bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and Magnetic Chirality of Cu2OSeO3
Authors: Dyadkin Vadim , Chernyshov Dmitry
Published: November 2015

We determine the chirality of the magnetic and crystal structures, respectively, for the magnetoelectric insulator Cu2OSeO3using small-angle diffraction of polarized neutrons and resonant contribution to X-ray single crystal diffraction of synchrotron radiation. This compound crystallizes in the P213 space group similar to other chiral but metallic magnets, such as MnSi, MnGe, MnSi1+xGex, Fe1+xCoxSi, Mn1+xFexSi, Mn1+xCoxSi, FeGe, Mn1+xFexGe. It has recently been shown that the structural and magnetic chiralities for metallic helimagnets are linked to each other [1], also in the so-called skyrmion phase [2]. Here we measure the spin chirality by comparing neutron scattering maps from Cu2OSeO3with the reference MnSi, which has left-handed magnetic spiral and absolute crystal structure denoted as left-handed [1]. Similar to the reference MnSi system, the crystallographic chirality of Cu2OSeO3is fixed on the basis of absolute structure determination taking into account the refinement of the Flack parameter. We find that the crystal and magnetic structures of Cu2OSeO3have the same chirality. The similar relationship is found for MnSi, Mn1+xFexSi, MnGe, while FeGe and Fe1+xCoxSi always show the opposite chiral correlation between magnetic and crystal structures. Notably, the relationship between two chiralities for Cu2OSeO3found in the experiment is opposite to that proposed from recent theoretical calculations [3], thus calling for a revision of the theory of possible microscopic mechanisms contributing to the phenomenological antisymmetric magneto-lattice coupling.
Spin chirality is flipped in transition-metal monogermanides
Authors: Siegfried S.-A. , Altynbayev E. V. , Chubova N. M. , Heinemann A. , Dyadkin V. A. , Moskvin E. V. , Menzel D. , Tsyashchenko A. V. , Lott D. , Schreyer A. , Grigoriev S. V.
Published: November 2015

Using high pressure method polycrystalline powder samples of Mn1-xFexGe and Fe1-yCoyGe have been synthesized with x/y running from 0.0 to 1.0. The crystallite size for these compounds is in the order of 10 microns. SQUID magnetization and small angle neutron scattering (using SANS-1 at the MLZ, Garching) have revealed the helical magnetic ordering of the samples within the concentration range of x = [0.0 – 1.0] and y = [0.0 – 0.8]. The values of the helical wavevector k have been taken from the SANS pattern. As it could be seen in Fig.1 a) for Mn1-xFexGe the wavevector k remains roughly constant around 2 nm^-1 for x ≤ 0.4, while going down to a minimum for (|k| -> 0) at xc ≍ 0.75 and increases again to a value of 0.09 nm^-1 for pure FeGe. For Fe1-yCoyGe the k value smoothly decreases from 0.09 nm-1 for pure FeGe to its minimum at yc ≍ 0.6 and increase again for y = 0.8 to its maximum of 0.14 nm^-1 (Fig.1 b). For x/y -> xc/yc we observe a transformation of the helical magnetic structure to a ferromagnetic-like one at the critical concentrations. The change of the magnetic structure from helimagnetic to ferromagnetic-like goes along with a different sign of the magnetic chirality for x/y < xc/yc and x/y > xc/yc [1,2].
Spin-1/2 frustrated zigzag chain compound beta-TeVO4
Authors: Zaharko Oksana , Pregelj Matej , Zorko Andrej , Arcon Denis , Nojiri Hiroyuki , Morioka Takayuki , Berger Helmut
Published: November 2015

We report on exotic magnetic ordered states and phase diagram of frustrated spin chain compound beta-TeVO4 studied by specific heat, neutron diffraction, and high-field magnetization measurements. This compound, comprising weakly coupled infinite chains of VO5 pyramids sharing corners, is proposed to be a new realization of the zigzag J1-J2 model [1]. In qualitative agreement with this proposal, we found an incommensurate, ICM, magnetic order with q1=(-0.208 0 0.436) below TN=4.65 K and a series of transitions between consecutive ICM magnetic phases, exhibiting pronounced temperature, T, and magnetic field, H, dependences. Of special interest is a long-scale modulated phase with high-order satellite magnetic reflections (fig. 1) that might reflect the formation of magnetic solitons [2] existing in a narrow T,H-range.
Large-Scale Computational Screening of Novel Compounds for Carbon Capture
Authors: Dunstan Matthew , Liu Wen , Ong Shyue Ping , Jain Anubhav , Persson Kristin , Dennis John , Scott Stuart , Grey Clare
Published: November 2015

