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  • International Union of Crystallography
  • Wiley-Blackwell
  • American Meteorological Society (AMS)
  • 2010-2014  (27,874)
  • 1950-1954  (11,056)
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  • 1
    Publication Date: 2020-12-15
    Description: We present a time-independent gridded earthquake rate forecast for the European region including Turkey. The spatial component of our model is based on kernel density estimation techniques, which we applied to both past earthquake locations and fault moment release on mapped crustal faults and subduction zone interfaces with assigned slip rates. Our forecast relies on the assumption that the locations of past seismicity is a good guide to future seismicity, and that future large-magnitude events occur more likely in the vicinity of known faults. We show that the optimal weighted sum of the corresponding two spatial densities depends on the magnitude range considered. The kernel bandwidths and density weighting function are optimized using retrospective likelihood-based forecast experiments. We computed earthquake activity rates (a- and b-value) of the truncated Gutenberg–Richter distribution separately for crustal and subduction seismicity based on a maximum likelihood approach that considers the spatial and temporal completeness history of the catalogue. The final annual rate of our forecast is purely driven by the maximum likelihood fit of activity rates to the catalogue data, whereas its spatial component incorporates contributions from both earthquake and fault moment-rate densities. Our model constitutes one branch of the earthquake source model logic tree of the 2013 European seismic hazard model released by the EU-FP7 project ‘Seismic HAzard haRmonization in Europe’ (SHARE) and contributes to the assessment of epistemic uncertainties in earthquake activity rates. We performed retrospective and pseudo-prospective likelihood consistency tests to underline the reliability of our model and SHARE’s area source model (ASM) using the testing algorithms applied in the collaboratory for the study of earthquake predictability (CSEP). We comparatively tested our model’s forecasting skill against the ASM and find a statistically significant better performance for testing periods of 10–20 yr. The testing results suggest that our model is a viable candidate model to serve for long-term forecasting on timescales of years to decades for the European region.
    Description: EC-Research FP7-projects, SHARE, under grant agreement No. 226967 and NERA, under grant agreement No. 262330
    Description: Published
    Description: 1159-1172
    Description: 2T. Tettonica attiva
    Description: 3T. Pericolosità sismica e contributo alla definizione del rischio
    Description: JCR Journal
    Description: restricted
    Keywords: Probabilistic forecasting ; Statistical seismology ; Europe ; 04. Solid Earth::04.06. Seismology::04.06.02. Earthquake interactions and probability ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2017-04-04
    Description: This paper describes an application of artificial neural networks for the recognition of volcanic lava flow hot spots using remote sensing data. Satellite remote sensing is a very effective and safe way to monitor volcanic eruptions in order to safeguard the environment and the people affected by such natural hazards. Neural networks are an effective and well-established technique for the classification of satellite images. In addition, once well trained, they prove to be very fast in the application stage. In our study a back propagation neural network was used for the recognition of thermal anomalies affecting hot lava pixels. The network was trained using the three thermal channels of the Advanced Very High Resolution Radiometer (AVHRR) sensor as inputs and the corre- sponding values of heat flux, estimated using a two thermal component model, as reference outputs. As a case study the volcano Etna (Eastern Sicily, Italy) was chosen, and in particular the effusive eruption which took place during the month of 2006 July. The neural network was trained with a time-series of 15 images (12 nighttime images and 3 daytime images) and validated on three independent data sets of AVHRR images of the same eruption and on two relative to an eruption occurred the following month. While for both nighttime and daytime validation images the neural network identified the image pixels affected by hot lava with a 100 per cent success rate, for the daytime images also adjacent pixels were included, apparently not interested by lava flow. Despite these performance differences under different illumination conditions, the proposed method can be considered effective both in terms of classification accuracy and generalization capability. In particular our approach proved to be robust in the rejection of false positives, often corresponding to noisy or cloudy pixels, whose presence in multispectral images can often undermine the performance of traditional classification algorithms. Future work shall address application of the proposed method to data acquired with a high temporal resolution, such as those provided by the spinning enhanced visible and infrared imager sensor on board the Meteosat second generation geostationary satellite.
    Description: Published
    Description: 1525-1535
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: Image processing ; Neural networks ; fuzzy logic ; Remote sensing of volcanoes ; Hot-spot detection ; Mt. Etna ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2017-04-04
    Description: We present a systematic study on the influence of pressure (0.1–600 MPa), temperature (750– 1200 ◦C), carbon dioxide fugacity (logfCO2 = −4.41 to 3.60) and time (2–12 hr) on the chemical and physical properties of carbonate rock. Our experiments aim to reproduce the conditions at the periphery of magma chamber where carbonate host rock is influenced by, but not readily assimilated by, magma. This permits the investigation of the natural conditions at which circulating fluids/gases promote infiltration reactions typical of metasomatic skarns that can involve large volumes of subvolcanic carbonate basements. Results show that, providing that carbon dioxide is retained in the pore space, decarbonation does not proceed at any magmatic pressure and temperature. However, when the carbon dioxide is free to escape, decarbonation can occur rapidly and is not hindered by a low initial porosity or permeability. Together with carbon dioxide and lime, portlandite, a mineral commonly found in voluminous metasomatic skarns, readily forms during carbonate decomposition. Post-experimental analyses highlight that thermal microcracking, a result of the highly anisotropic thermal expansion of calcite, exerts a greater influence on rock physical properties (porosity, ultrasonic wave velocities and elastic moduli) than decarbonation. Our data suggest that this will be especially true at the margins of dykes or magma bodies, where temperatures can reach up to 1200 ◦C. However, rock compressive strength is significantly reduced by both thermal cracking and decarbonation, explained by the relative weakness of lime + portlandite compared to calcite, and an increase in grain size with increasing temperature. Metasomatic skarns, whose petrogenetic reactions may involve a few tens of cubic kilometres, could therefore represent an important source of volcanic instability.
    Description: Published
    Description: 369-380
    Description: 2R. Laboratori sperimentali e analitici
    Description: JCR Journal
    Description: restricted
    Keywords: Volcanic hazards and risks ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2017-04-04
    Description: Interactions of conduit geometry with gas–liquid flows control volcanic activity, implying that the evaluation of volcanic hazards requires quantitative understanding of the inner structure of the volcano. The more established geophysical imaging techniques suffer from inherent ambiguity, may require spatially dense measurements in active areas and may not provide sufficient spatial resolution in the uppermost part of the conduit system. It is thus desirable to develop new imaging techniques allowing a better spatial resolution of a volcano's upper feeding system, with reduced ambiguity and a low level of risk for operators. Muon particles can be utilized to image the internal density distribution of volcanic structures. The principle of muon radiography is essentially the same as X-ray radiography, except for substituting penetrating particles in place of photons. Muons are more attenuated by higher density parts inside the target and thus information about its inner structure are obtained from the differential muon absorption. We report on a muon-imaging experiment that was conducted at Mt Etna in 2010. The target structure was one of the summit craters of the volcano. This experiment was performed using a muon telescope suitably designed to withstand the harsh conditions in the summit zone of a high volcano. We found a marked difference between synthetic and observed attenuation of muons through the target. This discrepancy is likely due to the bias on the observed flux, arising from false muon tracks. They are caused by low-energy particles that, by chance, hit simultaneously the two matrixes of the telescope, leading to detection of a false positive. We separated the useful from the unwanted signal through a first-order model of the background noise. The resulting signal is compared with the corresponding synthetic flux. Eventually, we found regions of higher- and lower-than-expected muon flux, that are possibly related to inner features of the target crater.
    Description: Published
    Description: 633-643
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Tomography; Volcano monitoring; Volcanic hazards and risks ; 04. Solid Earth::04.03. Geodesy::04.03.06. Measurements and monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: The identification of a source model for the catastrophic 1908 December 28 Messina earth- quake (Mw = 7.2) has been the subject of many papers in the last decades. Several authors proposed different models on the basis of seismological, macroseismic and geodetic data sets; among these models, remarkable differences exist with regard to almost all parameters. We selected a subset of six models among those most cited in literature and used them to model the post-seismic sea level variation recorded at the tide gauge station of Messina (until 1923), to attempt an independent discrimination among them. For each model, we assumed a simple rheological structure and carried out a direct-search inversion of upper crust thickness and lower crust viscosity to fit the post-seismic sea level signal. This approach enabled us to iden- tify a class of fault geometries which is consistent with the post-seismic signal at the Messina tide gauge and with the known structural and rheological features of the Messina strait
    Description: Published
    Description: 611-622
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: open
    Keywords: Sea level change ; Earthquake source observations ; Rheology: crust and lithosphere ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2017-04-04
    Description: When remote sensing users are asked to define their requirements for a new sensor, the big question that always arises is: will the technical specifications meet the scientific requirements? Herein, we discuss quantitative relationships between instrumental spectral and radiometric characteristics and data exploitable for lava flow subpixel temperature analysis. This study was funded within the framework of ESA activities for the IR GMES (Global Monitoring for Environment and Security) element mission requirements in 2005. Subpixel temperature retrieval from satellite infrared data is a well-established method that is well documented in the remote sensing literature. However there is little attention paid to the error analysis on estimated parameters due to atmospheric correction and radiometric accuracy of the sensor. In this study, we suggest the best spectral bands combination to estimate subpixel temperature parameters. We also demonstrate that poor atmospheric corrections may vanish the effectiveness of the most radiometrically accurate instrument.
    Description: Published
    Description: 112-125
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Remote sensing, error analysis, IR sensors, sub-pixel temperature, Numerical solutions; Non-linear differential equations; Effusive volcanism; Eruption mechanisms and flow emplacement; Remote sensing of volcanoes; Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2021-11-25
    Description: Here we inverted the GPS data to infer the coseismic slip of the Tohoku-Oki earthquake and the time-dependent afterslip distribution in the 4 months following the main shock. The Tohoku-Oki earthquake showed an unexpected magnitude and a characteristic depth-dependent differentiation of seismic energy radiation. In this context the estimation and comparison of the distribution of the fault portions that slip coseismically and post-seismically contribute to a better understanding of the variation of frictional characteristics of the plate interface. The inferred coseismic slip extends in a relatively compact region located updip from the hypocentre and reaches its highest value (about 60 m) near the trench. Afterslip occurs mostly outside the coseismic rupture and is distributed in two main modal centres. It reaches its largest values in an area located downdip of the coseismic slip and extends to a depth of 80 km. In the depth range between 30 and 50 km afterslip overlaps the portion of the fault that experienced historical moderate earthquakes, high-frequency seismic radiation and thrust-type aftershocks. The behaviour of this area can be explained by a rheologically heterogeneous region made of a ductile fault matrix interspersed with compact brittle asperities. On the contrary, the region beneath 50–60 km depth is probably characterized by a fully velocity strengthening behaviour. Southern afterslip, located off-Chiba Prefecture, is probably related to the Mw 7.9 Ibaraki-Oki aftershock. The northward extension of the afterslip stops at a latitude of about 40◦ N, just south of the off-Aomori region. This may be related to three large events occurred in this area during the last century and the consequent strong coupling or complete depletion of the accumulated strain that characterize this region.
