bluuebunny/crossref_metadata_2025 huggingface dataset:
Serial Femtosecond Crystallography user's consortium apparatus at European XFEL
Authors: Messerschmidt Marc , Chavas Leonard , Ananthaneni Sunil , Dadgostar Hamidreza , Graafsma Heinz , Liang Mengning , Mancuso Adrian , Raabe Steffen , Stern Stephan , Vagovic Patrik , Chapman Henry
Published: November 2015

The Serial Femtosecond Crystallography (SFX) user's consortium apparatus is to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument of the European X-ray Free-Electron Laser facility (XFEL.EU) [1, 2]. The XFEL.EU will provide ultra-short, highly intense, coherent X-ray pulses at an unprecedented repetition rate. The experimental setup and methodological approaches of many scientific areas will be transformed, including structural biology that could potentially overcome common problems and bottlenecks encountered in crystallography, such as creating large crystals, dealing with radiation damage, or understanding sub-picosecond time-resolved phenomena. The key concept of the SFX method is based on the kinetic insertion of protein crystal samples in solution via a gas dynamic virtual nozzle jet and recording diffraction signals of individual, randomly oriented crystals passing through the XFEL beam, as first demonstrated by Chapman et al. [3]. The SFX-apparatus will refocus the beam spent by the SPB instrument into a second interaction region, in some cases enabling two parallel experiments. The planned photon energy range at the SPB instrument is from 3 to 16 keV. The Adaptive Gain Integrating Pixel Detector (AGIPD) is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX-apparatus. The AGIPD is designed to store over 350 data frames from successive pulses, and aims to collect more than 3,000 images per second. Together with the implementation of automated procedures for sample exchange and injection, high-throughput nanocrystallography experiments can be integrated at the SFX-apparatus. In this work, we review the overall design of the SFX-apparatus and discuss the main parameters and challenges
The Coherent X-ray Scattering Beamline at Taiwan Photon Source
Authors: Lin Jhih-Min , Huang Yu-Shan , Chen Chun-Yu , Jeng U-Ser , Mou Chung-Yuan , Lin Tsang-Lang , Chen Hsin-Lung
Published: November 2015

The coherent X-ray scattering beamline is one of the phase I beamlines designed for the Taiwan Photon Source, a new 3 GeV ring under construction at the National Synchrotron Radiation Research Center in Taiwan. By using a pair of 2m-long in-vacuum undulators, this beamline will provide a highly coherent beam for X-ray photon correlation spectroscopy principally; moreover, it will share a part of beamtime for small-angle X-ray scattering (SAXS) experiments with similar setup of the beamline. The operating photon energy is designed within the range of 5-20 keV. In vertical direction, the beam spot size at sample position is 1 μm with focusing mirror and by using 1D compound refractive lenses (CRLs) the beam spot size is 10 μm. The horizontal beam spot size is in the range of 1 to 10 μm with a two-stage focusing design. The vertical and horizontal transverse coherence lengths of the 10 μm2 beam spot size at the photon energy of 5 KeV are 212 and 6 μm at sample position respectively. Beside XPCS the beamline configuration can cope with the requirements of most SAXS experiments, including anomalous measurements and micro-beam mapping. In addition, the increasing biological SAXS demand is also considered and the on-line fast performance liquid chromatography (FPLC) will be enclosed for biological users.
Automated protein crystal optimisation with TTP Labtech's dragonfly
Authors: Jenkins Joby , Cochrane Gary
Published: November 2015

The ability to crystallise proteins, nucleic acids or macromolecular complexes pose significant challenges to the protein crystallography community, from large scale screening assays for the determination of initial crystallization conditions, screen optimisation and final screen set-up. Protein crystal optimisation is vital to ensure high quality X ray diffraction data for the solving of high resolution structure. This process involves the set-up of a series of complex screening combinations where the ratios of the individual components identified from primary crystallisation studies are varied. In order to reduce the effort and tedium of this process, TTP Labtech have introduced dragonfly as an addition to their successful mosquito liquid handling portfolio for crystallisation screening. This poster demonstrates that "dragonfly" is a valuable, compact, low cost addition to the crystallographer's bench. It eliminates lengthy and complicated plate set-up at the optimisation stage of crystallisation.
Commissioning the Neutron Laue Diffractometer in Berlin
Authors: Iles Gail , Schorr Susan
Published: November 2015

