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IUCrJ

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https://www.readbyqxmd.com/read/29123683/thermomechanical-effect-in-molecular-crystals-the-role-of-halogen-bonding-interactions
#1
Sudhir Mittapalli, D Sravanakumar Perumalla, Jagadeesh Babu Nanubolu, Ashwini Nangia
The design and synthesis of mechanically responsive materials is interesting because they are potential candidates to convert thermal energy into mechanical work. Reported in this paper are thermosalient effects in a series of halogen derivatives of salinazids. The chloro derivative, with higher electronegativity and a weaker inter-halogen bond strength (Cl⋯Cl) exhibits an excellent thermal response, whereas the response is weaker in the iodo derivative with stronger I⋯I halogen bonding. 3,5-Di-chloro-salinazid (Compound-A) exists in three polymorphic forms, two room-temperature polymorphs (Forms I and II) and one high-temperature modification (Form III)...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123682/analysis-of-xfel-serial-diffraction-data-from-individual-crystalline-fibrils
#2
David H Wojtas, Kartik Ayyer, Mengning Liang, Estelle Mossou, Filippo Romoli, Carolin Seuring, Kenneth R Beyerlein, Richard J Bean, Andrew J Morgan, Dominik Oberthuer, Holger Fleckenstein, Michael Heymann, Cornelius Gati, Oleksandr Yefanov, Miriam Barthelmess, Eirini Ornithopoulou, Lorenzo Galli, P Lourdu Xavier, Wai Li Ling, Matthias Frank, Chun Hong Yoon, Thomas A White, Saša Bajt, Anna Mitraki, Sebastien Boutet, Andrew Aquila, Anton Barty, V Trevor Forsyth, Henry N Chapman, Rick P Millane
Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123681/lifetimes-and-spatio-temporal-response-of-protein-crystals-in-intense-x-ray-microbeams
#3
Matthew A Warkentin, Hakan Atakisi, Jesse B Hopkins, Donald Walko, Robert E Thorne
Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s(-1). At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123680/hit-detection-in-serial-femtosecond-crystallography-using-x-ray-spectroscopy-of-plasma-emission
#4
H Olof Jönsson, Carl Caleman, Jakob Andreasson, Nicuşor Tîmneanu
Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123679/mix-and-diffuse-serial-synchrotron-crystallography
#5
Kenneth R Beyerlein, Dennis Dierksmeyer, Valerio Mariani, Manuela Kuhn, Iosifina Sarrou, Angelica Ottaviano, Salah Awel, Juraj Knoska, Silje Fuglerud, Olof Jönsson, Stephan Stern, Max O Wiedorn, Oleksandr Yefanov, Luigi Adriano, Richard Bean, Anja Burkhardt, Pontus Fischer, Michael Heymann, Daniel A Horke, Katharina E J Jungnickel, Elena Kovaleva, Olga Lorbeer, Markus Metz, Jan Meyer, Andrew Morgan, Kanupriya Pande, Saravanan Panneerselvam, Carolin Seuring, Aleksandra Tolstikova, Julia Lieske, Steve Aplin, Manfred Roessle, Thomas A White, Henry N Chapman, Alke Meents, Dominik Oberthuer
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123678/rare-earth-based-quaternary-heusler-compounds-mcovz-m-lu-y-z-si-ge-with-tunable-band-characteristics-for-potential-spintronic-applications
#6
Xiaotian Wang, Zhenxiang Cheng, Guodong Liu, Xuefang Dai, Rabah Khenata, Liying Wang, Abdelmadjid Bouhemadou
Magnetic Heusler compounds (MHCs) have recently attracted great attention since these types of material provide novel functionalities in spintronic and magneto-electronic devices. Among the MHCs, some compounds have been predicted to be spin-filter semiconductors [also called magnetic semiconductors (MSs)], spin-gapless semiconductors (SGSs) or half-metals (HMs). In this work, by means of first-principles calculations, it is demonstrated that rare earth-based equiatomic quaternary Heusler (EQH) compounds with the formula MCoVZ (M = Lu, Y; Z = Si, Ge) are new spin-filter semiconductors with total magnetic moments of 3 µB...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123677/in-vivo-analysis-of-the-escherichia-coli-ultrastructure-by-small-angle-scattering
#7
Enrico F Semeraro, Juliette M Devos, Lionel Porcar, V Trevor Forsyth, Theyencheri Narayanan