    Description: Published
    Description: 580-596
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Satellite geodesy; Seismic cycle; Earthquake source observations; Subduction zone processes ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.04. Plate boundaries, motion, and tectonics ; 04. Solid Earth::04.07. Tectonophysics::04.07.06. Subduction related processes
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  • 8
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    Wiley-Blackwell
    In:  EPIC3Functional Ecology, Wiley-Blackwell, 28, pp. 1482-1493, ISSN: 0269-8463
    Publication Date: 2023-09-15
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 9
    Publication Date: 2024-05-09
    Description: Episodic gas seepage occurs at the seafloor in the Gulf of Izmit (Sea of Marmara, NW Turkey) along the submerged segment of the North Anatolian Fault (NAF), which ruptured during the 1999 Mw7.4 Izmit earthquake, and caused tectonic loading of the fault segment in front of the Istanbul metropolitan area. In order to study gas seepage and seismic energy release along the NAF, a multiparametric benthic observatory (SN-4) was deployed in the gulf at the western end of the 1999 Izmit earthquake rupture, and operated for about 1 yr at 166 m water depth. The SN-4 payload included a three-component broad-band seismometer, as well as gas and oceanographic sensors. We analysed data collected continuously for 161 d in the first part of the experiment, from 2009 October to 2010 March. The main objective of our work was to verify whether tectonic deformation along the NAF could trigger methane seepage. For this reason, we considered only local seismicity, that is, within 100 km from the station. No significant (ML ≥ 3.6) local earthquakes occurred during this period; on the other hand, the seismometer recorded high-frequency SDEs (short duration events), which are not related to seismicity but to abrupt increases of dissolved methane concentration in the sea water that we called MPEs (methane peak events). Acquisition of current velocity, dissolved oxygen, turbidity, temperature and salinity, allowed us to analyse the local oceanographic setting during each event, and correlate SDEs to episodic gas discharges from the seabed. We noted that MPEs are the result of such gas releases, but are detected only under favourable oceanographic conditions. This stresses the importance of collecting long-term multiparametric time-series to address complex phenomena such as gas and seismic energy release at the seafloor. Results from the SN-4 experiment in the Sea of Marmara suggest that neither low-magnitude local seismicity, nor regional events affect intensity and frequency of gas flows from the seafloor.
    Description: Published
    Description: 850-866
    Description: 1T. Geodinamica e interno della Terra
    Description: 3A. Ambiente Marino
    Description: 7A. Geofisica di esplorazione
    Description: JCR Journal
    Description: restricted
    Keywords: Time-series analysis ; Seismicity and tectonics ; Broad-band seismometers ; multiparametric seafloor observatory ; Izmit Gulf ; Sea of Marmara ; gas seepage ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 04. Solid Earth::04.04. Geology::04.04.04. Marine geology ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2014-05-31
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  • 11
    Publication Date: 2014-05-31
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  • 12
    Publication Date: 2014-05-31
    Description: Highly hygroscopic pyridineN-oxide, C5H5NO, dissolves in water absorbed from atmospheric air, but it crystallizes in the neat form of the aqueous solution under high pressure. The crystals grown at high-pressure isochoric conditions are of the same phase as that obtained from anhydrous crystallization at ambient pressure. This feature can be employed for retrieving compounds highly soluble in water from their aqueous solutions. The crystal structure is strongly stabilized by CH...O contacts. The crystal compression and thermal expansion as well as three shortest H...O distances comply with the inverse-relationship rule of pressure and temperature changes.
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  • 13
    Publication Date: 2014-05-24
    Description: Since simple data tables on phase transitions and structural systematics of the elements over a wide range of pressure and temperature are difficult to comprehend, this paper illustrates these systematics with some artwork together with an artist's view of the equations of states for the elements.
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  • 14
    Publication Date: 2014-05-24
    Description: Metal–organic frameworks (MOFs) are a class of porous crystalline materials of modular design. One of the primary applications of these materials is in the adsorption and separation of gases, with potential benefits to the energy, transport and medical sectors.In situcrystallography of MOFs under gas atmospheres has enabled the behaviour of the frameworks under gas loading to be investigated and has established the precise location of adsorbed gas molecules in a significant number of MOFs. This article reviews progress in such crystallographic studies, which has taken place over the past decade, but has its origins in earlier studies of zeolites, clathratesetc. The review considers studies by single-crystal or powder diffraction using either X-rays or neutrons. Features of MOFs that strongly affect gas sorption behaviour are discussed in the context ofin situcrystallographic studies, specifically framework flexibility, and the presence of (organic) functional groups and unsaturated (open) metal sites within pores that can form specific interactions with gas molecules.
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  • 15
    Publication Date: 2014-05-24
    Description: Sequential Rietveld refinements were applied on high-pressure synchrotron powder X-ray diffraction measurements of lanthanum ferrite (LaFeO3) revealing two phase transitions on the room-temperature isotherm up to a pressure of 48 GPa. The first structural phase transition of second order occurs at a pressure of 21.1 GPa, changing the space group fromPbnmtoIbmm. The second transition, involving a isostructural first-order phase transition, occurs at approximately 38 GPa, indicating a high-spin to low-spin transition of the Fe3+ion. Following the behavior of the volume up to the hydrostatic limit of methanol–ethanol it was possible to use inverted equations of state (EoS) to determine a bulk modulus ofB0= 172 GPa and a corresponding pressure derivative ofB′0= 4.3. In addition, the linearized version of the inverted EoS were used to determine the corresponding moduli and pressure derivatives for each lattice direction.
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  • 16
    Publication Date: 2014-05-24
    Description: The effect of pressure (up to 0.17 GPa) on the spin-crossover compound {Fe(pmd)2[Ag(CN)2]2}n[orthorhombic isomer (II), pmd = pyrimidine] has been investigated by temperature- and pressure-dependent neutron Laue diffraction and magnetometry. The cooperative high-spin ↔ low-spin transition, centred atca180 K at ambient pressure, is shifted to higher temperatures as pressure is applied, showing a moderate sensitivity of the compound to pressure, since the spin transition is displaced byca140 K GPa−1. The space-group symmetry (orthorhombicPccn) remains unchanged over the pressure–temperature (P–T) range studied. The main structural consequence of the high-spin to low-spin transition is the contraction of the distorted octahedral [FeN6] chromophores, being more marked in the axial positions (occupied by the pmd units), than in the equatorial positions (occupied by four [Ag(CN)2]−bridging ligands).
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  • 17
    Publication Date: 2014-05-24
    Description: This is a comparative study on the high-pressure behavior of microporous materials with an MFI framework type (i.e.natural mutinaite, ZSM-5 and the all-silica phase silicalite-1), based onin-situexperiments in which penetrating and non-penetrating pressure-transmitting media were used. Different pressure-induced phenomena and deformation mechanisms (e.g.pressure-induced over-hydration, pressure-induced amorphization) are discussed. The influence of framework and extra-framework composition and of the presence of silanol defects on the response to the high pressure of MFI-type zeolites is discussed.
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  • 18
    Publication Date: 2014-05-24
    Description: An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.
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  • 19
    Publication Date: 2014-03-28
    Description: Cu/Zn disorder in the kesterite Cu2ZnSnS4derivatives used for thin film based solar cells is an important issue for photovoltaic performances. Unfortunately, Cu and Zn cannot be distinguished by conventional laboratory X-ray diffraction. This paper reports on a resonant diffraction investigation of a Cu2ZnSnS4single crystal from a quenched powdered sample. The full disorder of Cu and Zn in thez= 1/4 atomic plane is shown. The structure, namely disordered kesterite, is then described in the I ar 42m space group.
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  • 20
    Publication Date: 2014-03-28
    Description: The crystal structures of a new polymorph and seven new derivatives of 2-(1-phenyl-1H-1,2,3-triazol-4-yl)pyridine have been characterized and examined along with three structures from the literature to identify trends in their intermolecular contact patterns and packing arrangements in order to develop an insight into the crystallization behaviour of this class of compound. Seven unique C—H...Xcontacts were identified in the structures and three of these are present in four or more structures, indicating that these are reliable supramolecular synthons. Analysis of the packing arrangements of the molecules usingXPacidentified two closely related supramolecular constructs that are present in eight of the 11 structures; in all cases, the structures feature at least one of the three most common intermolecular contacts, suggesting a clear relationship between the intermolecular contacts and the packing arrangements of the structures. Both the intermolecular contacts and packing arrangements appear to be remarkably consistent between structures featuring different functional groups, with the expected exception of the carboxylic acid derivative 4-(4-(pyridin-2-yl)-1H-1,2,3-triazol-1-yl) benzoic acid (L11), where the introduction of a strong hydrogen-bonding group results in a markedly different supramolecular structure being adopted. The occurrence of these structural features has been compared with the packing efficiency of the structures and their melting points in order to assess the relative favourability of the supramolecular structural features in stabilizing the crystal structures.
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  • 21
    Publication Date: 2014-03-17
    Description: Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed usingCRYSTAL09with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N—N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C—H...N, C—H...O and N—H...N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.
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  • 22
    Publication Date: 2014-03-17
    Description: A single-crystal X-ray diffraction structure analysis of decagonal Zn–Mg–Dy, a Frank–Kasper-type quasicrystal, was performed using the higher-dimensional approach. For this first Frank–Kasper (F–K) decagonal quasicrystal studied so far, significant differences to the decagonal Al–TM-based (TM: transition metal) phases were found. A new type of twofold occupation domain is located on certain edge centers of the five-dimensional unit cell. The structure can be described in terms of a two-cluster model based on a decagonal cluster (∼ 23 Å diameter) arranged on the vertices of a pentagon-Penrose tiling (PPT) and a star-like cluster covering the remaining space. This model is used for the five-dimensional refinements, which converged to anRvalue of 0.126. The arrangement of clusters is significantly disordered as indicated by high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). In order to check the structure and stability at higher temperatures,in-situhigh-temperature (HT) single-crystal X-ray diffraction experiments were conducted at 598 and 648 K (i.e.slightly below the decomposition temperature). The structure does not change significantly, however, the best quasiperiodic order is found at 598 K. The implication of these results on the stabilization mechanism of quasicrystals is discussed.
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  • 23
    Publication Date: 2014-03-17
    Description: The β-phase of Pigment Red 170, C26H22N4O4, which is used industrially for the colouration of plastics, crystallizes in a layer structure with stacking disorder. The disorder is characterized by a lateral translational shift between the layers with a componenttyof either +0.421 or −0.421. Order–disorder (OD) theory is used to derive the possible stacking sequences. Extensive lattice-energy minimizations were carried out on a large set of structural models with different stacking sequences, containing up to 2688 atoms. These calculations were used to determine the actual local structures and to derive the stacking probabilities. It is shown that local structures and energies depend not only on the arrangement of neighbouring layers, but also next-neighbouring layers. Large models with 100 layers were constructed according to the derived stacking probabilities. The diffraction patterns simulated from those models are in good agreement with the experimental single-crystal and powder diffraction patterns. Electron diffraction investigation on a nanocrystalline industrial sample revealed the same disorder. Hence the lattice-energy minimizations are able to explain the disorder and the diffuse scattering.