The Fast Acquisition Laue Camera for Neutrons (FALCON) is a thermal neutron Laue diffractometer situated in the experimental hall of the BER-II reactor at HZB in Berlin. The thermal beamtube, D1S, delivers a stream of neutrons direct to FALCON just 8m from the reactor core but with a low gamma radiation count. FALCON benefits from a beam that does not pass through any objects upstream whilst a beam definer delivers a highly focused neutron beam to the instrument with <10divergence. The instrument comprises two scintillator plate detectors coupled to four iCCD cameras each. The neutron beam passes through the detector units enabling one detector to be placed in the backscattering position and the second detector in the transmission position. The image-intensified CCDs are capable of obtaining 20-bit digitization Laue images in under ten seconds and variable sample table and detector positions allow a full range of sample environments to be utilised. Scientifically, FALCON offers the opportunity to study samples from a wide range of fields for example; low-temperature magnetic studies, high-temperature structural phase transitions, in-situ kinetics studies and point-defect analysis in compound semiconductors. Data from FALCON can be used to solve crystallographic structures and as a neutron instrument it has all the advantages of neutrons as a probe for condensed matter, for instance, identification of the location of hydrogen atoms within structures and differentiation between electronically similar elements. FALCON will now enter the commissioning phase using in-house samples to test both ambient and sample environment conditions on the instrument. We present here details of the upcoming commissioning tests and invite users to submit proposals for Laue diffraction experiments.
Towards routine study of hydrogenous materials using powder neutron diffraction
Authors: Henry Paul
Published: November 2015

Hydrogen (1H) is an element that is ubiquitous in chemistry and materials science. Neutron diffraction is the preferred technique for studying 1H-containing compounds, but is complicated by the high incoherent scattering cross section, which also varies with wavelength. This variation of scattering cross section as a function of wavelength/energy and chemical environment is not well understood.[1-2] This is surprising as it is the largest contributing factor to the scattering properties used in single crystal and powder neutron diffraction experiments to calculate the optimal sample size for hydrogen containing compounds and the tabulated data are given for fixed neutron velocity of 2200 m s-1 (approximately 1.8 Å). The use and current limitations of certain current generation neutron diffraction instruments to probe 1H materials has recently been described.[3] Here, I present work to validate an empirical correction for the incoherent scattering cross section of 1H as a function of incident neutron wavelength in the range 0.5 - 10 Å using continuous source, monochromatic wavelength measurements. The practical use of this is that a, potentially quantitative, correction for all neutron diffraction data, including time-of-flight (TOF) from pulsed sources, as a function of scattering angle and neutron path length will become possible. Implementation of methodology that allows routine H position definition from easily synthesised material (i.e. non-isotopically enriched, and in polycrystalline or small single crystal (≤ 50 μm) form) for both TOF and monochromatic neutron instruments would be both of widespread application. Additionally, i will present work on an instrument concept for a pulsed monochromatic powder diffractometer for the ESS, which will be built in Lund by the end of the current decade. This diffractometer will aim to specialise in the data collection and analysis of hydrogenous materials using a combination of diffraction and inelastic techniques.
Current Status of the Liquid-Metal-Jet X-ray Source Technology
Authors: Espes Emil , Hansson Björn , Gratorp Christina , Hemberg Oscar , Johansson Göran , Kronstedt Johan , Otendahl Mikael , Sundman Björn , Takman Per , Tuohimaa Tomi
Published: November 2015

High-end x-ray diffraction and scattering techniques such as high-resolution XRD, protein crystallography, and SAXS rely heavily on the x-ray source brightness for resolution and exposure time. Traditional solid or rotating anode x-ray tubes are typically limited in brightness by when the e-beam power density melts the anode. The liquid-metal-jet technology has overcome this limitation by using an anode that is already in the molten state. We have previously demonstrated prototype performance of a metal-jet anode x-ray source concept [1-3] with unprecedented brightness in the range of one order of magnitude above current state-of-the art sources. The technology has since been developed into a stable and reliable source for home-lab systems This presentation will review the current status of the technology specifically in terms of stability, lifetime, flux and brightness. It will also discuss details of the liquid-metal-jet technology with a focus on the fundamental limitations of the technology. It will furthermore refer to some recent data from applications within x-ray diffraction and SAXS.
Future developments for macromolecular crystallography at the CLS
Authors: Grochulski Pawel , Cygler Miroslaw , Fodje Michel , Labiuk Shaunivan , Gorin James , Janzen Kathryn
Published: November 2015

