bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian hierarchical models suggest oldest known plant-visiting bat was omnivorous
Authors: Yohe Laurel R. , Velazco Paúl M. , Rojas Danny , Gerstner Beth E. , Simmons Nancy B. , Dávalos Liliana M.
Published: November 2015

The earliest record of plant visiting in bats dates to the Middle Miocene of La Venta, the world's most diverse tropical palaeocommunity.Palynephyllum antimasteris known from molars that indicate nectarivory. Skull length, an important indicator of key traits such as body size, bite force and trophic specialization, remains unknown. We developed Bayesian models to infer skull length based on dental measurements. These models account for variation within and between species, variation between clades, and phylogenetic error structure. Models relating skull length to trophic level for nectarivorous bats were then used to infer the diet of the fossil. The skull length estimate forPalynephyllumplaces it among the larger lonchophylline bats. The inferred diet suggestsPalynephyllumfed on nectar and insects, similar to its living relatives. Omnivory has persisted since the mid-Miocene. This is the first study to corroborate with fossil data that highly specialized nectarivory in bats requires an omnivorous transition.
Aerobic scope explains individual variation in feeding capacity
Authors: Auer Sonya K. , Salin Karine , Anderson Graeme J. , Metcalfe Neil B.
Published: November 2015

Links between metabolism and components of fitness such as growth, reproduction and survival can depend on food availability. A high standard metabolic rate (SMR; baseline energy expenditure) or aerobic scope (AS; the difference between an individual's maximum and SMR) is often beneficial when food is abundant or easily accessible but can be less important or even disadvantageous when food levels decline. While the mechanisms underlying these context-dependent associations are not well understood, they suggest that individuals with a higher SMR or AS are better able to take advantage of high food abundance. Here we show that juvenile brown trout (Salmo trutta) with a higher AS were able to consume more food per day relative to individuals with a lower AS. These results help explain why a high aerobic capacity can improve performance measures such as growth rate at high but not low levels of food availability.
Climate and developmental plasticity: interannual variability in grapevine leaf morphology
Authors: Chitwood Daniel H , Rundell Susan M , Li Darren Y , Woodford Quaneisha L , Yu Tommy T , Lopez Jose R , Greenblatt Danny , Kang Julie , Londo Jason P
Published: November 2015

The shape of leaves are dynamic, changing over evolutionary time between species, within a single plant producing different shaped leaves at successive nodes, during the development of a single leaf as it allometrically expands, and in response to the environment. Notably, strong correlations between the dissection and size of leaves with temperature and precipitation exist in both the paleorecord and extant populations. Yet, a morphometric model integrating evolutionary, developmental, and environmental effects on leaf shape is lacking. Here, we continue a morphometric analysis of >5,500 leaves representing 270 grapevines of multiple Vitis species between two growing seasons. Leaves are paired one-to-one, vine-to-vine accounting for developmental context, between growing seasons. Linear Discriminant Analysis reveals shape features that specifically define growing season, regardless of species or developmental context. The shape feature, a more pronounced distal sinus, is associated with the colder, drier growing season, consistent with patterns observed in the paleorecord. We discuss the implications of such plasticity in a long-lived woody perennial, such as grapevine, with respect to the evolution and functionality of plant morphology and changes in climate.
Mapping the morphological changes of deposited gold nanoparticles across an imprinted groove
Authors: Roth Stephan Volkher , Döhrmann Ralph , Gehrke Rainer , Röhlsberger Ralf , Schlage Kai , Metwalli Ezzeldin , Körstgens Volker , Burghammer Manfred , Riekel Christian , David Christian , Müller-Buschbaum Peter
Published: November 2015

The gradient gold layer morphology below the percolation threshold along a channel groove imprinted into a pressure-sensitive adhesive polymer film is studied. In order to elucidate the complex nanostructure of the sputter-deposited gold nanoparticle layer, nanobeam grazing-incidence small-angle X-ray scattering and imaging ellipsometry are used. Thus, the complex nanostructure of this metal–polymer nanocomposite can be detected, distinguished and identified. The presence of macroscopically curved structures, as introduced by the imprinted ridges, can cause deviations from the mean metal nanoparticle morphology, probed on the `flat' sample area outside the ridges. The phase-separated morphology of the polymer film is rather unaffected by the imprint structure but leads, in addition, to a selective growth of gold on polystyrene-rich domains.
Logistic regression models to predict solvent accessible residues using sequence- and homology-based qualitative and quantitative descriptors applied to a domain-complete X-ray structure learning set
Authors: Nepal Reecha , Spencer Joanna , Bhogal Guneet , Nedunuri Amulya , Poelman Thomas , Kamath Thejas , Chung Edwin , Kantardjieff Katherine , Gottlieb Andrea , Lustig Brooke
Published: November 2015

