bluuebunny/crossref_metadata_2025 huggingface dataset:
A Rebirth of Laboratory XANES and XES
Authors: Seidler Gerald , Mortensen Devon , Pacold Joseph , Hoidn Oliver
Published: November 2015

We have recently launched a reinvestigation of laboratory-based measurement of x-ray absorption near edge structure (XANES) and high-resolution x-ray emission spectroscopy (XES). Driven by the roughly one-hundred-fold improvement in the efficiency of high resolution x-ray optics compared to the 1970's, we have demonstrated that surprisingly impressive performance is now possible with laboratory XES instruments and that quite useful performance is possible for laboratory XANES. For applications in the 5 keV- 10 keV energy range, i.e., appropriate for 3d transition metal K edges and lanthanide L edges, we find XES performance that is intermediate between what can be achieved at bending-magnet and insertion-device beamlines at third generation synchrotron light sources. In the same energy range, we find that high quality XANES measurements can be performed in transmission mode on concentrated samples with the present instrument and should be possible, in many cases, in fluorescence mode after a planned upgrade brings the monochromatic beam flux up to approximately 10M/sec.
Degenerate Sequence Recognition by AdpA
Authors: Ohtsuka Jun , Yao Ming Dong , Nagata Koji , Miyazono Ken-ichi , Zhi Yuehua , Ohnishi Yasuo , Tanokura Masaru
Published: November 2015

AdpA is the central transcriptional factor in the A-factor regulatory cascade of Streptomyces griseus and activates hundreds of genes required for both secondary metabolism and morphological differentiation, leading to onset of streptomycin biosynthesis as well as aerial mycelium formation and sporulation. It has been shown that AdpA binds to over 500 operator regions with the loosely conserved consensus sequence, 5'-TGGCSNGWWY-3' (S: G or C; W: A or T; Y: T or C; and N: any nucleotide). However, it is still obscure how AdpA can control hundreds of genes. To reveal the molecular basis of the low nucleotide sequence specificity, we have determined the crystal structure of the complex of DNA-binding domain of AdpA and a 14-mer duplex DNA with two-nucleotide overhangs at 5'-ends at 2.95-Å resolution. The crystal structure and electrophoretic mobility-shift assays showed that only two arginine residues, Arg262 and Arg266, are involved in the sequence recognition and determine the nucleotide specificity/preference of continuous five base-pairs of positions 1–5 in the consensus sequence. These results partially explain how AdpA directly controls hundreds of genes.
Crystal structure of the response regulator VraR fromStaphylococcus aureus
Authors: Lee Chieh-Shan , Liu Chia-I , Chang Wei-Jung , Jeng Wen-Yih
Published: November 2015

Staphylococcus aureusis one of the major causes of nosocomial infections today. Infections caused byS. aureusare a growing cause of concern owning to the widespread development of multiple antibiotic-resistant strains, particularly methicillin and vancomycin-intermediate resistant strains (MRSA and VISA). The VraSR two component system is reported to be highly related to the development of vancomycin resistance ofS. aureus. VraS is a membrane-bound sensor histidine kinase that received the signal stimulation from environment to regulate the phosphorylation status of its cognate response regulator protein VraR to control target genes transcription to result in the development of vancomycin resistance ofS. aureus.Here, we report the crystal structure of unphosphorylated VraR fromS. aureusin a dimeric form at 1.8 Å resolution. The crystals of VraR belong to the monoclinic space group C2 containing two protein molecules as a dimer in the asymmetric unit. The first β-strand at N-terminal end of each VraR subunit was inserted into the other subunit to form an intertwining dimer structure. Finally, according to previous reports and our crystal structure, we propose a regulation model for VraR. The feedback control ofvraSR operon would be the unphosphorylated dimeric VraR rather than the unphosphorylated monomeric VraR.
Structural studies of AraR from B. thetaiotaomicron
Authors: Chang Changsoo , Tesar Christine , Rodionov Dmitry , Li Xiaoqing , Jedrzejczak Robert , Kim Youngchang , Joachimiak Andrzej
Published: November 2015

The NrtR family of bacterial transcription factors is characterized by an N-terminal Nudix hydrolase-like effector binding domain and a C-terminal DNA binding domain. A bioinformatics analysis of the NrtR family represented by uncharacterized protein BT0354 in Bacteroides thetaiotaomicron suggests that these regulators control the catabolic pathways for L-arabinose. Many bacteria use L-arabinose as the sole source of carbon energy. The L-arabinose utilization pathway and its transcriptional regulation have been studied for a long time in several model microorganisms. Here we provide biochemical and structural characterization of the novel arabinose-responsive regulator of NrtR family protein BT0354, L-arabinose regulator from B. thetaiotaomicron (BtAraR). The BtAraR DNA binding and the role of effector molecule L-arabinose were confirmed using electrophoretic mobility shift assays. We have solved the crystal structures of BtAraR for two apo forms, and complexes with L-arabinose and double-stranded DNA target. The apo-1 form was solved as two dimers/AU in the R3 space group at 2.35 Å, while the apo-2 form was solved as one monomer/AU in the I213 space group at 2.56 Å resolution. The L-arabinose and DNA complex structures were solved as a dimer/AU in the P21 space group at 1.95 Å resolution and the P23 space group at 3.05 Å resolution, respectively. The biological unit of this protein is a dimer while the N-terminal ligand binding domain of the monomer adopts a Nudix hydrolase-like fold and the C-terminal DNA binding domain is a winged helix-turn-helix. The DNA binding-releasing mechanism can be rationalized through the comparison and analyses of these structures. The apo and DNA bound structures are more similar compared to the L-arabinose-bound structure. The r.m.s. deviation for the apo and DNA bound structures is 1.13 Å, while that for apo and the L-arabinose-bound structures is 4.54 Å. Details about the DNA binding mode, L-arabinose binding and L-arabinose induced structural change will be presented. This work was supported by National Institutes of Health grant GM094585 and by the U. S. Department of Energy, Office of Biological and Environmental Research, under contract DE-AC02-06CH11357.
Inhibitors of the DNA-cleavage gate of bacterial type IIA topoisomerases
Authors: Bax Ben , Fosberry Andrew , Spitzfaden Claus , Shillings Anthony , Pearson Neil , Chan Pan , Huang Jianzhong
Published: November 2015

