Journal of Synchrotron Radiation

Published by International Union of Crystallography
Online ISSN: 1600-5775
Publications
Article
Long horizontal parallel slits with angular apertures of 0.032 and 0.065 degrees were constructed for powder diffraction experiments with synchrotron radiation. They have been tested at the BL-4B experimental station at the Photon Factory by using a monochromated beam with a wavelength of 1.528 A. The horizontal parallel slits with the smaller aperture gave a full-width at half-maximum of 0.030 (1) degrees for the (200) reflection from CeO(2) and an intensity about one order of magnitude higher than that obtained with a receiving slit in the same angular resolution, demonstrating the finest horizontal parallel slits developed so far. The misalignment of the horizontal parallel slits does not affect the intensity whilst it shifts the Bragg-peak positions systematically.
 
Article
The use of soft X-rays near the carbon edge of absorption (270–300 eV) greatly enhances studies in various branches of science. However, the choice of reflecting coatings for mirrors operating in free-electron and X-ray free-electron laser (FEL and XFEL) beamlines in this spectral range is not so evident and experimental justifications of the mirror efficiency are rather limited. In the present paper it is demonstrated experimentally that the reflectivity of B 4 C- and Ni-coated grazing-incidence mirrors is high enough for their operation in FEL or XFEL beamlines near the carbon K -edge of absorption. The minimal reflectivity of both mirrors proves to exceed 80% near the carbon absorption edge at a grazing angle of 0.6°. An in-depth profile of the chemical elements composing the reflecting coatings is reconstructed based on analysis of a set of reflectivity curves measured versus the grazing angle at different photon energies in the soft X-ray spectral region. This allows us to predict correctly the mirror reflectivity at any X-ray energy and any grazing angle.
 
Article
Reliable knowledge of the complex x-ray form factor [Re(f) and f″] and the photoelectric attenuation coefficient (σPE) is required for crystallography, medical diagnosis, radiation safety, and XAFS studies. Discrepancies between currently used theoretical approaches of 200% exist for numerous elements from 1 to 3 keV x-ray energies. The key discrepancies are due to the smoothing of edge structure, the use of nonrelativistic wave functions, and the lack of appropriate convergence of wave functions. This paper addresses these key discrepancies and derives new theoretical results of substantially higher accuracy in near-edge soft x-ray regions. The high-energy limitations of the current approach are also illustrated. The energy range covered is 0.1 to 10 keV. The associated figures and tabulation demonstrate the current comparison with alternate theory and with available experimental data. In general, experimental data are not sufficiently accurate to establish the errors and inadequacies of theory at this level. However, the best experimental data and the observed experimental structure as a function of energy are strong indicators of the validity of the current approach. New developments in experimental measurement hold great promise in making critical comparisons with theory in the near future.
 
Article
A fast multigrid ion chamber for the detection of fluorescent X-rays has been developed. The structure of 17 grids with close separation was employed to maximize the time response as well as to give sufficient detection efficiency. The measured rise/fall response time to cyclic X-rays was shorter than that of an existing three-grid ion chamber by more than one order of magnitude. A 0.13 ms time response was obtained at the 500 V applied voltage, where the detector can stably operate without any discharge. The available frequency range is as high as 1 kHz with a practical amplitude response.
 
Article
The present status and accuracy of determining the electron momentum density from experimental Compton profiles is reviewed. The new spectrometers operating at third-generation synchrotron radiation sources have made possible measurements with 0.1% statistical accuracy at the Compton peak. A comparable accuracy of the Compton profiles is achieved only after careful corrections for departures from the impulse approximation, effects of multiple scattering, and variations in the analyser response function. Detailed descriptions are given of the correction procedures applied to the data collected by the Johann-type scanning spectrometer that is one of the Compton spectrometers in use at the ESRF. Special attention is paid to the calculation and correction of the glitches that are caused by extra reflections of the analyser crystal. The Fourier transform of the Compton profile, the reciprocal form factor, is calculated, and its use in data treatment and presentation is discussed.
 
Data-processing statistics.
Article
To bridge the gap between traditional multilayer and crystal optics a high-resolution multilayer monochromator with a bandwidth of 0.22% has been designed and installed on a bending-magnet beamline (F3) at the Cornell High Energy Synchrotron Source (CHESS) to provide an unfocused monochromatic X-ray beam for protein crystallography experiments. Crystallographic data of excellent quality from a medium-sized protein, Concanavalin A, were collected and processed using standard crystallographic programs. The data were successfully used for a structure solution and refinement. The flux from the multilayer monochromator is enhanced, relative to that from a flat Si(111) monochromator, by a factor of 5; consequently, data collection is faster and/or smaller samples may be used. At the same time, the bandwidth is narrow enough to avoid streaked spots. This experiment suggests that multilayer optics may play a valuable role in satisfying the demands of the structural biology community for rapid X-ray data collection, particularly at under-utilized bending-magnet beamlines.
 