Carbon capture and storage (CCS) applications offer a plausible solution to the urgent need for a carbon neutral energy source from stationary sources, including power plants and industrial processes. The most mature technology for post-combustion capture currently uses a liquid sorbent, amine scrubbing. However, with the existing technology, a large amount of heat is required for the regeneration of the liquid sorbent, which introduces a substantial energy penalty. Operation at higher temperatures could reduce this energy penalty by allowing the integration of waste heat back into the power cycle. New solid absorbents for use at intermediate to high temperatures, such as CaO, have shown promise in pilot plant studies, but are still far from ideal due to their poor capacity retention upon successive cycling. This presentation will describe our studies aimed at rationally selecting and designing materials for carbon capture and storage applications. We use ab initio calculations of oxide materials from the Materials Project database1 in an effort to screen for novel materials with optimal thermodynamic and kinetic properties for CO2 looping applications. From the determination of a material's optimised structure and ground state energy we have then constructed a screening routine for materials within the database based on simulating their carbonation equilibria and phase stability under differing atmospheric concentrations of CO2. A number of promising materials were identified from the screening, and we are currently investigating their properties experimentally, by using a combination of methods (including thermogravimetric analysis, in situ x-ray diffraction and microscopy). In this way we are able to assess the validity of the screening methodology, and use the insights afforded by experimental studies to iteratively improve the entire process.
Structure, bonding and dynamcs under extreme conditions
Authors: Tse John
Published: November 2015

Knowledge on the composition and structure of a material are essential to the understanding of the properties. Recent advances in structural prediction techniques from first-principles calculations have greatly enhanced the perspective on the large variety of new crystal types, particularly, under extreme conditions at high pressure and high temperature. The structural information helps to develop a new understanding on the change in chemical bonding in highly compressed solids. I will present the results and experience in the use of several structural prediction methods with examples drawn from recent studies on the outstanding problems in pressure-induced amorphization of SnI4, structural transformations, atomic dynamics and structural chemistry of simple elemental and molecular solids at high pressure and high temperature. Our results will highlight the successes, challenges and future development on the practical applications of these methods.
Looking into the structure of Ge nano-crystals through combined Diffraction/XAFS
Authors: Zhang Yuanpeng , Karatutlu Ali , Ersoy Osman , Sapelkin Andrei
Published: November 2015

Nano-particles of different materials including II-VI (ZnS, ZnO, etc.), III-V (AlN, GaN, etc.) and IV (Si, Ge, etc.) have been applied widely because of their superb optical-electrical properties. More importantly, the size & structure-dependent character of their physical properties due to the quantum confinement effect attracted much research interest during the past decades [1]. Ge is characterized by relatively large Exciton Bohr Radius (≍24nm) [3], which potentially favors the quantum confinement effects for tuning the photoluminescence (PL) properties. Besides, the low toxicity of Ge suggests potential biological applications such as cell imaging and labeling [4]. For the structure characterization of our prepared Ge quantum dots (QDs), we used the in-house X-ray pair distribution function (PDF) machine (X-ray from Ag source with wavelength down to 0.056nm) and Diamond light source synchrotron radiation source (XAFS, XRD, PL, etc.) to characterize the atomic structure. Several other methods such as TEM and SAED were used to provide a comprehensive picture of QDs on nanoscale. The results showed that our as-prepared Ge QDs are amorphous with small size, and annealing process could attenuate the Ge-O bonding. In both aged as prepared and fresh annealed samples we observed a diffraction peak corresponding to d-spacing around 2.8Å, which can be associated with either ST12 or BC8 metastable phase of Ge. Moreover, samples showing extra diffraction peaks also shows different XANES features from that of diamond Ge. The fdmnes calculation and FitIt fitting was carried out to further look into structural information.
In crystallo optical spectroscopy as a complementary tool to crystallography
Authors: Royant Antoine
Published: November 2015

The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially if these are applied to the crystals themselves. As a consequence, optical spectroscopies as applied in Structural Biology have become instrumental in assessing the relevance of many crystallographic results. Since the year 2000, such data can be recorded close to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This presentation will report the status of the current version of the Cryobench, now located on the MAD beamline ID29 and thus called ID29S-Cryobench, S standing for 'Spectroscopy'. In particular, the new on-line Raman data collection mode of ID29 will be described. Finally, it will review the diverse experiments that can be performed at the Cryobench, highlighting various scientific questions that can be addressed.
Defect induced forbidden X-ray reflections in RbH2PO4.
Authors: Richter Carsten , Novikov Dmitri , Mukhamedzhanov Enver , Borisov Michail , Ovchinnikova Elena , Oreshko Alexey , Akimova Ksenia , Dmitrienko Vladimir , Strempfer Jörg , Zschornak Matthias , Mehner Erik , Meyer Dirk
Published: November 2015

Resonant X-ray diffraction was used to study the proton jumps in hydrogen-bonded rubidium dihydrogen phosphate (RDP) crystals. In the paraelectric RDP phase, hydrogen is delocalized between two crystallographically equivalent positions. At lower temperatures, this symmetry can be broken, which defines the processes that lead to the para- to ferroelectric phase transition. We have measured the energy spectra of the forbidden reflections 006 and 550 at incident radiation energies close to the Rb K-edge in a wide temperature range, down to the temperature of the ferroelectric phase transition. In the paraelectric phase we observed a growth of integrated intensity for both forbidden reflections with temperature. This behavior is opposite to conventional non-resonant Bragg reflections, where the intensity decreases in accordance with the Debye-Waller factor. The developed theoretical model explains this effect with the thermal motion induced (TMI) scattering mechanism and also confirms the adiabatic approximation stating that electrons instantly follow the nuclei movements. In the 550 energy spectra, we have observed an additional contribution to the resonant structure factor which could be associated with the presence of transient Slater-type proton configurations (PC) in the half-filled hydrogen position.
Early stages of solid state reactions: insights from micro-XRD and XAS
Authors: Tarantino Serena , Ghigna Paolo , Achilli Elisabetta , Pin Sonia , Zema Michele , Spinolo Giorgio
Published: November 2015

