bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Modifications of Cold and Dense Cesium, Calcium, Barium, and Selenium
Authors: Desgreniers Serge , Tse John , Zhao Jianbao , Matsuoka Takahiro , Ohishi Yasuo
Published: November 2015

Following the development of high brilliance synchrotron x-ray sources, high density crystalline structures of elemental solids have been vastly studied at room temperature and elevated pressures. In the last decades, experimental and computational results have unveiled a vast diversity of crystalline structures adopted by many dense elements. Both complex modulated and exotic structures have been observed [1] and predicted [2]. In this communication, we report results of systematic searches for structural modifications taking place at very low temperature (T>10 K) and high pressure (P<50 GPa) in selected elementals solids. Results for cesium, calcium, barium, and selenium are presented. An extension of the known P-T phase diagram to lower temperature for cesium and selenium indicates that both elements do not adopt crystalline structures different that those already known and documented. We show that calcium at low temperature and high pressure, however, exhibits unusual and large dynamical fluctuations leading to a tetragonal distortion of the simple cubic structure known to exist at room temperature and about 30 GPa. The large amplitude fluxional behaviour leads to the appearance of a new phase, nested at T<30K between 40 and 45 GPa. Finally, barium when compressed at low temperature, transforms into a crystalline structure unobserved at high pressure and room temperature. It is found that, below 140K and in the pressure range of 13 to 35 GPa, barium does not adopt the phase IV structure, i.e., the modulated incommensurate cell, but undergoes a transition from phase II (P63/mmc) to an orthorhombic (Pmna) cell. This new structure corresponds to phase VI. On the basis of an x-ray diffraction study along quasi-isobaric and isothermal paths, we conclude that Ba-VI is most likely metastable. Our results suggest the need to scrutiny other dense elements at very low temperature. Under those conditions, unusual structural modifications are ought to be observed.
High-pressure synthesis of materials with new bonding patterns and stoichiometries
Authors: Goncharov Alexander
Published: November 2015

The search for new materials for advanced technological and practical applications requires breakthroughs in our understanding of how we can control matter most efficiently. Pressure is arguably the most revealing physical variable to delineate various competing physical and chemical phenomena. There are multiple theoretical predictions for existence of novel materials state via changes in the equilibrium chemical bonding at high pressures, but many of these reports do not take into account a possible change in the most stable chemical composition. Also, the implications of this novel extreme chemistry for synthesis of new materials for practical applications remain challenging because high-pressure bonding patterns are often thermodynamically unstable at ambient pressure. Search for a recovery mechanisms or attempts of synthesis in nominally metastable conditions require detailed knowledge of the energy landscape; extensive collaborative efforts of experiment and theory are needed for its determination and for validating the theoretical predictions. I will present new results on synthesis of materials with new bonding patterns and unusual stoichiometries containing hydrogen, nitrogen, carbon, sodium, and halogens. This work has been performed in collaboration with M. Somayazulu, V. V. Struzhkin, V. Prakapenka, E. Stavrou, T. Muramatsu, A. R. Oganov, W. Zhang, Q. Zhu, S. E. Boulfelfel, A. O. Lyakhov, Z. Konopkova, H.-P. Liermann, D.-Y. Kim. I acknowledge the support of DARPA, NSF, EFRee (DOE), Army Research Office, Deep Carbon Observatory, and Carnegie Institution of Washington.
X-ray investigation of polytype distribution in InAs nanowires during MBE growth
Authors: Pietsch Ullrich , Biermanns Andreas , Dimakis Emmanouil , Geelhaar Lutz , Davydok Anton , Takahashi Masumitu , Sasaki Takuo
Published: November 2015

The monolithic integration of III-V semiconductors with Si is the ideal way to combine the superior optoelectronic properties of the compound semiconductors with the mature Si technology. This integration can be realized by growing epitaxially dislocation-free III-V NWs on Si substrates either in the vapor-liquid-solid (VLS) or in the vapor-solid (VS) mode associated with the presence or absence, respectively, of group-III liquid droplets on the NW tips [1]. In this work, we investigate the correlation between the growth mode and the forming polytypes in InAs NWs grown on Si(111). The growth was performed in the molecular beam epitaxy chamber of beamline 11XU at Spring8 [2], while the structural dynamics was probed by in situ x-ray diffraction. Specifically, the time evolution of the formation of wurtzite (WZ) and zincblende (ZB) polytypes was monitored during the NW growth. Despite the As-rich growth conditions, a spontaneous build-up of liquid In on Si was found to be present in the nucleation phase, where the InAs nuclei mainly grow in the WZ phase with low number of stacking faults. Shortly after the nucleation, the liquid In is consumed by the excessive As, and the growth continues in the VS mode with an increasing density of stacking faults forming in the NW crystal. The time evolution of the liquid Indium signal (Fig. (a)) correlates well with the time evolution of wurzite growth rate (Fig (b)). The latter saturates at a time where the liquid indium disappers, i.e. where the VLS changes into the VS mode, whereas the zinc-blende polytypes grow almost continuous in both VLS and VS growth mode. The dynamics of stacking faults density was determined quantitatively by ex-situ X-ray diffraction measuring thestacking fault induced increase of the peak width of wurtzite reflections at InAs nanowire samples of different length ; i.e. growth time [3].
Structural Characterization of Mg2CoH5-based Nanocomposites for Hydrogen Storage
Authors: Leiva Daniel , Figueroa Santiago , Terra Bárbara , Zepon Guilherme , Lamas Diego , Floriano Ricardo , Jorge Junior Alberto , Botta Walter
Published: November 2015