Article
A novel processing scheme has been developed that allows for the single step processing of nanostructured complex oxides. This approach involves the high energy ball-milling (HEBM) of binary oxide precursors to form pure phase complex oxides at low-temperatures. Using this technique we have prepared La0.67Ca0.33MnO3-delta and studied the evolution of short range and long-range order, using EXAFS and XRD respectively, as a function of milling lime during the solid state transformation. Transport properties of the milled perovskites are also discussed.
 
Mn 2p X-ray absorption spectra for (a) La 0.46 Sr 0.54 MnO 3 and (b) Nd 0.46 Sr 0.54 MnO 3 . The vertical dashed line indicates the absorption edge, which corresponds to E F in metallic samples. A large increase in the intensity just above E F with decreasing temperature was observed only for La 0.46 Sr 0.54 MnO 3 .  
Temperature dependence of the HeI UPS valence band spectra for (a) (La 0.8 Nd 0.2 ) 0.46 Sr 0.54 MnO 3 and (b) Nd 0.46 Sr 0.54 MnO 3 . The backgrounds were subtracted by using the Shirley method, and the spectra were normalized by the maximum intensity. A large change in the shape of the spectrum at about 4±6 eV, which is indicated as the energy-range between the dotted lines, occurred across T C = 260 K only for (La 0.8 Nd 0.2 ) 0.46 Sr 0.54 MnO 3 .  
Article
High-resolution HeI photoemission spectroscopy (UPS), Mn 2p-3d resonant photoemission spectroscopy (RPES) and Mn 2p X-ray absorption spectroscopy (XAS) have been performed to investigate the electronic structure and its effect on the electrical resistivity in (La(1-z)Nd(z))(0.46)Sr(0.54)MnO(3) (z = 0, 0, 2, 0.6 and 1.0). It was found that in the UPS and RPES spectra the Fermi edge persisted over the temperature range 15 < or = T < or = 340 K regardless of the magnetic structure or the composition of the samples. The density of states at the Fermi level [N(E(F))] in the samples where 0 < or = z < or = 0.6 was increased drastically at the Curie temperature (T(C)) with decreasing temperature, but essentially kept unchanged across the Néel temperature (T(N)). A fairly large reduction at T(C) and a small increase at T(N) in the electrical resistivity with decreasing temperature are found to be well accounted for in terms of the temperature dependence of N(E(F)). The presence of a finite N(E(F)) in the insulating Nd(0.46)Sr(0.54)MnO(3) was also found. Thus the origin of the insulating behavior in this sample can be regarded as the Anderson localization associated with the small density of states and the chemical disorder between Nd and Sr.
 
Temperature-dependent MSRD of the Fe-As and Fe-Fe pairs (symbols) for Ba 0.5 K 0.5 (Fe 1-x TM x ) 2 As 2 compounds as a function of Mn/Zn doping concentrations and their simulations using the classical Einstein model (dotted lines).
Article
To clarify the contrasting impurity effects of Mn and Zn dopants on the critical temperature of optimally doped Ba0.5K0.5Fe2As2 superconductors, extended X-ray absorption fine-structure spectroscopy was implemented at the Fe and As K-edge. In Mn-doped compounds a gradual deviation of the symmetric FeAs4 tetrahedron and weakening of the Fe-As bond was observed. Conversely, in Zn-doped compounds the perfect FeAs4 tetrahedron is maintained and the Fe-As bond is rigid. The local structural details are consistent with the development of superconductivity in these two systems, suggesting a significant role played by the topology of the FeAs4 tetrahedron and rigidness of the Fe-As bond in Mn/Zn-doped Ba0.5K0.5Fe2As2 superconductors.
 
Article
Recently it was shown experimentally that regular arrays of tiny prisms can be used as X-ray monochromators providing a spectral bandwidth of below 2%. Successively the measured spectral transmission functions of monochromators operated under different conditions were found to be in agreement with expectations within an analytical model. This type of monochromator focuses chromatically and thus necessitates the use of an exit slit for the monochromatization. This contribution will show that the lower limit for the achievable bandpass can be predicted under practically feasible experimental conditions. Refractive monochromators based on prism arrays are found to be feasible solutions for monochromatization with high transmission to a spectral bandwidth of the order of 0.5%. The bandwidth can easily be increased by adjusting the exit slit setting accordingly. Consequently, the presented refractive devices would make for tunable monochromators with tunable bandwidth, which provides more flexibility for an intermediate bandwidth of <1%, which multilayer monochromators have difficulty providing routinely.
 