The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source (CLS) is a suite of fully automated beamlines, 08ID-1 and 08B1-1 [1]. It serves over 60 Canadian groups plus academic and commercial users in the US. Besides remote data collection, we offer Mail-In service where data are collected by CMCF staff. Beamline 08B1-1 has been in operation since 2011 and beamline 08ID-1 since 2006. When beamline 08ID-1 was designed, over 10 years ago, small crystals were defined as having sizes of 50-100 μm. Today, the most challenging experiments require more intense X-ray beams that can be focused to accommodate much smaller crystal sizes of less than 5 μm with flux on the order of 10^11 photons/s. To reach these stringent parameters, a new more powerful source of X-rays will be required, which will be provided by a longer small-gap in-vacuum undulator (SGU). To accommodate the higher power levels and to focus X-rays to a smaller focal spot with a high degree of spatial and temporal stability, the existing X-ray optical elements need to be upgraded. The remaining components of the project include a 5-axis alignment table for improving alignment of small samples with the microbeam, a high-efficiency robotic sample-changer and a single-photon X-ray detector. Several options for the new design will be discussed. These developments are consistent with the current direction of structural biology research at the CLS [2]. Since 2006 over 225 (240) papers and 400 (444) PDB deposits reported data collected at beamline 08ID-1. Parentheses indicate the total number for the CMCF. Many of these have been published in very high impact journals such as N. Engl. J. Med., Nature, Cell, Science, PNAS, among others (http://cmcf.lightsource.ca/publications/).
Launching the Theoretical Crystallography Open Database
Authors: Gražulis Saulius , Merkys Andrius , Vaitkus Antanas , Le Bail Armel , Chateigner Daniel , Vilčiauskas Linas , Cottenier Stefaan , Björkman Torbjörn , Murray-Rust Peter
Published: November 2015

As computational chemistry methods enjoy unprecedented growth, computer power increases and price/performance ratio drops, a large number of crystal structures can today be refined and their properties computed using modern theoretical approaches, such as DFT, post-HF, QM/MM, MCMM methods. Availability of several open source codes for computational and quantum chemistry and open-access crystallographic databases enables large scale computations of material structures and properties. We thus increasingly feel that an open collection of theoretically computed chemical structures would be a valuable resource for the scientific community. To address this need, we have launched a Theoretical Crystallography Open Database (TCOD, http://www.crystallography.net/tcod/). The TCOD sets a goal to collect a comprehensive set of computed crystal structures that would be made available under an Open Data license and invites all scientists to deposit their published results or pre-publication data. Accompanied with a large set of experimental structures in the COD database [1], the TCOD opens immediate possibilities for experimental and theoretical data cross-validation. To ensure high quality of deposited data, TCOD offers ontologies in a form of CIF [2] dictionaries that describe parameters of computed chemical and crystal structures, and an automated pipeline that checks each submitted structure against a set of community-specified criteria for convergence, computation quality and reproducibility. The scope of TCOD and validation tools make TCOD a high-quality, comprehensive theoretical structure database, useful in a broad range of disciplines. First-principle calculations are also of huge interest to simulate physical properties, either prospectively or for materials that do not grow as sufficiently large crystals. The property results can now be tested against the Material Properties Open Database [3] (http://www.materialproperties.org/) to ameliorate the used models.
Recent developments at the MX beamline X10SA at the SLS
Authors: Dworkowski Florian , Panepucci Ezequiel , Pradervand Claude , Fuchs Martin , Pauluhn Anuschka , Olieric Vincent , Ebner Simon , Thominet Vincent , Wang Meitian
Published: November 2015

The three macromolecular crystallography (MX) beamlines at the Swiss Light Source (SLS) rank among the most productive in Europe. The very successful design of the first beamline, X06SA, inaugurated in 2001, was the basis for the second beamline, X10SA, operated by the Paul Scherrer Institut and financed by the partners Max Planck Society, Novartis and Hofmann-La Roche. To keep up with the increasing demand for high throughput crystallographic experiments, especially in an industrial environment, as well as the rising interest in more challenging targets, the beamline is under constant development. Here we will present the recent advances in usability and performance, including software integration and automation with the completely new data acquisition software DA+, in-situ screening for diffraction candidates, (serial) micro-crystallography with micro-beam, and beamline hardware.
X-ray n-beam diffraction to study nanodefects of Xe+ implantation in Si(001)
Authors: Calligaris Guilherme , de Menezes Alan , Lang Rossano , dos Santos Adenilson , Bettini Jefferson , Cardoso Lisandro
Published: November 2015