Hydrogen is considered the ideal energy carrier, mainly due to its heating power, the highest among all chemical fuels, and to possibility of using it in fuel cells, therefore with efficiency and producing only water as by-product. However, the development of safe and effective hydrogen storage solutions remains as a challenge of applied research. MgH2, Mg2FeH6 and Mg2CoH5complex hydrides are promising materials for hydrogen storage, avoiding the inconvenient of gaseous or liquid storage alternatives. The main attractives of these phases are their volumetric and gravimetric hydrogen capacities, their reversibility during absorption/desorption cycles and the relatively low cost. Recently, we have achieved an important control of the synthesis of Mg-based complex hydrides with nanocrystalline structure, using reactive milling (RM) under hydrogen atmosphere as processing route [1, 2]. In this study, we present new results concerning the synthesis, hydrogen storage properties and structural characterization of MgH2–Mg2CoH5nanocomposites prepared by RM. The nanocomposites were produced by milling different Mg-Co starting compositions (2:1, 3:1, 5:1, 7:1, 1:0) for 12 h in a planetary mill under 3 MPa of H2. All samples were fully hydrogenated during milling, generating different MgH2–Mg2CoH5hydride mixtures. Mg presents the tendency of agglomerate during milling, so the sample that presents more MgH2shows larger agglomerates. This behavior causes a slight increase in the temperature of hydrogen desorption and the presence of two peaks, showed by DSC analysis for those samples which presents MgH2and Mg2CoH5. Using in-situ XRD and XANES during hydrogen desorption revealed that Mg and Co tend to remain coupled forming intermetallics after the complex hydride decomposition, differently from that was observed for Mg2FeH6. This effect is correlated to the high-reversibility exhibited by the Mg2CoH5phase. Furthermore, the nanocomposites of MgH2+Mg2CoH5showed better H-absorption/desorption kinetics than the Mg2CoH5or MgH2alone, as shown by volumetric measurements. The combination of MgH2and Mg2CoH5is therefore a promising strategy to produce hydrogen storage materials, matching the good reversibility and high capacity of magnesium hydride with the lower thermal stability.
Structural Studies on nanocrystalline ZnS and CdS
Authors: Deshpande Sunil , Pandey K. , Dharne Gopichand M. , Deshpande Shubhangi
Published: November 2015

II-VI semiconductor nanocrystals have attracted much attention due to their size dependent properties ranging from electronic to biological regimes. Herein results of ZnS and CdS ADXRD (Angle dispersive X-ray diffraction) data, recorded in transmission mode, on BL-11 Beamline of INDUS Synchrotron are reported. Semiconductors obtained using wet chemical co-precipitation method, were kept for a few hours in the deep freezer. The wavelength of x-rays was 0.04666 nm (27 keV). A MAR 3450 image plate was used as detector. Sample to detector distance was 185.9178 mm. XRD data were extracted using fit2d. ADXRD pattern was recorded in transmission mode. The fityk program was used to fit pseudo Voigt A function to the ADXRD data to get the half width at half maximum (HWHM) of the peaks. These HWHMs values as well as the Scherrer formula yielded the particle sizes. The Neilson-Riley method was used to refine the lattice parameters. Results of the ADXRD data analyses for both ZnS and CdS are given below:The Particle size (nm), Bravais Lattice, Lattice parameter (nm) and Eg (eV) [UV abs spectra] for ZnS are 2.81, F¯43m, 0.5371 and 3.82 respectively while for CdS these values are 3.03, F¯43m, 0.580, 2.59 respectively. From these data the metal-S and Metal-Metal distances were calculated and were found out for ZnS to be 0.2326 nm and 0.3798 nm while for CdS these distances are 0.251 nm and 0.41 nm respectively. These data match well with the literature/1/. Particle sizes were in agreement with Brus's /2/ method. Acknowledgements: One of the authors (SDD) acknowledges the financial assistance from the University Grant Commission, New Delhi (F-37/147/2009(SR)). The authors are also grateful to Dr. S. K. Deb, Head, INDUS Synchrotron Users' Division, Raja Ramanna Center for Advanced Technology, Indore, (M.P.) India.
Multiscale structure-properties analysis of photoactive nanocomposite materials
Authors: Bendeif EL-Eulmi , Hsieh Kuan-Ying , Schaniel Dominik , Gansmuller Axel , Pillet Sébastien , Woike Theo
Published: November 2015