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  • 24
    Publication Date: 2014-03-17
    Description: The structure of the δ1pphase in the iron−zinc system has been refined by single-crystal synchrotron X-ray diffraction combined with scanning transmission electron microscopy. The large hexagonal unit cell of the δ1pphase with the space group ofP63/mmccomprises more or less regular (normal) Zn12icosahedra, disordered Zn12icosahedra, Zn16icosioctahedra and dangling Zn atoms that do not constitute any polyhedra. The unit cell contains 52 Fe and 504 Zn atoms so that the compound is expressed with the chemical formula of Fe13Zn126. All Fe atoms exclusively occupy the centre of normal and disordered icosahedra. Iron-centred normal icosahedra are linked to one another by face- and vertex-sharing forming two types of basal slabs, which are bridged with each other by face-sharing with icosioctahedra, whereas disordered icosahedra with positional disorder at their vertex sites are isolated from other polyhedra. The bonding features in the δ1pphase are discussed in comparison with those in the Γ and ζ phases in the iron−zinc system.
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  • 25
    Publication Date: 2014-03-17
    Description: The structure of decagonal Al–Cu–Rh has been studied as a function of temperature byin-situsingle-crystal X-ray diffraction in order to contribute to the discussion on energy or entropy stabilization of quasicrystals. The experiments were performed at 293, 1223, 1153, 1083 and 1013 K. A common subset of 1460 unique reflections was used for the comparative structure refinements at each temperature. A comparison of the high-temperature datasets suggests that the best quasiperiodic ordering should exist between 1083 and 1153 K. However, neither the refined structures nor the phasonic displacement parameter vary significantly with temperature. This indicates that the phasonic contribution to entropy does not seem to play a major role in the stability of this decagonal phase in contrast to other kinds of structural disorder, which suggests that, in this respect, this decagonal phase would be similar to other complex intermetallic high-temperature phases.
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  • 26
    Publication Date: 2014-01-16
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  • 27
    Publication Date: 2014-12-01
    Description: Under accelerated and controlled evaporation, chain polymers crystallize from aqueous solutions of CaIIand MnIIhalides with enantiopure L-alanine or racemic DL-alanine. In all ten solids thus obtained zwitterionic amino acid ligands bridge neighbouring cations. The exclusively O-donor-based coordination sphere around the metal cations is completed by aqua ligands; the halides remain uncoordinated and act as counter-anions for the cationic strands. Despite the differences in ionic radii and electronic structure between the main group and the transition metal cation, their derivatives with L-alanine share a common structure type. In contrast, the solids derived from DL-alanine differ and adopt structures depending on the metal cation and the halide. Homochiral chains of either chirality or heterochiral chains with different arrangements of crystallographic inversion centres along the polymer strands are encountered. On average, the six-coordinated CaIIcations, devoid of any ligand field effect, show more pronounced deviation from idealized octahedral geometry than thed-block cation MnII.
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  • 28
    Publication Date: 2014-12-01
    Description: The crystal structure of the novel Al77Rh15Ru8phase (which is an approximant of decagonal quasicrystals) was determined using modern direct methods (MDM) applied to automated electron diffraction tomography (ADT) data. The Al77Rh15Ru8E-phase is orthorhombic [Pbma,a= 23.40 (5),b= 16.20 (4) andc= 20.00 (5) Å] and has one of the most complicated intermetallic structures solved solely by electron diffraction methods. Its structural model consists of 78 unique atomic positions in the unit cell (19 Rh/Ru and 59 Al). Precession electron diffraction (PED) patterns and high-resolution electron microscopy (HRTEM) images were used for the validation of the proposed atomic model. The structure of the E-phase is described using hierarchical packing of polyhedra and a single type of tiling in the form of a parallelogram. Based on this description, the structure of the E-phase is compared with that of the ε6-phase formed in Al–Rh–Ru at close compositions.
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  • 29
    Publication Date: 2014-10-01
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  • 30
    Publication Date: 2014-10-01
    Description: The aim of this study was to test the applicability of a Bruker AXS CMOS-type PHOTON 100 detector for the purpose of a fine charge density quality data collection. A complex crystal containing oxalic acid, ammonium oxalate and two water molecules was chosen as a test case. The data was collected up to a resolution of 1.31 Å−1with high completeness (89.1%;Rmrg= 0.0274). The multipolar refinement and subsequent quantum theory of atoms in molecules (QTAIM) analysis resulted in a comprehensive description of the charge density distribution in the crystal studied. The residual density maps are flat and almost featureless. It was possible to derive reliable information on intermolecular interactions to model the anharmonic motion of a water molecule, and also to observe the fine details of the charge density distribution, such as polarization on O and H atoms involved in the strongest hydrogen bonds. When compared with our previous statistical study on oxalic acid data collected with the aid of CCD cameras, the complementary metal-oxide semiconductor (CMOS) detector can certainly be classified as a promising alternative in advanced X-ray diffraction studies.
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  • 31
    Publication Date: 2014-01-16
    Description: Three nickel(II) isothiocyanato complexes of the formulatrans-[NiL4(NCS)2] (L= ethylisonicotinate, methylisonicotinate and 4-benzoylpyridine) have been prepared: [Ni(ethylisonicotinate)4(NCS)2] (I), [Ni(methylisonicotinate)4(NCS)2] (II) and [Ni(4-benzoylpyridine)4(NCS)2] (III). All three complexes are monomeric and have a distorted octahedral geometry around NiII. Despite their apparent molecular similarity, the crystal density of (III) (1.454 g cm−3) is significantly higher than that of (I) and (II) (both 1.408 g cm−3), suggesting that the molecular packing is most efficient in (III). A study of the molecular Hirshfeld surfaces, together with density functional theory (DFT) calculations, provide insights into the origin of the molecular packing features, and it is suggested that the greater crystal density of (III) results from smaller intermolecular electrostatic repulsions.
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  • 32
    Publication Date: 2014-12-01
    Description: High-resolution crystal structure determination and spherical and multipolar refinement enabled an organic solid solution of 1-(4′-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile and 5-bromo-1-(4′-chlorophenyl)-2-methyl-4-nitro-1H-imidazole to be found, which would not normally be revealed using only standard resolution data (ca0.8 Å), as the disordered part is only visible at high resolution. Therefore, this new structure would have been reported as just another polymorphic form, even more reasonably as isostructural with other derivatives. To the best of our knowledge this is the first example of organic solid solution modelledviacharge density Hansen–Coppens formalism and analysed by means of quantum theory of atoms in molecules (QTAIM) theory.
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  • 33
    Publication Date: 2014-12-01
    Description: The structure of cronstedtite-1Mwas refined using a crystal from Eisleben (Saxony-Anhalt, Germany). The space group isCm,a= 5.5033 (3),b= 9.5289 (6),c= 7.3328 (5) Å, β = 104.493 (7)°, composition (Fe2+2.461Fe3+0.539)(Si1.461Fe3+0.539)O5(OH)4,Z= 2. Despite diffusely streaked characteristic polytype reflections, the refinement converged toRobs= 0.0242 for 1117 independent reflections. SeparateRobsvalues of 0.0183 and 0.0553 were obtained for 415 subfamily and 702 characteristic reflections, respectively. The structure is built of one edge-sharing octahedral (Oc) and one corner-sharing tetrahedral (Tet) sheet forming the 1:1 layer by sharing apical corners of theTetsheet. Consecutive layers are shifted bya/3 of the hexagonal cell, the polytype belongs to the subfamily (Bailey's group) A. There are two octahedral sitesM1 (atm),M2 (in a general position) both fully occupied by Fe. Since theM2 octahedron is larger thanM1, theOcsheet ismeso-octahedral. TheTetsheet contains one tetrahedral position,T1, occupied by Si and Fe in the ratio 0.731:0.269 (9). The ring of tetrahedra is strongly ditrigonalized, α = +12.7°; Franzini type A. Of three H atoms localized, two are involved in hydrogen bonds, linking OH groups of theOcsheet with basal O atoms of theTetsheet. The basal O atoms (acceptors) of theTetsheet are rotated close to OH groups (donors) of theOcsheet of an adjacent layer in order to achieve reasonable lengths and geometries of hydrogen bonds. The structure is interpreted as an example of the order–disorder (OD) structure of more than one kind of layer with a very low degree of desymmetrization.
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  • 34
    Publication Date: 2014-11-08
    Description: The observed and calculated densities of nanodiamond cannot be reconciled, and the stability of diamond structure explained, if nanodiamond is regarded as a form ofpurecarbon. The surface-terminating hydrogen and functional groups are an integral part in the stability of these particles which therefore need not be as inert and non-toxic as bulk diamond, with important implications for nanomedicine.
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  • 35
    Publication Date: 2014-12-01
    Description: We have determined the crystal structure of ammonium carbonate monohydrate, (NH4)2CO3·H2O, using Laue single-crystal diffraction methods with pulsed neutron radiation. The crystal is orthorhombic, space groupPnma(Z= 4), with unit-cell dimensionsa= 12.047 (3),b= 4.453 (1),c= 11.023 (3) Å andV= 591.3 (3) Å3[ρcalc= 1281.8 (7) kg m−3] at 10 K. The single-crystal data collected at 10 and 100 K are complemented by X-ray powder diffraction data measured from 245 to 273 K, Raman spectra measured from 80 to 263 K and an athermal zero-pressure calculation of the electronic structure and phonon spectrum carried out using density functional theory (DFT). We find no evidence of a phase transition between 10 and 273 K; above 273 K, however, the title compound transforms first to ammonium sesquicarbonate monohydrate and subsequently to ammonium bicarbonate. The crystallographic and spectroscopic data and the calculations reveal a quite strongly hydrogen-bonded structure (EHB≃ 30–40 kJ mol−1), on the basis of H...O bond lengths and the topology of the electron density at the bond critical points, in which there is no free rotation of the ammonium cation at any temperature. The barrier to free rotation of the ammonium ions is estimated from the observed librational frequency to be ∼ 36 kJ mol−1. Thec-axis exhibits negative thermal expansion, but the thermal expansion behaviour of theaandbaxes is ormal.
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  • 36
    Publication Date: 2014-10-01
    Description: The new tetrachloroaurate ethanol hydrate HAuCl4·0.65C2H5OH·1.35H2O was prepared from chloroauric acid trihydrate in ethanol. The compound crystallizes in the triclinic space group P ar 1 (No. 2). The [AuCl4]−units in the structure have approximately square-planar symmetry, forming chains parallel to the crystallographicb-axis direction.
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  • 37
    Publication Date: 2014-09-18
    Description: The new generation of X-ray detectors, the hybrid pixel area detectors or `pixel detectors', is based on direct detection and single-photon counting processes. A large linearity range, high dynamic and extremely low noise leading to an unprecedented high signal-to-noise ratio, fast readout time (high frame rates) and an electronic shutter are among their intrinsic characteristics which render them very attractive. First used on synchrotron beamlines, these detectors are also promising in the laboratory, in particular for pump-probe or quasi-static experiments and accurate electron density measurements, as explained in this paper. An original laboratory diffractometer made from a Nonius Mach3 goniometer equipped with an Incoatec Mo microsource and an XPAD pixel area detector has been developed at the CRM2 laboratory. MoKα accurate charge density quality data up to 1.21 Å−1resolution have been collected on a sodium nitroprusside crystal using this home-made diffractometer. Data quality for charge density analysis based on multipolar modelling are discussed in this paper. Deformation electron densities are compared to those already published (based on data collected with CCD APEXII and CAD4 diffractometers).