Investigations about the nanocavities/bubbles formation by inert gas ion implantation in Si matrix and its properties have constituted an ongoing challenge in material science. Dislocation/extended defects (likely the {113} defects) are produced by post-implant annealing, which affect directly the nanocavities/bubbles structural evolution. In this work, the formation of defects induced by Xenon gas ion implantation in a Si sample (#Si-pristine) was studied by high-resolution reciprocal space mappings (RSM) and non-conventional X-ray Multiple Diffraction (XRMD) using synchrotron radiation. For this, Xe+ ions (80 keV; 5x1015 cm-2) were implanted in Si(001) at room temperature. Subsequently, the as-implanted samples were thermally annealed in air atmosphere at 600, 700 and 800 °C for 30 min in order to nucleate Xe nanobubbles that were detected in annealed samples by TEM images. Differences in the diffracted intensity pattern, along the crystal truncation rod, were detected in the Si (113) asymmetrical RSM for as-implanted and annealed samples, in comparison to pristine Si, indicating defect contribution along in-plane an out-of-plane directions. The ω(incident):Φ(azimuthal) coupled scans of two XRMD cases: 3-beam Bragg-Surface-Diffraction (BSD) (000)(002)(1-11) and the 4-beam (000)(002)(1-1-1)(1-13) have shown expected broader peaks (as-implanted sample) in comparison to the pristine sample, besides the ω-axis intensity asymmetry (c-axis strain induced). Furthermore, the analysis of all BSD mappings has provided: i) the annealing effect of reducing the lattice strain (600 and 700 °C samples), and ii) a huge surface effect through the diffuse scattering (800 °C-sample). As to the 4-beam case, a strong streak (diffraction condition trace) was observed for annealed sample patterns. This remarkable effect can be associated to the {113} defects, which are in the same direction of the secondary/coupling diffracting planes (XRMD phenomenon). It is believed that these defects break the spatial coherence, increasing the streak intensity. On the other hand, the streak is suppressed by the primary extinction effect in the pristine-Si and as-implanted samples. Financial support by Brazilian Synchrotron Light Laboratory (LNLS), CAPES, CNPq and FAPEMA.
Upgrading Existing Diffractometers with State-of-the-art Microfocus Sources
Authors: Beerlink André , Graf Jürgen , Wiesmann Jörg , Michaelsen Carsten
Published: November 2015

Modern microfocus X-ray sources define the state-of-the-art for a broad spectrum of applications in home laboratories, such as protein and small molecule crystallography, and small-angle scattering. These sources are combined with multilayer optics to image the source spot onto the sample. The optics provides a parallel or focused monochromatic X-ray beam, magnified to a suitable size. Low power sealed microfocus sources, such as Incoatec's IµS represent an attractive alternative to rotating anodes, with a significant reduction in cost and maintenance. Power loads of a few kW/mm2 in anode spot sizes below 50µm deliver a compact brilliant beam. For example, the IµSHighBrilliance delivers up to 1010 photons/s/mm2 in a spot size in the 100µm range. It is available for Cu, Mo, Ag, Cr and Co anodes. Since the launch in 2006 more than 400 IµS are now in operation worldwide for a large variety of applications in biology, chemistry, physics and material science. Are you tired of getting spare parts for an ancient rotating anode or is your detector performance only limited by your beam delivery system? We will demonstrate how to bring former high end diffractometers back to a superb performance for cutting edge science after an upgrade with an IµS source. Incoatec ensures full software and safety integration, and an installation hand in hand with the local service, providing a constant service support from your partners on site. In addition to all Bruker or Nonius systems, Incoatec also offers integrations into a wide range of instruments from Rigaku, Marresearch or STOE, also with Dectris or Huber components.
Structural effects of hinge length variation in a versatile foldamer backbone
Authors: Suhonen Aku , Laakkonen Heikki , Nissinen Maija
Published: November 2015

Foldamers are complex molecular scaffolds that mimic the form and function of biological molecules and are composed of simple repeating units.[1] Their potential applications include stereoselective and efficient organic catalysis mimicking the properties of enzymes, as well as bioreceptor mimics for new foldamer-protein interactions which could provide interesting possibilities for the medical industry.[2] In our previous studies we have investigated the folding properties of two oligoamides.[3] As the next step we prepared a series of aromatic oligoamide foldamers with several folding units and a hinge group between the units. The length of the hinge group is an important feature of the foldamer and understanding the properties the varying lengths is an integral step towards the preparation of foldamers with versatile conformational and functional properties. The prepared foldamers adopt a helical structure with multiple hydrogen bonds to single carboxyl oxygen. The structure is very compact and unlike many other aromatic foldamers, there is no void in the center of the structure resembling many of the biological helices formed in proteins. The diameter of the fold is roughly 11 Å, fairly close to the diameter of the biological alpha-helix (12 Å). The structure also has vast potential for a specific functionalization because of the aromatic rings, and desired properties can be produced with minimal variation in the secondary structure of the foldamer.
Thermosalient crystals – new materials for clean energy conversion
Authors: Skoko Željko , Naumov Panče
Published: November 2015