In the last decades, the confinement of various types of functional material in mesoporous silica matrices has been used to design hybrid organic-inorganic nanocomposites with unique and fascinating properties. Such nanocomposites have attracted considerable interest owing to their potential applications in various domains [1-2], while reports with precise structural information of such molecular nanomaterials are still rather scarce and quite disparate. However, in order to be able to derive a structure-functionality relationship of such hybrid complexes, a detailed description of the structural organisation of the guest species and of their immediate surrounding is absolutely mandatory. We show in this contribution that detailed structural information can be obtained by using an appropriate multiscale approach combining various experimental techniques such as X-ray total scattering coupled to atomic pair distribution function (PDF) and solid-state NMR spectroscopy. This multiscale approach does provide more extensive and accurate structural information [3]. The PDF approach has allowed the identification of the nature of the incorporated species and their arrangement as well as the distinction of the various existing phases: isolated molecules and nanoparticles. The multi-nuclei Solid State NMR investigation has provided information on both the amorphous host and the molecular guest and adds a dynamic dimension to the classical static structural characterisation. We also discuss the influence of the structural changes on the physical properties of the investigated materials
Nanoparticles: from wulff to winterbottom, plasmonics & catalysis
Authors: Marks Laurence
Published: November 2015

Understanding the structure of nanoparticles is a problem with over a century of history from the first analysis by Wulff which was only proved during WWII by von Laue with the extension for supported particles on a flat substrate by Winterbottom. All these analyses have focused on single crystals, but often nanoparticles have different structures as first shown by of Ino and Ogawa who published just ahead of Allpress and Sanders. These structures, called multiply-twinned particles or MTPs remained incompletely understood until a variant of a Wulff construction was shown to explain their equilibrium shapes. Given the growth of nanotechnology in the last decades, significant advances in synthesis and characterization methods have been made so it is time to return to some of these topics and look further. It appears there is still a fair amount of science left to be done, ranging from Wulff shapes for alloys to understanding the growth shapes of nanoparticles based upon a kinetic variant of the modified Wulff construction. Some recent results such as finite size effects for alloys and single-phase nanoparticles as well as corner rounding and how these couple to the chemical potential and substrate interfacial energy, as well as how these relate to applied topics such as nanoplasmonics and face-selective catalysis will be described.
In situ oxidation kinetics of magnetite nanoparticles by total scattering
Authors: Cervellino Antonio , Frison Ruggero , Guagliardi Antonella , Cernuto Giuseppe , Masciocchi Norberto , Colonna Gian Maria
Published: November 2015

Iron oxide nanoparticles (NPs) show different structures as a function of oxidation state. In particular, magnetite (Fe3O4) NPs are easily oxidized in air at moderate temperatures, eventually yielding maghemite (Fe2O3). Oxidation proceeds via the creation of iron vacancies. While the vacancies may be created with a random distribution throughout the octahedral Fe sites, they eventually order over a specific subset of these sites, lowering the symmetry from F-centered (magnetite) to P-centered (cubic maghemite). By ex situ X-ray Total Scattering studies of magnetite-maghemite NPs in different oxidation states[1] we have recently studied, by the DFA method[2], the correlation between particle diameter, stoichiometry and lattice parameter in polydisperse NP samples unraveling also the size dependence of lattice parameter and composition. Moreover, we have shown indirect evidence of the formation of a polycrystalline surface layer of maghemite on a magnetite core in the intermediate oxidation states. Motivated by the excellent ex-situ results, we have also performed in-situ studies where magnetite NPs were oxidised in air at moderate temperatures (50-200 C). We present here an in-situ study performed at the X04SA-Materials Science beamline of the Swiss Light Source synchrotron[3]. Total Scattering X-ray diffraction patterns were collected every few minutes, while the oxidation was completed within several hours. The mechanism of NPs oxidation - whereas a surface oxidised layer is formed by outwards diffusion of Fe, then the vacancies so created order themselves giving rise to the maghemite-magnetite phase transition, will be examined in great detail. We will discuss, on robust statistical basis, the calculation of kinetic and diffusion constants, the temperature effect on the lattice constant and on the thickness of the surface oxidised layer; the different possible structural models for the cubic-maghemite NPs. We thank for support Fondazione Cariplo (2009-0289).
Revealing Intricacies of Nano-Sized Intermetallic GaPd2Catalysts
Authors: Leary Rowan , de la Peña Francisco , Barnard Jon , Luo Yuan , Armbrüster Marc , Thomas John , Midgley Paul
Published: November 2015

The use of intermetallic compounds in catalysis is a promising means of achieving well-defined catalytic active sites with high selectivity. Simultaneously, it is desirable to nanostructure the catalyst to maximize activity. However in nanoparticulate form, structures and properties quite distinct from bulk systems may arise. Thorough characterization of the nano-sized catalyst is therefore required, for which the high-resolution analysis provided by transmission electron microscopy (TEM) can be invaluable. The directly interpretable imaging provided by aberration-corrected annular dark-field scanning TEM especially, can reveal atomic-scale intricacies and intrapopulation heterogeneities with clarity. Recently, a promising new class of selective hydrogenation catalyst has emerged based on intermetallic Ga-Pd compounds [1]. In foundational studies, use of bulk or powdered model systems led to insights into the relationship between structural and electronic properties and catalytic performance. Aiming for industrial applicability, attention is now being given to high-performance nanoparticulate Ga-Pd catalysts. Through high-resolution imaging, spectroscopic and 3D tomographic TEM studies, significant insight into the crystallographic status of unsupported Ga-Pd nanocatalysts, GaPd2 in particular, has been possible [2,3]. Further to direct verification of the distinctive intermetallic structure in nano-sized particles, catalytically significant and crystallographically intriguing deviations compared to the 'ideal' bulk crystal are revealed. These include strong surface segregation, lattice relaxation and particularly interesting morphologies of the small (<10 nm) particles that comprise both nanocrystalline 'fcc-like' and 'non-crystallographic' five-fold twinned structures. The extent to which the intermetallic structure may be maintained in nanoscale morphologies and the nature of the resultant catalytically active sites are important aspects to be addressed.
Freshwater pearls as near single crystals for vaterite structure resolution
Authors: Farre Bastien , Dellicour Aline , Bourrat Xavier , Lutterotti Luca , Pérez Olivier , Chateigner Daniel
Published: November 2015