A working example of relative solvent accessibility (RSA) prediction for proteins is presented. Novel logistic regression models with various qualitative descriptors that include amino acid type and quantitative descriptors that include 20- and six-term sequence entropy have been built and validated. A domain-complete learning set of over 1300 proteins is used to fit initial models with various sequence homology descriptors as well as query residue qualitative descriptors. Homology descriptors are derived from BLASTp sequence alignments, whereas the RSA values are determined directly from the crystal structure. The logistic regression models are fitted using dichotomous responses indicating buried or accessible solvent, with binary classifications obtained from the RSA values. The fitted models determine binary predictions of residue solvent accessibility with accuracies comparable to other less computationally intensive methods using the standard RSA threshold criteria 20 and 25% as solvent accessible. When an additional non-homology descriptor describing Lobanov–Galzitskaya residue disorder propensity is included, incremental improvements in accuracy are achieved with 25% threshold accuracies of 76.12 and 74.79% for the Manesh-215 and CASP(8+9) test sets, respectively. Moreover, the described software and the accompanying learning and validation sets allow students and researchers to explore the utility of RSA prediction with simple, physically intuitive models in any number of related applications.
Structural chemistry and number theory amalgamized: crystal structure of Na11Hg52
Authors: Hornfeck Wolfgang , Hoch Constantin
Published: November 2015

The recently elucidated crystal structure of the technologically important amalgam Na11Hg52is described by means of a method employing some fundamental concept of number theory, namely modular arithmetical (congruence) relations observed between a slightly idealized set of atomic coordinates. In combination with well known ideas from group theory, regarding lattice–sublattice transformations, these allow for a deeper mutual understanding of both and provide the structural chemist with a slightly different kind of spectacles, thus enabling a distinct viw on complex crystal structures in general.
Structural studies of metal–organic frameworks under high pressure
Authors: McKellar Scott C. , Moggach Stephen A.
Published: November 2015

Over the last 10 years or so, the interest and number of high-pressure studies has increased substantially. One area of growth within this niche field is in the study of metal–organic frameworks (MOFs or coordination polymers). Here we present a review on the subject, where we look at the structural effects of both non-porous and porous MOFs, and discuss their mechanical and chemical response to elevated pressures.
Metal–organic frameworks: the pressure is on
Authors: Coudert François-Xavier
Published: November 2015

Metal–organic frameworks (MOFs) demonstrate a wide variety of behavior in their response to pressure, including anomalous mechanical properties, negative linear compressibility, pressure-induced crystal-to-crystal and crystal-to-amorphous structural transitions. The discovery of framework materials combining novel pressure responses and high mechanical stability is key in the quest for applications of MOFs at the industrial level.
Five closely related 4-chloro-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepines: similar molecular structures but different supramolecular assemblies
Authors: Acosta Lina M. , Jurado Jorge , Palma Alirio , Cobo Justo , Glidewell Christopher
Published: November 2015

Dibenz[b,f]azepine (DBA) is a privileged 6-7-6 tricyclic ring system of importance in both organic and medicinal chemistry. Benzo[b]pyrimido[5,4-f]azepines (BPAs), which also contain a privileged 6-7-6 ring system, are less well investigated, probably because of a lack of straightforward and versatile methods for their synthesis. A simple and versatile synthetic approach to BPAs based on intramolecular Friedel–Crafts alkylation has been developed. A group of closely-related benzo[b]pyrimido[5,4-f]azepine derivatives, namely (6RS)-4-chloro-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine, C14H14ClN3, (I), (6RS)-4-chloro-8-hydroxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine, C14H14ClN3O, (II), (6RS)-4-chloro-8-methoxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine, C15H16ClN3O, (III), and (6RS)-4-chloro-8-methoxy-6,11-dimethyl-2-phenyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine, C21H20ClN3O, (IV), has been prepared and their structures compared with the recently published structure [Acosta-Quinteroet al.(2015).Eur. J. Org. Chem.pp. 5360–5369] of (6RS)-4-chloro-2,6,8,11-tetramethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine, (V). All five compounds crystallize as racemic mixtures and they have very similar molecular conformations, with the azepine ring adopting a boat-type conformation in each case, although the orientation of the methoxy substituent in each of (III) and (IV) is different. The supramolecular assemblies in (II) and (IV) depend upon hydrogen bonds of the O—H...N and C—H...π(arene) types, respectively, those in (I) and (V) depend upon π–π stacking interactions involving pairs of pyrimidine rings, and that in (III) depends upon a π–π stacking interaction involving pairs of phenyl rings. Short C—Cl...π(pyrimidine) contacts are present in (I), (II) and (IV) but not in (III) or (V).
Structural Evolution according to the temperature of the Compound LiNbO3
Authors: Tabti Charef , Chouaih Abdelkader , Hamzaoui Fodil
Published: November 2015

Structural evolution of LiNbO3 with temperature. A comparative study was made by X-ray diffraction on a single crystal of lithium niobate (LiNbO3) at low temperature (120K) and room temperature (293K). LiNbO3 is a ferroelectric compound particularly interesting for applications in the nonlinear optics field. After a recording of high resolution X-ray diffraction data, we used Blessing formalism for the reduction and the processing of the raw data. Structure refinement was carried out by program SHELXL. The results of the refinement led to a reliability factor of about 6% at T = 293K and of 3% at T = 120K. The structure evolution study of lithium niobate with temperature made it possible to highlight the compound stability in the investigated temperature range. Results show a light displacement (about 0.01Å) of oxygen atoms around the Li - Nb bond.
CTD Code: a Combinatorial Code for Eukaryotic Transcription
Authors: Zhang Yan Jessie
Published: November 2015