Article
The effect of dynamical interactions between reflections involved in 000/111/220 multiple diffraction by an In(0.5)Ga(0.5)P/GaAs heteroepitaxial structure was observed, which significantly increases the intensity of the (111) reflection in the region of the total (220) reflection from the substrate during Renninger-like scanning. The amplitude of the peak is roughly five times as great as the peak of detoured excitation for ideal GaAs. Possible applications of the observed feature in synchrotron-radiation-based studies are discussed.
 
Article
The use of temperature-gradient analyzers for non-resonant high-resolution inelastic X-ray scattering is investigated. The gradient compensates for geometrical broadening of the energy resolution by adjusting the lattice spacing of the analyzer crystal. Applying a ∼12 mK temperature gradient across a 9.5 cm analyzer, resolutions of 0.75 (2) meV FWHM at 25.7 keV for Si(13 13 13) and 1.25 (2) meV at 21.7 keV for Si(11 11 11) were measured, while retaining large (250 mm) clearance between the sample position and detector, and reasonable (9.3 mrad × 8.8 mrad) analyzer acceptance. The temperature control and stability are discussed.
 
Article
Thin Co films (1-8 nm) were directly, sequentially, and co-deposited with Si (3.6-29.2 nm) on the (square root of 3 x square root of 3)-R30 degrees reconstruction of 6H-SiC(0001). The films were annealed over a temperature range of 823-1373K and investigated with XAFS, XPS, AES and AFM. After annealing up to 1373K directly deposited Co films do not transform entirely to cobalt disilicide and C segregation is observed on the surface of the films. On the other hand, sequentially and co-deposited films do form cobalt disilicide after annealing at 823K, but also show islanding after annealing at 923K.
 
Article
We present temperature-dependent measurements via the element-specific XMCD technique for Co/Cu/Ni trilayers for cases where the ordering temperature of Co is lower than the one of Ni. Our work focuses mainly on the influence of the interlayer coupling on the shape of the temperature-dependent magnetization curves of Ni. By electing 1.3 ML of Co and 4 ML of Ni we get a lower T(C)(Co) approximately 90 K and a higher T(C)(Ni) approximately 180 K. The crossing of the M(T) curves leads to a rotation of the remanent magnetization of Ni. A case where the sublayer magnetizations change gradually their angle as a function of the temperature is recorded and attributed to a competition between coupling and anisotropy mechanisms.
 
Article
Using X-ray Magnetic Circular Dichroism, the spin and orbital magnetic moments were determined through the sum rules for ultrathin (2-4 ML) films of 3d elements on Cu(001). The fct Co ultrathin films, contrary to the fct Ni, show an enhancement of the orbital moment. The influence of direct coupling in Fe/Ni and Co/Fe bilayers is investigated. In Fe/Ni, an enhancement of the Ni (15 ML) orbital moment is observed. The easy axis of the Fe (3 ML) magnetisation changes from out of plane to in plane by capping it with Co.
 
Article
Three-dimensional images of the near-surface atom arrangement were calculated from two-dimensional photoelectron diffraction data by several imaging algorithms: (i) a basic method with a Fourier transformation at one kinetic energy over k space, considering the phase factor due to the path-length difference; (ii) energy summation of the above results; (iii) Fourier transformation within small k-space windows; and (iv) their combinations. Atomic images produced by these methods from the experimental Si 2p photoelectron diffraction patterns of an Si(001) surface are compared with the crystal geometry. The results show that the energy-summed small-window method, called SWEEP, gives the best images.
 
EXAFS multishell fits results for the parallel and perpendicular polari- sations First neighbor distancesÅdistances˚distancesÅ 2 ˚ A 2
Article
Diffraction Anomalous Fine Structure (DAFS) and EXAFS measurements have been performed on a (Fe0.7Mn0.3)/Ir(100)40 super-lattice at the K-edges of Fe and Mn. Theoretical EXAFS spectra have been refined: a slight difference in the first neighbor distance suggests a non homogeneous distribution of the Mn in the alloy. The smooth features of the DAFS spectra have been modeled to study the composition and the strain profile along the growth axis.
 
GISAXS patterns of Si-capped Ge nanodots in SX and HX regions. (a) ' = 0 for SX, (b) ' = 22.5 for SX, (c) ' = 0 for HX, (d) ' = 22.5 for HX.
Schematic illustration of the spatial alignment of nanodots and the corresponding structure function used in the present model calculation; the grey area represents the probability distribution of the Ge nanodot location.
Article
Grazing-incidence small-angle X-ray scattering (GISAXS) measurements with soft X-rays have been applied to Ge nanodots capped with a Si layer. Spatially anisotropic distribution of nanodots resulted in strongly asymmetric GISAXS patterns in the q y direction in the soft X-ray region, which have not been observed with conventional hard X-rays. However, such apparent differences were explained by performing a GISAXS intensity calculation on the Ewald sphere, i.e. taking the curvature of Ewald sphere into account.
 