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  • 38
    Publication Date: 2014-10-01
    Description: The orientation relations (ORs) of the cubic icosahedral quasicrystal approximant phase α-Al(Fe,Mn)Si have been studied after low temperature annealing of a 3xxx wrought aluminium alloy by transmission electron microscopy. From diffraction studies it was verified that the most commonly observed OR for the α-Al(Fe,Mn)Si dispersoids is [1 ar 11]α // [1 ar 11]Al, (5 ar 2 ar 7)α // (011)Al. This orientation could be explained by assuming that the internal Mackay icosahedron (MI) in the α-phase has a fixed orientation in relation to Al, similar to that of the icosahedral quasi-crystals existing in this alloy system. It is shown that mirroring of the normal-to-high-symmetry icosahedral directions of the MI explains the alternative orientations, which are therefore likely to be caused by twinning of the fixed MI. Only one exception was found, which was related to the Bergman icosahedron internal to the T-phase of the Al–Mg–Zn system.
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  • 39
    Publication Date: 2014-09-18
    Description: VF3-type FeF3is generally considered as a perovskite with a completely vacantAsite. The high-pressure structural evolution of FeF3has been studied by both X-ray diffraction and theoretical simulation up to 62.0 GPa. Experimental and theoretical results demonstrate that VF3-type FeF3is stable up to 50 GPa. The structural evolution presents three features at different pressure ranges. AtP〈 10 GPa, the volume reduction is dominated by the FeF6octahedral rotation, and a small octahedral strain develops upon compression, which represents an elongation of FeF6octahedra along thecaxis. Between 10 and 25 GPa, the volume reduction is mainly attributed to the Fe—F bond length decreasing, and the octahedral strain gradually disappears. Between 25 and 50 GPa, an octahedral elongation along theaaxis quickly develops, resulting in a substantial structural distortion. Structural instability is predicted atP〉 51 GPa on the basis of a soft mode occurring in phonon calculations. The pressure–volume relationship is described by a third-order Birch–Murnaghan equation-of-state withB0= 14 (1) GPa,B0′ = 17 (1) by experiment andB0= 10.45 (1) GPa,B′10= 12.13 (1) by calculation.
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  • 40
    Publication Date: 2014-07-31
    Description: Donor-stabilized addition complexes of nickel(II) with disubstituted diphenyldithiophosphates, [{(ArO)2PS2}2NiL2] {Ar = 2,4-(CH3)2C6H3[(1), (5)], 2,5-(CH3)2C6H3[(2), (6)], 3,4-(CH3)2C6H3[(3), (7)] and 3,5-(CH3)2C6H3[(4), (8)];L= C5H5N [(1)–(4)] and C7H9N [(5)–(8)]}, were successfully isolated and characterized by elemental analysis, magnetic moment, IR spectroscopy and single-crystal X-ray analysis. Compound (4) crystallizes in the monoclinic space groupP21/nwhereas compounds (7) and (8) crystallize in the triclinic space group P ar 1. The single-crystal X-ray diffraction analysis of (4), (7) and (8) reveals a six-coordinated octahedral geometry for the NiS4N2chromophore. Two diphenyldithiophosphate ions act as bidentate ligands with their S atoms coordinated to the Ni centre. Each of them forms a four-membered chelate ring in the equatorial plane. The N atoms from two donor ligands are axially coordinated to the Ni atom.
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  • 41
    Publication Date: 2014-07-31
    Description: A series of temperature-dependent single-crystal and powder diffraction experiments has been carried out using synchrotron radiation in order to characterize the monogermanides of Mn, Fe and their solid solutions. The MnGe single crystal is found to be enantiopure and we report the absolute structure determination. The thermal expansion, parametrized with the Debye model, is discussed from the temperature-dependent powder diffraction measurements for Mn1−xFexGe (x= 0, 0.1, 0.2, 0.25, 0.3, 0.4, 0.5, 0.6, 0.7, 0.75, 0.8, 0.9). Whereas the unit-cell dimension and the Debye temperature follow a linear trend as a function of composition, the thermal expansion coefficient deviates from linear dependence with increasing Mn content. No structural phase transformations have been observed for any composition in the temperature range 80–500 K for both single-crystal and powder diffraction, indicating that the phase transition previously observed with neutron powder diffraction most probably has a magnetic origin.
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  • 42
    Publication Date: 2014-05-01
    Description: This paper presents the basic tools commonly used to describe the atomic structures of quasicrystals with a specific focus on the icosahedral phases. After a brief recall of the main properties of quasiperiodic objects, two simple physical rules are discussed that lead one to eventually obtain a surprisingly small number of atomic structures as ideal quasiperiodic models for real quasicrystals. This is due to the fact that the atomic surfaces (ASs) used to describe all known icosahedral phases are located on high-symmetry special points in six-dimensional space. The first rule ismaximizing the densityusing simple polyhedral ASs that leads to two possible sets of ASs according to the value of the six-dimensional lattice parameterAbetween 0.63 and 0.79 nm. The second rule ismaximizing the number of complete orbits of high symmetryto construct as large as possible atomic clusters similar to those observed in complex intermetallic structures and approximant phases. The practical use of these two rules together is demonstrated on two typical examples of icosahedral phases,i-AlMnSi andi-CdRE (RE = Gd, Ho, Tm).
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  • 43
    Publication Date: 2014-09-20
    Description: Convergent-beam electron diffraction (CBED) recorded using nanometre-sized probes, in principle, can detect the highest symmetry in a crystal. However, symmetry reduction may occur by overlapping crystal domains along the beam direction. Thus, delineating the relationship between the recorded and the crystal symmetry is important for studying crystals with complex nanodomains. This paper reports a study of the averaged local symmetry of 71°/109° rhombohedral (R), 90° tetragonal (T) and 180° monoclinic (M) nanodomain structures. The averaged symmetry of nanodomain structures is investigated by CBED simulations using the multislice method. The simulation results show that the 71°-R, 109°-R and 90°-T nanodomain structures partially mimic the monoclinic symmetries ofCmandPmthat have been proposed by the adaptive phase model. This study is also compared to the reported experimental CBED patterns recorded from PMN-31%PT.
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  • 44
    Publication Date: 2014-08-05
    Description: Envenoming due to snakebites is an important public health problem in many tropical and subtropical countries which, in addition to mortality, may result in permanent sequelae as a consequence of local tissue damage, i.e. necrosis and hemorrhage. Toxins that play a leading role in the complex pathogenesis of these feared venom actions have been identified as members of the phospholipase A2 (PLA2) and metalloproteinase protein families. Phospholipases A2 are enzymes responsible for cellular membrane disruption through Ca2+-dependent hydrolysis of phospholipids. A class of these proteins (Lys49-PLA2s) does not show catalytic activity but can exert a pronounced local myotoxic effect that is not neutralized by serum therapy. After more than 20 years of structural, biochemical and biological studies with this class of proteins, its biological mechanism still remain not totally understood. Here, based in a comprehensive study including over than 30 crystallographic structures, Small Angle X-ray Scattering, Dynamic Light Scattering, Isothermal Titration Calorimetry, Biochemical, Bioinformatics, Phylogenic and Myografic experiments, we proposed a complete myotoxic mechanism. This work confirms the biological dimer indicated by recent studies in which both C-termini are in the dimeric interface. In this configuration, we propose that the myotoxic site of these toxins is composed by the Lys 20, Lys115 and Arg118 residues. The extensive structural analysis also include: (i) the function of hydrophobic long-chain molecules as Lys49-PLA2s inhibitors, (ii) the role of Lys122, previously indicated as being responsible for Lys49-PLA2s catalytic inactivity, (iii) a structural comparison of the Ca2+-binding loop region between Lys49 and Asp49-PLA2s, (iv) the importance of Tyr119 residue, (v) the role of different classes of inhibitors and (vi) the role of hydrophobic knuckle. Taking into account all these issues we were able to propose a complete mechanism of action of these proteins and also proposed the different ways to inhibit them. These results may be useful to guide new experiments that can definitively clarify the action mechanism of snake venom PLA2s and lead to the design of structure-based inhibitors to complement the serum therapy.
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  • 45
    Publication Date: 2014-05-28
    Description: The temperature dependence of H-UisoinN-acetyl-L-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uisobelow 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.
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  • 46
    Publication Date: 2014-08-05
    Description: SHELXT is intended for robust routine solution of small molecule crystal structures. It makes the simple but powerful assumption that the structure consists of resolved atoms, but unlike classical direct methods it is not required that the atoms are 'equal'. This enables it to succeed with poor or incomplete data but makes it unsuitable for structures that are twinned, modulated or contain severe (e.g. 'whole molecule') disorder. SHELXT is a dual-space program that starts with a Patterson minimum superposition and iteratively applies the random omit procedure (also used in SHELXD) with data expanded to space group P1, but does not use phase probability relations or solvent flipping. In the SHELX system it will probably obsolete SHELXS but not SHELXD, which is better for large equal-atom and twinned structures. SHELXT reads any legal SHELX format .ins and (HKLF3 or 4) .hkl files. It extracts the Laue group and tries to find space groups in this Laue group and origin shifts to fit the phases from the best P1 solution, and makes an approximate assignment of element types using the elements specified on the SFAC instruction (and maybe a couple more). This is followed by an isotropic refinement and an attempt to assign the absolute structure if the space group is non-centrosymmetric. It is hoped to release SHELXT as part of the SHELX system (http://shelx.uni-ac.gwdg.de/SHELX/index.php) in time for the 2014 Montreal IUCr Meeting.
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  • 47
    Publication Date: 2014-08-05
    Description: We present recent experimental X-ray Absorption Fine Structure (XAFS) data of the Nickel K-edge, measured at temperatures of 15, 70 and 140 K. This study has taken elements of the X-ray Extended Range Technique (XERT) and for the first time, applied them to a cryostat cold cell system. These measurements permit critical tests of XAFS theory, with emphasis on quantification of the Debye-Waller factor and static vs. thermal disorder. X-ray Absorption Fine Structure contains vital information about the surrounding system of an absorbing atom including crystal structure, bond distances and coordination number. It is crucial that we understand all processes that may affect the measured XAFS spectra. The aim of this study is to investigate thermal effects and quantify thermal and static disorder [1]. The XERT is an experimental technique developed by our group, capable of measuring X-ray mass attenuation coefficients on an absolute scale with accuracies down to 0.02% [2]. This study has taken crucial elements from the XERT and applied them to complex experimental systems. This includes, but is not limited to high accuracy energy calibration [3], quantification and correction of beam harmonics and fluorescence. Our robust technique allows us to take the high accuracy data required to determine fundamental structural and crystallographic properties. These developments give great insight into our understanding of more complex systems such as organometallic molecules and biological systems.
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  • 48
    Publication Date: 2014-05-17
    Description: The physical property coefficients that arise in a phase transition which are zero in the high-symmetry phase and nonzero in the low-symmetry phase are calledspontaneous coefficients. For all 1601 Aizu species of phase transitions, matrices have been constructed which show the nonzero coefficients of a wide variety of magnetic and nonmagnetic physical properties including toroidal property coefficients in the high-symmetry phase and their corresponding spontaneous coefficients in the low-symmetry phase. It is also shown that these spontaneous coefficients provide for the distinction of and switching between nonferroelastic domain pairs.