The flagellated Gram-negative bacterium Escherichia coli is one of the most studied microorganisms. Despite extensive studies as a model prokaryotic cell, the ultrastructure of the cell envelope at the nanometre scale has not been fully elucidated. Here, a detailed structural analysis of the bacterium using a combination of small-angle X-ray and neutron scattering (SAXS and SANS, respectively) and ultra-SAXS (USAXS) methods is presented. A multiscale structural model has been derived by incorporating well established concepts in soft-matter science such as a core-shell colloid for the cell body, a multilayer membrane for the cell wall and self-avoiding polymer chains for the flagella...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123676/merging-single-shot-xfel-diffraction-data-from-inorganic-nanoparticles-a-new-approach-to-size-and-orientation-determination
#8
Xuanxuan Li, John C H Spence, Brenda G Hogue, Haiguang Liu
X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123675/the-potential-of-hexatungstotellurate-vi-to-induce-a-significant-entropic-gain-during-protein-crystallization
#9
Christian Molitor, Aleksandar Bijelic, Annette Rompel
The limiting factor in protein crystallography is still the production of high-quality crystals. In this regard, the authors have recently introduced hexatungstotellurate(VI) (TEW) as a new crystallization additive, which proved to be successful within the liquid-liquid phase separation (LLPS) zone. Presented here are comparative crystal structure analyses revealing that protein-TEW binding not only induces and stabilizes crystal contacts, but also exhibits a significant impact on the solvent-driven crystallization entropy, which is the driving force for the crystallization process...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123674/characterization-of-temporal-coherence-of-hard-x-ray-free-electron-laser-pulses-with-single-shot-interferograms
#10
Taito Osaka, Takashi Hirano, Yuki Morioka, Yasuhisa Sano, Yuichi Inubushi, Tadashi Togashi, Ichiro Inoue, Kensuke Tono, Aymeric Robert, Kazuto Yamauchi, Jerome B Hastings, Makina Yabashi
Temporal coherence is one of the most fundamental characteristics of light, connecting to spectral information through the Fourier transform relationship between time and frequency. Interferometers with a variable path-length difference (PLD) between the two branches have widely been employed to characterize temporal coherence properties for broad spectral regimes. Hard X-ray interferometers reported previously, however, have strict limitations in their operational photon energies, due to the specific optical layouts utilized to satisfy the stringent requirement for extreme stability of the PLD at sub-ångström scales...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123673/cryo-em-reconstruction-of-the-chlororibosome-to-3-2%C3%A2-%C3%A3-resolution-within-24%C3%A2-h
#11
Björn O Forsberg, Shintaro Aibara, Dari Kimanius, Bijoya Paul, Erik Lindahl, Alexey Amunts
The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123672/the-science-is-in-the-data
#12
REVIEW
John R Helliwell, Brian McMahon, J Mitchell Guss, Loes M J Kroon-Batenburg
Understanding published research results should be through one's own eyes and include the opportunity to work with raw diffraction data to check the various decisions made in the analyses by the original authors. Today, preserving raw diffraction data is technically and organizationally viable at a growing number of data archives, both centralized and distributed, which are empowered to register data sets and obtain a preservation descriptor, typically a 'digital object identifier'. This introduces an important role of preserving raw data, namely understanding where we fail in or could improve our analyses...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123671/theoretical-prediction-of-strain-tuneable-quaternary-spintronic-heusler-compounds
#13
Jan-Willem G Bos
Heusler materials have attracted a large amount of attention in the development of spintronic technologies. In this issue, Wang et al. [IUCrJ (2017), 4, 758-768] show how strain can be used to tune the band structure of these materials.