Type IIA topoisomerases resolve topological problems in DNA by making a double-stranded break in one DNA segment, passing another DNA duplex through this break, and then resealing the break. Drugs (such as the widely used fluoroquinolone antibacterials and anti-cancer compounds such as etoposide) that stabilize double-strandedly cleaved DNA complexes with type IIA topoisomerases are cytotoxic. In GlaxoSmithKline a new class of novel bacterial topoisomerase inhibitors (NBTIs) have been developed. A 2.1Å crystal structure of a complex of GSK299423 with DNA and S. aureus DNA gyrase showed how the NBTI inhibits the enzyme by interacting with both the DNA and the protein. A pocket occupied by the compound in the protein (at the dimer interface) is absent in the apo structure, while the pocket occupied by the compound in the DNA has been formed by the enzyme stretching and untwisting the DNA between the two active sites. The NBTI structure has trapped a pre-cleavage complex of the enzyme, before the four base-pair double stranded break has occurred, and the structure gives insights into the role of metal ions in the cleavage mechanism of type IIA topoisomerases. Stuctures suggest how relatively small movements at the active sites (for example an ~3Å movement of a magnesium ion) can cause the cleavage of phosphate ester bonds and are coupled to the large domain movements involved in the catalytic cycle of these conformationally flexible enzymes. The binding site for the NBTI is close to but distinct from those for fluoroquinolones. Structures shows how the fluoroquinolone interacts with both the protein and the DNA by binding a non-catalytic magnesium ion and four associated waters. This provides a structural explanation for both fluoroquinolone resistance mutations and SAR (structure-activity relationships). Mechanistic implications of recent structural studies will be discussed.
Creation of nanomaterials by extreme pressure-temperature conditions
Authors: Solozhenko Vladimir
Published: November 2015

Nanomaterials in the form of zero-, one- and two-dimensional nanostructures make a high-impact background for both science and technology. At the same time, the synthesis of bulk nanostructured materials remains the least-explored but challenging domain that allows combining the desired physical, chemical and mechanical properties and gives rise to nanoelectronics, nanomechanics, band-gap engineering, etc. The common methods of soft chemistry allow obtaining nanoparticles whose direct sintering unavoidably leads to the grain growth and lost of nanostructure. The extreme pressure is a parameter of choice to suppress the self-diffusion responsible for high-temperature recrystallization. The bulk nanostructured materials shows the superior fracture toughness and extremely high hardness as compared to corresponding microcrystalline bulks. The remarkable changes in physical and mechanical properties, however, do not affect the original thermal and chemical stability of the phase(s). All this opens unique opportunities for high-temperature superabrasive and electronic applications of such materials. Finally, the extreme pressure-temperature conditions are powerful and promising tool for grain-size control during direct solid-state phase transformations. The simultaneous variation of pressure and temperature makes possible to combine different nucleation, growth and aggregation regimes with high flexibility, and, therefore, to go deep into nanoscale engineering.
Structure analysis of an Fe-interlayer expanded zeolite.
Authors: Gies Hermann , Feyen Mathias
Published: November 2015

Interlayer expansion using silylating agents to connect layer silicates to 3D framework structures has proofed to be a versatile synthesis route to new micro-porous frameworks (1). We show here that also Me-cations can be used as linker agents. An acidic Fe-chloride solution was used in a hydrothermal reaction to convert the hydrous layer silicate RUB-36 into an interlayer expanded zeolite, containing Fe at the linker site. Structure analysis of the new material Fe-COE-3, Si19.14Fe0.86O42, showed that the porous framework is stable after calcination and contains Fe on T-sites at the linker position which connects the two silicate layers. From chemical analysis it is confirmed that every other linker site is occupied by iron. The material crystallizes in space group Pm with a = 12.200(9) Å, b = 13.981(8) Å, c = 7.369(2) Å, ß = 106.9(1)0. Fig. 1 shows the results of the final Rietveld analysis (chi2= 8.8) and a projection of the framework structure along [001]. Because of the limited crystallinity of the material also the quality of the structure refinement is constricted. However, including complementary information from adsorption experiments, IR-, and UV-spectroscopy the structure model is confirmed without any doubt. Besides, the Rietveld analysis of the XRD data is the analytical tool to gain more detailed geometric information of the metallosilicate framework. The synthesis procedure is flexible and can be extended to other Me-cations as linker sites. We have prepared isostructural interlayer expanded metallosilicates of similar crystallinity with Ti, Sn, Zn, Eu, and Al as active centers. This method of inserting Me-cations as linkers in hydrous layer silicates shows for the first time that the active sites in the generated microporous silicate framework can be obtained in a controlled manner on well defined T-sites.
Symmetry reduction in thortveitites: incommensurability and polytypism
Authors: Stöger Berthold
Published: November 2015