Thermosalient compounds, colloquially known as "jumping crystals", are promising materials for fabrication of actuators that are also being considered as materials for clean energy conversion because they are capable of direct conversion of thermal energy into mechanical motion. During heating and/or cooling, these materials undergo rapid phase transitions accompanied by large and anisotropic change in their unit-cell dimensions at relatively small volume change, causing the crystals to jump up to height of several centimeters. Although the list of about a dozen reported thermosalient materials has been expanded recently, this extraordinary phenomenon remains poorly understood. The main practical burden with the analysis of these crystals is their propensity to disintegrate during the transition. By using a combination of structural, microscopic, spectroscopic, and thermoanalytical techniques, we have investigated the thermosalient effect in a prototypal example of a thermosalient solid, the anticholinergic agent oxitropium bromide, and we proposed the mechanism responsible for the effect. We found that heating/cooling over the phase transition causes conformational changes in the oxitropium cation, which are related to increased separation between the ion pairs in the lattice. On heating, this change triggers rapid anisotropic expansion by 4% of the unit cell, whereby the b axis increases by 11% and the c axis decreases by 7%. The phase transition is reversible, and shows a thermal hysteresis of approximately 20 K. Additional interesting observations were that the high-temperature phase of this material can also be obtained by short exposure of the room temperature phase to UV light or with grinding.
Strategies for distinguishing between B and C atoms in metallacarborane cages
Authors: Rosair Georgina , Welch Alan , McAnaw Amelia , Ellis David , Scott Greig , Lopez Maria
Published: November 2015

Carboranes and metallacarboranes demonstrate diverse geometric structures. Carborane cages are comprised of a mixture of carbon and boron vertices whereas metallacarboranes contain one or more metal atoms in addition to C and B atoms. The most common structure is the 12 vertex icosahedron but sub-icosahedral and supraicosahedral (13 vertex and even 14 and 15 vertex) cages are known. A common problem in structural studies of such species is how to distinguish between C and B given their very similar X-ray scattering powers. Usually in crystallography, displacement parameters and the Hirshfeld test are used as tools to check whether elemental assignment is correct. Although these are very useful in many circumstances, there are occasions when the displacement parameters are less well-defined and the Hirshfeld results consequently unreliable. Since correct element assignment is crucial in understanding the chemistries of carboranes and metallacarboranes we have developed new techniques to distinguish the C atom positions from the B atom positions in these cages. At Heriot-Watt University we have recently reported the Vertex-to-Centroid Distance (VCD) method [1] and a complementary approach, the Boron–H Distance (BHD) method [2], which was first communicated in 2002 [3]. The VCD and BHD methods have been used to distinguish between cage B and cage C atoms in a wide range of crystallographically-determined structures, both leading to the same clear conclusions and thus allowing the identities of these species to be established unambiguously. The methods are particularly useful when traditional approaches, e.g. using displacement parameters, fail, as demonstrated for asymmetric 14-vertex metallacarboranes [2] (Figure).
Temperature / pressure-dependent luminescence spectra of square-planar complexes
Authors: Poirier Stéphanie , Reber Christian , Libioulle Pierre
Published: November 2015

Luminescence properties of square-planar complexes of platinum(II) and palladium(II) with a d8 electron configuration were investigated. Blue shift of the maxima of the luminescence spectra occur for pressure-dependent spectra of several complexes of both metals. This is due to a structural compression of the crystalline lattice, which causes a destabilization of the LUMO orbital for theses complexes. Other structural changes can also occur, providing a more important slope of the blue shift. Also, intermolecular interactions cause a red shift in pressure-dependent spectra. In temperature-dependent spectra, opposite trends occur for several analog complexes. Palladium(II) complexes show a red shift of luminescence maxima with increasing temperature. Platinum(II) compounds exhibit a blue shift. This difference is explained with theoretical calculations of luminescence spectra. In these trends, the dominant effect is due to an increase of vibronic contributions with temperature. We also present a complex of platinum(II) in which the structural effect is dominant in the spectra with increasing temperature, leading to a red shift. This rare effect allows the study of structural changes with temperature for square-planar platinum(II) complex.
Calix[4]arene-Based MOFs Controlled by Length of Alkyldiammonium Guests
Authors: Park Ki-Min , Lee Eunji , Ju Huiyeong , Moon Suk-Hee , Lee Shim Sung
Published: November 2015