In eukaryotes, the C-terminal domain of RNA polymerase II (CTD) orchestrates the temporal and spatial control of transcription and is involved in the epigenetic regulation of gene expression. Errors in CTD regulation can result in cell death, cancer and severe developmental defects. The CTD executes its function as transcription modulator through various post-translational modifications on its heptad repeat sequences. Recently, novel modifications on new regulatory sites of CTD have been identified, setting the stage for the possibility of combinatorial mechanisms for transcription regulation. We focused on two well-characterized modification of CTD, namely serine phosphorylation and prolyl isomerization, and discuss the interplay between the enzymes regulating these modification states. Our results established that the selectivity of prolyl isomerization state of CTD on phosphatases can lead to differentiated outcome for the CTD phosphorylation state and therefore, transcription. To further investigate the prolyl selectivity, we developed chemical compounds that can be used to probe such subtle structural variation in the CTD binding proteins. These compounds closely mimic the cis or trans proline state and can be effectively recognized by CTD phosphatases. The application of such chemical probes can help us understand the molecular mechanism of the interplay between phosphorylation and prolyl isomerization state and how that affect the conformational status of CTD in transcription temporally and spatially.
Hydrogen Bonded Charge Transfer Complex of Chloranilic Acid With Benzimidazole
Authors: Marfo-Owusu Prof. Emmanuel , Thompson Dr. Amber
Published: November 2015

The crystal structure of 1:1:1 complex of chloranilic acid with benzimidazole and water determined by X-ray diffraction methods is reported. It crystallizes in the monoclinic (space group, P21/c) crystal system. Both chloranilic acid and benzimidazole molecules adopt a face-to-face stacking arrangement along the b-axis. An interaction beween adjacent layers is a π...π stacking interactions between chloranilic acid molecules. The dihedral angle between the interacting chloranilic acid ring planes is only 1.22 (7)0with an interplanar spacing between C10...C12 (3.383 (16) Å) and C13...C15 (3.351 (14) Å ). Water influences proton transfer in the hydrogen bonded charge transfer complex, and contributes to generating increased number of hydrogen bonds utilized in the stabilzaation of the crystal structure of the complex. Water serves as an efficient bridge between the chloranilic acid molecules through O-H...O intermolecular hydrogen bonds to form a zigzag channel, as well as directly linking chloranilic acid molecules with benzimidazole molecules which are strongly entrapped within the zigzag channel by intermolecular hydrogen bonding network involving the N-H...O, C-H...O, and C-H...Cl interactions. In the chloranilate anion structure, an intramolecular hydrogen bonding involving O2-H7 and O1 (dO2... O1 and dH7... O1 = 2.670 (12) and 2.25 Å) occurs. The supramolecular architecture of the hydrogen bonded charge complex exhibits a three-dimensional hydrogen bonding network
Structural Features of Biomimetic Complexes: The Role of Axial Donor Ligands
Authors: Palluccio Taryn , Colona-Guifarro Celeo , Rybak-Akimova Elena
Published: November 2015

An ongoing theme in our research group involves the development of biomimetic transition metal complexes that serve to activate small molecules, promote reactions similar to those of metalloenzymes, and provide new synthetic routes to novel ligands. In one instance, we have developed models of iron-containing bleomycin that rely on robust tetradentate aminopyridine macrocyclic (PyMAC) ligands. These simple systems serve as rigid scaffolds that are suitable for coordination of transition metal ions and their success as structural and functional models has led to the design and study of more elaborate ligand architectures. Our group has developed novel PyMACs containing functionalized pendant arms that can provide an additional donor atom as well as modulate the spin state of the metal center. A second area of focus involves the template synthesis of a wide range of imidoylamidines promoted by a urease model complex containing Ni(II) supported by tert-butyl-dipicolylamine (tBuDPA). Structures of the model complex with a bound imidoylamidine reveal that the tertiary amine donor atom of tBuDPA behaves in a similar fashion to pendant arm donor atoms in PyMAC ligands and its degree of coordination dictates the metal's spin state. Novel iron(II) and copper(II) complexes supported by our modified PyMAC ligands as well as examples of our structurally characterized nickel(II) imidoylamide and imidoylamidine complexes will be presented.
Gemstones and Salts as Light Emitters for Learning X-ray Detectors
Authors: Arakawa Etsuo , Voegeli Wolfgang , Kamezawa Chika , Iwami Ryutaro , Shirasawa Tetsuroh , Yamaguchi Yudai , Kamogawa Masashi , Nakata Masataka , Hyodo Kazuyuki
Published: November 2015

The scintillation counter is a widely-used X-ray detector. It contains a scintillator as a luminescent material that converts X-rays into visible light, which is detected with a sensor. A well-known scintillator in the X-ray region is sodium iodide, NaI, an ionic crystal. Before use, it is important to understand how the detector works. For students, the material name and the chemical formula of the scintillator are not familiar, however. In addition, students cannot watch or touch the key element in the detector, because the scintillator is installed inside the housing. Many jewels emit visible light or change their colors under ultraviolet light irradiation. Under X-ray irradiation, the same jewels exhibit similar responses as well. If popular jewels instead of special ionic crystals were used as scintillators, students might show interest in these materials. We propose that photographs of beautiful, brightly shining gemstones and salts could be used as visual educational materials for students to learn the principles of X-ray detectors. Different gemstones and salts were irradiated by intense white synchrotron X-ray radiation at beamline NE7A1 of the PF-AR synchrotron radiation facility at KEK, Japan. Photographs of fluorescence and phosphorescence from the gemstones, and of color changes due to the irradiation, were taken with a remote controlled digital camera. It should be noted that the experimental setup of this study is an easily understood handmade X-ray detector. We will present photographs of exciting gemstones such as Fluorite from the US, Hackmanite from Afghanistan, Mangano Calcite from China, Ruby from Brazil, Selenite from Canada, and Black Opal from Australia. We also irradiated different kinds of colored Himalayan Rock Salt from India or Pakistan, shown in Fig. 1. We will explain basic concepts of X-ray detectors, such as photon counting, dead time, recording, and quantum efficiency, with these photographs.
Structural analysis of tRNA(His) guanylyltransferase comlexed with tRNA
Authors: Nakamura Akiyoshi , Nemoto Taiki , Tanaka Isao , Yao Min
Published: November 2015