The mechanism of a solid state reaction in its early stages can be explored by investigating the time evolution of a model reactive system made of a thin layer of one reagent deposited onto a single crystal slab of the other reagent. Insights can be retrieved by comparing results at both local and long length scales obtained with films of different thicknesses and deposited onto different crystal orientations. In particular, reaction between ZnO and Al2O3has been chosen, as the spinel-forming reactions have been and still remain a model experimental system for investigating solid state reactions and because in the ZnO/Al2O3phase diagram, spinel is the only stable compound. The reaction initial steps have been investigated by using synchrotron X-ray diffraction, atomic force microscopy and X-ray absorption spectroscopy at the Zn-K edge starting from zincite films deposited onto (110)-, (012)-, (001)-oriented corundum single crystals [1,2]. The reaction eventually yields ZnAl2O4spinel but via a complex mechanism involving side and intermediate non-equilibrium compounds that do not appear in the equilibrium phase diagram of the pseudo-binary system. Spinel, when occurs, is polycrystalline at the end but initially forms with a few preferred orientations. Intermediate phases form before and in parallel with the growth of the spinel. Their number, composition, structure and kinetic role strongly depend on substrate orientation and film thickness. A more detailed understanding of the reactivity can be inferred by comparing EXAFS results to those of grazing incidence diffraction experiments of the films deposited on the (001) face of Al2O3and heat-treated at 10000C for different lengths of time. Information on the structure of the intermediate phases is given and results are discussed by comparing different films thickness to clarify the role of interfacial free energy and crystallographic orientation.
NMR crystallography driven structure determination
Authors: Martineau Charlotte , Bouchevreau Boris , Taulelle Francis
Published: November 2015

Because solid-state nuclear magnetic resonance (ss-NMR) spectroscopy is sensitive to local order and is selective to the nature of the atoms, this technique has emerged as ideally complementary to powder diffraction for structure determination of a wide range of solids. Here, we will illustrate with the example of hybrid solids (aluminophosphates) the role of high-resolution one and two-dimensional solid-state NMR data to drive the search for a structure model from powder diffraction data. Great progresses have been made in the field of ss-NMR in the past few years (higher magnetic field, more robust pulse sequences, etc.) that now allows access to NMR spectra with very high resolution in such compounds [1]. From these NMR data, information about the cations (number, coordination number, etc) and the connectivity between the cation polyhedra are readily available. Such knowledge allows performing a more constraint structure search, thus increasing the chance to obtain a solution [2]. NMR data further provide information about the non-periodic sub-networks in hybrid compounds (water molecules, OH groups, templates...), allowing to draw very detailed pictures of the solids [3].
Sturucture of the stress response protein SAV1875 from S. aureus
Authors: Kim Hyojung , Kwon Aeran , Lee Bongjin
Published: November 2015

The DJ-1/ThiJ/PfpI superfamily is a large protein group over diverse organisms, under this superfamily, there are multi-types of proteins such as protease, chaperones, heat shock protein, human parkinson's disease protein. The conserved protein from Staphylococcus aureus SAV1875 is a member of DJ-1 superfamily, but its function is unknown. We have determined the crystal structure of SAV1875 to a resolution of 1.8Å . As expected, the overall fold of the core domain of SAV1875 is similar to that of DJ-1. SAV1875 appears to be a dimer both in solution and the crystal, displaying an oligomerization interface similar to that observed for DJ-1. SAV 1875 contains a possible catalytic triad (Cys105-Glu17-His106) analogous to PfpI, YhbO, and DR1199. The cysteine in this triad (Cys-105) is oxidized in this crystal structure, similar to modifications seen in the cysteine of the DJ-1. This Cys-sulfenic acid is stabilized by hydrogen bonding with Glu17, Gly72, His106. We also have determined the crystal structure of mutated form of reactive Cys, SAV1875 C105D to a resolution of 2.1 Å. Aspartate mutation mimics the the Cys-sulfinic acid, more oxidized form. The aspartate stabilization by hydrogen bonding with neighboring residues are maintained. On the basis of these results, we suggest that SAV1875 might work as a general stress protein involved in the detoxification of the cell from oxygen reactive species.
Hidden Hoogsteens in the Data
Authors: Hintze Bradley , Zhou Huiqing , Al-Hashimi Hashim , Richardson David , Richardson Jane
Published: November 2015

Although extremely rare in the crystallographic database, Hoogsteen (HG) base pairs have been modeled, especially at duplex termini, protein-DNA interfaces, damaged DNA and DNA mismatches. Formation of HG base pairs in duplex DNA requires a 180 degree rotation along the glycosidic bond of the purine relative to the canonical Watson-Crick (WC) base-pair. In a recent survey of the PDB we identified 75 HS base pairs in 2,910 x-ray derived models. Recent evidence suggests that the prevalence of HG base pairs in nature to be greater than previously thought. Due to electron density density ambiguity at mid to low resolution, it is possible for bases to be modeled incorrectly. We have developed a high-throughput method which examines the difference density around DNA to identify mis-modeled bases. Here we show where bases were incorrectly modeled and our subsequent fixes which show pairs modeled as WC that really are HG, vice versa, and evidence of WC-HG alternates. This research shows that base pairing conformations in DNA are more heterogeneous than previously thought.
Piecing together the ryanodine receptor with crystal structures and cryo-EM
Authors: Lau Kelvin , Van Petegem Filip
Published: November 2015