Our interest in the development of MOFs with the cavities controlled by guest species has led us to investigate the MOFs based on calix[4]arene derivatives, in which metal ions link the calix unit to give the networks with the cavities accommodating several guest species, because the calix[4]arene-based MOFs contain porosity associated with both the ligand itself and the structural framework. In the present work, we employed a low rim-functionalized calix[4]arene tetraacetic acid (H4CTA) with 1,3-alternative conformation as a multidentate building block and alkyldiamines as the guest molecules. In the solvothermal reaction of H4CTA and Zn(II) ion in the presence of alkyldiamines, two types of new MOFs based on calix[4]arene tetraacetate (CTA4-) depending on the lengths of α,ω–alkyldiammonium guests have been synthesized by including suitable alkyldiammonium guests. Their single-crystal X-ray diffraction analyses reveal that the short alkyldiammonium guests such as ethyldiammonium, propyldiammonium, and butyldiammonium lead to form two-dimensional framework with the cavity consisting of two CTA4-and four Zn(II) ions whereas the alkyldiammonium guests such as heptyldiammonium, octyldiammonium, nonyldiammonium, and decyldiammonium give rise to generate three-dimensional network with the cavity surrounded by six CTA4-and four Zn(II) ions. The alkyldiammonium guests in both MOFs are well accommodated by each cavity via a variety of supramolecular interactions including electrostatic interactions, hydrogen bonds and van der Waals interactions. We will present and discuss a study on the syntheses and characterization of two new MOFs based on calix[4]arene derivative.
Chemical information presentation in the Crystallography Open Database
Authors: Merkys Andrius , Matusevičiūtė Agnė , Vaitkus Antanas , Le Bail Armel , Chateigner Daniel , Lutterotti Luca , Quirós-Olozábal Miguel , Okulič-Kazarinas Mykolas , Moeck Peter , Murray-Rust Peter , Downs Robert , Girdzijauskaitė Saulė , Gražulis Saulius
Published: November 2015

Crystallography Open Database (COD, http://www.crystallography.net/) is the largest to date curated open-access collection of small to medium sized unit cell crystal structures [1,2]. Over 11 years of development, COD has accumulated over 1/4 million structures from the peer reviewed press and personal communications. COD has an automated data submission Web site, performs routine automatic quality checks on all incoming structures and is now recommended as a database for crystallographic deposition by several scientific journals. To facilitate automatic use and discoverability of COD data, and to increase usefulness of our database for chemists, two steps were undertaken. COD was now supplemented with software and data from the CrystalEye data aggregator. The new software permits extracting chemical data and presenting them as structural formula, unique moieties, and chemically significant fragments. We have also implemented search of crystal structures by the structural chemical formulae of the target compounds. The search is first of all performed among 70 000 hand-curated chemical structure descriptors, and can be extended to automatically generated descriptors. To facilitate data curation, a new software platform for data review is being developed. All COD structures will be evaluated using statistical distributions of observed geometrical and chemical properties (bond lengths, angles, dihedrals, planarities). The most statistically unusual structures will be forwarded to a COD reviewer Internet forum, where qualified reviewers will be asked whether they find provided evidence for a particular structure convincing or not. In this way, a set of human review indicators (convincing/unconvincing) will be available along with the match against the bulk of data (usual structure/unusual). Such indicators would be especially useful for deciding which COD records require special attention and which subsets of COD should be selected for reliable scientific inferences.
Old structures revisited: Better insights from new data
Authors: Díaz de Delgado Graciela , Ramírez V. Belkis , Velásquez William , Trejo Dávila Julio , Chen Chun-Hsing , González Teresa , Delgado J. Miguel
Published: November 2015

The need for improving the description of structural features with better quality data, at low temperature and with modern 2D detectors of certain materials, sometimes leads to surprisingly new insights into a previously reported structure. When attempting to grow single crystals of maleamic acid, good crystals of ammonium maleate, NH4(Mal), were obtained. Although the structure of this material has been reported at room temperature, in space group Pbcm with V=613.2(5) Å3[1], synchrotron data were collected at low temperature to examine the behavior of the ammonium moiety. The data collected lead to a structure better described in Pbca, a=8.9687(12), b=8.1604(8), c=16.348(2) Å, V=1196.5(2) Å3, Z=8. The refinement converged to R=0.0438, wR2=0.1156, S=1.02. An examination of the new data indicates that reflections with h odd are systematically weak but, nevertheless, present. The Ca derivative of valproic acid (a common anticonvulsant) was reported as monoclinic, C2/c, with a=16.250(8), b=18.471(17), c=7.729(7) Å, β=109.71(5)0, V=2183.97 Å3, Z=4, and R=10.94% [2]. However, data collection at room temperature and under a stream of nitrogen on several newly prepared crystals always lead to a triclinic, P-1 cell, with approximately half the volume of the reported cell. Attempts to index the dataset using the known monoclinic cell resulted in high uncertainties for the unit cell parameters and high Rint values since reflection spots showed splitting and diffuse scattering. The new cell had dimensions a=7.6995(4) Å, b=11.7444(6) Å, c=11.7708(6) Å, α=91.089(3)0, β=101.643(3)0, γ=102.041(3)0, V=1017.47(99) Å3, Z=2. Although the initial refinement was discouraging (R=0.1172, wR2=0.360, S=1.12) the analysis with PLATON indicated the presence of twining and, after considering the twin law, the refinement improved significantly (R=0.059, wR2=0.1472, S=0.99). Several examples where a new data collection resulted in interesting results will be presented.
The Physical Origins of the Chemical Bond
Authors: Brown Ian
Published: November 2015

