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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
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
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
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
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
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
Keitaro Yamashita, Naoyuki Kuwabara, Takanori Nakane, Tomohiro Murai, Eiichi Mizohata, Michihiro Sugahara, Dongqing Pan, Tetsuya Masuda, Mamoru Suzuki, Tomomi Sato, Atsushi Kodan, Tomohiro Yamaguchi, Eriko Nango, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Hiroshi Manya, Tamao Endo, Ryuichi Kato, Toshiya Senda, Hiroaki Kato, So Iwata, Hideo Ago, Masaki Yamamoto, Fumiaki Yumoto, Toru Nakatsu
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX...
September 1, 2017: IUCrJ
James M Parkhurst, Andrea Thorn, Melanie Vollmar, Graeme Winter, David G Waterman, Luis Fuentes-Montero, Richard J Gildea, Garib N Murshudov, Gwyndaf Evans
An algorithm for modelling the background for each Bragg reflection in a series of X-ray diffraction images containing Debye-Scherrer diffraction from ice in the sample is presented. The method involves the use of a global background model which is generated from the complete X-ray diffraction data set. Fitting of this model to the background pixels is then performed for each reflection independently. The algorithm uses a static background model that does not vary over the course of the scan. The greatest improvement can be expected for data where ice rings are present throughout the data set and the local background shape at the size of a spot on the detector does not exhibit large time-dependent variation...
September 1, 2017: IUCrJ
Haomin Chen, Stefan Adams
Based on a description of bond valence as a function of valence electron density, a systematic bond softness sensitive approach to determine bond-valence parameters and related quantities such as coordination numbers is elaborated and applied to determine bond-valence parameters for 706 cation-anion pairs. While the approach is closely related to the earlier softBV parameter set, the new softNC1 parameters proposed in this work may be simpler to apply in plausibility checks of crystal structures, as they follow the first coordination shell convention...
September 1, 2017: IUCrJ
Julien R Lhermitte, Aaron Stein, Cheng Tian, Yugang Zhang, Lutz Wiegart, Andrei Fluerasu, Oleg Gang, Kevin G Yager
Small-angle X-ray scattering (SAXS) often includes an unwanted background, which increases the required measurement time to resolve the sample structure. This is undesirable in all experiments, and may make measurement of dynamic or radiation-sensitive samples impossible. Here, we demonstrate a new technique, applicable when the scattering signal is background-dominated, which reduces the requisite exposure time. Our method consists of exploiting coherent interference between a sample with a designed strongly scattering 'amplifier'...
September 1, 2017: IUCrJ
Jian Kang, Yali Yang, Xiaolong Qian, Kai Xu, Xiaopeng Cui, Yifei Fang, Venkatesh Chandragiri, Baojuan Kang, Bin Chen, Alessandro Stroppa, Shixun Cao, Jincang Zhang, Wei Ren
Spin reorientation is a magnetic phase transition in which rotation of the magnetization vector with respect to the crystallographic axes occurs upon a change in the temperature or magnetic field. For example, SmFeO3 shows a magnetization rotation from the c axis above 480 K to the a axis below 450 K, known as the Γ4 → Γ2 transition. This work reports the successful synthesis of the new single-crystal perovskite SmFe0.75Mn0.25O3 and finds interesting spin reorientations above and below room temperature...
September 1, 2017: IUCrJ
Craig L Bull, Giles Flowitt-Hill, Stefano de Gironcoli, Emine Küçükbenli, Simon Parsons, Cong Huy Pham, Helen Y Playford, Matthew G Tucker
Glycine is the simplest and most polymorphic amino acid, with five phases having been structurally characterized at atmospheric or high pressure. A sixth form, the elusive ζ phase, was discovered over a decade ago as a short-lived intermediate which formed as the high-pressure ∊ phase transformed to the γ form on decompression. However, its structure has remained unsolved. We now report the structure of the ζ phase, which was trapped at 100 K enabling neutron powder diffraction data to be obtained. The structure was solved using the results of a crystal structure prediction procedure based on fully ab initio energy calculations combined with a genetic algorithm for searching phase space...
September 1, 2017: IUCrJ
Carsten Fortmann-Grote, Alexey Buzmakov, Zoltan Jurek, Ne-Te Duane Loh, Liubov Samoylova, Robin Santra, Evgeny A Schneidmiller, Thomas Tschentscher, Sergey Yakubov, Chun Hong Yoon, Michael V Yurkov, Beata Ziaja-Motyka, Adrian P Mancuso
Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs...
September 1, 2017: IUCrJ
Chenyang Shi, Rattavut Teerakapibal, Lian Yu, Geoff G Z Zhang
Using high-brilliance high-energy synchrotron X-ray radiation, for the first time the total scattering of a thin organic glass film deposited on a strongly scattering inorganic substrate has been measured in transmission mode. The organic thin film was composed of the weakly scattering pharmaceutical substance indomethacin in the amorphous state. The film was 130 µm thick atop a borosilicate glass substrate of equal thickness. The atomic pair distribution function derived from the thin-film measurement is in excellent agreement with that from bulk measurements...
September 1, 2017: IUCrJ
Vanessa K Peterson, Josie E Auckett, Wei-Kong Pang
Energy materials form the central part of energy devices. An essential part of their function is the ability to reversibly host charge or energy carriers, and analysis of their phase composition and structure in real time under non-equilibrium conditions is mandatory for a full understanding of their atomic-scale functional mechanism. Real-time powder diffraction is increasingly being applied for this purpose, forming a critical step in the strategic chemical engineering of materials with improved behaviour...
September 1, 2017: IUCrJ
Masaki Yamamoto, Kunio Hirata, Keitaro Yamashita, Kazuya Hasegawa, Go Ueno, Hideo Ago, Takashi Kumasaka
The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features...
September 1, 2017: IUCrJ
Anne T Tuukkanen, Alessandro Spilotros, Dmitri I Svergun
Small-angle X-ray scattering (SAXS) is an established technique that provides low-resolution structural information on macromolecular solutions. Recent decades have witnessed significant progress in both experimental facilities and in novel data-analysis approaches, making SAXS a mainstream method for structural biology. The technique is routinely applied to directly reconstruct low-resolution shapes of proteins and to generate atomistic models of macromolecular assemblies using hybrid approaches. Very importantly, SAXS is capable of yielding structural information on systems with size and conformational polydispersity, including highly flexible objects...
September 1, 2017: IUCrJ
Ilme Schlichting
A synopsis of and prospects for de novo phasing using diffraction data collected at X-ray free-electron lasers are given.
September 1, 2017: IUCrJ
I David Brown
Two recent systematic determinations of bond-valence parameters addressed the problem of the correlation between R0 and b in different ways raising the question of which is to be preferred.
September 1, 2017: IUCrJ
Alexander A Matvienko, Daniel V Maslennikov, Boris A Zakharov, Anatoly A Sidelnikov, Stanislav A Chizhik, Elena V Boldyreva
For martensitic transformations the macroscopic crystal strain is directly related to the corresponding structural rearrangement at the microscopic level. In situ optical microscopy observations of the interface migration and the change in crystal shape during a displacive single crystal to single crystal transformation can contribute significantly to understanding the mechanism of the process at the atomic scale. This is illustrated for the dehydration of samarium oxalate decahydrate in a study combining optical microscopy and single-crystal X-ray diffraction...
September 1, 2017: IUCrJ
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