There has been lots of controversies about vaterite structure in the past decades. Extra peaks occurring out of the hexagonal structure and best described by Kamhi [1] still resist any indexing. Lower space group symmetries, superspace groups, microtwinning, and first-principle calculations [2], all failed in taking account of these minor peaks, surprisingly always present in all synthetic and biogenic vaterite formations. Recently, secondary interspersed domains observed in high-resolution TEM images indicated their incoherence and rather incompatible character with the vaterite matrix [3]. One of the major difficulty in resolving the vaterite structure lies in the absence of single crystals. Powder diffraction patterns are always composed of hexagonal and extra, but small, peaks, and temptation to index the pattern as a single phase is large, particularly since x-ray fluorescence invariably probes for CaCO3. We used Hyriopsis cumingii freshwater mussel pearls to help proving that vaterite is definitely crystallizing within the original hexagonal space group. Some of these pearls suffer defective growth toward vaterite. In such cases the hexagonal peaks clearly exhibit a strong texture while the extra peaks look more random. This is an invaluable evidence of the existence of clearly separated phases, though the minor phase (or phases) still resist indexing. The hexagonal structure refinement, thanks to the strong vaterite texture, is obtained with larger resolution than before.
Microstructural Evolution of Monolithic Fuel Foils During Processing
Authors: Brown Donald , Okuniewski Maria , Clausen Bjorn , Sisneros Thomas , Balogh Levente
Published: November 2015

Residual stresses are expected in monolithic, aluminum clad uranium 10 weight percent molybdenum (U-10Mo) nuclear fuel plates because of the large mismatch in thermal expansion between the two bonded materials. Previous high energy x-ray diffraction measurements successfully profiled the residual stresses in the U-10Mo, but were unable to probe either the Al cladding or the 15micron Zr diffusion prevention barrier due to poor grain statistics. Neutron diffraction, with its inherently more divergent incident be alleviates this problem and, moreover, allowed for the determination of the dislocation density and texture in all three phases. Several samples were examined as a function of processing step and the phase stresses, dislocation density and texture are monitored with respect to the processing conditions.
Substrate Induced Polymorphism in Organic Thin Films
Authors: Chattopadhyay Basab , Geerts Yves
Published: November 2015

The presence of substrate induced polymorphic phases in thin films is an intriguing phenomenon with the physical and chemical factors responsible for its formation are not yet clearly understood. In particular, this is really crucial in the field of organic electronics, where the charge-transport properties are highly dependent on crystal packing, especially for organic field-effect transistors where charge transport occurs at the interface between the organic semiconductor and the dielectric. In pharmaceutical sector, thin film drug delivery is the new emerging alternative to traditional tablets and oral suspensions. The need to identify and control polymorphism induced by the substrate is thus very crucial. In this presentation, we report the structure and morphological changes associated with a substrate induced polymorphic phases in a discotic liquid crystal and a rod shaped DPP-thiophene-based molecule [1, 2]. The bulk compound and the thin films are characterized by a combination of various X-ray diffraction methods to investigate the structural properties. Atomic force microscopy and polarized optical microscopy are used to determine the thin film morphologies. This is the first experimental proof of presence of a substrate induced phase in discotic liquid crystal showcasing an unique example where the 2-D liquid crystalline phase converts to a 3-D crystal plastic phase due to nucleation caused by the solid substrate over a time scale of a month or longer. The presentation also highlights the importance of polymorphism in DPP-thiophene-based material and the specific organization that could arise from the interaction with the substrate depending on the growing conditions. Here the exact structural and the spectroscopic signatures of different polymorphic forms in bulk and in thin films could be identified. These are clearly factors to consider to induce the formation of a particular polymorph and to help to design deposition methodologies.
Suppressing twin formation in Bi2Se3thin films
Authors: Tarakina Nadezda , Schreyeck Steffen , Luysberg Martina , Schumacher Claus , Karczewski Grzegorz , Brunner Karl , Gould Charles , Buhmann Hartmut , Dunin-Borkowski Rafal , Molenkamp Laurens
Published: November 2015