For many years periodicity was the defining property of crystalline materials. The discovery of numerous aperiodic materials like incommensurately modulated phases or quasi-crystals led to a paradigm shift and since 1992 crystallinity is defined by the IUCr via the discreteness of the diffraction pattern [1]. A different class of materials lacking periodicity in three dimensions, albeit following strict building principles, are polytypes. Polytypes are composed of modules that can be arranged in different but energetically similar ways. On the example of the thortveitite family of compounds it will be shown that these seemingly disparate phenomena can be linked to the same underlying cause, namely symmetry reduction. Many bivalent transition metal diphosphates(V), diarsenates(V) and divanadates(V) of general formula M2X2O7 (X=P, As, V) crystallize in the thortveitite structure type. The high temperature β-M2X2O7 phases feature one crystallographically unique X2O7 group located on a centre of inversion. Due to the unfavourable X-O-X angle of 1800these phases transform on cooling into lower symmetry structures. Thus, numerous superstructures based on the thortveitite aristotype have been described. Incommensurate structures can be considered as superstructures with symmetry reduction by an index of ∞. The first example in the thortveitite family was described by Palatinus et al. [2]. Since then we found several other incommensuarte thortveitites with varying modulation functions and phase-transition behaviour. If the symmetry reduction leads to layers with different local symmetry, the resulting structures are order-disorder (OD) polytypes [3], resulting in twinning or diffuse scattering. In (Co,Ni)2As2O7 both features, incommensurate modulation and systematic twinning, are combined. An overview of the crystal-chemistry and the complex phase-transition behaviour of the incommensurately modulated and/or polytypic thortveitite phases will be given.
Freeze Frames vs. Movies
Authors: Müller Carola , Lidin Sven
Published: November 2015

Sometimes, model building in crystallography is like resolving a puzzle: All obvious symmetrical or methodological errors are excluded, you apparently understand the measured patterns in 3D, but the structure solution and/or refinement is just not working. One such nerve-stretching problem arises from metrically commensurate structures (MCS). This expression means that the observed values of the components of the modulation wave vectors are rational by chance and not because of a lock-in. Hence, it is not a superstructure - although the boundaries between the two descriptions are blurry. Using a superstructure model for a MCS decreases the degrees of freedom, and forces the atomic arrangement to an artificial state of ordering. Just imagine it as looking at a freeze frame from a movie instead of watching the whole film. The consequences in structure solution and refinement of MCS are not always as dramatically as stated in the beginning. On the contrary, treating a superstructure like a MCS might be a worthwhile idea. Converting from a superstructure model to a superspace model may lead to a substantial decrease in the number of parameters needed to model the structure. Further, it can permit for the refinement of parameters that the paucity of data does not allow in a conventional description. However, it is well known that families of superstructures can be described elegantly by the use of superspace models that collectively treat a whole range of structures, commensurate and incommensurate. Nevertheless, practical complications in the refinement are not uncommon. Instances are overlapping satellites from different orders and parameter correlations. Notably, MCS occur in intermetallic compounds that are important for the performance of next-generation electronic devices. Based on examples of their (pseudo)hexagonal 3+1D and 3+2D structures, we will discuss the detection and occurrence of MCS as well as the benefits and limitations of implementing them artificially.
Surveying the higher dimensions of the aperiodic composite nonadecane/urea
Authors: McIntyre Garry , Lemée-Cailleau Marie-Hélène , Toudic Bertrand
Published: November 2015

We recently observed for the first time that there exist phase transitions where the structural changes correspond just to degrees of freedom hidden in the internal (super)space of an aperiodic material, here the composite nonadecane/urea [1]. A key factor in the discovery of this type of transition [2] was the examination of the diffraction pattern in 3D, only possible at the time on a four-circle triple-axis neutron spectrometer, the analyzer used in zero-energy transfer to reduce the background and improve resolution. Despite the greater accessibility in reciprocal space, the weak intensity of the superlattice reflections limited the volume of reciprocal space that could be explored. Modern neutron Laue diffractometers with large image-plate detectors permit rapid and extensive exploration of reciprocal space with high resolution in the two-dimensional projection and a wide dynamic range with negligible bleeding of intense diffraction spots [3]. Surveying nonadecane/urea with neutron Laue diffraction from 300K to 4K reveals further detail of the superspace-driven phase transition, notably an increase in misorientation in the plane perpendicular to the composite misfit axis, as well as a first-order transition to a new phase at lower temperature. These new observations shed further light on how nature can use the degrees of freedom hidden in the internal superspace to form states that cannot be envisaged in the usual 3D real space.
Wide Range Solid Solutions with Composite Modulated Structures
Authors: Schmid Siegbert
Published: November 2015