The properties of the chemical bond are the same as those of the electrostatic flux that links the cores of two bonded atoms via their bonding electrons. Both the bond and the flux depend only on the number of electrons that form the bond, and significantly, neither depends on how the electron density is distributed. This allows the rules of chemical bonding to be developed using classical electrostatic theory without the need to know how the electron density is distributed. The magnitude of the flux is equal to the bond order (bond valence) and hence correlates with the bond length [1]. A network of bonds is equivalent to a capacitive electric circuit which allows one to predict the bond fluxes, hence also the bond lengths. Bond angles are determined by the spherical symmetry of the flux around each atom, and the resulting bonding geometry can be predicted using little more than a pocket calculator. The rules of all the predictive bond models: the VSEPR model, the ionic model, the covalent bond model and the bond valence model can be derived using classical electrostatics without introducing problematic concepts such as hypervalency, dative bonding, hybridization and the dichotomy between ionic and covalent bonding, thus eliminating the paradoxes created by the physically questionable Lewis and orbital models. Quantum effects are rarely important except in the transition metals where in some cases they perturb the bonding geometry.
The phase transition in bis(methyl(2-phenylethyl)ammonium) tetrabromidocuprate(II)
Authors: Bond Marcus
Published: November 2015

Bis(methyl(2-phenylethyl)ammonium) tetrachloridocuprate(II) is a well-known thermochromic compound that exhibits an abrupt color change (from green to yellow) at 353 K that is caused by a change in coordination geometry from square planar to flattened tetrahedral [1]. As part of a reinvestigation of established thermochromic chloridocuprate(II) and their related compounds, the bromide analog [bis(methyl(2-phenylethyl)ammonium) tetrabromidocuprate(II)] has been studied anew. The structure redetermination at ambient temperature agrees with the original [2] (CSD refcode: FUTTIX), i.e. alternating layers of flattened tetrahedral tetrabromidocuprate(II) complexes and of organic cations stacked along the a-axis of the monoclinic C2/c unit cell. A DSC scan from ambient temperature to 183 K reveals an exothermic peak (and corresponding endothermic peak upon heating) at 215 K. Single crystal structures, determined from ambient temperature to 120 K in steps of ~20 K, track a steady increase in b-axis length on cooling to the transition temperature. Across the transition temperature abrupt 1.1% and 0.74% increases in lengths of the b- and c-axes, respectively. and a 0.23% decrease in the a-axis length are observed with no change in space group. Slight changes of the organic cation phenyl group conformation are observed across the transition temperature that cause the organic layer to spread out and become thinner so that neighbouring layers are stacked more closely together along a. However, the flattened tetrahedral geometry of the tetrabromidocuprate(II) complex remains essentially unchanged across the transition.
Crystal structures of two molecules with small chemical structure difference
Authors: Berzins Agris , Actins Andris
Published: November 2015

Droperidol and benperidol, neuroleptic pharmaceuticals, both are used as antipsychotics. The chemical structure of these two compounds differs only by one double bond in the middle of the molecule (see Scheme). It is known that both of these substances can form several polymorphs and solvates. Crystal structures of most of these phases are known [1, 2]. Despite the molecular structure similarities, there are no known droperidol polymorph or solvate isostructural to those of benperidol. Although there has been studies characterizing the crystal structures of chemically very similar compounds, general explanation to observed structural differences was not found (e.g. [3]). In this study we analyse the crystal structures of benperidol and droperidol by comparing the molecule conformation and packing in crystal structures of both of these compounds. Molecule conformation is compared and torsion angles which differ and therefore lead to different crystal structures are identified. Theoretical calculation of potential energy surfaces of these torsion angles are performed in Gaussian09. Intermolecular interactions and molecule packing in all crystal structures are compared by trying to understand the general differences between both molecules. Analysis of structures deposited in Cambridge Structural Database is performed to find conformations and intermolecular interactions characteristic for similar molecules by therefore trying to generalize structural formation possibilities for both pharmaceuticals and understand the reasons for crystallization of only observed structures. Theoretical calculations of benperidol and droperidol crystal structures where benperidol molecules are replaced by droperidol and vice versa are performed in CASTEP to compare the energy of experimentally observed crystal structure with that of theoretically possible structure isostructural to double-bond-different molecule.
The crystal structure of the cytochrome P450 enzyme TxtE
Authors: Yu Feng , Li Minjun , Xu Chunyan , Wang Zhijun , Zhou Huan , Yang Min , Chen Yaxing , He Jianhua
Published: November 2015