The ryanodine receptor is the largest ion channel known. It is responsible for the release of calcium ions from the intracellular stores of the sarcoplasmic/endoplasmic reticulum. The release of calcium signals for a wide assortment of cellular processes, most importantly, muscle contraction in skeletal and cardiac tissue. Only two regions of this receptor have been described by high-resolution crystal structures. In addition these two domains have been docked into low-resolution cryo-EM structures. Here, I will present a x-ray crystal structure of a novel domain from the ryanodine receptor of both skeletal and cardiac isoforms. Stability of the wild-type versus those of mutants will be discussed as well as the implications of the structure of a mutant linked to cardiac hypertrophy and a loss of function phenotype. The docked location of the domain within the whole channel may suggest its functional properties.
Which metal or ion? Identification of metals and ions in protein structures
Authors: Dohnalek Jan
Published: November 2015

Identification of ligands in single crystals of biomolecules is often uneasy. The target molecules undergo expression, purification, and special pre-crystallization treatment and even trace impurities in known chemicals become a source of potential ligands. The final "binders" belong to a large set of both natural cofactors and chemicals encountered before the diffraction experiment. Some promiscuous metal binding sites can bind different types of metals of the fourth period and activity towards the same substrate can be measured with different divalent metals in active sites of nucleases, anhydrolases, etc. Therefore, 1) Not all structures have correct ions; 2) Ion identification in all structures requires high attention, especially in metal-dependent proteins. To date 98% of X-ray structures in the PDB have the high diffraction limit of 1.2 Å or worse. Thus we must rely on other indicators as for the ion type than just the height of electron density because our data often provide an accurate picture of a mixture of states. Therefore, essential determinants (relative heights of unbiased electron density maxima, anomalous signal, the shortest interatomic distances, stability of atoms in refinement, nature of coordinating atoms) must be distinguished from marginal factors which can be smeared by worse data quality, resolution limits, position in protein chain or local disorder (atomic displacement parameters, occurrence of longer coordination distances, missing vertices of the first coordination sphere). We have applied the described approach to identify cations, such as Cu2+, Mn2+, Zn2+, Ni2+, Ca2+, Mg2+, Na+ and other ionic ligands, for instance Cl-, PO43-, SO42- [1]. The available tools for identification of metals/ions also include statistics on coordination and bonding distances [2], absorption edge detection and fluorescence [1] or microbeam proton induced X-ray emission [3]. The work was supported by MEYS CR (EE2.3.30.0029) and BIOCEV (CZ.1.05/1.1.00/02.0109).
Check your metal - not every density blob is a water molecule
Authors: Zheng Heping , Chordia Mahendra , Cooper David , Shabalin Ivan , Chruszcz Maksymilian , Müller Peter , Sheldrick George , Minor Wladek
Published: November 2015

Metals play vital roles in both the mechanism and architecture of biological macromolecules, and are the most frequently encountered ligands (i.e. non-solvent heterogeneous chemical atoms) in the determination of macromolecular crystal structures. However, metal coordinating environments in protein structures are not always easy to check in routine validation procedures, resulting in an abundance of misidentified and/or suboptimally modeled metal ions in the Protein Data Bank (PDB). We present a solution to identify these problems in three distinct yet related aspects: (1) coordination chemistry; (2) agreement of experimental B-factors and occupancy; and (3) the composition and motif of the metal binding environment. Due to additional strain introduced by macromolecular backbones, the patterns of coordination of metal binding sites in metal-containing macromolecules are more complex and diverse than those found in inorganic or organometallic chemistry. These complications make a comprehensive library of "permitted" coordination chemistry in protein structures less feasible, and the usage of global parameters such as the bond valence method more practical, in the determination and validation of metal binding environments. Although they are relatively infrequent, there are also cases where the experimental B-factor or occupancy of a metal ion suggests careful examination. We have developed a web-based tool called CheckMyMetal [1](http://csgid.org/csgid/metal_sites/) for the quick validation of metal binding sites. Moreover, the acquired knowledge of the composition and spatial arrangement (motif) of the coordinating atoms around the metal ion may also help in the modeling of metal binding sites in macromolecular structures. All of the studies described herein were performed using the NEIGHBORHOOD SQL database [2], which connects information about all modeled non-solvent heterogeneous chemical motifs in PDB structure by vectors describing all contacts to neighboring residues and atoms. NEIGHBORHOOD has broad applications for the validation and data mining of ligand binding environments in the PDB.
Porous metal-organic frameworks incorporating mixed ligands
Authors: Oliver Clive
Published: November 2015