Article
Using the In-L fluorescence produced by normal-incidence X-ray standing waves, we have measured the layer perfection and positions of 1 and 1/2 monolayer (ML) InAs quantum wells buried in GaAs(001). Growth temperature effects were studied in a series of samples produced by metalorganic vapor phase epitaxy (MOVPE) at temperatures between 400 and 600 degrees C. The coherent position of the In atoms decreases with temperature in the 1 ML samples, and the optimal growth temperature is near 550 degrees C, as evidenced by the coherent position of 1.15+/-0.02, and the relatively high coherent fraction of 0.72+/-0.08. These results are corroborated by 1.6 K photoluminescence (PL) measurements in which the most sharp and intense In-excitonic emission is obtained from a sample grown at 530 degrees C. For the 1/2 ML samples, growth temperatures of 400 degrees C and 600 degrees C produce similar standing wave results: coherent positions of 1.09+/-0.02 and 1.10+/-0.02, coherent fractions of 0.75+/-0.10 and 0.74+/-0.11, respectively. However, PL reveals the higher temperature sample to be of far superior quality, due to excessive carbon incorporation at 400 degrees C.
 
Article
The X-ray lithography beamline on Indus-2 is now operational, with two modes of operation. With a pair of X-ray mirrors it is possible to tune the energy spectrum between 1 and 20 keV with a controlled spectral bandwidth. In its `no optics' mode, hard X-rays up to 40 keV are available. Features and performance of the beamline are presented along with some example structures. Structures fabricated include honeycomb structures in PMMA using a stainless steel stencil mask and a compound refractive X-ray lens using a polyimide-gold mask in SU-8.
 
Article
Beamline 08B1-1 is a recently commissioned bending-magnet beamline at the Canadian Light Source. The beamline is designed for automation and remote access. Together with the undulator-based beamline 08ID-1, they constitute the Canadian Macromolecular Crystallography Facility. This paper describes the design, specifications, hardware and software of beamline 08B1-1. A few scientific results using data obtained at the beamline will be highlighted.
 
Article
It is now possible to perform X-ray absorption spectroscopy (XAS) on metalloprotein crystals at the Canadian Macromolecular Crystallography Facility bend magnet (CMCF-BM) beamline (08B1-1) at the Canadian Light Source. The recent addition of a four-element fluorescence detector allows users to acquire data suitable for X-ray absorption near-edge structure and extended X-ray absorption fine-structure based studies by monitoring fluorescence. CMCF beamline users who wish to supplement their diffraction data with XAS can do so with virtually no additional sample preparation. XAS data collection is integrated with the established Mx Data Collector software package used to collect diffraction data. Mainstream XAS data-processing software packages are available for the users; assistance with data processing and interpretation by staff is also available upon request.
 
Article
Beamline 08ID-1 is the prime macromolecular crystallography beamline at the Canadian Light Source. Based on a small-gap in-vacuum undulator, it is designed for challenging projects like small crystals and crystals with large cell dimensions. Beamline 08ID-1, together with a second bending-magnet beamline, constitute the Canadian Macromolecular Crystallography Facility (CMCF). This paper presents an overall description of the 08ID-1 beamline, including its specifications, beamline software and recent scientific highlights. The end-station of the beamline is equipped with a CCD X-ray detector, on-axis crystal visualization system, a single-axis goniometer and a sample automounter allowing remote access to the beamline. The general user program is guaranteed up to 55% of the useful beam time and is run under a peer-review proposal system. The CMCF staff provide `Mail-in' crystallography service to the users with the highest-scored proposals.
 
Article
Ruddlesden-Popper phase, La(n+1)Ni(n)O(3n+1 (n=1, 2, and infinity) compounds were prepared by citrate sol-gel method. We revealed the origin of the variation of the electrical conductivities in La(n+1)Ni(n)O(3n+1 (n=1, 2, and infinity) using resistivity measurements, Rietveld analysis, and X-ray absorption spectroscopy. According to the XANES spectra, it is found that the degree of 4p(pi) - 4psigma energy splitting between 8345 eV and 8350 eV is qualitatively proportional to the elongation of the out-of-plane Ni-O bond length. With the decrease of 4p(pi) - 4psigma splitting, the strong hybridization of the sigma-bonding between Ni-3d and O-2p orbitals creates narrow antibonding sigma* bands, which finally results in the lower electrical resistivity.
 