Systems that form modulated structures are a fascinating class of materials, which lack lattice periodicity but may still be perfectly long-range ordered [1]. Such systems exist across the whole range of chemical disciplines from organic conductors to high-Tc superconductors and minerals. The importance of modulated structures has been recognised, but there have been few systematic studies across composition ranges of wide-range solid solutions that form composite modulated structures. Such a systematic investigations further our understanding of crystal chemical and structural aspects of modulated structures as well as the reasons for their existence. Examples for such wide-range solid solutions will be presented, with structures investigated using X-ray and neutron powder diffraction as well as transmission electron microscopy.
Time-resolved Crystallographic Developments Utilising Detector Gating Techniques
Authors: Warren Mark , Allan Dave , Raithby Paul , Christensen Jeppe , Trincao Jose , Hamilton Michelle , Hatcher Lauren , Thomas Lynne , Pearson Arwen , Marchal Juilien
Published: November 2015

The X-ray scattering process occurs on the time scale of about 10-18 seconds; the complete data collection is in the order of hours at synchrotron sources and consequently gives a time-averaged structure of the crystalline material. Previously on beamline I19 at Diamond Light Source we have used a method which involves mechanically chopping the X-ray beam to produce a pulsed source. The pulsed X-ray beam can then be used to probe the crystal a short period after the sample has been photo-activated by a laser beam. This method can be repeated changing the period between the laser (pump) and X-ray pulse (probe) until the entire time series is obtained. Beamline I19 in collaboration with the Dynamic Structural Sciences Consortium at the Research Complex at Harwell have designed a novel strategy to collect an entire time-series (zero to 100 ms) in one data collection utilising the fast image collection time of the Pilatus detector. The 300K Pilatus detector has a readout out time of 2.7 ms and can be gated down to 200 ns. This means that we can use this gating (instead of the mechanical chopper) to obtain single crystal time-resolved structures. This technique shortens the data collection time and as the entire series is obtained from one crystal during the same data collection, this reduces decay and scaling issues.
Probing the Giant Piezoelectric response of ferroelectric perovskites
Authors: Rouquette Jerome , Hinterstein Manuel , Haines Julien , Knapp Michael , Glaum Julia , Eckert Jurgen , Fuess Hartmud , Dammak Hichem
Published: November 2015

By analogy with ferromagnetism and the hysteresis of the magnetic moment with a magnetic field, materials that exhibit a macroscopic spontaneous polarization Ps, which can be reversed under electric field E were defined as ferroelectrics. Ps, the directional order parameter can give rise to different polar structural phase transitions and finally disappear as a function of temperature T and/or hydrostatic pressure P in a transformation from a non-centrosymmetric to a centrosymmetric space group. The physical properties of ferroelectric materials are the basis of many technological applications based on their hysteretic properties (Ps / E in ferroelectric random access memories) or based on their coupled properties (η (mechanical strain)/ E in piezoelectric applications). In order to understand the origin and the mechanisms associated with the ferroelectric properties, "in-situ" structural studies as a function of E, T and P have to be performed. In addition ferroelectric materials exhibit based on their directional properties (Ps) a particular domain configuration which makes the structural understanding of these compounds much more complex. Different scales should be taken into account: from the atomic scale (individual polar displacements) to the macroscopic scale (macroscopic piezoelectric effect) and finally the mesoscopic scale in between, which is governed by the domain wall motion. High piezoelectric/ferroelectric properties in lead perovskite materials (PZT, PMN, PZN) are structurally linked to strong disorder which can be characterized by the presence of diffuse scattering in diffraction experiments and by nanosized domains. Here we will present "in-situ" characterization in lead perovskite materials as a function of the applied electric field based on X-ray and neutron diffraction and EXAFS techniques. A brief overview of the challenges to solve in future studies as a function of pressure and temperature will also be discussed.
Neutron and X-ray Diffraction from Exotic Magnets in Pulsed Magnetic Fields
Authors: Gaulin Bruce
Published: November 2015

Magnetic fields obtained by discharging a large capacitor bank through Helmholtz coils can be produced in excess of 25 T for relatively short periods of time, ~ 1 msec and longer. When combined with modern facilities for diffraction at modern neutron and synchrotron x-ray sources, one can study the structure and phase diagrams of new materials under extremes of magnetic field. I will present two such studies, each focussing on a new magnetic material which exhibit exotic low temperature states. I will show time-resolved neutron Laue diffraction on the multiferroic magnet MnWO4 [1], and time-resolved synchrotron x-ray studies of large magneto-elastic effects in the geometrically-frustarted pyrochlore magnet Tb2Ti2O7 [2], both in magnetic fields up to ~ 30 T. Such studies of new materials in extreme sample environments can be very revealing as to the nature of their exotic low temperature states.
Structure determination from X-ray powder diffraction data at low resolution
Authors: Xu Hongliang
Published: November 2015