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  • 49
    Publication Date: 2014-07-10
    Description: The subgroup structure of the hyperoctahedral group in six dimensions is investigated. In particular, the subgroups isomorphic to the icosahedral group are studied. The orthogonal crystallographic representations of the icosahedral group are classified and their intersections and subgroups analysed, using results from graph theory and their spectra.
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  • 50
    Publication Date: 2014-07-10
    Description: Symmetric Bragg-case reflections from a thick, ideally imperfect, crystal slab are studied mostly by analytical means. The scattering transfer function of a thin mosaic layer is derived and brought into a form that allows for analytical approximations or easy quadrature. The Darwin–Hamilton equations are generalized, lifting the restriction of wavevectors to a two-dimensional scattering plane. A multireflection expansion shows that wavevector diffusion can be studied independently of the real-space coordinate. Combining analytical arguments and Monte Carlo simulations, multiple Bragg reflections are found to result in a minor correction of the reflected intensity, a moderate broadening of the reflected azimuth angle distribution, a considerable modification of the polar angle distribution, and a noticeable shift and distortion of rocking curves.
    Electronic ISSN: 2053-2733
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  • 51
    Publication Date: 2014-07-10
    Description: A low-discrepancy cubic variant of β-Mn is presented exhibiting local octagonal symmetry upon projection along any of the three mutually perpendicular 〈100〉 axes. Ideal structural parameters are derived to be x(8c) = (2-sqrt{2}) ig/16 and y(12d) = 1 ig/(4 sqrt{2}) for theP4132 enantiomorph. A comparison of the actual and ideal structure models of β-Mn is made in terms of the newly devised concept of geometrical discrepancy maps. Two-dimensional maps of both the geometrical star discrepancyD*and the minimal interatomic distancedminare calculated over the combined structural parameter range 0 leq x(8c) ,lt, 1/8 and 1/8 leq y(12d), lt, 1/4 of generalized β-Mn type structures, showing that the `octagonal' variant of β-Mn is almost optimal in terms of globally minimizingD*while at the same time globally maximizingdmin. Geometrical discrepancy maps combine predictive and discriminatory powers to appear useful within a wide range of structural chemistry studies.
    Electronic ISSN: 2053-2733
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  • 52
    Publication Date: 2014-02-26
    Description: The chain of algebraic geometry and topology constructions is mapped on a structural level that allows one to single out a special class of discrete helicoidal structures. A structure that belongs to this class is locally periodic, topologically stable in three-dimensional Euclidean space and corresponds to the bifurcation domain. Singular points of its bounding minimal surface are related by transformations determined by symmetries of the second coordination sphere of the eight-dimensional crystallographic latticeE8. These points represent cluster vertices, whose helicoid joining determines the topology and structural parameters of linear biopolymers. In particular, structural parameters of the α-helix are determined by the seven-vertex face-to-face joining of tetrahedra with theE8non-integer helical axis 40/11 having a rotation angle of 99°, and the development of its surface coincides with the cylindrical development of the α-helix. Also, packing models have been created which determine the topology of theA,BandZforms of DNA.
    Electronic ISSN: 2053-2733
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  • 53
    Publication Date: 2014-02-20
    Description: The fullerenes of the C60series (C60, C240, C540, C960, C1500, C2160etc.) form onion-like shells with icosahedralIhsymmetry. Up to C2160, their geometry has been optimized by Dunlap & Zope from computations according to the analytic density-functional theory and shown by Wardman to obey structural constraints derived from an affine-extendedIhgroup. In this paper, these approaches are compared with models based on crystallographic scaling transformations. To start with, it is shown that the 56 symmetry-inequivalent computed carbon positions, approximated by the corresponding ones in the models, are mutually related by crystallographic scalings. This result is consistent with Wardman's remark that the affine-extension approach simultaneously models different shells of a carbon onion. From the regularities observed in the fullerene models derived from scaling, an icosahedral infinite C60onion molecule is defined, with shells consisting of all successive fullerenes of the C60series. The structural relations between the C60onion and graphite lead to a one-parameter model with the same Euclidean symmetryP63mcas graphite and having ac/a= τ2ratio, where τ = 1.618… is the golden number. This ratio approximates (up to a 4% discrepancy) the value observed in graphite. A number of tables and figures illustrate successive steps of the present investigation.
    Electronic ISSN: 2053-2733
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  • 54
    Publication Date: 2014-02-12
    Description: The potential of mathematical crystallography as an emerging field is examined from a sociological point of view. Mathematical crystallography is unusual as an emerging field as it is also an old field, albeit scattered, with evidence of continued substantial activity. But its situation is similar to that of an emerging field, so we analyse it as such. Comparisons with past emergent efforts suggest that a new field can grow if given an economic demand for its product and a receptive environment. Developing a field entails developing a sense of identity, developing infrastructure and recruiting practitioners.
    Electronic ISSN: 2053-2733
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  • 55
  • 56
    Publication Date: 2014-02-20
    Description: The structure of quasicrystals is aperiodic. Their diffraction patterns, however, can be considered periodic. They are composed solely of series of peaks which exhibit a fully periodic arrangement in reciprocal space. Furthermore, the peak intensities in each series define the so-called `envelope function'. A Fourier transform of the envelope function gives an average unit cell, whose definition is based on the statistical distribution of atomic coordinates in physical space. If such a distribution is lifted to higher-dimensional space, it becomes the so-called atomic surface – the most fundamental feature of higher-dimensional analysis.
    Electronic ISSN: 2053-2733
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  • 57
    Publication Date: 2014-08-05
    Description: A series of copper(II) complexes containing phosphonium substituted hydrazone, (L) with the formulations [CuL]Cl and [Cu(L')L]Cl, where L = doubly deprotonated hydrazone; L' = 1,10'-phenanthroline, 2,2'-bipyridine, 4,4-bipyridine and 5,5'-dimethyl-2,2'-bipyridine has been synthesized. The compounds were characterized by elemental analysis, IR and NMR spectroscopic methods and in the case of crystalline products by X-ray crystallography. The crystal structure of [CuL]Cl and the extent of distortion from ideal square pyramidal geometry for CuL')(l)]Cl will be discussed. The cytotoxicity and topoisomerase I (topo I) inhibition activities of these compounds were also studied. It is noteworthy that the addition of N,N-ligands to the copper(II) complex lead to the enhancement in the cytotoxicity of the compounds, especially against human prostate adenocarcinoma cell line (PC-3). The complexes can also inhibit topo I through the binding to DNA and the enzyme.
    Electronic ISSN: 2053-2733
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  • 58
    Publication Date: 2014-08-05
    Description: CEL-III is a hemolytic lectin isolated from the sea cucumber Cucumaria echinata. This lectin is composed of two carbohydrate-binding domains (domains 1-2) and one oligomerization domain (domain 3). After binding to the cell surface carbohydrate chains through domains 1-2, domain 3 self-associates to form transmembrane pores, leading to cell lysis or death, which resembles other pore-forming toxins of diverse organisms. To elucidate the pore-formation mechanism of CEL-III, the crystal structure of the CEL-III oligomer was determined. The CEL-III oligomer has a heptameric structure with a long β-barrel as a transmembrane pore. This β-barrel is composed of 14 β-strands resulting from a large structural transition of α-helices accommodated in the interface between domains 1-2 and domain 3 in the monomeric structure, suggesting that the dissociation of these α-helices triggered their structural transition into a β-barrel. After heptamerization, domains 1-2 form a flat ring, in which all carbohydrate- binding sites remain bound to cell surface carbohydrate chains, stabilizing the transmembrane β-barrel in a position perpendicular to the plane of the lipid bilayer.
    Electronic ISSN: 2053-2733
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  • 59
    Publication Date: 2014-08-05
    Description: Human general transcription factor TFIID is a megadalton sized multiprotein complex containing the TATA-box binding protein (TBP) and 13 TBP Associated Factors (TAFs). Structural studies by cryo-electron microscopy (cryo-EM) have uncovered the overall architecture of TFIID, providing valuable insight into subunit assembly and promoter recognition at medium resolution. Despite considerable effort, high resolution structural information of TAFs to date have been largely limited to structures of individual domains and assemblies of TAF histone-fold pairs, which are prevalent in TFIID. We used our MultiBac baculovirus/insect cell technology to obtain recombinant TFIID complexes including holo-TFIID in unprecedented quality and quantity, setting the stage for high resolution structural analysis by X-ray crystallography. We identified stable subassemblies of the TFIID complexes by limited proteolysis, and utilized a rapid combinatorial co-expression approach to produce and purify specimens for high-throughput crystallization. We crystallized a thus defined complex formed by TAF5, TAF6 and TAF9 and determined the structure to a resolution of 2.7 Å, revealing intricate molecular interactions at the core of human TFIID.
    Electronic ISSN: 2053-2733
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  • 60
    Publication Date: 2014-08-05
    Description: Vertebrate cell growth, division, migration, morphogenesis, and development, rely on the dynamic interactions of cells with components the extracellular matrix (ECM) via cell surface complexes. These focal adhesions (FAs) are comprised of integrin receptors, associated signaling molecules, and talin, which is required for "inside-out" signaling that stabilizes contacts of integrin receptors with the ECM by linking FAs to the actin cytoskeleton by binding to vinculin. The highly dynamic interactions with the actin cytoskeleton are also essential for the formation of membrane protrusions (lamellopodia and filopodia). Second messengers are found at the plasma cell membrane and include signaling lipids such as phosphoinositides, which play essential roles in signal transduction pathways and in directing the oligomerization of cytoskeletal proteins that function as essential links of FAs to the actin cytoskeleton. Notably, the most abundant phosphoinositide, phosphatidyl (4,5) bisphosphate (PIP2), directly binds to key cytoskeletal proteins, where it triggers homotypic and heterotypic interactions that amplify binding to the actin network. Binding of the inositol head group and the hydrophobic acyl chain pose difficulties in generating protein/PIP2 complex crystals and here we present the only second non-membrane protein structure of such a complex. Our crystal structure and biochemical approaches define the roles of PIP2 in controlling the oligomerization of cytoskeletal proteins and their binding to adhesion receptors and to the actin cytoskeleton. Importantly, we also determined the contribution of PIP2-directed oligomerization of cytoskeletal proteins to the formation and stabilization of adhesion complexes. These studies provide important new insights into how dynamic interactions of cytoskeletal proteins with the lipid membrane, adhesion complexes, and the actin network direct the mechanical behaviors of cells.