tRNA(His) guanylyltransferase (Thg1) of eukaryote adds a guanylate to the 5' end of immature or incorrectly processed tRNAs (3'-5' polymerization) by three reaction steps: adenylylation; guanylylation and dephosphorylation. This additional guanylate provides the major identity element for histidyl-tRNA synthetase to recognize its cognate substrate tRNA(His) and differentiates tRNA(His) from the pool of tRNAs present in the cell (1). Previous studies indicate that Thg1 is a structural homolog of canonical 5'-3' polymerases in the catalytic core with no obvious conservation of the amino acid sequence(2). However, the substrate binding of Thg1 is unclear and requires information on the three-dimensional structure in complex with tRNA. In this study, we determined the crystal structures of Thg1 from Candida albicans (CaThg1) in tRNA-bound (CaThg1-tRNA), ATP-bound (CaThg1-ATP), and GTP-bound (CaThg1-GTP) form, and elucidated how Thg1 functions as a reverse polymerase to add nucleotide(3). The crystal structures of CaThg1-tRNA complex shows that two tRNAs are bound to tetrameric Thg1 in parallel orientation which is consistent with SAXS (Small angle X-ray scattering) and gel filtration analysis. One tRNA interacts with three monomers for its positioning, anticodon recognition, and catalytic activation. The end of the acceptor stem and the anticodon loop are both recognized by the same sub-domain belonging to the different monomers. Moreover, the structural comparison of Thg1-tRNA with canonical 5'-3' polymerase shows that the domain architecture of Thg1 is reversed to that of canonical 5'-3' polymerase.
The many faces of SRP RNA
Authors: Wild Klemens , Kempf Georg , Grotwinkel Jan , Sinning Irmgard
Published: November 2015

The signal recognition particle (SRP) is a ribonucleoprotein complex that plays an essential role in co-translational targeting of membrane proteins. It is found in all three domains of life and exhibits a high diversity regarding composition and structure. In most organisms, SRP can be divided into two functional domains. The S domain mediates recognition and transport of ribosome-nascent chain complexes to the translocation channel, while the Alu domain stalls elongation of the ribosome until the complex has been faithfully delivered._x000B_Here we present the crystal structures of the complete bacterial SRP Alu domain and the ternary complex of human SRP S domain RNA, SRP19, and the SRP68-RBD. Together with previous structures, our data underline the taxon-specific evolutionary adaptation of SRP RNA that has important implications in SRP-mediated targeting.
New applications of sapphire crystals
Authors: Alexeev Pavel , Asadchikov Victor , Bessas Dimitrios , Butashin Andrey , Cecilia Angelica , Deryabin Alexander , Hermann Raphael , Jafari Atefeh , Kanevsky Vladimir , Roshchin Boris
Published: November 2015

Results of studies of sapphire as a prospective material for different modern applications are presented. An analysis of different growth techniques was performed and a crystalline surface treatment technique developed. Processes of high-temperature surface recrystallization have been studied and the structure of dislocations in the crystals examined. Some applications for sapphires are shown. The following techniques were applied: RHEED, AFM, HRTEM, X-ray scattering, topography, and tomography, using both x-ray tubes and synchrotron radiation sources. High-temperature annealing of super-smooth sapphire surfaces (RMS roughness < 0.2 nm) produces terrace-step structures on the surface. The influence of the miscut parameters and annealing conditions on the structures is analyzed. The substrates with such surface structures were used to form regular ensembles of gold nanoparticles and for the epitaxy processes of AIIBVI thin films. The availability of sapphires that are perfect from the X-ray optics point of view can overcome major limiting factors for meV resolved nuclear resonance scattering and other high energy-resolution X-ray spectroscopy techniques. The analysis made by different X-ray topographic methods shows that the presence of dislocations limits the size of useful reflective area of the crystal. It is shown, that only Kyropoulos-grown crystals demonstrate very low dislocation densities, as low as 100 cm^-2, and the most narrow backscattering spectral reflectivity band. This work is supported by the Russian Foundation for Basic Researches (Grants No. 13-02-01065a and 13-02-91325), Presidium of the Russian Academy of Sciences (Program No.24) and Helmholtz association of German Research Centers (HRJRG-402 project). We thank A. Danilewsky, J. Härtwig, A. Muslimov, I. Prokhorov, A. Vasilyev, V. Vlasov for their assistance as well as principal investigators of the project: A. Chumakov, H.-C. Wille, I. Sergueev, S. Stankov.
Ab-initio study of the orthorhombic ndmno3 perovskite
Authors: Bentata Samir , Bouadjemi Bouabdellah , Lantri Tayeb , Benstaali Wissem
Published: November 2015

