like domain (Ubl) binds adjacent to the REP through the hydrophobic surface centered around Ile44 and regulate parkin activity. Mutagenesis and NMR titrations verified interactions observed in the crystal. We also proposed the putative E2 binding site on RING1 and confirmed it by mutagenesis and NMR titrations. Importantly, mutations that disrupt these inhibitory interactions activate parkin both in vitro and in cells. The structure of the E3-ubiquitin ligase provides insights into how pathological mutations affect the protein integrity. Current work is directed towards obtaining high-resolution structure of full-length parkin in complex with E2 and substrates. The results will lead to new therapeutic strategies for treating and ultimately preventing PD.
Human intestinal glucosidases MGAM and SI: Roles in Health and Disease
Authors: Rose David
Published: November 2015

The way to a person's heart is through their stomach - not just their heart. All aspects of health are affected by sources of nutrition; not just health but social and political issues, too. The metabolism of starch into glucose is linked directly to the development of the human brain. There is considerable interest worldwide into the processing of starch and other foods by the intestinal microbiome. This talk will focus on the main mammalian intestinal enzymes that process starch, their structures, functions and potential roles in human health and disease. The alpha-glucosidases maltase-glucoamylase (MGAM) and sucrase-isomaltast (SI) are resident in the small-intestinal lumen and are responsible for generating glucose from a wide variety of starch structures. Their malfunction is responsible for many nutritional intolerances and diseases including diabetes, gastrointestinal cancers and obesity. A pediatric nutritional disorder directly associated with mutations in SI, Congenital Sucrase-Isomaltase Deficiency (CSID) has significant occurrence, especially in northern and indigenous populations. The structural analyses presented in this talk will shed light on the molecular basis for this disease, as well as the development of inhibitor analyses that are designed to investigate the roles of human intestinal glucosidases in health and disease.
Structural studies on M. tuberculosis O6-methylguanine methyltransferase
Authors: Rizzi Menico , Miggiano Riccardo , Lahiri Samarpita , Perugino Giuseppe , Ciaramella Maria , Rossi Franca
Published: November 2015

Mycobacterium tuberculosis (MTB) is an extremely well adapted human pathogen capable to survive for decades inside the hostile environment represented by the host's infected macrophages despite exposure to multiple potential DNA-damaging stresses. In order to maintain a remarkable low level of genetic diversity, MTB deploys different strategies of DNA repair, including multi-enzymatic systems, such as Nucleotide Excision Repair, and single-step repair. In particular, to counteract the mutagenic effects of DNA alkylation, MTB performs the direct alkylated-base reversal by sacrificing one molecule of a DNA-protein alkyltransferase, such as O6-methylguanine methyltransferase (OGT; orf: Rv1316c). We present here the biochemical and structural characterization of recombinant mycobacterial OGT (MtOGT) in its wild-type form along with its mutated variants mimicking the ones occurring in relevant clinical strains (i.e. MtOGT-T15S and MtOGT-R37L). Our studies reveal that MtOGT-R37L is severely impaired in its activity as consequence of its ten-fold lower affinity for modified double-stranded DNA (dsDNA) (1). Further investigations on a new structure-based panel of OGT versions, designed to explore different molecular environment at position 37, allowed us a better understanding of the functional role of the MtOGT Arg37-bearing loop during catalysis. Moreover, we solved the crystal structure of MtOGT in covalent complex with modified dsDNA that reveals an unprecedented MtOGT::DNA architecture, suggesting that the MtOGT monomer performing the catalysis needs assisting unreacted subunits during cooperative DNA binding. This work is supported by European Community FP7 program SYSTEMTB (Health-F4-2010-241587)