    Electronic ISSN: 2053-2733
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  • 61
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 62
    Publication Date: 2014-08-05
    Description: Aldehyde oxidases (AOX; E.C. 1.2.3.1) are molybdo-flavoenzymes with broad substrate specificity, oxidizing aldehydes and N-heterocycles. AOX belongs to the xanthine oxidase (XO) family of Mo-containing enzymes. The true physiological function of AOX is still unknown, although it is recognized to play a role in the metabolism of compounds with medicinal and toxicological relevance [1]. AOX importance has increased in recent years since it is substituting Cyt-P450 as the central drug-metabolizing system in humans. We have solved the 3D structure of mouse AOX3 to 2.9 Å resolution [2] that was the first structure of an aldehyde oxidase, providing important evidences on substrate and inhibitor specificities between AOX and XO. The complement of AOX proteins in mammals varies from one in humans (hAOX1) to four in rodents (mAOX1, mAOX3, mAOX4 and mAOX3L1) as a result of evolutionary genetic events. Due to this unusual complement of AOX genes in different animal species, conclusions regarding protein metabolism in humans cannot be taken exclusively from the mouse model. Using the human aldehyde oxidase (hAOX1) purified after heterologous expression in Escherichia coli we were able to crystallize it and solve its 3D structure to 2.7 Å resolution (submitted). In addition to the native protein we also solved the structure of an inhibited form of the enzyme to 2.6Å resolution. Analysis of the protein active site and comparison with the structure of the mouse isoform (mAOX3) allowed us to identity, for the first time, the unique features that characterize hAOX1 as an important drug-metabolizing enzyme. In spite of the similarities of both enzymes, they show marked and relevant differences at the Mo active site, substrate tunnel as well as at the FAD site. The ensemble of these structures provides important insights into the role of aldehyde oxidases, contributing to elucidate the clinical metabolism implications of hAOX1 in humans which has particular relevance for novel drug design studies.
    Electronic ISSN: 2053-2733
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  • 63
    Publication Date: 2014-08-05
    Description: Hypertension is considered a multi-factorial disease being an important worldwide public-health challenge due to its high frequency and concomitant risks of cardiovascular and other diseases. It has been identified as the leading risk factor for mortality, and is ranked as the third cause of disability-adjusted life-years[1]. The LASSBio-1289 compound was designed from the lead compound LASSBio-294 through the use of medicinal chemistry strategy of bioisosteric replacement of aromatic rings[2]. Many factors are involved in the task of describing the relationship between chemical structure and pharmacological activity of a prototype of a new drug. Among these factors the study of atomic-level structure can be included. The aim of this work is to carry out the structural characterization of LASSBio-1289, in solid-state. Since many NAH derivatives, as LASSBio-1289, do not form single crystals for proper structure determination, this task was overcome by using X-ray powder diffraction data and an ab initio simulated annealing procedure. This study can contribute to better understand the full pharmacodynamic profiles and physicochemical properties of this class of compounds. The LASSBio-1289 compound was synthesized following the procedure described in literature[3]. The sample was sofly hand-grinded in an agate mortar in order to get a fine powder suitable for X-ray powder diffraction analysis. The final refined values for the unit-cell parameters after the Rietveld fit were: a = 14.5119(3) Å, b = 12.1375(2) Å, c = 7.5498(1) Å, β = 91.113(1) Å, Z = 4, Z' = 1 and ρcalc = 1.44039(5) g.m-3. The goodness-of-fit indicator and R-factors were: χ2 = 1.290, RBragg = 1.749%, Rwp = 4.903%, Rexp = 3.802% and Rp = 3.661%. The crystal structure of LASSBio-1289 compound consists of four formula units per unit cell (Z = 4), accommodating one molecule in the asymmetric unit (Z' = 1). The sample was indexed as monoclinic space group (P21/c).
    Electronic ISSN: 2053-2733
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  • 64
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 65
    Publication Date: 2014-08-05
    Description: Methylated cytosine of CpG dinucleotides in vertebrates may be oxidized by Tet proteins, a process that can lead to DNA demethylation. The predominant oxidation product, 5-hydroxymethylcytosine (5hmC), has been implicated in embryogenesis, cell differentiation and human diseases. Recently, the SRA domain of UHRF2 (UHRF2-SRA) has been reported to specifically recognize 5hmC, but how UHRF2 recognizes this modification is unclear. Here we report the structure of UHRF2-SRA in complex with a 5hmC-containing DNA. The structure reveals that the conformation of a phenylalanine allows the formation of an optimal 5hmC-binding pocket, and a hydrogen bond between the hydroxyl group of 5hmC and UHRF2-SRA is critical for their preferential binding. Further structural and biochemical analyses unveiled the role of SRA domains as a versatile reader of modified DNA, and the knowledge should facilitate further understanding of the biological function of UHRF2, and the comprehension of DNA hydroxymethylation in general.
    Electronic ISSN: 2053-2733
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  • 66
    Publication Date: 2014-08-05
    Description: 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
    Electronic ISSN: 2053-2733
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  • 67
    Publication Date: 2014-08-05
    Description: Inspired from the work of Van Meersshe and Feneau-Dupont (1984), the ternary representation of the basic models in crystallography offers interesting perspectives to illustrate quantum orbitals, the classical S, P, D and F orbitals, by using a 3D representation of a trigonal system in place of the orthogonal system . On the other hand, the studies of the molecular orbitals of orthohydrogen (spins in the same sense) induces the hypothesis of a singularity zone between the atoms of hydrogen which could be a neutral zone favourable to the emergence of neutral particles and potentially can reorganize the repartition of electronic orbitals. Therefore, the nuclear spins can be related to the quantum orbitals distribution. Finally, by associating the ternary system in crystallisation with the orientation of nuclear spins and chemical bonds between the elements, we could work out a "trigonal" representation for the first elements of the periodic table, from hydrogen to calcium. The trigonal approach can facilitate the 3D representation of complex orbital systems. It offers a theoretical potential for crystallographic studies and it can support a large program of experimentation about the formation of the isotopes, the ionic character of covalent bonds and the gas state at low temperature for the electronegative elements of the periodic table.
    Electronic ISSN: 2053-2733
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  • 68
    Publication Date: 2014-08-05
    Description: Coat proteins of several isometric viruses consist of two domains, a disordered N-terminal R-domain consisting of several positively charged residues and a shell (S) domain characterized by a jelly roll β-barrel structure. The three-dimensional structure of Sesbania mosaic virus (SeMV), a T=3 plant virus, has been determined at 3 Å resolution. The full length coat protein, when expressed in E. coli, assembles into T=3 icosahedral shells (VLPs) resembling native virus particles. In the present investigations, the role of N-terminal R domain in the assembly of VLPs was explored by replacing the R domain with a presumably globular domain (SeMV-P10) and other intrinsically disordered (SeMV-P8, and SeMV-VPg) SeMV encoded domains. The R domain was also replaced with the non-viral globular B-domain of Staphyloccocus aureus protein A. These domains were of nearly the same size as that of the R-domain. Most of the chimeric coat proteins, when expressed in E.coli, formed VLPs, which could be purified by ultra-centrifugation. The purified VLPs were examined by transmission electron microscopy (TEM), which suggested that a fraction of the expressed proteins could assemble into T=3 VLPs, although often, the particles were heterogeneous. Interestingly, the SeMV NΔ65B CP could also be purified by Ni-NTA chromatography as a dimer which assembled into T=1 VLPs under crystallization conditions. The structure of NΔ65B-CP VLPs revealed that the assembled particles were devoid of divalent metal ions at the canonical site and there was no density corresponding to the B domain. However, the S domain could be superimposed on that of SeMV NΔ65VLPs determined earlier. The other VLPs- SeMVNΔ65P10 CP, SeMVNΔ65P8 CP and SeMVNΔ65VPg could not be crystallized because of their heterogeneity. These studies suggest a subtle interplay between the length, sequence and structure of the R-domain polypeptide and the assembly of particles.
    Electronic ISSN: 2053-2733
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  • 69
    Publication Date: 2014-08-05
    Description: Ternary chalcogenides with the spinel crystal structure have been widely studied for the last 60 years. These compounds are more covalent and allow different interactions between ions when compared to corresponding oxides while maintaining the versatility of the spinel structure. Particularly, spinels with formula AIn2S4(A= Mn-Ni) are found to be semiconductors with a large band gap (~2.0 eV), showing mainly antiferromagnetic interactions at temperatures below 100 K. These properties are dependent on the distribution of cations between octahedral and tetrahedral sites in the structure and also on the synthesis method. Syntheses of these compounds have been extensively reported, involving long heating periods of mixtures of elements or binary sulfides inside evacuated quartz ampoules, lasting for up to two weeks or longer. We report two new, faster synthesis methods for polycrystalline samples of indium thiospinels avoiding evacuated ampoules. Polycrystalline FeIn2S4and MnIn2S4samples were synthesized from stoichiometric mixtures of binary sulfides, heating in a constant gas flow of 1% H2in Ar at 1073 K for 6 and 24 hours respectively. Polycrystalline samples of FeIn2S4, CoIn2S4and NiIn2S4have also been synthesized in a piston-cylinder press, from stoichiometric mixtures of the binary sulfides, at a pressure of 3.5 GPa at 1173 K for 1 hour. From x-ray powder diffraction data all crystal structures were refined by means of Rietveld analysis. Refined cell parameters are in agreement with previous reports. Different degrees of inversion were obtained for each sample. NiIn2S4and both FeIn2S4samples are in accordance with previous reports, while MnIn2S4and CoIn2S4differ from reported values [1]. FeIn2S4and MnIn2S4synthesized in H2/Ar flux were characterized by Raman spectroscopy to further assess cation distribution. In addition, their thermal stability in air was tested by Thermogravimetric Analysis (TGA).
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  • 70
    Publication Date: 2014-08-05
    Description: The ABC toxin complexes produced by certain bacteria are of interest owing to their potent insecticidal activity and potential role in human disease. These complexes comprise at least three proteins (A, B and C), which must assemble to be fully toxic. The carboxy-terminal region of the C protein is the main cytotoxic component, and is poorly conserved between different toxin complexes. A general model of action has been proposed, in which the toxin complex binds to the cell surface via the A protein, is endocytosed, and sub-sequently forms a pH-triggered channel, allowing the translocation of C into the cytoplasm, where it can cause cytoskeletal disruption in both insect and mammalian cells. We have determined the three-dimensional structure of the complex formed between the B and C proteins by X-ray crystallography to 2.5Å. These proteins assemble to form an unprecedented, large hollow structure that encapsulates and sequesters the cytotoxic, C-terminal region of the C protein like the shell of an egg. The shell is decorated on one end by a β-propeller domain, which mediates attachment of the B–C heterodimer to the A protein in the native complex. The structure reveals how C auto-proteolyses when folded in complex with B. The C protein is the first example of a structure that contains rearrangement hotspot (RHS) repeats, and illustrates a striking structural architecture that we predict to be conserved across both this widely distributed bacterial protein family and the related eukaryotic tyrosine-aspartate (YD)-repeat-containing protein family, which includes the teneurins. The structure provides the first clues about the function of these protein repeat families, and suggests a generic mechanism for protein encapsulation and delivery. We have been able to model the complete ABC toxin complex for the by docking the B–C complex and both associated chitinase enzymes, Chi1 and Chi2, onto the single-particle electron microscopy structure of the Y. entomophaga A pentamer. The structure of the complete complex presented here reveals how the cytotoxic C proteins of ABC-type toxin complexes are processed and protected, demonstrates the function of the B protein within the complex and provides a framework for further experiments to build a complete mechanistic model of action for this class of toxins. More broadly, it also illuminates the function of the widely distributed RHS- and YD-repeat families of proteins, which had previously been unknown.