We investigate the structural, electronic and magnetic properties of the orthorhombic Perovskite oxyde NdMnO3 through density-functional-theory (DFT) calculations using both generalized gradient approximation GGA+U, where U is on-site Coulomb interaction correction. The electronic band structure, the partial and total density of states (DOS) and the magnetic moment are determined. The results show a half-metallic ferromagnetic ground state for the orthorhombic NdMnO3.
Gold, Glass, and Garnets: A Micromanufactured Diode Beamstop
Authors: Bryant Diane , Morton Simon , Allaire Marc , Pepper John , Dimaggio Scott , Krueger Kurt , Royal Kevin , Dickert Jeff , Zwart Peter , Ralston Corie
Published: November 2015

Beamline improvements through the years have been critical for maintaining high throughput and reliability on macromolecular crystallography synchrotron beamlines. At the BCSB, development of microparts and assembly procedures are becoming more important in order to continually evolve our beamlines. I will present innovations and improvements in potential beam measurement strategies utilizing a diode beamstop system, developed in house at the BCSB. There have been four generations in the development process of the diode beamstop (DBS), resulting in the development of unique micromanufacturing processes. These will be described, and the specifics of each generation of the DBS as well as the most recent results from the use of the DBS will be presented.
Structure for the N-terminal domain of HCV glycoprotein E1
Authors: El Omari Kamel , Iourin Oleg , Kadlec Jan , Sutton Geoff , Fearn Richard , Hall David , Harlos Karl , Grimes Jonathan , Stuart Dave
Published: November 2015

Single-wavelength anomalous dispersion of sulfur atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy atom incorporation or selenomethionine derivatization. Nevertheless this technique has been limited by the paucity of the signal at usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here we report the data collection and structure solution of the N-terminal domain of the ectodomain of Hepatitis C virus (HCV) E1, from crystals that diffracted very weakly. By combining the data from 32 crystals it was possible to solve the sulfur substructure and calculate initial maps at 7Å resolution, and after density modification and phase extension, using a higher resolution native dataset, to 3.5Å resolution, model building was achievable. The crystal structure of the N-terminal domain of reveals a complex network of covalently linked intertwined homodimers that do not harbor the expected truncated class II fusion protein fold.
IYCr Open Factory: Inviting Young Crystallographers to Europe – Status & Outlook
Authors: Fark Martin , Richter Jens , Brönnimann Christian , Schulze-Briese Clemens , Høghøj Peter , Bossan Frédéric , Hartmann Thomas
Published: November 2015

The STOE DECTRIS Xenocs OpenFactory will take place from 10 to 19 September 2014. Participants receive seven days of intensive training by STOE, DECTRIS and Xenocs staff and guest scientists in cooperation with the IUCr. The training will focus on teaching participants the relevant theoretical skillset as well as giving practical training. In Grenoble, the delegates will spend significant time at the ESRF (European Synchrotron) and will be trained in Small Angle X-ray scattering at Xenocs' headquarters. In Darmstadt, the participants will be trained in Single Crystal and Powder XRD at STOE's headquarter. Delegates will have the opportunity to visit beamlines and interact with scientists at ESRF. Starting on 18 September, all OpenFactory participants will join the STOE annual user meeting. The user meeting is a platform for the exchange of ideas among its participants as well as speeches to highlight recent research results. It will be a unique opportunity for OpenFactory participants to interact with highly experienced XRD users and to build up relevant networks. This presentation and poster will highlight the activity, the focus of the program and present the selected participants for the OpenFactory event. The intention is to update on the status of the OpenFactory, but even more important, to encourage similar activities within and after the International Year of Crystallography. In this context, the presenter will discuss any insights from the applications received, i.e. geographies with particular high interest in the OpenFactory, which could be used to follow up on the OpenFactory with future events.
Charge-Induced Defect Formation in LixCoO2 Battery Cathodes: XRD and PA Spectroscopy Study
Authors: Bitschnau Brigitte , Mautner Franz , Parz Peter , Puff Werner , Würschum Robert , Fuchsbichler Bernd , Koller Stefan
Published: November 2015

Lithium-ion batteries have developed into most advanced battery systems, e.g. laptops and mobile phones. LiCoO2 is a typical intercalation battery cathode material. However, reversible charge-discharge cycling of LiCoO2 is only possible down to 50% of the available Li-ions since further removal of Li-ions drastically reduces the capacity and cycle stability. The formation of vacancy-type defects during the charging process in LixCoO2 battery cathodes was investigated by XRD and position life-time spectroscopy and Doppler broadening of positron-electron annihilation (PA) radiation as defect specific techniques [1]. Li+-extraction, which in a battery mode corresponds to charging, was performed at 293 K under electrochemical control in a 3-electrode test-cell with a Maccor Series 4000 battery tester. The composition of the lithium-ion electrode material used was: 88wt.% LiCoO2 particles, 7 wt.% carbon black as conducting agent, 5 wt.% binder material (polyvinylidene difluoride hexafluoropropylene copolymer). Structural analysis of the electrode samples was performed by means of X-Ray diffraction using a Bruker D8 Advance diffractometer in Bragg-Brentano geometry with Cu-Kα radiation. Diffractograms were measured in the 2-Theta angle range from 150to 1300and were analysed by Rietveld refinement with the programs FULLPROF [2] and X'PertHighScorePlus (Panalytical). For positron annihilation measurements a positron source (22NaCl) was sandwiched between two identical LiCoO2 electrode samples. Positron lifetime measurements were performed with a fast-fast spectrometer with a time resolution of 221 ps. The spectra were analysed by using the program pfposfit [3]. Doppler broadening (DB) measurements were performed in a coincidence setup with two high purity Ge detectors.with energy resolution for the 511 keV annihilation γ-line in the detector system corresponds to ca. 0.88keV (FWHM). Both the Doppler broadening S parameter as well as the positron lifetime component τ1 exhibit a characteristic variation with increasing amount of Li+-extraction; the S-parameter and τ1 first increases upon decreasing x from 1 to 0.6. Further Li+-extraction causes a decrease of S and τ1 (x = 0.55), followed by a re-increase for x<0.55. Conclusions: The regime of reversible charging is dominated by vacancy-type defects on the Li+-sublattice the size of which increases with increasing Li+-extraction. Indication is found that Li+-reordering which occurs at the limit of reversible Li+-extraction (x = 0.55) causes a transition from the two-dimensional agglomerates into one-dimensional vacancy chains. Degradation upon further Li+-extraction is accompanied by the formation of vacancy complexes on the Co- and anion sublattice.
Complexes of Mn(II) with imidazole and 2-thiophene acetic acid ligands
Authors: Boudraa M'hamed , Bouchareb Hasna , Bouacida Sofiane , Merazig Hocine
Published: November 2015