Knowledge of the structural arrangement of atoms in solids is necessary to facilitate the study of their properties. The best and most detailed structural information is obtained when the diffraction pattern of a single crystal a few tenths of a millimeter in each dimension is analyzed, but growing high-quality crystals of this size is often difficult, sometimes impossible. However, many crystallization experiments that do not yield single crystals do yield showers of randomly oriented micro-crystals that can be exposed to X-rays simultaneously to produce a powder diffraction pattern. Direct Methods routinely solve crystal structures when single-crystal diffraction data are available at atomic resolution (1.0-1.2Å), but fail to determine micro-crystal structures due to reflections overlapping and low-resolution powder diffraction data. By artificially and intelligently extending the measured data to atomic resolution, we have successfully solved structures having low-resolution diffraction data that were hard to solve by other direct-method based computation procedures. The newly developed method, Powder Shake-and-Bake, is implemented in a computer program PowSnB. PowSnB can be incorporated into the state-of-the-art software package EXPO that includes powder data reduction, structure determination and structure refinement. The new combination could have potential to solve structures that have never been solved before by direct-methods approach.
Atomic structure of Li2-xMnO3studied by neutron diffraction and STEM
Authors: Wang Fangwei , Li Xiyang Li , He Lunhua , Wang Rui Wang , He Xiaoqing , Gu Lin , Li Hong , Chen Liquan
Published: November 2015

Li2MnO3 is an important cathode material with extra high capacity (>300mAh g-1 for the first charge process). The exact charge-discharge mechanism and the structure evolution still remain controversial. Here the atomic structures of Li2MnO3 after partial delithiation and lithiation are investigated by neutron powder diffraction and spherical aberration-corrected scanning transmission electron microscopy (STEM). Neutron diffraction experiments are performed on Li2-xMnO3 (x=0, 0.25) in a bulk level. It can be found that the volume of the unit cell almost keeps constant, while the lattice constants in the a, b direction increases after the chemical delithiation, but the c direction decreases. For the delithiated compound Li1.75MnO3, the Li occupancies are 0.7(+-0.3), 0.9(+-0.1) for the 2c and 4h sites, respectively, resulting in the Li-concentration of 1.75(+-0.27), while the 2b sites are fully occupied. Furhtermore, the isotropic thermal vibration factors of the 2c and 4h Li atoms are considerably larger than that of the 2b Li atoms, also seemingly implying the feasible delithiation of Li atoms at the 2c and 4h sites in the Li-O layer. It is interesting to note that the thermal factor of Mn atoms is slightly larger than O atoms, which probably means that the Mn atoms are more mobile than O atoms. The STEM results suggest that the Li ions can be extracted both from the LiMn2 planes and Li planes, and the Mn ions can move reversibly in the (110) plane during delithiation and lithiation.
XANES studies of zirconia-ceria/Ni during partial/total methane oxidation
Authors: Bacani Rebeca , Fantini Márcia , Martins Tereza , Larrondo Susana , Lamas Diego
Published: November 2015

Zirconia-ceria solid-solutions are extensively used as promoters for three-way catalysts, in addition, these materials can be used as anodes in solid oxide fuel cells (SOFCs) operated with hydrocarbons. The structural features of ZrO2-CeO2 materials in combination with oxygen storage/release capacity (OSC) are crucial for various catalytic reactions. The direct use of hydrocarbons as fuel for the SOFC (instead of pure H2), without the necessity of reforming and purification reactors can improve global efficiency of the system. The samples preparation method was developed using Zr and Ce chloride precursors, HCl aqueous solution, Pluronic P123, NH4OH and a Teflon autoclave. The samples were dried and calcined, until 540°C. The NiO impregnation was made with an ethanol dispersion of Ni(NO3)×6H2O, calcinated in air until 350°C for 2 hours. In-situ XANES experiments are capable to evaluate the reduction/oxidation potencial of Ni and Ce species in ZrO2-CeO2/Ni samples during partial/total methane oxidation and reduction reactions with H2. The experiments at the Ni K-edge/Ce L3-edge were collected at the LNLS D06A-DXAS beam line in transmission mode, using a Si(111) monochromator and a CCD camera as detector. The data were acquired during a series of temperature programmed reduction steps (TPR), under a 5% H2/He until 600°C, and mixtures of 20%CH4:5%O2/He with 2:1, 1:1 and 1:2 ratios. After each process with CH4 and O2, a TPR procedure was performed in order to evaluate the reduction capacity of the sample after reactions with CH4. The results demonstrated that NiO embedded in the porous ZrO2-CeO2 matrix, reduces at lower temperatures than standard NiO, measured in the same conditions, revealing that the mesoporous support improves the reduction of impregnated NiO. For both edges, there was formation of H2 during partial methane oxidation at 600°C. The total oxidation of methane was observed in lower temperatures (500°C). These results reveal that a high ceria content (90%) could be a great candidate for the SOFC anode.
Tracking chemical reactions with ultrafast X-ray spectroscopies and scattering
Authors: Gawelda Wojciech , Britz Alexander , Assefa Tadesse , Galler Andreas , Vanko György , Sundström Villy , Gaffney Kelly , Nielsen Martin Meedom , Bressler Christian
Published: November 2015