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  • 71
    Publication Date: 2014-08-05
    Description: Haloalkane dehalogenases (EC 3.8.1.5; HLDs) are microbial enzymes with catalytic activity for the hydrolytic conversion of xenobiotic and highly toxic halogenated aliphatic compounds to the corresponding alcohols. Biodegradation, biosensing, biocatalysis and cellular imaging are potentially practical applications for the HLDs. Two newly isolated and purified psychrophilic haloalkane dehalogenases, exhibiting interesting catalytic properties, DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17, were used for the crystallization experiments and structure determination. Diffracted crystals of DpcA(left) and DmxA(right) (see figure, the scale bar -100μm) were refined up to the 1.05 Å and 1.45 Å resolutions, respectively. Diffraction data for DpcA were collected on beamline 14.2 at the BESSY II electron-storage ring (Helmholtz-Zentrum Berlin (HZB), Germany) and equipped with a Rayonics MX-225 CCD detector at the wavelengths of 0.978 Å, and for DmxA were collected using Pilatus 6M-F detector at the wavelengths of 0.972 Å on the beamline ID29, at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France). Crystals of DpcA belonged to P21 space group with unit-cell parameters: a = 41.3, b = 79.4, c = 43.5 A °, α = β = 90.0, γ = 95.0 and contained 1 molecule in the asymmetric unit. Crystals of DmxA belonged to P212121 space group, with unit-cell parameters: a = 43.371, b = 78.343, c = 150.51; α = γ = β = 90.0 and contained 2 molecules in the asymmetric unit. The structures were solved by molecular replacement with MOLREP from the CCP4 software suite. The coordinates of Xanthobacter autotrophicus (PDB code: 1B6G; 40% sequence identities for 121 residues and 53% sequence similarity was used as search model for DpcA structure and for DmxA from Rhodococcus rhodochrous (PDB entry 4E46; 48% sequence identity for 142 residues and 63% sequence similarity). Belonging to the superfamily of α/β - hydrolases, according to the catalytic pentad, HLDs are subdivided onto the three subfamilies. DpcA belongs to the HLD - I: Asp- His - Asp + Trp - Trp and DmxA to the HLD – II: Asp - His - Glu + Asn - Trp. We thank M. Weiss and S. Pühringer (BESSY). This work is supported by the Grant Agency of the Czech Republic (P207/12/0775).Also by the Ministry of Education of the Czech Republic (CZ.1.05/2.1.00/01.0024 and CZ.1.05/2.1.00/01.0001). The support of the Academy of Sciences of the Czech Republic is acknowledged as well.
    Electronic ISSN: 2053-2733
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  • 72
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 73
    Publication Date: 2014-08-05
    Description: Renewable energy today comprises wind, photovoltaics, geothermal, and biofuels. Biomass is the leading source of renewable, sustainable energy used for the production of liquid transportation fuels. While the focus is shifting today from the ethanol towards next generation or advanced biofuels the real challenge however remains the same: reducing the recalcitrance of biomass to deconstruction, which yields the sugars needed for further processing. NREL's Biosciences Center conducts studies of the fundamental nature of the plant cell wall; as well as those enzyme systems utilized in Nature to deconstruct it. These systems could be classified in two ways: the "free enzymes" and the "cellulosomes." Cellulosomes are self-assembling, multi-enzyme machinery that can include dozens and hundreds of catalytic domains and cellulose binding modules interconnected by linker peptides. We will present a structural overview of the biomass degrading enzymes from fungi using Trichoderma reesei and Penicillum funiculosum as examples. The bacterial cellulosome system discussed will be from a thermophile Clostridium thermocellum and bacterial free enzyme example will be the hyperthermophile, Caldicellulosiruptor bescii. To study these systems, we combined classical biochemistry and molecular biology, mass spectrometry, electron microscopy, high throughput robotics, macromolecular crystallography, and molecular dynamics. We seek to understand the properties and structure of biomass and plant cell walls, the structure-function relationships of the relevant hydrolytic enzymes, and the ways these enzymes interact with and alter the biomass during the degradation. Thorough understanding of the details of the molecular machinery at work has led to the development of improved enzyme cocktails that have reduced the cost of biomass conversion to renewable fuels so that today, this technology is becoming competitive with traditional fossil fuels.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 74
    Publication Date: 2014-08-05
    Description: Diaminopropionate ammonia lyase (DAPAL) is a non-stereo specific fold-type II pyridoxal 5' phosphate (PLP) dependent enzyme that catalyzes the conversion of both D/L isoforms of the nonstandard amino acid Diaminopropionate (DAP) to pyruvate and ammonia. DAP is important for the synthesis of nonribosomal peptide antibiotics such as viomycin and capreomycin. Earlier structural studies on EcDAPAL bound to a reaction intermediate (aminoacrylate) suggested that the enzyme follows a two base mechanism, where Asp120 and Lys77 function as general bases to abstract proton from D-DAP and L-DAP respectively. A novel disulfide was observed near the active site, although its functional significance was not clear. In the present study, structural and biochemical characterization of active site mutants Asp120 (Asp120Asn/Ser/Thr/Cys) and Lys77 (Lys77His/ Thr/Ala/Val) of EcDAPAL has been carried out. Reduction of catalytic efficiency (Kcat/Km) of D120N EcDAPAL for D-DAP by 140 fold and presence of the uncatalyzed ligand at the active site in the crystal structure suggested that Asp120 indeed abstracts proton from D-DAP. Lys77, which was speculated to be important for proton abstraction from L DAP, however seemed to be crucial for PLP binding only. Presence of non-covalently bound PLP in the L77W mutant and occurence of both the ketoenamine, enolimine forms of internal aldimine in L77R mutant provided an in depth insight into the unique chemistry of internal aldimine formation in PLP dependent enzymes. To investigate the role of the novel disulfide bond near the active site, C265 and C291 were mutated to Serine. Studies on these mutants show that this disulfide bond gives additional stability to the protein and might regulate the entry of substrates to the active site. Thus, these studies provide deeper insights into the reaction mechanism of EcDAPAL, representing the overall reaction mechanism followed by several other fold-type II PLP pendent enzymes.
    Electronic ISSN: 2053-2733
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  • 75
    Publication Date: 2014-08-05
    Description: As a part of exploration of novel bacterial genes coding for insecticidal proteins, we have initiated structural and functional studies on oxalate decarboxylase from Photorhabdus luminescens, a symbiotic bacteria inhabiting guts of nematodes that parasitize insects. Oxalate decarboxylases (OXDC) are enzymes that catalyze the conversion of oxalate to formate and carbondioxide (CO2) in the presence of manganese and dioxygen. Structures of OXDC in complex with ethylene glycol (EDO), EDO/formate (FMT) and FMT/CO2 were determined at resolutions of 1.97Å, 2.36Å and 2.5Å, respectively. The asymmetric unit of these crystals contained a trimeric molecule. A protomer of the enzyme consists of two β-barrel domains belonging to the cupin family of proteins. All the three ligand bound structures of OXDC resemble the closed form of OXDC from B. subtilis reported earlier. Comparison of these structures with the open and closed forms of B. subtilis OXDC indicated that the conformation of Glu166 (corresponding to Glu162 of B. subtilis) in cupin domain I but not in domain II is in a conformation suitable to function as the catalytic base/acid and hence only domain I may be catalytically active. It is observed that the hydrogen bonding interaction between Arg95 and Thr169 of cupin domain I is essential for the positioning of Glu166 for catalysis. A corresponding threonine residue is absent in cupin domain II. An analysis of the similarities and differences between OXDC structures from P. luminescens and other reported bacterial OXDC structures and oxalate oxidase from Hordeum vulgare has been carried out with the view of understanding substrate and functional specificities of these enzymes. The structure provides the molecular framework required to investigate the mode of action of the enzyme, which may be a suitable candidate for developing P. luminescens as a bio-insecticide against plant pests.
    Electronic ISSN: 2053-2733
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  • 76
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 77
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 78
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 79
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 80
    Publication Date: 2014-08-05
    Description: Drugs may present polycrystalline polymorphism (property of a substance to crystallize in more than one form or crystal structure). These variations can cause changes in physical-chemical properties and differences between the polymorphs as shape, solubility, density, melting range, among other consequences, leading to formulations that are not effective, although the chemical formula is the same [1]. Drugs such as albendazole (C12H15N3O2S, which is one of the most effective anthelmintics, [2] showing activity against nematodes, trematodes and cestodes, reasons that added to its safety and low cost have made it a drug widely used in human medicine and veterinary), has more than two different crystal structures, and only two of them are known. The X-ray powder diffraction is a powerful technique used in the structural characterization of drugs, and coupled with the Rietveld method [4], the quantification of the active phases, through the knowledge of their crystal structures, becomes possible. In this paper we discuss results on the differences between the polymorphs of albendazole, with data obtained by means of X-ray diffraction, thermal analysis (differential scanning calorimetry and thermogravimetric analysis), Fourier transform infrared spectroscopy and scanning electron microscopy.
    Electronic ISSN: 2053-2733
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  • 81
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 82
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 83
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 84
    Publication Date: 2014-08-05
    Description: Recently we reported a new possibility for stabilizing highly reactive organoselenenyl(II) chlorides by N-functionalization of an organyl substituent and the subsequent addition of a hydrochloric acid molecule [Ref.]. It is well-known that organotellurenyl(II) chlorides are even less stable than the related organoselenenyl(II) chlorides. This fact prompted us to apply the same approach to organotellurenyl(II) chlorides containing an N-functionalized aryl substituent. In the present work, a novel facile route for stabilizing highly reactive Ar*TeCl species (Ar* = nitrogen-containing aryl) by hydrochloric acid addition has been demonstrated, exemplified by two new T-shaped tellurenyl chloride adducts, viz. 1H-pyridine-2-tellurenyl-dichloride (Fig.) and 4,6-dimethyl-1H-pyrimidine-2-tellurenyl-dichloride. Their quasi-planar zwitterionic structures with strong intramolecular N–H...Cl hydrogen bonds have been evidenced by experimental (single-crystal X-ray diffraction, multi-nuclear NMR, vibrational spectroscopy) and theoretical (DFT and QTAIM) methods. Due to this structure, the studied heteroaryl tellurenyl dichlorides react with alkenes in a similar manner to the corresponding monomeric tellurenyl chlorides affording the same cycloaddition products. The described approach to difficult-to-obtain, extremely unstable organotellurenyl(II) chlorides opens alluring prospects in the synthesis and study of low-valent chalcogen compounds.
    Electronic ISSN: 2053-2733
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  • 85
    Publication Date: 2014-08-05
    Description: Porous molecular crystals that retain their structure in the absence of trapped solvent molecules are rare, given the flexibility of most non-covalent interactions. The crystal structure of microporous 1,3,5-tris(4-carboxyphenyl)benzene (tcpb) is notable for its large void volume and thermal stability, which stems from a complex polycatenation of its hydrogen-bonded network. Our group is exploring the crystallography of derivatives of this model compound with an eye towards tuning the dimensions and polarity of its pore structure. In one synthetic pathway, tritolylarenes are prepared as intermediates. We have discovered that even these molecules, which have no hydrogen-bond forming groups, tend towards complex crystal packings that exhibit disorder, aperiodicity, and solvent-filled voids. Additional exploration of co-crystals of these propeller shaped entities produced a pseudohexagonal columnar structure assembled from π-stacked helices. These helices enclose channels containing disordered tetrafluoroborate counterions, suggesting the possibility of ion exchange properties.