The reactions of 2-thiophene acetic acid and imidazole with manganese (II) chloride resulted in mononuclear [Mn(C6H5O2S)2(C3H4N2)6] (1), or binuclear [Mn2(C6H5O2S)4(C3H4N2)4] (2) and [Mn2(C6H5O2S)4(C3H4N2)4(H2O)] (3) complexes. In the complex (1), the Mn ion is octahedral coordinated by six nitrogen atoms from six imidazole rings and the Mn-O bond lengths are in the range 2.261(4) to 2.275(6) Å. The crystal packing is stabilized by weak C-H...O and N-H...O hydrogen bonds. In the structure of (2), the asymmetric unit is formed from an Mn ion bonded to two N atoms from two imidazole ligands and to three O atoms from three different thiophene acetic acid ligands. Two of these ligands are deprotonated and bridge by the same oxygen atoms between the second manganese ion giving rise to an binuclear complex. In this complex, each Mn cation is located in a slightly distorted square-planar environment and the Mn-N bond lengths are in the range 1,960(3) to 1.976(2) Å. The Mn-O bonds lengths in the square base of the two pyramids are in the range 1.956(5) to 2.000(1) Å. The Mn-O axial bond distance is quite longer than the Mn-O equatorial bond distances and is 2.458(2)Å [1,2]. The crystal packing is stabilized by weak C-H...O and N-H...O hydrogen bonds forming connected layers parallel to (001) planes. When an oxygen of one molecule of water bridges the two metal centers in the complex (2), the environment of the two Mn becomes octahedral and thus we obtain the complex (3). In this latter complex, the Mn-N bonds are in the range 2.192(4) to 2.245(4). All Mn-O bonds are between 2.148(6) and 2.232(7)Å. All structures are disordered in all thiophenyl rings occupy alternatively two positions related to one another by an 180o rotation about the C–C sigma bond [3]. The sulfur and one carbon atom of the ring occupy the same position. The complexes were structurally characterized by single crystal X-ray diffraction analyses, infrared spectroscopy (IR), elemental analyses and thermogravimetric analyses (TGA). Cristal data: (1): MnC30H34N12O4S2 in C2/c, a=11.3492(6), b=13.9186(7), c=22.2101(13), beta= 94.963(4) (2): Mn2C36H36N8O8S4 in P21/n, a=15.996(2), b=10.274(13), c=26.141(3), beta=97.715(9) (3): Mn2C24H38N8O9S4 in P21/n, a=26.206(2), b=8.5421(8), c=19.0694(17), beta= 92.229(4)
Plasmodium falciparum DHODH inhibitor complexes reveal flexible binding site
Authors: Rowland Paul , SINGH Onkar , Ross Leila , Gamo Francisco , Lafuente-Monasterio Maria , Wiegand Roger , Wirth Dyann
Published: November 2015

Malaria is a preventable and treatable disease, yet annually there are still hundreds of thousands of malaria-related deaths. The disease is caused by infection with mosquito-borne Plasmodium parasites. With hundreds of millions of cases each year there is a very high potential for drug resistance and this has compromised many existing therapies. One target under investigation is the enzyme dihydroorotate dehydrogenase (DHODH) which catalyses the rate-limiting step of pyrimidine biosynthesis and is an essential enzyme in the malaria parasite. There are currently several Plasmodium-selective DHODH inhibitors under development. To investigate the potential for drug resistance against DHODH inhibitors in vitro resistance selections were carried out using known inhibitors from different structural classes [1]. These studies identified point mutations in the drug binding site which lead to reduced sensitivity to the inhibitors, and in some cases increased sensitivity to a different inhibitor, suggesting a novel combination therapy approach to combat resistance. To help understand the significance of the inhibitor binding site mutations we determined the crystal structures of P. falciparum DHODH in complex with the inhibitors Genz-669178, IDI-6253 and IDI-6273. Co-crystallisation experiments led to a new crystal form in each case. Here we describe the crystal structures, the binding modes of the inhibitors and the great flexibility of the binding site, which is able to adjust to accommodate different inhibitor series. The structural role of the resistance mutations is also discussed.
DSR- A tool for disorder refinements with SHELXL
Authors: Kratzert Daniel , Krossing Ingo
Published: November 2015