Metal-organic frameworks (MOFs), infinite systems built up of metal ions and organic ligands have been extensively studied in materials and supramolecular chemistry due their structural diversity and application as porous materials, in catalysis, ion exchange, gas storage and purification. [1] A novel, 2-fold interpenetrated, pillared, cadmium metal-organic framework was synthesized using trimesic acid and 1,2-bis(4-pyridyl)ethane.[2] Single crystal X-ray analysis revealed a 2-fold interpenetrated, 3-dimensional framework which exhibits a 3,5-connected network with the Schläfli symbol of [(6^3)(6^9.8)] and hms topology. This compound exhibits a temperature-induced single-to-crystal-single-crystal (SC–SC) transformation upon the release of N,N'-dimethylformamide (stable up to 3000C). SC–SC transformation was also observed when the desolvated form absorbed selected polar and non-polar organic solvents. In addition, gas (N_2, CO_2 and N_2O) sorption experiments were performed showing 2.5% N_2, 4.5% CO_2 and 3.4% N_2O absorption by mass at room temperature and moderate gas pressures (~10 bar). A similar MOF was produced when 1,3,5-benzenetricarboxylic acid was replaced with 5-nitro-1,3-benzenedicarboxylic acid. This MOF displays 4-fold interpenetration and also maintains the host framework structure upon heating.
Dynamic porous property in a new heterometallic supramolecular compound
Authors: Kenfack Patrice , Wenger Emmanuel , Dahaoui Slimane , Lambi John , Durand Pierrick , Ponou Siméon , Lecomte Claude
Published: November 2015

Supramolecular compounds have attracted considerable interest to chemists, physicists and materials scientists due to their fascinating structures and potential applications as porosity [1-3] but one of the most appealing aims today, is to build multifunctional compounds. We are interested to rationalize the synthesis of porous heterometallic compounds by self- assembly via hydrogen bonds. In this communication, we present a stacked 2D Catena-{Co(amp)3Cr(ox)3.6H2O} (amp = 2-picolylamine, ox=oxalate). It is built by layers in which both (Co(amp)3+ (D) and Cr(ox)3- ( A)) ionic units are linked in a repeating DADADA...pattern along both the a and c axis with four and two hydrogen bonds respectively. These layers host very well resolved dodecameric discrete ring water clusters (R12) built by six independent molecules located around the centrosymmetric Wyckoff position's of the P21/n space group in which the compound crystallizes. The clusters are ranged along the [001] direction, occupy 807.6 Å3 (23.9%) of the unit cell and have a chair conformation via 10 hydrogen bonds. The dehydration process of the compound occurs in one step around 77oC and the dehydrated compound remains crystalline although all framework atoms move by 2.25 Å along a mean vector (dm= 2.21 i + 0.17 j + 0.37 k) during the process. The unit cell is then reduced by 12.34 % along a, 12.22% along b and 2. 03% along c reducing V by 22.03%. By exposure to air, the regeneration of the compound needs 90 min, following the first kinetic Avrami's model.
In-situ analysis of gas-loaded porous materials
Authors: Barbour Len
Published: November 2015

In order to understand gas sorption processes at the molecular level it is important to correlate physico-chemical data (e.g. sorption isotherms and calorimetric analysis) with structural data. It is therefore desirable to carry out structural elucidation and calorimetric analysis under conditions that closely mimic those of the sorption/desorption experiments. However, the crystallographic analysis of samples under controlled gas environments poses significant technical challenges, particularly given the limited space associated with the sample compartment of standard commercial diffractometer. In this regard, an environmental gas cell has been developed in parallel with a pressure-programmed differential scanning calorimeter. Use of these complementary techniques has provided new insight into features such as pressure-induced phase transformations that give rise to inflections and hysteresis in sorption isotherms. The influence of guest molecules on aspects such as structural flexibility, linear thermal expansion and changes in network interpenetration will be discussed.
Amorphous Metal-organic Frameworks: Structure, Properties and Application
Authors: Bennett Thomas
Published: November 2015

A small but growing number of cases of MOFs lacking the long-range order characteristic of crystalline structures are steadily capturing scientific interest (though they remain woefully under represented), despite the phenomenon being known in inorganic zeolites. The majority of work has been performed on a sub-family of MOFs called zeolitic imidazolate frameworks (ZIFs), which consist of tetrahedral metal centers (typically Zn2+ or Co2+), connected by Imidazolate-type (C3H3N2-) organic ligands in zeolitic topologies. Recently, we discovered that ZIFs could be amorphized by ball-milling and heating, and that the resultant amorphous material has a similar topology to that of silica glass.(Bennett et al., 2010, Bennett et al., 2011) Similarly, they can also be amorphized by pressure, though there is considerable debate about the reversibility of the process. Amorphous MOFs, whilst significantly harder to characterise, are more mechanically stable than their well-known crystalline counterparts. They also offer routes to functional glass materials, through melting of functionalised parent frameworks (incoporating lanthanide ions or chiral ligands). Some of these glasses have been shown to be topologically `perfect' with fragilities lower than that of aSiO2. Recently, we have shown that the release in-vitro of ibuprofen and caffeine stored within ZIF-8 can be tailored by ball-milling inducing collapse of the framework, whilst I2 has also been irreversible captured using similar methodology.(Bennett et al., 2013) Significant challenges exist in exploring the field of amorphous hybrid frameworks, though access to a multitude of functional materials is indeed a worthwhile reward.
Observation of electron transfer associated with enzymatic process by muSR
Authors: Kiyotani Tamiko , Kobayashi Masayoshi , Tanaka Ichiro , Niimura Nobuo
Published: November 2015

