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Olivier Jeannin, Eric W Reinheimer, Pascale Foury-Leylekian, Jean-Paul Pouget, Pascale Auban-Senzier, Elzbieta Trzop, Eric Collet, Marc Fourmigué
A mixed-valence conducting cation radical salt of the unsymmetrically substituted o -Me2 TTF donor molecule (TTF is tetrathiafulvalene) was obtained upon electrocrystallization in the presence of the non-centrosymmetric NO3 - anion. It crystallizes at room temperature in the monoclinic P 21 / c space group, with the anion disordered on an inversion centre. The donor molecules are stacked along the a axis. A 90° rotation of the longest molecular axis of o -Me2 TTF generates a chessboard-like structure, preventing lateral S⋯S contacts between stacks and providing a strongly one-dimensional electronic system, as confirmed by overlap interaction energies and band structure calculations...
May 1, 2018: IUCrJ
Felix Lehmkühler, Florian Schulz, Martin A Schroer, Lara Frenzel, Holger Lange, Gerhard Grübel
We report on the self-assembly of gold nanoparticles coated with a soft poly(ethylene glycol) shell studied by X-ray cross-correlation analysis. Depending on the initial concentration of gold nanoparticles used, structurally heterogeneous films were formed. The films feature hot spots of dominating four- and sixfold local order with patch sizes of a few micrometres, containing 104 -105 particles. The amplitude of the order parameters suggested that a minimum sample amount was necessary to form well ordered local structures...
May 1, 2018: IUCrJ
Koji Yonekura, Rei Matsuoka, Yoshiki Yamashita, Tsutomu Yamane, Mitsunori Ikeguchi, Akinori Kidera, Saori Maki-Yonekura
Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac-Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O- . Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology...
May 1, 2018: IUCrJ
Katarzyna Ostrowska, Davide Ceresoli, Katarzyna Stadnicka, Marlena Gryl, Marco Cazzaniga, Raffaella Soave, Bogdan Musielak, Łukasz J Witek, Piotr Goszczycki, Jarosław Grolik, Andrzej M Turek
The structural origin of absorption and fluorescence anisotropy of the single crystal of the π-conjugated heterocyclic system 5,6,10b-tri-aza-acephenan-thrylene, TAAP, is presented in this study. X-ray analysis shows that the crystal framework in the space group P [Formula: see text] is formed by centrosymmetric dimers of face-to-face mutually oriented TAAP molecules joined by π-π non-covalent interactions. The conformation of the TAAP molecule is stabilized by intramolecular C-H⋯N( sp 2 ), N( sp 2 )H⋯π(CN), and C-H⋯O( sp 2 ) hydrogen bonds...
May 1, 2018: IUCrJ
Akira Takada, Kathryn J Glaser, Robert G Bell, C Richard A Catlow
Structural changes in tridymite have been investigated by molecular dynamics simulation. Two thermal processes were carried out, one cooling from the high-temperature hexagonal structure of tridymite (HP-tridymite) and the other heating from the low-temperature monoclinic structure of tridymite (MX1-tridymite). The former process showed that HP, LHP (low-temperature hexagonal structure), OC (orthorhombic structure with C 2221 symmetry) and OP (orthorhombic structure with P 21 21 21 symmetry)-like structures appeared in sequence...
May 1, 2018: IUCrJ
Abida Rehman, Amit Delori, David S Hughes, William Jones
Pharmaceutical salt solvates (dimethyl sulfoxide, DMSO) of the drug triamterene with the coformers acetic, succinic, adipic, pimelic, azelaic and nicotinic acid and ibuprofen are prepared by liquid-assisted grinding and solvent-evaporative crystallization. The modified Δp K a rule as proposed by Cruz-Cabeza [(2012 ▸). CrystEngComm , 14 , 6362-6365] is in close agreement with the results of this study. All adducts were characterized by X-ray diffraction and thermal analytical techniques, including single-crystal X-ray diffraction, powder X-ray diffraction, differential scanning calorimetry and thermal gravimetric analysis...
May 1, 2018: IUCrJ
Roland Resel, Andrew O F Jones, Guillaume Schweicher, Roland Fischer, Nicola Demitri, Yves Henri Geerts
The origin of unknown polymorphic phases within thin films is still not well understood. This work reports on crystals of the molecule terthio-phene which were grown by thermal gradient crystallization using glass-plate substrates. The crystalline domains displayed a plate-like morphology with an extended lateral size of about 100 µm, but a thickness of only a few µm. Specular X-ray diffraction patterns confirmed the presence of a new polymorph of terthio-phene. Crystal structure solution from a single crystal peeled from the film revealed a structure with an extremely large unit-cell volume containing 42 independent molecules...
May 1, 2018: IUCrJ
Ekaterina N Zorina-Tikhonova, Aleksandr S Chistyakov, Mikhail A Kiskin, Aleksei A Sidorov, Pavel V Dorovatovskii, Yan V Zubavichus, Eugenia D Voronova, Ivan A Godovikov, Alexander A Korlyukov, Igor L Eremenko, Anna V Vologzhanina
Photoinitiated solid-state reactions are known to affect the physical properties of coordination polymers, such as fluorescence and sorption behaviour, and also afford extraordinary architectures ( e.g. three-periodic structures with polyorganic ligands). However, the construction of novel photo-sensitive coordination polymers requires an understanding of the factors which govern the mutual disposition of reactive fragments. A series of zinc(II) malonate complexes with 1,2-bis(pyridin-4-yl)ethylene and its photo-insensitive analogues has been synthesized for the purpose of systematic analysis of their underlying nets and mutual disposition of N -donor ligands...