The goal of the present work was to reveal the origin of the formation of different structural defects in Bi2Se3 thin films. We conducted a detailed comparative study of layers grown on InP(111)A and -B terminated flat and rough substrates using reflection high-energy electron diffraction (RHEED), atomic force microscopy (AFM), X-ray reflectivity (XRR), X-ray diffraction (XRD) and probe-corrected scanning transmission electron microscopy (STEM). This choice of substrate reduces the formation of mosaicity twist sufficiently due to an almost perfect lattice match (0.2%) between InP and Bi2Se3. The use of substrates with different terminations and roughnesses allows the factors that define twin formation to be identified, providing conclusions about how twinning can be controlled and suppressed. In particular we have shown that growth using molecular beam epitaxy on rough Fe-doped InP(111) substrates leads to the formation of high quality thin films, with very low mosaicity twist and with complete suppression of twins in the Bi2Se3 thin films. No extra layer was observed at the interface between the film and the substrate. We also showed that the substrate surface termination (A or B) defines which family of twin domains dominates. The only types of structural defects that remain in the films are antiphase grain boundaries associated with the variation in substrate height. We believe that our study is relevant not only for Bi2Se3 growth but that it also provides essential insight for obtaining monocrystalline A2B3 (A = Bi, Sb; B = Se, Te) chalcogenide thin films and for realizing desirable electrical properties within this class of materials.
Thin film stress and microstructure analysis by energy-dispersive diffraction
Authors: Genzel Christoph
Published: November 2015

The most important advantage of energy dispersive (ED) diffraction compared with angle dispersive methods is that the former provides complete diffraction patterns in fixed but arbitrarily selectable scattering directions. Furthermore, in experiments that are carried out in reflection geometry, the different photon energies E(hkl) of the diffraction lines in an ED diffraction pattern can be taken as an additional parameter to analyze depth gradients of structural properties in the materials near surface region. For data evaluation advantageous use can be made of whole pattern methods such as the Rietveld method, which allows for line profile analysis to study size and strain broadening [1] or for the refinement of models that describe the residual stress depth distribution [2]. Concerning polycrystalline thin films, the features of ED diffraction mentioned above can be applied to study residual stresses, texture and the microstructure either in ex-situ experiments or in-situ to monitor, for example, the chemical reaction pathway during film growth [3]. The main objective of this talk is to demonstrate that (contrary to a widespread opinion) high energy synchrotron radiation and thin film analysis may fit together. The corresponding experiments were performed on the materials science beamline EDDI at BESSY II which is one of the very few instruments worldwide that is especially dedicated to ED diffraction. On the basis of selected examples it will be shown that specially tailored experimental setups allow for residual stress depth profiling even in thin films and multilayer coatings as well as for fast in situ studies of film stress and microstructure evolution during film growth.
Water Oxidation in Natural Photosynthesis
Authors: Kern Jan , Tran Rosalie , Chatterjee Ruchira , Han Guangye , Alonso-Mori Roberto , Bergmann Uwe , Yachandra Vittal , Yano Junko
Published: November 2015

The photosynthetic water oxidation reaction is energetically demanding and mechanistically complex because of the difficulties in managing the four electron, four proton redox chemistry required for the evolution of molecular oxygen starting from two water molecules. The reaction takes place in Photosystem II (PS II), a multi-subunit membrane protein present in plants, algae, and cyanobacteria. This sunlight-driven reaction is catalyzed by an oxygen-evolving complex (OEC), that consists of an oxo-bridged four Mn and one Ca cluster. O2 is formed and released only after four oxidation equivalents are accumulated at the OEC. The structure of the Mn4CaO5 cluster has been studied by various spectroscopic and diffraction methods. The recent XRD study by Umena et al.[1] has shown the oxo-bridged Mn4Ca cluster structure at 1.9 Å resolution. Based on this high-resolution XRD structure, there have been efforts to obtain chemically optimized structures and structural changes of the Mn4CaO5 cluster during the catalytic cycle using spectroscopic parameters and theoretical approaches. EXAFS spectra of the PS II S states show that the structure of the Mn4CaO5 cluster changes during the catalytic cycle.[2] In particular, the short Mn-Mn distances change in the range of 2.7 to 2.9 Å. Such changes in oxygen-bridged Mn-Mn distances can reflect several chemical parameters; Mn oxidation state changes, protonation state changes of bridging oxygens, ligation modes (e.g. bidentate/monodentate), as well as fundamental changes in geometry. We have also used femtosecond X-ray spectroscopy and crystallography to study the catalytic process of the OEC.[3] The femtosecond X-ray pulses of the free-electron laser allows us to out-run X-ray damage at room temperature, and the time-evolution of the photo-induced reaction can be probed using a visible laser-pump followed by the X-ray-probe pulse. We will discuss a possible water oxidation mechanism based on these results.
Characterization of Chloroquine-Ferriheme Solution Structure Using EXAFS and MD
Authors: Kuter David , Streltsov Victor , Davydova Natalia , Venter Gerhard , Naidoo Kevin , Egan Timothy
Published: November 2015