Article
The saccharification process is essential for bioethanol production from woody biomass including celluloses. Cold-adapted cellulase, which has sufficient activity at low temperature (<293 K), is capable of reducing heating costs during the saccharification process and is suitable for simultaneous saccharification and fermentation. Endo-1,4-β-glucanase from the earthworm Eisenia fetida (EF-EG2) belonging to glycoside hydrolase family 9 has been shown to have the highest activity at 313 K, and also retained a comparatively high activity at 283 K. The recombinant EF-EG2 was purified expressed in Pichia pastoris, and then grew needle-shaped crystals with dimensions of 0.02 × 0.02 × 1 mm. The crystals belonged to the space group P3221 with unit-cell parameters of a = b = 136 Å, c = 55.0 Å. The final model of EF-EG2, including 435 residues, two ions, seven crystallization reagents and 696 waters, was refined to a crystallographic R-factor of 14.7% (free R-factor of 16.8%) to 1.5 Å resolution. The overall structure of EF-EG2 has an (α/α)6 barrel fold which contains a putative active-site cleft and a negatively charged surface. This structural information helps us understand the catalytic and cold adaptation mechanisms of EF-EG2.
 
Article
The Ser/Thr kinase CK2 consists of two catalytic subunits (CK2α) and a dimer of the regulatory subunits (CK2β), and is a ubiquitous enzyme that regulates growth, proliferation and the survival of cells. CK2 is a remarkable drug target for potentially treating a wide variety of tumours and glomerulonephritis. The purified CK2α protein was crystallized using ethylene glycol as a precipitant. The crystal structure of CK2α with 21 loci of alternative conformations, including a niacin, 19 ethylene glycols and 346 waters, was determined at 1.06 Å resolution to an R work of 14.0% (R free = 16.5%). The alternative ensemble in the internal hydrophobic core underpins the plasticity of the αD-helix responsible for the regulation of ATP/GTP binding. The clear density map indicates that a niacin molecule, contained in the Escherichia coli culture medium, binds to the ATP binding site. An ethylene glycol molecule binds in the hydrophobic pocket lateral to the αD-helix forming the rim of the active site. The other ethylene glycol molecules occupy physiologically significant sites, including the CK2β binding interface and substrate binding site, as well as the gap in the crystal packing. Together with water molecules in the active site, these structural insights should facilitate drug discovery.
 
Article
The crystal and local atomic structure of monoclinic ReO2 (alpha-ReO2) under hydrostatic pressure up to 1.2 GPa was investigated for the first time using both X-ray absorption spectroscopy and high-resolution synchrotron X-ray powder diffraction and a home-built B4C anvil pressure cell developed for this purpose. Extended X-ray absorption fine-structure (EXAFS) data analysis at pressures from ambient up to 1.2 GPa indicates that there are two distinct Re-Re distances and a distorted ReO6 octahedron in the alpha-ReO2 structure. X-ray diffraction analysis at ambient pressure revealed an unambiguous solution for the crystal structure of the alpha-phase, demonstrating a modulation of the Re-Re distances. The relatively small portion of the diffraction pattern accessed in the pressure-dependent measurements does not allow for a detailed study of the crystal structure of alpha-ReO2 under pressure. Nonetheless, a shift and reduction in the (011) Bragg peak intensity between 0.4 and 1.2 GPa is observed, with correlation to a decrease in Re-Re distance modulation, as confirmed by EXAFS analysis in the same pressure range. This behavior reveals that alpha-ReO2 is a possible inner pressure gauge for future experiments up to 1.2 GPa.
 
Article
The fully ordered high-pressure crystal structure of cyclopentanol (C5H10O) has been solved using single-crystal X-ray diffraction techniques on station 9.8 at the SRS Daresbury Laboratory. At pressures above 1.5 GPa, cyclopentanol crystallizes in the monoclinic P2(1)/c space group with a=17.882 (3), b=5.4573 (3), c=9.6817 (14) A, beta=104.699 (8) degrees and Z'=2. The crystal structure is characterized by the formation of hydrogen-bonded molecular chains, denoted C_2;2(4) in graph set notation, which lie parallel to the crystallographic c-axis, with the molecules adopting a pseudo fourfold arrangement around the central core of hydrogen bonds.
 