May 1, 2018: IUCrJ
Sam Horrell, Demet Kekilli, Kakali Sen, Robin L Owen, Florian S N Dworkowski, Svetlana V Antonyuk, Thomas W Keal, Chin W Yong, Robert R Eady, S Samar Hasnain, Richard W Strange, Michael A Hough
High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition...
May 1, 2018: IUCrJ
Åsa Janfalk Carlsson, Paul Bauer, Doreen Dobritzsch, Shina C L Kamerlin, Mikael Widersten
The epoxide hydrolase StEH1 catalyzes the hydrolysis of trans -methylstyrene oxide to 1-phenyl-propane-1,2-diol. The ( S , S )-epoxide is exclusively transformed into the (1 R ,2 S )-diol, while hydrolysis of the ( R , R )-epoxide results in a mixture of product enantiomers. In order to understand the differences in the stereoconfigurations of the products, the reactions were studied kinetically during both the pre-steady-state and steady-state phases. A number of closely related StEH1 variants were analyzed in parallel, and the results were rationalized by structure-activity analysis using the available crystal structures of all tested enzyme variants...
May 1, 2018: IUCrJ
Samuel Savitz, Mehrtash Babadi, Ron Lifshitz
For many years, quasicrystals were observed only as solid-state metallic alloys, yet current research is now actively exploring their formation in a variety of soft materials, including systems of macromolecules, nanoparticles and colloids. Much effort is being invested in understanding the thermodynamic properties of these soft-matter quasicrystals in order to predict and possibly control the structures that form, and hopefully to shed light on the broader yet unresolved general questions of quasicrystal formation and stability...
May 1, 2018: IUCrJ
Gongrui Guo, Martin R Fuchs, Wuxian Shi, John Skinner, Evanna Berman, Craig M Ogata, Wayne A Hendrickson, Sean McSweeney, Qun Liu
With the recent developments in microcrystal handling, synchrotron microdiffraction beamline instrumentation and data analysis, microcrystal crystallo-graphy with crystal sizes of less than 10 µm is appealing at synchrotrons. However, challenges remain in sample manipulation and data assembly for robust microcrystal synchrotron crystallography. Here, the development of micro-sized polyimide well-mounts for the manipulation of microcrystals of a few micrometres in size and the implementation of a robust data-analysis method for the assembly of rotational microdiffraction data sets from many microcrystals are described...
May 1, 2018: IUCrJ
John C H Spence
Recent advances in the application of X-ray lasers to structural biology are providing time-resolved high-resolution imaging of many processes, from enzyme kinetics to the riboswitch in action, drug action, and light-sensitive proteins.
May 1, 2018: IUCrJ
Magali Saez-Ayala, Elsie Laban Yekwa, Mauro Carcelli, Bruno Canard, Karine Alvarez, François Ferron
The Arenaviridae family, together with the Bunyaviridae and Orthomyxoviridae families, is one of the three negative-stranded RNA viral families that encode an endonuclease in their genome. The endonuclease domain is at the N-terminus of the L protein, a multifunctional protein that includes the RNA-dependent RNA polymerase. The synthesis of mRNA in arenaviruses is a process that is primed by capped nucleotides that are 'stolen' from the cellular mRNA by the endonuclease domain in cooperation with other domains of the L protein...
March 1, 2018: IUCrJ
Ariana Peck, Frédéric Poitevin, Thomas J Lane
Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals...
March 1, 2018: IUCrJ
Kangsa Amporndanai, Rachel M Johnson, Paul M O'Neill, Colin W G Fishwick, Alexander H Jamson, Shaun Rawson, Stephen P Muench, S Samar Hasnain, Svetlana V Antonyuk
Cytochrome bc 1 , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc 1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc 1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc 1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host...
March 1, 2018: IUCrJ
Gemma Tinti, Erik Fröjdh, Eric van Genderen, Tim Gruene, Bernd Schmitt, D A Matthijs de Winter, Bert M Weckhuysen, Jan Pieter Abrahams
Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2 , frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data...
March 1, 2018: IUCrJ
In-Hyeok Park, Huiyeong Ju, Kihwan Kim, Shim Sung Lee, Jagadese J Vittal
The existence of isomerism in coordination polymeric structures offers opportunities to understand structure-function relationships. Herein the serendipitous isolation is reported of two isomeric double-pillared-layer coordination polymeric structures arising from two different types of carboxyl-ate bonding of benzene-1,4-di-carboxyl-ate ligands to zinc(II), which constitutes a new type of structural isomerism. The different bonding modes not only alter the shape and size of the pores, but also the nature of interpenetration and photoreactivity...
March 1, 2018: IUCrJ
Michael E Wall
Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure...
March 1, 2018: IUCrJ
Pavol Skubák, Demet Araç, Matthew W Bowler, Ana R Correia, Andre Hoelz, Sine Larsen, Gordon A Leonard, Andrew A McCarthy, Sean McSweeney, Christoph Mueller-Dieckmann, Harm Otten, Gabriel Salzman, Navraj S Pannu
Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data...
March 1, 2018: IUCrJ
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