    Electronic ISSN: 2053-2733
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  • 86
    Publication Date: 2014-08-05
    Description: 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
    Electronic ISSN: 2053-2733
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  • 87
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
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  • 88
    Publication Date: 2014-08-05
    Description: Lactoperoxidase is a member of mammalian heme peroxidase superfamily that consists of lactoperoxidase (LPO), myloperoxidase (MPO), thyroid peroxidase (TPO), eosinophil peroxidase (EPO). So far crystal structures of only two mammalian peroxidases LPO and MPO have been determined. The structures of LPO have been determined from the samples obtained from bovine, buffalo, goat and sheep. Their complexes have also been determined with inhibitors and substrate analogues. However, the structures of EPO and TPO have not been obtained so far. Due to significant sequence identity between LPO and TPO, the structures of these proteins are expected to be similar. Similarly their substrates will also have similarity as well as the substrate and enzyme interactions will be similar. Therefore, a complex of LPO was prepared with propylthiouracil (PTU), a compound used as a drug in thyroid ailments. The complex was crystallized using co-crystallization. The crystals of native LPO were also soaked in the solution containing PTU. The crystals belonged to monoclinic space group with cell dimensions a = 80.2 Å, b = 82.5, c = 95.0, β = 73.7° There were four molecules of LPO in the asymmetric unit. The structure determination of the complex revealed that PTU binds to the LPO at the distal heme site. It is held at this site through several hydrogen bonds and van der Waals contacts. The mode of binding and number of interactions suggest that a similar mode of binding may occur with TPO. Based on the information of interactions and the missing potential interactions, the modifications in the structure of PTU are suggested so that the improved design of the TPO inhibitor is obtained.
    Electronic ISSN: 2053-2733
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  • 89
    Publication Date: 2014-08-05
    Description: 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)
    Electronic ISSN: 2053-2733
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  • 90
    Publication Date: 2014-08-05
    Description: With 2014 marking the International Year of Crystallography (IYRc) one can't help but look back in awe with respect to how far the science has come. At the same time, we are always looking forward to new techniques, technologies and transformational methods that push our science even further. So what is the state of the union, what are the major areas for growth, and what will crystallography look like in 5, 10, 25 and 100 years? In seeking to answer these questions, we are providing conference attendees an opportunity to peer into their crystal balls and answer these questions.
    Electronic ISSN: 2053-2733
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  • 91
    Publication Date: 2014-08-05
    Description: The development of the seriesInternational Tables for Crystallographysince the 2011 Congress in Madrid will be discussed. The series includes eight published volumes with a ninth expected before the end of 2014 and definite plans for a tenth. A new edition of Volume A (Space-group symmetry, Editor Mois Aroyo) is nearly ready. A great deal of work has been done on the associated onlineSymmetry Database. Volume A1 (Symmetry relations between space groups, 2011, editors Hans Wondratschek and Ulrich Müller) is the companion volume. Work on a revision of theBrief Teaching Editionwill begin once the new Volume A is finished. Volume B (Reciprocal space, 2010; Editor Gervais Chapuis, who succeeded Uri Shmueli in 2011) and Volume C (Mathematical, physical and chemical tables, 2006, Editor Richard Welberry) are undergoing revisions, which will be major. The volumes will be reorganized with those topics connected to reciprocal space in B and those connected to direct space in C. A new edition of Volume D (Physical properties of crystals, Editor André Authier) was completed in 2013. A new edition of Volume F (Crystallography of biological macromolecules, Editors Eddy Arnold, Daniel Himmel, and Michael Rossmann) appeared in 2012. A new Volume H onPowder diffraction(Editors Chris Gilmore, Jim Kaduk, and Henk Schenk) is nearing completion. A new Volume I onXAFS(Editors Chris Chantler, Federico Boscherini, and Bruce Bunker) is in the planning stage. The Commission on Magnetic Structures is developing plans for a volume. In the meantime Danny Litvin's compilation of 1-, 2-, and 3-dimensional magnetic subperiodic groups and space groups was published as an e-book by the IUCr in 2013. Ideas for future developments will be welcome.
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  • 92
    Publication Date: 2014-08-05
    Description: Two high resolution crystal structures of isatin hydrolase (IH) from the Baltic seabed bacteria Labrenzia aggregata are presented. The crystals structure capture both the apo and the product state. This hydrolase present a new fold and the first metal-dependent hydrolase with this fold to be functionally characterized[1]. The Isatin hydrolase catalyze the reaction that convert isatin to isatinate and belongs to a novel family of metalloenzymes that include bacterial kynurenine formamidase (KynB) also recently published, however hoste a binclear zink site in the active site[2] as compared to a single manganese in IH. The product state, mimicked by thioisatinate, has captured an additional water molecule that bridges the thioisatinate to a water channel and that could act as a proton wire and thus allows the proton to be released during the hydrolysis reaction only when the product is formed. The functional proton wire is therefore locked by thioisatinate and represents a unique catalytic feature trapped and visualized. Biochemical evidence for the proton wire is also presented as single point mutation from S225C enhances the Vmax of the enzyme. Ser-225 is the only side chain residue that is included in the proton wire. The molecular basis for thioisatinate recognition allows stronger and more confident identification of orthologous genes encoding isatin hydrolases within the prokaryotic kingdom. The isatin hydrolase orthologues found in human gut bacteria raise the question as to whether the indole-3-acetic acid degradation pathway is present in human gut flora.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 93
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 94
    Publication Date: 2014-08-05
    Description: An impressive comparison of G(r) calculated with PDFgetX2(1) from data of Naphthalen taken at room temperature with a Stoe Stadi P powder diffractometer in Transmission mode equipped with a Ag-tube, a Ge(111)-monochromator for pure Ag-Kα1-radiation (0.5594 Å) as well as the Dectris MYTHEN 1K with1mm chip size and from synchrotron data, beamline X17A, NSLS Brookhaven with a wavelength of 0.1839 Å, yields amazingly similar peak widths for both experiment sites. To observe the temperature dependence of this resolution, the same laboratory setup with an additional Oxford Cryosystems Cobra or a Stoe furnace has been chosen to compare the signal width as a function of T. Low temperature data for these PDF calculation experiments has been taken from LaB6 as a crystalline standard and Naphthalene as well known organic phase. In addition high temperature G(r)-data from Ammonium Nitride will be demonstrated.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 95
    Publication Date: 2014-08-05
    Description: Synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of rapidly-synthesized crystal sponges using high-flux synchrotron radiation are presented [1]. The synthetic procedure for the zinc-based metal-organic framework (MOF) used in preliminary crystal sponge reports [2, 3] has been modified to afford suitable sponges in 3 days instead of 2 weeks. These sponges were tested on some small molecules, with two being difficult cases for in-house diffraction analysis in regards to data quality and determination of space group. These issues were readily resolved by the use of high-flux synchrotron radiation with
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 96
    Publication Date: 2014-08-05
    Description: Local structures surrounding Co dopoant atoms in (Y,Co) codoped CeO2 nanocrystals prepared by a chemical method followed by a series of thermal annealing and x-ray exposure have been probed using x-ray absorption fine structure (XAFS) techniques. These material systems are of great interest for catalytic applications. Our x-ray results show systematic variation of local structures surrounding Co atoms due to thermal annealing at different temperatures. It was also found that x-ray exposure with sufficient incident photon energy can substantially neutralize the structural effects of annealing. A theoretical model based on calculation using the Vienna ab initio Simulation Package (VASP) was proposed to identify relevant dopant locations that lead to the observed XAFS results and to explain the migration of Co in the CeO2 host due to the x-ray and thermal treatments. Manipulation of dopant atoms using x-ray exposure may provide unprecedented opportunities for tuning the physical properties of these materials for catalytic applications.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 97
    Publication Date: 2014-08-05
    Description: 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.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 98
    Publication Date: 2014-08-05
    Description: The arrangement of the molecules in their crystal structure is controlled by the non-covalent intermolecular interactions other than the effectual space filling. The role of strong hydrogen bonds in guiding the crystal packing is well-known in the literature. But, how significant are the weak interactions in the field of crystal engineering, has yet not been fully understood. Our aim is to comprehend the nature and strength of the weak interactions involving fluorine in guiding the packing of small organic molecules in their respective crystal structure. The reason being the controversies, which are involved regarding the interactions offered by "organic fluorine"[1] and also due to the importance of these interactions in the pharmaceutical industry. Some of the research groups indicate the incapability of interactions offered by fluorine in the formation of supramolecular motifs, whereas other groups have indicated that substantial role is being played by fluorine in constructing the lattice through C-H···F, C-F···F and C-F···π interactions in the presence and absence of strong hydrogen bond donor and acceptor groups. To understand more about these interactions, we have chosen a model system of halogen substituted N-benzylideneanilines[2]. In this system, we have analysed the impact of fluorine mediated interactions on the crystal packing by having fluorine as a substituent on both the phenyl rings. Then the robustness of the synthons offered by organic fluorine has been anticipated in the same system, but with one of the substituent as chlorine or bromine in either of the phenyl ring. It has been observed that the replacement of the non-interacting fluorine by its heavier analogue has not altered the supramolecular motif, which was formed by the other fluorine. But the crystal packing has been found to be completely altered in the molecules where the interacting fluorine was replaced by its heavier analogue. Salient features of our computational studies, which include the calculation of the stabilization energies of the studied dimers using MP2 method and their topological analysis using AIM2000, to support the experimental observations will also be presented to highlight the sturdiness of the synthons formed by so called "organic fluorine".
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 99
    Publication Date: 2014-08-05
    Description: Anion deficiency in perovskite-based ferrites containing lone pair cations Pb2+ and Bi3+ can be accommodated by the formation of crystallographic shear (CS) planes. In this contribution, using (Pb1-zSrz)1-xFe1+xO3-y as a model system, we demonstrate that the lone pair cations are not only responsible for the formation of the CS planes, but also control their orientation. The isovalent substitution of Pb2+ by stereochemically inactive Sr2+ highlights the influence of the A-cation electronic structure owing to very close ionic radii of these cations. Employing a combination of transmission electron microscopy and X-ray and neutron powder diffraction, we have systematically investigated the structure evolution of the compounds with changing P/Sr ratio. Two compositional ranges with distinct orientations of the CS planes have been identified in the system: 0.05 ≤ z ≤ 0.2, where the CS planes orientation systematically varies but stays close to (203)p, and 0.3 ≤ z ≤ 0.45 with the (101)p CS planes. The incommensurate structure of Pb0.792Sr0.168Fe1.040O2.529, a representative compound of the first range, has been refined from the neutron powder diffraction data (S.G. X2/m(α0γ), X = [1/2,1/2,1/2,1/2], a = 3.9512(1)Å, b = 3.9483(1)Å, c = 3.9165(1)Å, β = 93.268(2)0, q = 0.0879(1)a* + 0.1276(1)c*, RF = 0.023, RP = 0.029, T = 900K). Comparing the CS structures in both compositional ranges, we demonstrate that the orientation of the CS planes is primarily governed by a specific bonding configuration of the lone pair cations with the anions.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 100
    Publication Date: 2014-08-05
    Description: A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36)3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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