We propose muSR experiments on trypsin-BPTI complex to visualize the electron and proton transfer processes occurring in the catalytic reaction of the trypsin. The mechanism of an inhibitory effect of the BPTI is interpreted that the reaction products of BPTI remain at a part of the structure and the reverse reaction reforms the stable trypsin–BPTI complex, which has been confirmed by neutron diffraction experiment of the trypsin-BPTI complex [1]. However, it never sees the real image of the proton and electron transfer processes directly. According to the model provided by the results of neutron diffraction experiments, the proton and electron transfer processes are continuously occurring in a crystal of trypsin-BPTI complex and the process induces the local magnetic field. The slow muon is very adequate because the position, where mu+ is captured, is absolutely negatively charged oxyanion hole close to the reaction center of Trypsin. The distance between the oxyanion hole and the active peptide bond is about 10Å. When the turn over time of the catalytic reactions is assumed to be 10msec or so, the induced magnetic field would be estimated as 0.2 micro-T. In order to check the effectiveness of the measurement of the μSR experiments on trypsin-BPTI complex, another measurement of the muSR experiments on the trypsin- MIP complex is adequate [2]. Here, MIP is a kind of the trypsin inhibitor, which completely stops the catalytic reaction of trypsin. In the trypsin-MIP complex, no electron and proton transfers at all in the active site of trypsin and captured mu+ at the oxyanion hole would never be sensitive to the induced magnetic field [3].
A pipeline for the rapid generation of difference maps from protein crystals
Authors: Wojdyr Marcin , Keegan Ronan , Winter Graeme , Ashton Alun , Lebedev Andrey , Krissinel Eugene
Published: November 2015

"In 2013 MX beamlines at the Diamond synchrotron deployed an automated software pipeline, called DIMPLE, for rapid processing of crystals that contain a known protein and possibly a ligand bound. DIMPLE takes the already known ""apo"" structure for the target protein, compares it with the electron density map from X-ray diffraction images, and visualizes areas of the electron density unaccounted for by the structure model. When processing batches of crystals, such feedback allows the user to better decide what to measure next which leads to a more efficient use of the beam time. This year we've enhanced the pipeline to cover more complex cases, including changes in the space group and some changes in conformation. With multiple molecular replacement computations run in parallel, the time from shooting to viewing the difference map is still only a few minutes. While the software is developed primarily for use at synchrotron beamlines, it is included in the CCP4 suite and can be used as well for in-house automation."
Color Symmetry of Certain Tilings with a Singular Center
Authors: Evidente Imogene , Felix Rene , Loquias Manuel Joseph
Published: November 2015

"Tilings with singular points, or tilings that are not locally finite, are classified in [1] among tilings that are not ""well-behaved"". In [2], colorings of tilings with a singular center were obtained from certain colorings of regular Euclidean tilings. It was observed that not all such colorings could be transformed into colorings of tilings with a singularity. Moreover, the existence of maximum color indexes was surmised. In this paper, we provide a mathematical basis for the said observations by utilizing conformal maps that distort a regular Euclidean tiling into a tiling with a singular center. That is, we determine conditions so that a coloring of a regular Euclidean tiling can be transformed into a coloring of a tiling with a singular center. In addition, we establish that a maximum number of colors exists. Finally, we give conditions so that the symmetry group of the tiling with a singular center induces a permutation of the colors."
Nanocrystalline Oxides: CdS nanowires synthesized by solvothermal method
Authors: Hadia Nomery , Garcia-Granda Santiago , Garcia Jose
Published: November 2015

Recent advances in the field of nanotechnology produced an assortment of one-dimensional (1D) structures, such as nanowires and nanorods. These fascinating materials are the potential building blocks for a wide range of nanoscale electronics, optoelectronics, magnetoelectronics, or sensing devices [1]. Parallel to the success with group IV and groups III–V compounds semiconductor nanostructures, semiconducting metal oxide materials with wide band gaps are attracting attention [2-3]. The main aim of this communication is to report our results on the application of several new techniques, particularly the use of hydrothermal synthesis, to fabricate single crystal one-dimensional nanostructured materials, study their growth processes, understand the growth mechanisms and investigate their physical properties. A wide range of remarkable features are then presented, to cover a number of metal oxides, such as ZnO, Sb2O3, CdS, MgO, α-Fe2O3, or TiO2, describing their structures, optical, magnetic, mechanical and chemical sensing properties. These studies constitute the basis for developing versatile applications based on metal oxide 1D systems as well as highlighting the current progress in device development. To exemplify, the as-prepared CdS nanowires have average 28 nm in diameter and length up to several micrometres. The direct band gap of the CdS nanowires is 2.56 eV calculated by the UV-vis absorption spectra. The PL spectrum has two distinct emission bands at 502 nm and 695 nm, which are associated with the near-band-edge emission and defect emission, respectively. These synthesized single-crystal CdS nanowires have a high potential in the optoelectronic applications of nanolasers, solar cells, lighting-emitting diodes or photodetectors. Acknowledgments: Erasmus Mundus MEDASTAR (Mediterranean Area for Science, Technology and Research) Programme, 2011–4051/002–001-EMA2, Spanish MINECO (MAT2010-15094, Factoría de Cristalización – Consolider Ingenio 2010) and ERDF.
Structural basis for error-free bypass of bulky adduct by DNA polymerase Polκ
Authors: Jha Vikash , Ling Hong
Published: November 2015