Article
The crystal structure of a brominated oligonucleotide d(CGCG(Br)CG), chemical formula C(114)N(48)O(68)P(10)Br(2), has been analysed by multiwavelength anomalous dispersion (MAD) methods. The oligonucleotide crystallizes in space group P2(1)2(1)2(1) with a = 17.97, b = 30.98, c = 44.85 A, alpha = beta = gamma 90 degrees . Data to a resolution of 1.65 A were collected at four wavelengths about the K-absorption edge of the bromine atom (lambda(1) = 0.9323 A, a reference wavelength at the long-wavelength side of the edge; lambda(2) = 0.9192 A, at the absorption-edge inflection point; lambda(3) = 0.9185 A, at the ;white line' absorption maximum; lambda(4) = 0.8983 A, a reference wavelength at the short-wavelength side) using synchrotron radiation at Station PX9.5, SRS, Daresbury. Multiwavelength data could be collected on a single-crystal as the sample was radiation stable. Anomalous and dispersive Patterson maps were readily interpretable to give the bromine anomalous scatterer positions. Phase calculations to 1.65 A, resolution, using all four wavelengths, gave a figure of merit of 0.825 for 2454 reflections. The electron-density map was readily interpretable showing excellent connectivity for the sugar/phosphate backbone and each base was easily characterized. The two nucleotide strands paired up as expected in an antiparallel Watson-Crick-type manner. The structure was refined to 1.65 A using all the data (R-factor = 17.0% based on 3151 reflections, with a data-to-parameter ratio of 2.6). In addition to the four-wavelength analysis, a variety of other phasing strategies, and the associated quality of the resulting electron-density maps, were compared. These included use of either of the reference wavelength data sets in the two possible three-wavelength phasing combinations to assess their relative effectiveness. Moreover, the time dependence upon measuring the Bijvoet differences and its effect upon phasing was also investigated. Finally, the use of only two wavelengths, including Friedel pairs, is demonstrated (the theoretical minimum case); this is of particular interest when considering overall beam time needs and is clearly a feasible experimental strategy, as shown here.
 
Data collection statistics for SMS Hb. Values in parentheses are for the highest-resolution shell. 
Article
Haemoglobin (Hb) is a tetrameric iron-containing protein that carries oxygen from the lungs to tissues and carbon dioxide from tissues back to the lungs. Pisces are the advanced aquatic vertebrates capable of surviving at wide depth ranges. The shortfin mako shark (SMS) is the pelagic, largest, fastest and most sophisticated species of the shark kingdom with well developed eyes. Mostly the pisces species are cold blooded in nature. Distinctly, the SMSs are warm-blooded animals with an advanced circulatory system. SMSs are capable of maintaining elevated muscle temperatures up to 33 K above the ambient water temperatures at a depth of 150-500 m. SMSs have a diverged air-breathing mechanism compared with other vertebrates. The haemoglobin molecule consists of four polypeptide chains, namely two α chains, each with 140 amino acids and two β chains each having 136 amino acids. The SMS Hb was found to crystallize in monoclinic space group P21 using the hanging-drop vapour-diffusion method at room temperature. The crystal packing parameters for the SMS Hb structure contain one whole biological molecule in the asymmetric unit with a solvent content of 47%. The SMS Hb quaternary structural features interface-interface interactions and heme binding sites are discussed with different state Hbs and the results reveal that SMS Hb adopts an unliganded deoxy T state conformation.
 
Article
Beamline 10.3.2 at the ALS is a bend-magnet line designed mostly for work on environmental problems involving heavy-metal speciation and location. It offers a unique combination of X-ray fluorescence mapping, X-ray microspectroscopy and micro-X-ray diffraction. The optics allow the user to trade spot size for flux in a size range of 5-17 microm in an energy range of 3-17 keV. The focusing uses a Kirkpatrick-Baez mirror pair to image a variable-size virtual source onto the sample. Thus, the user can reduce the effective size of the source, thereby reducing the spot size on the sample, at the cost of flux. This decoupling from the actual source also allows for some independence from source motion. The X-ray fluorescence mapping is performed with a continuously scanning stage which avoids the time overhead incurred by step-and-repeat mapping schemes. The special features of this beamline are described, and some scientific results shown.
 
Comparison of HK97 tetragonal crystal reflections recorded (A) without and (B, C) with convergent focusing optics. The maximum resolutions of images A, B, and C were 4.5 A ˚ , 5.6 A ˚ and 3.8 A ˚ , respectively.
Article
Studies of icosahedral virus capsids provide insights into the function of supramolecular machines. Virus capsid crystals have exceptionally large unit cells; as a result, they diffract weakly compared with protein crystals. HK97 is a dsDNA lambda-like bacteriophage whose 13 MDa capsid expands from 550 A to 650 A with large subunit conformational changes during virus maturation. The HK97 penultimate maturation intermediate was crystallized in a tetragonal unit cell that has lattice constants of 1010 A x 1010 A x 730 A. The crystals could be cryoprotected, but diffracted to a modest resolution of 5 A at a bending-magnet beamline. When these crystals were optimally exposed with two orders-of-magnitude more photons from a new insertion-device beamline, data extending to better than 3.8 A resolution were obtained. Here, the strategies to collect and process such data are described. These strategies can be adapted for other crystals with large unit cells and for microcrystals.
 