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123670/crystal-engineering-structure-property-and-beyond
#14
EDITORIAL
Gautam R Desiraju
Crystal engineering, which was considered to be crystal structure engineering, is now transforming into crystal property engineering. The same or similar crystal structures could have different properties while different crystal structures could have similar properties.
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28989725/crystallographic-features-of-the-martensitic-transformation-and-their-impact-on-variant-organization-in-the-intermetallic-compound-ni50mn38sb12-studied-by-sem-ebsd
#15
Chunyang Zhang, Yudong Zhang, Claude Esling, Xiang Zhao, Liang Zuo
The mechanical and magnetic properties of Ni-Mn-Sb intermetallic compounds are closely related to the martensitic transformation and martensite variant organization. However, studies of these issues are very limited. Thus, a thorough crystallographic investigation of the martensitic transformation orientation relationship (OR), the transformation deformation and their impact on the variant organization of an Ni50Mn38Sb12 alloy using scanning electron microscopy/electron backscatter diffraction (SEM/EBSD) was conducted in this work...
September 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28989724/charge-transport-properties-of-4-1-2-2-tri-phenyl-vinyl-aniline-salicylaldehyde-hydrazone-tight-packing-induced-molecular-hardening
#16
Huipeng Ma, Shuo Chai, Dengyi Chen, Jin-Dou Huang
Based on first-principles calculations, the relationship between molecular packing and charge-transport parameters has been investigated and analysed in detail. It is found that the crystal packing forces in the flexible organic molecule 4-(1,2,2-triphenylvinyl)-aniline salicylaldehyde hydrazone (A) can apparently overcome the dynamic intramolecular rotations and the intramolecular steric repulsion, effectively enhancing the molecular rigidity and decreasing the internal reorganization energy. The conducting properties of A have also been simulated within the framework of hopping models, and the calculation results show that the intrinsic electron mobility in A is much higher than the corresponding intrinsic hole mobility...
September 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28989723/single-particle-cryo-em-using-alignment-by-classification-abc-the-structure-of-lumbricus-terrestris-haemoglobin
#17
Pavel Afanasyev, Charlotte Seer-Linnemayr, Raimond B G Ravelli, Rishi Matadeen, Sacha De Carlo, Bart Alewijnse, Rodrigo V Portugal, Navraj S Pannu, Michael Schatz, Marin van Heel
Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets...
September 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28989722/a-closer-look-into-close-packing-pentacoordinated-silicon-in-a-high-pressure-polymorph-of-danburite
#18
Anna Pakhomova, Elena Bykova, Maxim Bykov, Konstantin Glazyrin, Biliana Gasharova, Hanns-Peter Liermann, Mohamed Mezouar, Liudmila Gorelova, Sergey Krivovichev, Leonid Dubrovinsky
Due to their high technological and geological relevance, silicates are one of the most studied classes of inorganic compounds. Under ambient conditions, the silicon in silicates is almost exclusively coordinated by four oxygen atoms, while high-pressure treatment normally results in an increase in the coordination from four- to sixfold. Reported here is a high-pressure single-crystal X-ray diffraction study of danburite, CaB2Si2O8, the first compound showing a step-wise transition of Si coordination from tetrahedral to octahedral through a trigonal bipyramid...
September 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28989721/a-distance-geometry-based-description-and-validation-of-protein-main-chain-conformation
#19
Joana Pereira, Victor S Lamzin
Understanding the protein main-chain conformational space forms the basis for the modelling of protein structures and for the validation of models derived from structural biology techniques. Presented here is a novel idea for a three-dimensional distance geometry-based metric to account for the fine details of protein backbone conformations. The metrics are computed for dipeptide units, defined as blocks of C(α)i-1-O i-1-C(α)i -O i -C(α)i+1 atoms, by obtaining the eigenvalues of their Euclidean distance matrices...
September 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28989720/one-enzyme-many-reactions-structural-basis-for-the-various-reactions-catalyzed-by-naphthalene-1-2-dioxygenase
#20
Daniel J Ferraro, Adam Okerlund, Eric Brown, S Ramaswamy
Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecific cis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidation etc. NDO itself catalyzes a variety of these reactions...
September 1, 2017: IUCrJ
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