Ultrafast structural dynamics is an emerging field aiming to deliver a detailed understanding of the elementary steps in reacting chemical species, which involve changes in their nuclear, electronic and spin states. Such processes are vital ingredients in chemistry and biology, but also in technological applications, including efficient charge transport in solar energy converters and ultrafast switchable molecular magnets. In order to unravel the complex dynamic behavior in photoexcited molecules we have implemented a suite of ultrafast x-ray spectroscopic and scattering tools to zoom into both the electronic and nuclear structures, with the goal to ultimately deliver a molecular movie of ongoing chemical processes. In view of the many potential applications in chemical and biological dynamics it is desirable to increase the signal-to-noise (S/N) level of such experiments as well as to decrease the time resolution into the femtosecond time domain. We present our benchmark results using a versatile setup that permits simultaneous measurements of ultrafast x-ray absorption and emission spectroscopies combined with x-ray diffuse scattering. This combined scattering and spectroscopic approach has recently been established by us at different synchrotron [1-2] and XFEL [3] lightsources. We applied it to study different photochemical systems in liquid media, ranging from nascent radicals in solution to photocatalytic systems, with the goal to deliver a deeper understanding of the elementary steps in chemical reactivity.
Status and future for time-resolved applications at Japanese XFEL facility SACLA
Authors: Yabashi Makina
Published: November 2015

Following the five-year construction and commissioning, SACLA has started operation for users in March 2012. As typical parameters, SACLA provides XFEL light in a photon energy range from 4 to 15 keV with a pulse energy of 0.5 mJ at 10 keV and a pulse duration less than 10 fs[1a,b]. Various fields of researches, including SFX/CDI, ultrafast chemistry, AMO, HEDS, and X-ray quantum optics are performed [2a]. ~50 proposals are performed per every year. For expanding the capacity, we are constructing new XFEL beamline, which will be open in 2015. For conducting high-resolution time-resolved experiments, it is crucially important for compensating possible timing jitter between XFEL and optical laser pulses. For this purpose, we have developed a timing diagnostic scheme, which utilizes x ray-pumped transient absorption of optical laser in semiconductor. We have evaluated a typical jitter as 130 fs in rms [2b]. Based on the scheme, we are constructing a dedicated system for post-process analysis, which will be operated in the autumn of 2014. We have developed a new scheme for time-resolved absorption spectroscopy, which combines a dispersive spectrometer with a grating-based beam splitter. Following the proof-of-principle test [3 a], we have successfully observed transient absorption signal in iron complex [3 b] in sub-ps resolution. For performing jitter-free X-pump/X-probe experiments, we have developed a two-color double-pulse scheme that uses variable-gap undulators and a small chicane [3 c]. A large and flexible wavelength separation of more than 30% with an ultraprecisely controlled time interval in the attosecond regime was achieved.
Structural determinants of ssDNA- and HIV-1 Vif-binding in APOBEC3F
Authors: Siu Karen , Sultana Azmiri , Azimi Farshad , Lee Jeffrey
Published: November 2015

The human APOBEC3 family of DNA cytosine deaminases serves as a front-line intrinsic immune response to inhibit the replication of diverse retroviruses. APOBEC3F and APOBEC3G are the most potent factors against HIV-1. As a countermeasure, HIV-1 viral infectivity factor (Vif) targets APOBEC3s for proteasomal degradation. Here, we report the crystal structure of the Vif-binding domain in APOBEC3F and a novel assay to assess Vif-APOBEC3 binding. Our results reveal a conserved, amphipathic surface in APOBEC3s that is critical for Vif binding. APOBEC3F-Vif interaction is likely mediated via electrostatic interactions. Moreover, structure-guided mutagenesis reveals a straight ssDNA-binding groove in APOBEC3F, and an `aromatic switch' is proposed to explain the different DNA substrate specificities across the APOBEC3 family. This study opens new lines of inquiry that will further our understanding of APOBEC3-mediated retroviral restriction and provides an accurate template for structure-guided development of inhibitors targeting the APOBEC3-Vif axis.
Physical Analysis of Kidney Stones:Metabolic Basis and Physical Practice
Authors: Kishorkumar Poriya
Published: November 2015

The kidneys play an important role in eliminating waste products from the body. Kidneys are a major source of morbidity and health care expenditure. They play an equally vital role in conservation of salt and water as the regulation of body's "internal environment". The past century has witnessed remarkable technological advances in the treatment and removal of Kidney Stones. Artificial Kidney and transplantation of Kidneys are today's reality, but advanced in prevention have been delayed by the incomplete understanding of what causes of stone formation. It is still unclear that how the Kidney Stones are grown in Kidneys. Investigation of kidney stone is based on urine chemistry, rather than physical analysis of stone itself. Such investigations does not explain the pathophysiology of stone formations. Chemical analysis and investigations can only be determines radical and ions but cannot resolve the crystalline entities. The present communication is an attempt to collect and prepared a huge data base for such samples. Naturally grown and surgically removed kidney stones were collected from various urological hospitals of Gujarat State with prescribe format. Such samples were analyzed with data analysis, and sophisticated physical tools like Scanning Electron Microscopy(SEM), Electron Dispersion Analysis by X-Rays(EDAX), Etching studies of such samples were made using inhibitor drug component as an Etchant.
Application of maximum entropy method to neutron protein crystallography
Authors: Yamamura Shigefumi , Sugawara Yoko
Published: November 2015