The complex formed between the antimalarial drug chloroquine (CQ) and its target iron(III)protoporphyrin IX (ferriheme) in aqueous solution is of considerable importance in understanding its mechanism of antimalarial activity. Recently, convincing evidence showed that CQ induces the μ-oxo dimeric form of ferriheme in aqueous solution, but the structure of this complex in solution is uncertain.[1] Molecular dynamics (MD) simulations in aqueous solution were used to model the structure of μ-oxo ferriheme and two possible conformations of the CQ-ferriheme complex, one in which CQ π-stacked with the unligated face of ferriheme and the other in which CQ was docked between the porphyrin rings. The EXAFS spectrum of μ-oxo ferriheme obtained from frozen solution strongly supported the hydrated structure determined from MD simulation where an excellent fit to the spectrum was only obtained when incorporating waters of hydration at regions identified by computation. On the other hand, the EXAFS spectrum recorded on the dried solid of μ-oxo ferriheme required no solvating waters to produce excellent agreement with the crystal structure of μ-oxo ferrihaem dimethyl ester.[2] The EXAFS spectrum recorded on a frozen aqueous solution of the CQ-ferriheme complex was able to distinguish between the two conformations modeled computationally. Fits to the EXAFS spectrum using the π-stacked structure produced poor agreement while those obtained using the docked conformation reproduced the spectrum well. This indicated that the latter is the most likely form of the CQ-ferriheme complex in aqueous solution.
Crystallographic fragment screening: challenges, opportunities, lessons learned
Authors: Heine Andreas , Radeva Nedyalka , Schiebel Johannes , Park Ahyoung , Köster Helene , Ühlein Monika , Sparta Karine , Weiss Manfred , Mueller Uwe , Klebe Gerhard
Published: November 2015

Fragment-based approaches are now routinely applied for lead development in pharmaceutical drug research. Usually, a small but well selected library of low molecular weight compounds is pre-screened by biochemical or biophysical methods such as surface plasmon resonance (SPR), nuclear magnetic resonance (NMR) or thermal shift assay; often followed for promising hit candidates by X-ray crystallography. We designed a small fragment library consisting of 364 compounds that is not strictly compliant to the otherwise often followed Astex rule of three for fragment library composition.[1] Thereafter, our library was validated on the pepsin-like aspartyl protease endothiapepsin, which serves as a model system for proteins that are involved in serious diseases such as malaria (plasmepsins), hypertension (renin) and Alzheimer's disease (ß-secretase) and therefore, is a valid target for further drug development. Due to the small size of fragments, they frequently exhibit only low affinity to the applied target protein and thus are often hard to detect in any screening approach, reflected in little overlap between different screening methods. After initial screening, we decided to validate the entire library by X-ray crystallography, which requires a steady supply of crystals, reproducible soaking conditions and a reliable setup at a synchrotron source, such as HZB BESSY II BL14.1 [2], preferably with some automation in initial data processing and refinement. A total hit rate greater than 10% was obtained, which will be compared to results from other screening methods. The resulting crystal structures will be discussed and provide an ideal basis for further lead development.
Determinants of nucleoside specificity of a macrolide phosphotransferase
Authors: Fong Desiree , Blanchet Jonathan , Berghuis Albert
Published: November 2015

2'-macrolide phosphotransferase type I [MPH(2')-I] is an antibiotic kinase that renders many macrolides, such as erythromycin, inactive by catalyzing the transfer of a phosphate group from a nucleoside triphosphate to the hydroxyl at the 2'-position of the antibiotic. MPH(2')-I is functionally and structurally analogous to the aminoglycoside kinases (APHs). However, it is distinct from most APHs in that it utilizes GTP exclusively as its phosphate donor. We will present the crystal structure of MPH(2')-I in its apo and ternary complex forms with guanosine nucleotide and different macrolide substrates. We will compare its nucleoside-binding pocket to that of the 2''-aminoglycoside phosphotransferases [APH(2'')], a subclass of aminoglycoside kinases that are capable of utilizing GTP as a phosphate donor. To further decipher the structural basis of the nucleoside specificity of MPH(2')-I, mutations of amino acid resides in the nucleoside-binding pocket have been carried out and their effects on the binding affinity of purine nucleotides were examined by isothermal titration calorimetry. Our preliminary results show that the "gatekeeper" residue plays a role in governing the nucleoside selectivity.
A catalytic switch uncovered in gentamicin resistance kinase APH(2'')-Ia
Authors: Caldwell Shane , Berghuis Albert
Published: November 2015

The APH(2'')-Ia domain of the bifunctional aminoglycoside resistance enzyme AAC(6')-Ie/APH(2'')-Ia confers high-level resistance to aminoglycoside antibiotics. Crystal structures of this kinase domain in complex with GTP analogues and acceptor substrates have uncovered a surprising conformational bistability of the GTP substrate, which may reduce futile hydrolysis of the cofactor by the enzyme. This conformational switch is influenced by the binding of aminoglycosides, and may represent an adaptive feature of the enzyme, improving its evolutionary fitness in bacterial populations. This mechanism combines with a remarkable flexibility observed in the binding of diverse aminoglycoside substrates to make this enzyme a formidable antibiotic resistance machine.
Study of 2'-macrolide phosphotransferase selectivity for different substrates
Authors: Blanchet Jonathan , Fong Desiree , Berghuis Albert
Published: November 2015