Article
Some points concerning the characteristics of the X-ray simulation code SHADOW [Welnak et al. (1994). Nucl. Instrum. Methods, A347, 344-347] are clarified which are not correctly mentioned by Yamada et al. [J. Synchrotron Rad. (2001), 8, 1047-1050]. It is shown that, contrary to the Authors' statement, some functionality of their new program is not original. In particular, we show that SHADOW can deal correctly with crystal monochromators.
 
Article
An X-ray beam of 3 x 10(7) photons s(-1) with 2 x 10(8) relative energy resolution has been obtained at a third-generation synchrotron undulator X-ray source using the (13 13 13) Bragg reflection from a silicon perfect crystal. The production of these 25.70 keV X-rays with 450 +/- 50 mueV bandpass opens up new possibilities in X-ray optics and spectroscopies.
 
Article
The high-quality aspects of magnified X-ray images recorded using MIRRORCLE-6X are reported. MIRRORCLE-6X is inherently suitable for hard X-ray imaging owing to its magnified projection X-ray imaging, micrometre-size X-ray source point, wide radiation emission angle, X-ray spectrum ranging from 10 keV to 6 MeV, natural refraction contrast imaging and high flux output. Images produced with 11x geometrical magnification display a sharply enhanced edge effect when generated using a 25 microm rod electron target. Image contrast is enhanced 2x owing to refraction when compared with absorption contrast images. An imitation tumour implanted in a human chest phantom was made clearly visible by using edge enhancement on images. Soft tissue becomes highly visible as a natural consequence of refraction contrast when using hard X-rays for imaging. The authors believe that novel imaging provided by MIRRORCLE makes it a superior instrument for medical diagnosis.
 
Article
In this study, five epitaxial [Co(t nm)/Pt(1 nm)]30, multilayer samples (t=0.16-1.07 nm) were studied using polarized X-ray absorption spectroscopy method. These samples were prepared on Mo(110)/ Al2O3(11-20) substrates by MBE technique. The results show that the Co layer is more like an fcc pseudomorphic structure for the Co thickness of less than 0.3 nm. For Co layer thickness of 1 nm, the first shell distance is 0.25 nm, which is very close to the Co-Co distance of bulk hcp Co. On the other hand, for Co layer of less than 0.3 nm, the in plane first shell distance is expanded by 4% and most of the neighboring atoms are Pt atoms. The fitting results of the Co/Pt multilayers seem to support a sharp boundary model rather than an interdiffusion model.
 
Article
W 4f core-level spectra of Gd films on W(110) show components which can be identified as being due to bulk and interface W. The results suggest that the W/Gd interface is abrupt, i.e. no interface alloying occurs. At submonolayer coverages a further component is seen which is attributable to intermediate (n x 2) phases.
 
Article
The two-dimensional electronic band structure of monolayer Bi on GaP(110) has been mapped using angle-resolved UV photoelectron spectroscopy (ARUPS) with synchrotron radiation. Surface photovoltage effects are corrected for by simultaneous second-order core spectroscopy. From valence-band spectra along the four symmetry directions of the surface Brillouin zone at three photon energies it is possible to distinguish three states as surface related. The topmost band is found to be inside the fundamental band gap, at ca 0.75 eV above the bulk valence-band maximum. Comparison with other V/III-V(110) systems shows that this system is not significantly different, despite the relatively large size of the Bi atoms with respect to the GaP lattice; in a selective comparison with InP and GaAs it would appear that Bi-substrate anion bonding is a more important factor than strain.
 
Article
Cu K-edge XAFS of Cu/TiO2(110) was measured by polarization-dependent total-reflection fluorescence XAFS technique. XAFS of [001], [110], and [110] directions were measured to elucidate the three dimensional structure of Cu species on the TiO2(110) surface prepared by the deposition of Cu(DPM)2 followed by reduction with H2. Simulation of the EXAFS functions as well as conventional curve fitting analysis revealed that plane Cu3,4 small clusters with similar structure to Cu(111) plane were formed by the reduction at 363 K. The small clusters converted into spherical metallic Cu particles by the reduction at 473 K.
 
Article
A new X-ray diffraction technique has been developed in order to measure the strain field near a solid surface under ultrahigh vacuum (UHV) conditions. The X-ray optics use an extremely asymmetric Bragg-case bulk reflection. The glancing angle of the X-rays can be set near the critical angle of total reflection by tuning the X-ray energy. Using this technique, rocking curves for Si surfaces with different surface structures, i.e. a native oxide surface, a slightly oxide surface and an Si(111) 7 x 7 surface, were measured. It was found that the widths of the rocking curves depend on the surface structures. This technique is efficient in distinguishing the strain field corresponding to each surface structure.
 