Humans are frequently exposed to the environmentally ubiquitous and potentially carcinigenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). BP is metabolized to highly reactive benzo[a]pyrene diol epoxides (BPDEs) in the cells. BPDEs react with DNA predominantly at the N2 position of guanine and form bulky adducts. The major BP adduct is (+)-trans-anti-[BP]-N2-dG (BP-N2-dG) that is carcinogenic. The bulky adduct block DNA synthesis by replicative or high-fidelity DNA polymerases. Some of the specialized lesion bypass polymerases (mostly belonging to Y-family) can replicate through this bulky adduct but often in an error prone manner, resulting in mutagenesis. Among the four human Y-family polymerases Polη, Polκ, Polι and Rev1, Polκ is unique in its ability for efficient and error-free replication through BP induced BP-N2-dG adduct. In this study, we determined the crystal structures of human Polκ (hPolκ) in ternary complex with DNA and an incoming nucleotide dCTP analogue. The crystals contain DNA with either G base or (+)-trans-anti-[BP]-N2-dG adduct at a template-primer junction and diffract to 2.5 Å and 2.8 Å, respectively. The structures reveal that hPolκ is able to accommodate the bulky adducted DNA in its minor groove without base flipping and nucleotide looping out. The bulky adduct has the polycyclic BP moiety in the minor groove in the regular helical conformation. Polκ has a unique active site that is more open at the minor groove side than other Y-family polymerases. The damaged guanine is in the anti-conformation, the dCMPNPP incoming nucleotide maintains normal Watson-Crick pairing with the G* base. This is the first structure of eukaryotic Y-family polymerase carrying the minor groove BP adduct. The structure and biochemical analysis provides a basis for understanding how hPolκ can correctly bypass and tolerate BP induced BP-N2-dG adduct in human cells.
Regulation of the ribosome and protein synthesis by RNAi
Authors: Flygaard Rasmus , Kidmose Rune , Nielsen Maja , Jenner Lasse
Published: November 2015

In many biological processes, e.g. the development of multicellular organisms, a tight regulation of the protein synthesis is a necessity. Among numerous mechanisms for translational control, RNA interference (RNAi) based mechanisms have been shown to regulate the translation of messenger RNA (mRNA) and hence regulate the synthesis of proteins. The key proteins in all RNAi mechanisms are the argonaute proteins. The only catalytically active argonaute protein is denoted argonaute2 (Ago2) in humans. This single chain protein is comprised of four globular domains arranged in a crescent shape tertiary structure [1]. The guide RNA binding specificity lies within the Mid and PAZ domain while the active site resides in the PIWI domain. In 2011 it was reported that the receptor for activated C-kinase (RACK1), an integral protein of the ribosomal 40S subunit, directly binds the microRNA induced silencing complex (miRISC) [2] and thereby contributes to gene repression through RNAi mediated knockdown. This interaction of RACK1 with miRISC was furthermore shown to be a specific interaction between Ago2 and RACK1. Structural investigation of this interaction will be of great interest to elucidate how Ago2 is positioned in relation to ribosome bound mRNA and if this positioning of Ago2 on the ribosome facilitates mRNA binding to the guide RNA bound in Ago2. In our studies we will co-crystallize recombinantly expressed Ago2 with 80S ribosome from S. cerevisiae [3] and solve the structure by x-ray crystallography. Recent project progress will be presented on the conference poster.
Structural and functional studies of the decapping exoribonucleases
Authors: Chang Jeong Ho , Tong Liang
Published: November 2015

Recent studies showed that two homologous yeast proteins, Rai1 and Dxo1, function in a quality control mechanism to clear cells of incompletely 5' end-capped messenger RNAs (mRNAs). Rai1 possesses a novel decapping activity that can remove the entire cap structure dinucleotide from an mRNA. This activity is targeted preferentially towards mRNAs with unmethylated caps in contrast to the canonical decapping enzyme, Dcp2, which targets mRNAs with a methylated cap. Dxo1 also has robust decapping activity on RNAs with unmethylated caps, but it has no detectable pyrophosphohydrolase activity. Unexpectedly, we found that Dxo1 also possesses distributive, 5'-3' exoribonuclease activity, and we named Dxo1 (originally Ydr370C) for this new eukaryotic enzyme with both decapping and exonuclease activities. Studies of yeast in which both Dxo1 and Rai1 are disrupted reveal that mRNAs with incomplete caps are produced even under normal growth conditions, in sharp contrast to current understanding of the capping process. Here, we introduce that their mammalian homolog, Dom3Z (referred to as DXO), possesses pyrophosphohydrolase, decapping, and 5'-3' exoribonuclease activities. Surprisingly, we found that DXO preferentially degrades defectively capped pre-mRNAs in cells. Additional studies show that incompletely capped pre-mRNAs are inefficiently spliced at all introns, a fact that contrasts with current understanding, and are also poorly cleaved for polyadenylation. Crystal structures of DXO in complex with substrate mimic and products at a resolution of up to 1.5 Å provide elegant insights into the catalytic mechanism and molecular basis for their three apparently distinct activities. Our data reveal a pre-mRNA 5' end capping quality control mechanism in mammalian cells, indicating DXO as the central player for this mechanism, and demonstrate an unexpected intimate link between proper 5' end capping and subsequent pre-mRNA processing.
Structural studies of Mot1 and NC2 in transcription initiation process
Authors: Butryn Agata , Schuller Jan , Stöhr Gabriele , Förster Friedrich , Hopfner Karl-Peter
Published: November 2015