Macrolides are antibiotics that have been in use since the late 1950s to treat a wide range of bacterial infections (e.g. upper respiratory infections, skin and soft–tissue infections, stomach ulcers and some venereal diseases). The structure of these antibiotics contains a lactone ring of either 14, 15, or 16 members, with a variety of sugar moieties attached. Resistance to this class of antibiotics may result from the reaction carried out by macrolide phosphotransferases [MPHs]. MPHs belong to the family of antibiotic kinases which catalyzes the transfer of a phosphate group from a nucleoside triphosphate to a specific hydroxyl on the antibiotic. However, unlike most antibiotic kinases, MPHs utilize GTP as the phosphate donor. Specifically, 2'-macrolide phosphotransferase type I [MPH(2')-I] transfers the gamma-phosphate from GTP to the 2'-hydroxyl of 14- and 15-membered ring macrolides. Crystal structure of the ternary complexes of MPH(2')-I with both 14- and 15-membered lactone macrolides have been determined. To study the basis of substrate selectivity, we have generated mutations of several amino acid residues in the macrolide-binding pocket and examined the catalytic activities of these mutants on the different classes of macrolides, including those containing a 16-membered lactone. Furthermore, we will present kinetic studies of MPH(2')-I containing mutations in the nucleoside-binding pocket in order to study the mechanism for the enzyme's preference for GTP.
Structural biology of Alzheimer's disease
Authors: Miles Luke , Crespi Gabriela , Nero Tracy , Parker Michael
Published: November 2015

Alzheimer's disease (AD) is the most prevalent neurodegenerative disease in humans with age being the biggest risk factor. The mechanisms by which the disease progresses to cognitive decline in the sufferer are complex and not fully elucidated. A defining pathological feature is the deposition of extracellular plaques composed primarily of misfolded amyloid beta (Aβ) peptide: a proteolytic breakdown product of the much larger Amyloid Precursor Protein. While Aβ peptides are the main constituents of amyloid plaques that burden the diseased brain, plaque burden correlates poorly with the severity of the disease. There is accumulating evidence that a prefibrillar or protofibrillar soluble form of Aβ can compromise neuronal functions and trigger cell death. Immunotherapy targeting Abeta is a promising direction in AD research with active and passive immunotherapies shown to lower cerebral Aβ levels and rescue cognitive function in animal models. Anti-Aβ immunotherapies are a significant class of AD therapeutics currently in human clinical trials. We have been examining the molecular basis of antibody engagement of Aβ epitopes to inform the analysis of clinical trial data and to guide the engineering of anti-Aβ antibodies with optimised specificity and affinity. We have determined the structures of three different AD antibodies in complex with Ab peptides: (1) WO2, which recognises the N-terminus of Aβ, (2) Mab 2286, which like the AD immunotherapeutic Ponezumab (Pfizer), shows specificity for the C-terminus of Aβ40 but has no significant cross-reactivity with Aβ42/43, and (3) Bapineuzumab, a humanized antibody developed by Pfizer and Johnson & Johnson which recognises the N-terminus of Aβ but cannot recognize N-terminally modified or truncated Aβ peptides (1). All these studies reveal surprising aspects of Aβ peptide recognition by the antibodies and suggest new avenues for AD antibody development.
AGIPD detector for Serial Femtosecond Crystallography Apparatus at European XFEL
Authors: Stern Stephan , Chavas Leonard , Chapman Henry , Mancuso Adrian , Aquila Andrew , Giewekemeyer Klaus , Becker Julian , Graafsma Heinz , Schmitt Bernd
Published: November 2015

The European X-ray Free-Electron Laser (XFEL.EU) [1] will provide ultra-short, highly-intense, coherent x-ray pulses at an unprecedented repetition rate, transforming experiments in many scientific areas, including serial femtosecond crystallography (SFX). For the purpose of SFX experiments at the XFEL.EU, a dedicated endstation is being developed to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument [2]. The setup will refocus the beam spent by SPB into a second interaction region, thereby enabling two parallel experiments. In order to overcome various challenges in XFEL crystallography, and to optimize the output for SFX experiments at XFEL.EU, the Adaptive Gain Integrating Pixel Detector (AGIPD) [3] is currently under development and is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX apparatus. The AGIPD is a hybrid-pixel detector with pixels of 200 x 200 micron^2 each. The gain of each single pixel dynamically and independently adapts to the incoming signal. Thus, diffraction patterns of high dynamic range can be recorded, with the measured signal within a single data frame ranging from single photons and up to 1e+4 photons at 12 keV. Moreover, the AGIPD is designed to store over 350 data frames from successive pulses prior to digitization and read-out, thereby enabling operation at the European XFEL with its challenging repetition rate with 10 Hz pulse trains and a 4.5 MHz intra-train repetition rate. Furthermore, the incorporation of a veto system in AGIPD will allow one to potentially store only the frames that contain diffraction data from actual crystal hits, which ultimately increases the efficiency of the detector and DAQ systems dramatically. In the present work, we will review the design of the 4Mpix AGIPD for the SFX apparatus and discuss simulations and tests of its expected performance under the conditions foreseen for SFX experiments at the XFEL.EU.
Fast Neutron Laue Diffraction with CCD Detectors
Authors: Ouladdiaf Bachir , Lemée-Cailleau Marie-Hélène , Allibon John , Rodriguez-Carvajal Juan , Chapon Laurent
Published: November 2015