Article
A study of the coherence and wavefront properties of a pseudo-channel-cut monochromator in comparison with a double-crystal monochromator is presented. Using a double-grating interferometer designed for the hard X-ray regime, the complex coherence factor was measured and the wavefront distortions at the sample position were analyzed. A transverse coherence length was found in the vertical direction that was a factor of two larger for the channel-cut monochromator owing to its higher mechanical stability. The wavefront distortions after different optical elements in the beam, such as monochromators and mirrors, were also quantified. This work is particularly relevant for coherent diffraction imaging experiments with synchrotron sources.
 
Article
The adsorption of 1-butanethiol on Cu(111) and square root of 7 x square root of 7 R19.1 degrees S/Cu(111) surfaces has been studied by S K-edge near edge X-ray absorption fine structure (NEXAFS) spectroscopy and thermal desorption spectroscopy. Upon adsorption on clean Cu(111) surface at room temperature, butanethiolate as well as atomic sulfur is formed. For the butanethiolate, the S-C bond is found predominately perpendicular to the surface as revealed by polarization analysis. In contrast, on square root of 7 x square root of 7 R19.1 degrees S/Cu(111) surface, the S-H and S-C bonds of the butanethiol stay intact, resulting in a weakly chemisorbed butanethiol.
 
Article
This study has revealed the advantages of the use of 116 keV X-rays as an excitation source of X-ray fluorescence (XRF) analyses. This technique is suitable for nondestructive multielemental analyses of heavy elements such as rare-earth elements. The lowest MDL value evaluated for the bulk analysis of a JG-1 standard reference sample (granite rock) was 0.1 ppm for W for a 500 s measurement. The spectrum of standard glass samples of SRM612 demonstrated clearly resolved K-line peaks of more than 30 elements, including all the existing rare-earth elements, at 50 ppm levels. The calibration curve for the determination of a rare-earth element shows a linear relation between the XRF intensity and concentrations from 10 to 0.03 ng. This powerful technique should be useful for nondestructive analyses of rare-earth and heavy elements in geological, geochemical and archaeological samples as well as industrial materials.
 
Article
The design and performance of a new soft X-ray beamline BL-11A at the Photon Factory (PF) are presented. A Hettrick-type grazing-incidence monochromator equipped with three varied-line-spacing plane gratings was designed and constructed at a bending-magnet source of the PF 2.5 GeV storage ring. An 800 lines mm(-1) laminar grating produced by aspheric-wavefront holographic recording optics, as well as a mechanically ruled blazed one, were tested. A resolving power of more than 4500 was achieved at 400 eV with either grating, and approximately 10(10) photons s(-1) are available at a resolving power of 2000. High photon flux enables low-concentration samples, such as surface adsorbates, to be studied. A simple scanning mechanism for a wide energy range is quite useful for EXAFS measurements on light elements such as C, N and O.
 
Article
A report on the 11th International Conference on Biology and Synchrotron Radiation, which took place on 8-11 September 2013, in Hamburg, Germany, is presented.
 
Article
We synthesized (Pb,Cd)Sr-2(Y,Ca)Cu2O7+x phase superconductor. After substitution of ph with Bi, the BiCd1212 phase shows no superconductivity. Although previous EXAFS study has shown the local structure environment of the Cu is similar in both compounds, EXAFS results of Bi and Pb here demonstrate that sigma(2) of Pb-Oin-plane is larger than that of Bi-Oin-plane, whereas sigma(2) of Pb-O-apical is smaller than that of Bi-O-apical. The Sr shell features are also different. It appeared that superconductivity needs some disorder in carrier reservoir layer, which is due to the substitutional defect caused by different ionic radii.
 
Article
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Article
A rotating glass capillary cell with a gas handling system has been built to allow in situ studies by powder X-ray diffraction. The cell can be used to condense volatile compounds, or to follow solid-state chemical reactions under vacuum or at gas pressures up to around 7 x 10(5) Pa. Using the cell, cooled by a stream of helium gas, the solid phases of 1,2-dichlorotrifluoroethane (HCFC-123a) and 2-chloro-1,1,1,2-tetrafluoroethane (HCFC-124) have been investigated using powder synchrotron X-ray radiation. These were found to have disordered hexagonal structures, with a = 4.018 (5), c = 6.553 (1) A and a = 4.048 (1), c = 6.625 (1) A, respectively, at 64 K.
 
Top-cited authors
Anna Bergamaschi
  • Paul Scherrer Institut
Marco Stampanoni
Beat Henrich
  • Paul Scherrer Institut
A. Snigirev
  • Immanuel Kant Baltic Federal University
J. Krempaský
  • Paul Scherrer Institut