Thaxtomins, a family of phytotoxins produced by Streptomyces spp., can causes plant cell necrosis at nanomolar concentrations. Thaxtomin A is the dominant form from Streptomyces scabies and has demonstrated herbicidal action. TxtE, a cytochrome P450 enzyme from S. scabies 87.22, catalyzes direct nitration of the indolyl moiety of L-tryptophan to L-4-nitrotryptophan using nitric oxide, dioxygen and NADPH, which is the key step of Thaxtomin A biosynthesis. NO-related nitration is a common chemical process in organisms, particularly for tyrosine nitration. However, TxtE is the first reported enzyme that catalyzes a direct nitration reaction specifically in a biosynthetic pathway and thus it can potentially be developed for industrial applications. The crystal structure of TxtE was determined at 2.1 angstrom. A clearly defined substrate access channel is observed and can be classified as channel 2a, which is common in bacteria cytochrome P450 enzymes. A continuous hydrogen bond chain from the active site to the external solvent is observed. Compared with other cytochrome P450 enzymes, TxtE shows a unique proton transfer pathway which crosses the helix I distortion. Polar contacts of Arg59, Tyr89, Asn293, Thr296, and Glu394 with L-tryptophan are seen using molecular docking analysis, which are potentially important for substrate recognition and binding. After mutating Arg59, Asn293, Thr296 or Glu394 to leucine, the substrate binding ability of TxtE was lost or decreased significantly. According to docking and mutagenesis experiments, we propose a possible substrate recognition and binding mechanism, a possible mechanism for substrate recognition and binding is proposed.
Facilities for Macromolecular Crystallography at the HZB
Authors: Förster Ronald , Hellmig Michael , Röwer Martin , Sparta Karine , Steffien Michael , Ühlein Monika , Mueller Uwe , Weiss Manfred
Published: November 2015

The Macromolecular Crystallography (MX) group at the Helmholtz-Zentrum Berlin (HZB) has been in operation since 2003. Since then, three state-of-the-art synchrotron beam lines (BL14.1-3) for MX have been built up on a 7T-wavelength shifter source [1,2]. Currently, the three beam lines represent the most productive MX-stations in Germany, with more than 1100 PDB depositions (Status 02/2014). BLs14.1 and 14.2 are energy tuneable in the range 5.5-15.5 keV, while beam line 14.3 is a fixed-energy side station operated at 13.8 keV. All three beam lines are equipped with state-of-the-art detectors: BL14.1 with a PILATUS 6M detector and BLs14.2 and 14.3 with large CCD-detectors. BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600 user shifts to approximately 70 research groups across Europe. BL14.3 has been equipped with a HC1 crystal dehydration device in 2011. In addition to serving the user community mainly as a screening and test beam line, it is currently the only MX beamline in Europe with a HC1 device permanently installed. Additional user facilities include office space adjacent to the beam lines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. On the poster, a summary on the experimental possibilities of the beam lines and the ancillary equipment provided to the user community will be given.
Structural analysis of Pore-Forming CEL-III
Authors: Unno Hideaki , Goda Shuichiro , Hatakeyama Tomomitsu
Published: November 2015

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.
Crystal structure of the novel haloalkane dehalogenases
Authors: Tratsiak Katsiaryna , Prudnikova Tatyana , Drienovska Ivana , Chrast Lukas , Damborsky Jiri , Rezacova Pavlina , Kuty Michal , Chaloupkova Radka , Kuta Smatanova Ivana
Published: November 2015

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.
Structure of the S.coelicolor A3(2) N-acetylhexosaminidase provides insight into GH20 catalysis
Authors: Thi Nguyen Nhung , Doucet Nicolas
Published: November 2015

β-N-acetylhexosaminidases (HEX - EC 3.2.1.52) are glycosidases that catalyze the glycosidic linkage hydrolysis of gluco- and galacto-configurations of N-acetyl-β-D-hexosaminides. These enzymes have shown considerable interest due to their importance in human physiology and their potential use for the enzymatic synthesis of carbohydrates and glycomymetics. HEX can cleave the β-1,4-glycosidic bonds of polymers with long saccharide chains, and utilize a double-displacement retaining mechanism with neighboring group participation to yield an oxazolinium intermediate. In this study, the three-dimensional structure of the wild-type and catalytically impaired E302Q HEX variant from the soil bacterium Streptomyces coelicolor A3(2) (ScHEX-family GH20) were solved in ligand-free forms and in the presence of 6-acetamido-6-deoxy-castanospermine (6-Ac-Cas). The E302Q variant was also trapped as an intermediate with oxazoline bound to the active center. The complexed structures reveal an active pocket with multiple subsites packed with four Trp, providing a hydrophobic environment that forms a small active-site architecture suitable for holding polysaccharide chains and protecting the formed oxazolinium intermediate during catalysis. Crystallographic evidence highlights structural variations in the loop 3 environment, suggesting conformational heterogeneity for important active-site residues of this GH20 family member.