Hydrogen atoms or hydrogen bonds play important roles in protein functions. Neutron diffraction is very powerful tool to detect hydrogen atoms. However it is often obtained rather poor resolution data compared with X-ray data due to weak neutron source intensity and large incoherent scattering from hydrogen atoms. The maximum entropy method (MEM) is noble method to obtain high resolution electron or nuclear density distribution from even limited number of diffraction data. The MEM has been applied to not only X-ray data of small molecules but also those of proteins. For the application to neutron data, so far, only small molecules are reported. When preliminary application of the MEM to 1.1 Å resolution partially deuterated neutron protein data (Protein Data Bank ID : 4fc1) is carried out, most of hydrogen and deuterium atoms are observed (Fig. 1). Since this resolution is unusually high, it is of interest that ability of the MEM for usual or low resolution data. In this paper, effects of resolution and data quality for the MEM are examined. Large deuterated crystals are necessary for neutron experiment to reduce incoherent scattering from hydrogen atoms and to improve data resolution. However deuterated condition is not usual for biomolecules. If no deuteration is need for low resolution data by using the MEM, it would be able to observe biomolecules as they are.
Single crystals of Al-rich complex metallic alloys grown by Czochralski method
Authors: Meisterernst Birgitta , Gille Peter
Published: November 2015

In quasicrystal-forming systems very often complex metallic phases exist which show similar structure motifs as the neighbouring quasicrystals but are periodic in all three directions. Therefore these phases are called approximants. They have similar chemical compositions as their parent quasicrystalline phases and can show the same periodicity of stacking of planes as for example found in decagonal quasicrystals. Using the Czochralski method cm3-size single-grain approximants of the Al4TM type, as orthorhombic Al4(Cr,Fe) and hexagonal Al4Cr and of the Al13TM4type, as monoclinic Al13(Co,Ni)4, orthorhombic Al13Co4, monoclinic Al13Fe4and its ternary extensions Al13(Fe,Cr)4and Al13(Fe,Ni)4have been grown from Al-rich solutions [1,2]. The Czochralski method has proven to be a suitable technique for growing single crystals from off-stoichiometric melts due to easy seeding, good mixing of the melt and by allowing good observation of the growth process. To meet the special needs of Al-rich melts a fully metal-sealed growth chamber is used to prevent almost any contact to traces of oxygen. Simultaneously to pulling the change of the liquidus temperature during the growth process has to be compensated by slightly decreasing the temperature using ramps of -(0.1 - 0.8) K/h. For seeding native seeds in different orientations were used. Pulling rates as low as (0.05 - 0.15) mm/h were necessary for growing because of matter transport limits in solution growth and kinetic reasons. Growing the approximant phases the same slow growth kinetics as known from the decagonal quasicrystals was found. Therefore, it might be concluded that the growth of quasicrystalline phases is primarily not limited by the absence of periodicity but by the large clusters that are a common feature in the crystal structures of both, quasicrystals and their approximants.
Phase transition and atomic structure of Cd6Tb 1/1 approximant to quasicrystal
Authors: Liu Dan , Yamada Tsunetomo , Gómez Cesar , Petricek Vaclav , Dusek Michal , Tamura Ryuji , Hiroto Takanobu , Beutier Guillaume , Fertey Pierre , De Boissieu Marc
Published: November 2015

We present an in-situ temperature study of the atomic structure of the 1/1 Cd6Tb approximant to an icosahedral quasicrystal. It belongs to the `Tsai' type family of quasicrystal and approximants whose archetype is the well-studied Cd-Yb system[1]. Its high temperature structure can be described as a bcc packing of a large Tsai atomic cluster, whose inner shell is a disordered tetrahedron at room temperature. As for most of the Cd6RE (RE=rare earth) approximant, the Cd6Tb phase undergoes a phase transition at 190 K to a phase of lower symmetry, resulting from an ordering of the inner tetrahedron[2]. Moreover, it has been shown that this phase undergoes a magnetic phase transition below 20 K, with an antiferromagnetic ordering of the Tb moment bearing atoms. It is thus particularly important to have a detailed structural study of this phase. We have carried out a systematic in situ measurement on a single grain from room temperature down to 40K on the crystal beam line located at the Soleil synchrotron. The structural phase transition is observed at about 190K. Using different attenuation, we have collected integrated intensity in a large dynamical range, leading to more than 60000 unique reflections in the C2/c monoclinic low temperature phase. The final wR2 values for room temperature and 40K are equal to 0.0726 and 0.0905 respectively. The resulting atomic structure will be compared to the well-studied approximant Zn6Sc, which is isostructural to Cd6Tb[3]. The ordering of the innermost tetrahedron leads to the distortion of the successive shells. The evolution of the high temperature phase, in particular just above Tc where pretransitional diffuse scattering is observed will be presented.
Average unit cell for the Generalized Penrose Tiling
Authors: Chodyn Maciej , Kuczera Pawel , Wolny Janusz
Published: November 2015