X-ray crystallography as a method used for identifying the atomic and molecular structure of a crystal has led to a better understanding of chemical bonds. It is an essential tool to determine the absolute configuration of molecules, has been important for the characterization of coordination complexes, as well as identifying supramolecular assemblies in biology and material science. Being so successful, one of the remaining problems in practical crystallography is the description of disorder in crystal structures. The Cambridge Structural Database includes 23% of disordered structures in its collection of nearly 700000.[1] The program described here is able to simplify many aspects of disorder modelling. The modelling of disorder with SHELXL is possible since its early stages. SHELXL is able to treat almost every possible kind of disorder but with a lot of manual work. It needs a free variable and a part number in combination of displacement parameters and bond length restraints. DSR (Disordered Structure Refinement) transfers a molecular fragment from a database of molecular fragments to the desired position in the unit cell automatically and generates restraints to stabilize the model (Figure 1). In practice, the user writes a command line into the SHELXL .res file, which subsequently is interpreted by DSR. The command line's main purpose is to tell DSR, which source atom of the fragment should go on which target coordinates in the .res file. The user has to choose a minimum of three atoms from the database fragment (source atoms) and the same amount of target positions (target atoms) where the fitting fragment should be placed on. Molecular fragments can be either imported directly from the GRADE server of Globalphasing Ltd.[4], from existing crystal structures or from ab initio calculations. DSR offers several more options available to make disorder modelling a convenient process. DSR can be obtained from http://goo.gl/BL6wP1.
Active Pharmaceutical Ingredients co-crystals via solvent-free reactions
Authors: Halim Nadiah , Nadzri Noor Izzati , Sanghiran Lee Vannajan
Published: November 2015

Dual-drug co-crystals comprising of active pharmaceutical ingredients (APIs); uracil and 5-fluorouracil with urea have been obtained by mechanochemical reactions. The formation of these co-crystals is typically towards drug design which is to help enhancing the solubility, stability and bioactivity in pharmaceutical development without changing the chemical composition of the APIs. These organic molecules undergo molecular recognition process to obtain a range of two dimensional networks through persistent hydrogen-bonding patterns adopted by certain functional groups, which acts as template and rely on the robustness of such motifs to create new solid- state structures. Hence, here we report the characterization, structural studies, binding energy and also the CDOCKER interaction of the co-crystals.
Crystal Structures of 1,3-Thiaza-4-one Heterocycles
Authors: Yennawar Hemant , Silverberg Lee , Tierney John , Cannon Kevin , Bendinsky Ryan , Cali Aaron , Coyle David , Minehan Michael
Published: November 2015

The five-, six-, and seven-membered 1,3-thiaza-4-one heterocycles are known for their bioactivity. Five-membered 1,3-thiazolidin-4-ones are known to have a very wide range of biological activity, so much that the ring system has been referred to as a "magic moiety" or "wonder nucleus" [1]. Six-membered 1,3-thiazin-4-ones have often been investigated for their biological activity and are of potential medicinal use [2]. The activity of seven-membered 1,3-thiazepan-4-ones is exemplified by the investigational compound omapatrilat [3]. Crystal structures of 1,3-thiaza-4-one heterocycles recently obtained in our laboratory will be presented.
Hydrogenation properties of as quenched Ti45Zr38Ni17quasicrystalline alloys
Authors: Shaz Mohammad , Shahi Rohit , Yadav Thakur , Srivasatava Onkar , van Smaalen Sander
Published: November 2015

The present study deals with the microstructural changes with respect to the processing parameter (quenching rate) and their correlation with hydrogen storage characteristics of Ti45Zr38Ni17 quasicrystalline alloys. The ribbons of the alloy have been synthesized at different quenching rates obtained through different wheel speeds (35, 40, 45 and 50 m/s) and investigated for their hydrogen storage characteristics. The lower cooling rate obtained through low wheel speed (35 m/s) produces, i-phase grains whose size ranges from 300- 350 nm, whereas higher cooling rates obtained through high wheel speed (45 and 50 m/s) promote the formation of grains with size ranges from 100-150 nm in Ti45Zr38Ni17 ribbons. It has been found that the ribbons synthesized at 35 m/s absorbed ∼2.0 wt%, whereas ribbons synthesized at 50 m/s absorbed ∼2.84 wt. % of hydrogen. Thus the hydrogen storage capacity of ribbon increases for the ribbons produced at higher quenching rate. One of the salient features of the present study is that the improvement of hydrogen storage capacity obtained through higher quenching rates (∼45 to 50 m/s wheel speed) leading to the formation of lower grain size.
Local-site cation ordering of Ln3+ions in doped PbTiO3
Authors: Madrigal Arbelio , González Yanela , Barranco Aime , Rosabal Beatriz , Rams Ernesto , Figueroa Santiago , de Oliveira Luiz Augusto
Published: November 2015