The large area neutron Laue diffractometer based on CCD detectors (CYCLOPS [1]) has been developed and recently completed at the ILL. High-quality Laue patterns covering an angular range of 3600horizontally and 920vertically, can be obtained in only few seconds. The diffractometer excels for fast survey of reciprocal space and fast data collections through phase transitions as well as in-situ experiments on single crystals with time resolution similar to that obtained with powder diffraction. The detector is being upgraded with new faster CCD cameras having a larger dynamic range. A protocol for detector corrections from spatial distortions and uniformity response has been established which allows to obtain accurate integrated intensities leading to good structural refinements. Examples of results of phase transitions and structural investigations will be presented.
A 3D CZT High Resolution Detector for X-and gamma-ray applications.
Authors: Kuvvetli Irfan , Budtz-Jørgensen Carl , Auricchio Natalia , Stephen John , Caroli Ezio , Benassi Giacomo , Zambelli Nicola , Zappettini Andrea
Published: November 2015

A high resolution three dimensional (3D) position sensitive CdZnTe-based detector was developed to detect high energy photons (10 keV-1MeV). The design of the 3D CZT detector, developed at DTU Space, is based on the CZT Drift Strip detector principle. The prototype detector contains 12 drift cells, each comprising one collecting anode strip with 3 drift strips, biased such that the electrons are focused and collected by the anode strips. The anode pitch is 1.6mm. The position determination perpendicular to the anodes, the X-direction, is performed using a novel interpolating technique. The position determination along the detector depth direction, Y-direction, is made using the depth sensing technique. The position determination along the anode strips, Z-direction is made with the help of 10 cathode strips orthogonal to the anode strips. REDLEN CZT crystals (20 mm x 20 mm x 5 mm) were used for the proto type detectors. IMEM-CNR fabricated the proto type detectors using a special surface treatment method and electrode attachment process. A novel method was applied to reduce the surface leakage current between the strips. The proto type detector was investigated at the European Synchrotron Radiation Facility, Grenoble which provided a fine 50 x 50 μm2 collimated X-ray beam covering an energy band up to 600 keV. At 400 keV we measured position resolutions of 0.2 mm FWHM in the X- and Y-direction and 0.6 mm FWHM in the Z-direction. The measured energy resolution of the detector was ~5.5 keV FWHM at 400 keV. The electronic noise contribution of the detector setup was 3.7 keV FWHM . The detector provides 3D position with very good spatial resolution as well as high resolution energy information and is therefore a well suited candidate e.g. as a Compton telescope detector, or for any application fields (medicine, security, science) where imaging and spectroscopy of high energy photons in the 10keV-1MeV range are required.
Halogen bonding in iron(II) and cobalt(II) tris(dichloroglyoximates)
Authors: Vologzhanina Anna , Lyssenko Konstantin
Published: November 2015

The understanding of the interplay between intermolecular strong and weak interactions requires approaches that are able to identify and quantify all of them, and are applicable to as large number of objects as possible. The QTAIM approach [1] nicely meets the first criteria. Less rigorous approaches, such as the Stockholder [2] and the Voronoi [3] partitioning have the second advantage. The latter can also give qualitative, quantitative and visual representation of intermolecular interactions. We compared how all these approaches would perform for two polymorphs of Fe(Cl2Gm)3(BCH3)2 (monoclinic C (1a), and less stable monoclinic P (1b)) and Co(Cl2Gm)3(BCH3)2 (2) isostructural with 1b (Cl2Gm = dichloroglyoximate). The Voronoi and Stockholder partitionings showed that three fourths of molecular surfaces were attributed to Cl...X (X = Cl, O, N) and C-H...Cl bonds. According to the QTAIM theory, each chlorine atom takes part in at least four intermolecular contacts. The Voronoi tessellation was found to be valid for determinating of the graph of intermolecular bonding. Indeed, in the isostructural 1b and 2 the sets of weak interactions do not coincide due to various conformations of iron- and cobalt-containing clathrochelate cages. Nevertheless, the resulting graph of intermolecular bonding (the gpu-x net) is the same. Qualitative (for all three approaches) and quantitative (for two partitionings) correlation for various methods was demonstrated. This study was supported by the Council of the President of the Russian Federation (MK-5181.2013.3 and MD- 3589.2014.3).
Intermolecular interactions in inclusion complexes
Authors: Suwinska Kinga
Published: November 2015

The whole range of interactions can be found between host and guest in supramolecular assemblies from ion-ion interactions, ion-dipole interactions, dipol-dipol interactions through hydrogen bonding, cation-π interactions, π-π stacking to van der Waals forces. Additionally, the same interactions exist between the supramolecular complex and its surrounding, i.e. solvent molecules, neighboring complexes, gases, etc. Recently the interest of scientists in the field of supramolecular chemistry is focused on design and synthesis of water-soluble synthetic macrocyclic ligands which are good receptors for biologically important guest molecules and can mimic the models of biological systems. Studying such complexes may provide new insight into the mechanisms of the formation of similar natural systems and as a consequence will help in better understanding the processes which occur in biological systems and in developing new materials with specific properties and functions. In this presentation the interactions which are stabilizing inclusion complexes of calix[n]arenes and cyclodextrins (host molecules) with guest molecules of biological interest, especially drug molecules will be discussed. This research was partly financed by the European Union within the European Regional Development Fund (POIG.01.01.02-14-102/09)