The Generalized Penrose Tiling (GPT) can be considered a promising alternative for Penrose Tiling (PT) as a model for decagonal quasicrystal refinement procedure, particularly in the statistical approach (also called the Average Unit Cell (AUC) approach) [1]. The statistical method using PT has been successfully applied to the structure optimization of various decagonal phases [2]. The application of the AUC concept to the GPT will be presented. In the higher dimensional (nD) approach, PT is obtained by projecting a 5D hypercubic lattice through a window consisting of four pentagons, called the atomic surfaces (ASs), in the perpendicular space. The vertices of these pentagons together with two additional points form a rhombicosahedron. The GPT is created by projecting the 5D hypercubic lattice through a window consisting of five polygons, generated by shifting the ASs along the body diagonal of the rhombicosahedron. Three of the previously pentagonal ASs will become decagon, one will remain pentagonal and one more pentagon will be created (for PT it is a single point). The structure of GPT will depend on the shift parameter, its building units are still thick and thin rhombuses, but the matching rules and the tiling changes. In the AUC concept the probability distribution for rhombuses of PT can be obtained as an oblique projection of the ASs on the physical space. This holds true also for the GPT. The derivation of the AUC distribution for a given type of rhomb in a given orientation of an arbitrarily chosen GPT will be presented. In the PT, these distributions are triangular, whereas in the case of the GPT they are triangular (originating from the pentagonal AS) or hexagonal (originating from the decagonal AS). The AUC of GPT for shift parameters 0.2 and 0.5 has been calculated. The derivation of the analytical formula for structure factor using AUC formalism, for the decorated GPT is made similarly to the calculation for the PT [3].
In-situ high-temperature diffraction studies of ion-exchanged umbite
Authors: Grieve Stephen , Green Hayley , Hall Reece , Readman Jennifer
Published: November 2015

Microporous materials such as zirconium silicates have the potential to be of importance in the nuclear industry for the selective uptake of cationic radionuclides and environmental pollutants. The structural behaviour of these materials at elevated temperatures is of interest for two reasons, the first is the densification of the exchanged materials prior to long term storage and the second is the formation of new porous phases which may have increased ion exchanged affinity for certain cations. The work presented here focuses on the umbite system. Umbite is a naturally occurring microporous zirconium titanium silicate found in northern Russia and synthetic analogues, K2ZrSi3O9·H2O, can be prepared using hydrothermal methods. It has an orthorhombic cell with a = 10.2977(2)Å, b = 13.3207(3)Å and c = 7.1956(1)Å. The ion-exchange of umbite with cations such as rubidium, caesium and strontium and the structures of the resulting exchanged materials have been studied. Exchanges with certain cations were found to cause a change in crystal system to a monoclinic cell. Recently Rocha and co-workers found that synthetic umbite will undergo a topotactic transformation when heated 9100C to form a new microporous zirconium silicate (AV-15) with the formula K2ZrSi3O9·2H2O, but to date no in-situ work has been carried out on this phase transition. In this work the high temperature structural behaviour of five umbite samples with different exchanged cations (K+, Na+, Mg2+Ca2+and Cu2+) was studied up to a temperature of 10000C. All samples behaved very differently, indicating that the nature and location of the charge balancing cation plays an important part in determining which high temperature phases are formed. Certain general trends were observed, with group 1 cations the samples remain crystalline to high temperatures. With group 2 cations dense phases are formed at high temperatures and with transition metal cations there is a loss of crystallinity at low temperature.
New representatives of solid acid conductors: CsmHn((HSO4),(H2PO4))m+n
Authors: Makarova Irina , Grebenev Vadim , Dmitricheva Elena , Komornikov Vladimir
Published: November 2015

Crystals - superprotonics are extensively studied with the goal of elucidating the influence of the hydrogen subsystem on the physicochemical properties and designing new functional materials. As opposed to other hydrogen-containing compounds, phase transitions in these crystals are accompanied by a hydrogen-bond network rearrangement, resulting in radical changes of their properties, in particular, in the appearance of proton conductivity about 10–1 Ω–1 cm–1. These crystals are unique in the class of proton conductors, since the superprotonic conductivity is related to the structural features of these compounds rather than to the presence of doping additives. The occurrence of high superprotonic conductivity in the Me3H(XO4)2 (Me = K, Rb, Cs, NH4; X = S, Se, P, As) crystals is associated with the formation of a qualitatively new and dynamically disordered hydrogen-bond system [1]. In K9H7(SO4)8·N2O crystals, the only known representative of the Me9H7(XO4)8·xN2O family, the occurrence of high conductivity is associated with the outward diffusion of water molecules, the hydrogen-bond network rearrangement, and the formation of channels for the possible motion of K+ ions [2]. The hydrogen-bond rearrangement and the hindered back diffusion of water to the crystal bulk stabilize the high-temperature crystal structure and ensure its supercooling to low temperatures. The new crystals of Cs3(HSO4)2(H2PO4), Cs4(HSO4)3(H2PO4) and Cs6H(HSO4)3(H2PO4)4 were grown up in the CsHSO4–CsH2PO4-H2O system - enough big, with good optic quality [3]. The thermal and optical properties of crystals as well as their conductivity have been investigated in the temperature range 295 – 445 K. It was observed superprotonic phase transitions at 409, 411 and 365 K correspondingly. The distinction in the properties of Cs3(HSO4)2(H2PO4) and Cs4(HSO4)3(H2PO4) (sp. gr. C2/c at 295 K) is related to differences in nets of hydrogen bonds formed between different-occupied XO4 tetrahedra. Cs6H(HSO4)3(H2PO4)4 srystals (sp. gr. I-43d at 295 K) have the net of hydrogen bonds which is completely different. After cooling the high-temperature superprotonic phase preserves long enough without essential decrease in conductivity. This study was supported by the Russian Foundation for Basic Research (projects 13-03-12216 and 13-02-92693).