The study of doped PbTiO3 with lanthanide (Ln3+) elements is an alternative way in order to obtain high density samples with near optimal piezoelectric properties, avoiding at the same time a high porosity microstructure and a crystal structure with a large c/a ratio. X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS), and scanning electron microscopy experiments were carried out in the (Pb0.88Ln0.08)TiO3 ferroelectric system with a perovskite type structure (Ln = La, Sm; Eu, Gd and Dy). Qualitative EXAFS analysis has shown that Ln ions substitute to Pb2+ and Ti4+ ions at A and B sites of the ABO3 structure, respectively except for La doped PbTiO3. The XRD pattern refinement was consistent with the Ln ion substitution at both A and B sites, which provides the formation of donor and acceptor type defects. The shape of the observed X-ray lines profiles has shown features, which are known for this kind of ferroelectric material to be typical of the ferroelectric domains microstructure. A phenomenological model has been used for fitting the diffraction profiles by the Rietveld method [1]. A two phase model considering isotropic size and anisotropic strain broadening was used as a suitable approximation for describing the peculiar peak shapes of the diffraction pattern[2], resulting in a useful approach for analyzing the effects of the domains microstructure. As example, the figure 1 shows the result of the XRD pattern refinement for the sample (Pb0.88Eu0.08)TiO3 taking into account asymmetric and anisotropic effects [3]. The observed and calculated patterns are denoted with dots and continuous lines, respectively. Bragg reflections are represented by vertical marks. The difference between the observed and the calculated data is plotted at the bottom.
Rietveld Method Applied for Triacylglycerol Polymorphism Analysis
Authors: Calligaris Guilherme , Ribeiro Ana Paula , dos Santos Adenilson , Cardoso Lisandro
Published: November 2015

The characterization of the fat components becomes very useful in the formulation of shortening, margarines and fatty products due to their unique properties of plasticity, texture, solubility and aeration. The qualitative analysis obtained by X-ray diffraction (XRD) can be further improved in order to fulfill the lack of information on the triacylglycerol (TAG) in the hardfat systems aiming a complete polymorph characterization. In this work, as an attempt to quantify the distinct β and β' TAG polymorphs, XRD was combined with Rietveld refinement method and applied to two types of samples: mixtures (M) and blended hardfats (B) samples involving fully hydrogenated of soybean (FHSO) and palm (FHPO) oils. M-samples were prepared with linear concentrations of FHSO (β) and FHPO (β') and their Rietveld analysis have provided the expected content trend through the involved polymorphic phases with a very good agreement (~5%). This result validates the Rietveld method applicability on this kind of materials. The Rietveld method applied for B-samples has shown that β' polymorphic form prevails over the β-form, even for samples originally prepared with FHSO (β)/FHPO (β') = 60/40 ratio (see figure). This result indicates the influence of the seeding process (earlier crystallization of β' phase). This first quantitative approach for blended samples represents a very useful contribution towards the full characterization of fats.
Chemical ordering in Al-Co-Ni approximants studied by Cs-corrected STEM with EDS
Authors: Yasuhara Akira , Yubuta Kunio , Hiraga Kenji
Published: November 2015

Six-types of decagonal quasicrystals (DQCs) and some crystalline approximants have been found in Al-Co-Ni alloys with a wide compositional range from 8 to 25.5 at.% Co and from 20 to 5 at.% Ni with a nearly constant Al content of around 70 at.%, and so the stability of the six DQCs is considered to depend on a ratio of Co/Ni associated with chemical ordering of Co and Ni. However, the study of the chemical ordering of Co and Ni in the Al-Co-Ni DQCs is difficult because of next atomic numbers of Co and Ni, though arrangements of transition-metal (TM) atoms have been determined by Cs-corrected HAADF-STEM observations [1-2]. Besides, it was impossible to distinguish between Co and Ni in a W-(AlNiCo) crystalline approximant by single-crystal X-ray diffraction [3]. Our intention in the present paper is two-fold; the first is to study the structure of the Al-Co-Ni crystalline approximant by Cs-corrected HAADF- and ABF- STEM observations, and the second is to investigate the chemical ordering of Co and Ni in the structure. Using a Cs-corrected scanning transmission electron microscope (JEM-ARM200F), HAADF and ABF images were simultaneously acquired with an incident beam parallel to the b-axis. And atomic-resolution elemental maps were taken with a newly developed silicon drift detector (SDD). The chemical ordering of Co and Ni is clearly seen in the acquired elemental maps. Co atoms are enriched in atomic columns with a decagonal section of 1.2 nm in diameter, and Ni atoms are located in gaps between two-dimensional arrangements of the 1.2 nm atom clusters. It can be concluded that the area ratio of the Co-rich 1.2 nm atom clusters to the Ni-rich gaps results in various types of Al-Co-Ni DQCs with different arrangements of the 1.2 nm clusters.
The upgraded and refurbished High Resolution Powder Diffraction beamline at ESRF - ID22
Authors: Watier Yves , Mairs Trevor , Fihman François , Fitch Andrew
Published: November 2015

This poster will present the novelties and first results of the upgraded and refurbished high resolution powder diffraction beamline ID22 (former ID31) at ESRF. Ongoing projects and future developments will also be discussed.
How to use "random" microseeding before you get your first crystals
Authors: Shaw Stewart Patrick
Published: November 2015

Random Microseed Matrix-Screening (rMMS), where seed crystals are added automatically to random crystallization screens, is a significant recent breakthrough in protein crystallization [1]. One industrial group used the method to solve 38 out of 70 structures generated in a three year period, finding particular success with antibody complexes [2]. rMMS not only produces more hits, it also generates better-diffracting crystals - because crystals are more likely to grow in the metastable zone. This assumes, however, that you have some initial crystal hits to make a seed stock from. This presentation will look at unusual methods of nucleation, including cross-seeding [3], heterogeneous nucleation, and nucleation with precipitants [4].