Regulation of protein–nucleic acid interactions plays a key role in various cellular processes. The SNF2/SWI2 protein family forms a large and diverse class of proteins and multiprotein assemblies, which use energy derived from ATP hydrolysis to disrupt or modify protein-DNA interactions. They possess a conserved helicase-like domain accompanied by protein-specific targeting and regulation regions. The SNF2/SWI2 family member Mot1 (Modifier of transcription 1, also known as BTAF1) is a single polypeptide ATP-dependent remodeler. Mot1 acts directly on TBP (TATA-box binding protein) regulating RNA polymerase II preinitiation complex formation in the first stages. Global distribution of TBP on promoter regions is also modulated by NC2 (Negative Cofactor 2). It has been suggested that Mot1 and NC2 can co occupy the same promoter sites influencing the assembly of the transcription machinery simultaneously. Our understanding of the molecular mechanism of SWI2/SNF2 family ATPases is very limited. Previously, we have reported the crystal structure of the complex of Encephalitozoon cuniculi N terminal domain of Mot1 (Mot1NTD) with its substrate, TBP [1]. Here we present the crystal structure of the TBP NC2 Mot1NTD complex bound to a promoter DNA fragment at 3.9Å resolution. In our studies we have applied a combined structural biology approach using crystallography, electron microscopy reconstructions and chemical cross-linking. We probed the conformational changes of the complex during the ATP hydrolysis cycle and unveiled the structural basis of the Mot1–NC2 interplay. Our findings greatly contribute not only to our limited understanding of Mot1 action, but all SNF2/SWI2 family remodeling enzymes.
Regulation of Pseudomonas aeruginosa virulence by the ExsACDE Signaling Cascade
Authors: Bernhards Robert , Yi Xiao , Shrestha Manisha , Schubot Florian
Published: November 2015

Pseudomonas aeruginosa requires its type III secretion system (T3SS) to facilitate acute infections. T3SS-related gene expression is controlled by the AraC-type transcriptional activator ExsA. A signaling cascade involving ExsA and three additional proteins -ExsC, ExsD, and ExsE directly ties the up-regulation of transcription to the activation of the type III secretion apparatus. In order to characterize the molecular interactions underlying the signaling process the crystal structures of the unique T3SS chaperone ExsC in complex with its cognate effector ExsE, the structure of the negative regulator ExsD and that of the regulatory domain of ExsA have been determined. The ExsC-ExsE structure revealed two Arg-X-Val-X-Arg motifs in ExsE that form identical interactions along opposite sides of the ExsC dimer. The structure of ExsD not only provided insights into the interactions of how ExsD is sequestered by ExsC but also revealed surprising similarities between ExsD and DNA binding proteins. Based on these findings, a new model for the ExsC-ExsD complex is proposed to explain its distinctive 2:2 stoichiometry and why ExsC displays a weaker affinity for ExsD than for ExsE. Lastly, we have determined the structure of ExsA regulatory domain revealing the protein's dimerization interface. The position of the interface appears to postulate interesting conformational changes upon binding of ExsA to DNA. The crystal structures of ExsD and the ExsA domain also serve as road maps for determining the interface for the critical interactions between these two proteins at the bottom of this unique signaling cascade.
Magneto-structural relationships in Cu(II) containing hybrid materials
Authors: Rademeyer Melanie , Bothma Shalene , Coetzee Stefan , Liles David , Turnbull Mark , Landee Christopher
Published: November 2015

The combination of inorganic Cu(II) halides with organic amine moieties within a single hybrid material allows for the combination of the properties of both components in a single material. Cu(II) ions may afford magnetic properties to such a hybrid material, while the organic component can be employed to template the structure and to shield the magnetic ions, thereby controlling the magnetic dimensionality of the structure. In this investigation, structural characterisation by single crystal X-ray diffraction and magnetic susceptibility measurements employing SQUID magnetometry, allows for the identification of magneto-structural relationships in the materials. Examples highlighting the magneto-structural properties in these Cu(II) containing hybrid materials will be presented. The effect of changes in organic component or anion on the structural characteristics will be analysed using the principles of crystal engineering, while the magnetic data is fitted to suitable quantum mechanical models to allow for the identification of magnetic exchange pathways and -parameters. It will be shown how computational techniques may assist in the interpretation of the magnetic data.
Investigation of the Orbital and magnetic orderings in VF3
Authors: Nénert Gwilherm , Reuvekamp Patrick , Drathen Christina , Eger Roland , Kraus F , Köhler J , Kremer Reinhard
Published: November 2015

We report on a magnetic and structural investigation of layered antiferromagnetic system vanadium (III) fluoride. VF3 crystallizes in a distorted ReO3 structure (R-3c) with rotated undistorted VF6 octahedra. The V3+ cations are arranged in a triangular lattice with the possibility of exhibiting magnetic frustration. Polycrystalline samples of VF3 were investigated using heat capacity, dielectric, magnetic susceptibility, synchrotron and neutron powder diffraction methods. Combining our results, we report the first evidence for a first order phase transition resulting from the ordering of the t2g orbitals below 105-110 K. This transition reduces the symmetry to C2/c. We further confirm that VF3 undergoes a long-range antiferromagnetic order at ∼19 K in accordance with literature [1]. The antiferromagnetic order results in a magnetic structure with the magnetic moments alternating between a parallel and b parallel alignments in the ab plane.