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IUCrJ

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https://read.qxmd.com/read/30713712/microbatch-under-oil-salt-screening-of-organic-cations-single-crystal-growth-of-active-pharmaceutical-ingredients
#1
Martin Babor, Philipp P Nievergelt, Jan Čejka, Vít Zvoníček, Bernhard Spingler
Multicomponent solid forms of active pharmaceutical ingredients represent a modern method of tuning their physicochemical properties. Typically, salts are the most commonly used multicomponent solid form in the pharmaceutical industry. More than 38% are formulated as organic cations. Salt screening is an essential but demanding step when identifying the most appropriate formulation. The microbatch under-oil crystallization technique of proteins has been combined with the previously developed high-throughput vapour-diffusion screening for use as a novel method of primary salt screening of organic cations...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713711/a-jumping-crystal-predicted-with-molecular-dynamics-and-analysed-with-tls-refinement-against-powder-diffraction-data
#2
Jacco van de Streek, Edith Alig, Simon Parsons, Liana Vella-Zarb
By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that of the low-temperature phase...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713710/synthesis-of-new-ln-4-al-2-o-6-f-2-o-2-ln-sm-eu-gd-phases-with-a-cuspidine-related-structure
#3
Aroa Morán-Ruiz, Aritza Wain-Martin, Alodia Orera, María Luisa Sanjuán, Aitor Larrañaga, Peter R Slater, Maribel Arriortua
The first fluorination of the cuspidine-related phases of Ln4 (Al2 O7 □)O2 (where Ln = Sm, Eu, Gd) is reported. A low-temperature reaction with poly(vinyl-idene difluoride) lead to the fluorine being substituted in place of oxygen and inserted into the vacant position between the dialuminate groups. X-ray photoelectron spectroscopy shows the presence of the F 1 s photoelectron together with an increase in Al 2 p and rare-earth 4 d binding energies supporting F incorporation. Energy-dispersive X-ray spectroscopy analyses are consistent with the formula Ln4 (Al2 O6 F2 )O2 , confirming that substitution of one oxygen by two fluoride atoms has been achieved...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713709/structure-model-of-%C3%AE-al-2-o-3-based-on-planar-defects
#4
Martin Rudolph, Mykhaylo Motylenko, David Rafaja
The defect structure of γ-Al2 O3 derived from boehmite was investigated using a combination of selected-area electron diffraction (SAED) and powder X-ray diffraction (XRD). Both methods confirmed a strong dependence of the diffraction line broadening on the diffraction indices known from literature. The analysis of the SAED patterns revealed that the dominant structure defects in the spinel-type γ-Al2 O3 are antiphase boundaries located on the lattice planes , which produce the sublattice shifts . Quantitative information about the defect structure of γ-Al2 O3 was obtained from the powder XRD patterns...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713708/incommensurate-structures-of-the-ch-3-nh-3-co-cooh-3-compound
#5
Laura Canadillas-Delgado, Lidia Mazzuca, Oscar Fabelo, J Alberto Rodriguez-Velamazan, Juan Rodriguez-Carvajal
The present article is devoted to the characterization of the structural phase transitions of the [CH3 NH3 ][Co(COOH)3 ] ( 1 ) perovskite-like metal-organic compound through variable-temperature single-crystal neutron diffraction. At room temperature, compound 1 crystallizes in the orthorhombic space group Pnma (phase I ). A decrease in temperature gives rise to a first phase transition from the space group Pnma to an incommensurate phase (phase II ) at approximately 128 K. At about 96 K, this incommensurate phase evolves into a second phase with a sharp change in the modulation vector (phase III )...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713707/deformation-pathway-and-defect-generation-in-crystals-a-combined-group-theory-and-graph-theory-description
#6
Yipeng Gao, Yunzhi Wang, Yongfeng Zhang
The generation and motion of crystalline defects during plastic deformation are critical processes that determine the mechanical properties of a crystal. The types of defect generated are not only related to the symmetry of a crystal but also associated with the symmetry-breaking process during deformation. Proposed here is a new mathematical framework to capture the intrinsic coupling between crystal symmetry and deformation-induced symmetry breaking. Using a combination of group theory and graph theory, a general approach is demonstrated for the systematic determination of the types of crystalline defect induced by plastic deformation, through the construction of a crystal deformation group and a deformation pathway graph...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713706/framework-disorder-and-its-effect-on-selective-hysteretic-sorption-of-a-t-shaped-azole-based-metal-organic-framework
#7
Sujuan Wang, Zhang-Wen Wei, Jianyong Zhang, Long Jiang, Dingxin Liu, Ji-Jun Jiang, Rui Si, Cheng-Yong Su
Metal-organic frameworks with highly ordered porosity have been studied extensively. In this paper, the effect of framework (pore) disorder on the gas sorption of azole-based isoreticular Cu(II) MOFs with rtl topology and characteristic 1D tubular pore channels is investigated for the first time. In contrast to other isoreticular rtl metal-organic frameworks, the Cu(II) metal-organic framework based on 5-(1 H -imidazol-1-yl)isophthalate acid has a crystallographically identifiable disordered framework without open N-donor sites...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713705/-spind-a-reference-based-auto-indexing-algorithm-for-sparse-serial-crystallography-data
#8
Chufeng Li, Xuanxuan Li, Richard Kirian, John C H Spence, Haiguang Liu, Nadia A Zatsepin
SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008 ▸), Acta Cryst...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713704/k-paracelsian-kalsi-3-o-8-%C3%A2-h-2-o-and-identification-of-a-simple-building-scheme-of-dense-double-crankshaft-zeolite-topologies
#9
Cristian-R Boruntea, Peter N R Vennestrøm, Lars F Lundegaard
During screening of the phase space using KOH and 1-methyl-4-aza-1-azoniabicyclo-[2.2.2]octane hydroxide (1-methyl-DABCO) under hydrothermal zeolite synthesis conditions, K-paracelsian was synthesized. Scanning electron microscopy, energy dispersive X-ray spectroscopy and ex situ powder X-ray diffraction analysis revealed a material that is compositionally closely related to the mineral microcline and structurally closely related to the mineral paracelsian, both of which are feldspars. In contrast to the feldspars, K-paracelsian contains intrazeolitic water corresponding to one molecule per cage...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713703/direct-air-capture-of-co-2-topological-analysis-of-the-experimental-electron-density-qtaim-of-the-highly-insoluble-carbonate-salt-of-a-2-6-pyridine-bis-iminoguanidine-pybigh-2-co-3-h-2-o-4
#10
Christopher G Gianopoulos, Zhijie Chua, Vladimir V Zhurov, Charles A Seipp, Xiaoping Wang, Radu Custelcean, A Alan Pinkerton
Chemical bonding and all intermolecular interactions in the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2 )(CO3 )(H2 O)4 , recently employed in the direct air capture of CO2 via crystallization, have been analyzed within the framework of the quantum theory of atoms in molecules (QTAIM) based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. Accurate hydrogen positions were included based on an analogous neutron diffraction study at 100 K...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713702/computational-design-of-symmetrical-eight-bladed-%C3%AE-propeller-proteins
#11
Hiroki Noguchi, Christine Addy, David Simoncini, Staf Wouters, Bram Mylemans, Luc Van Meervelt, Thomas Schiex, Kam Y J Zhang, Jeremy R H Tame, Arnout R D Voet
β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713701/structure-factor-amplitude-reconstruction-from-serial-femtosecond-crystallography-of-two-dimensional-membrane-protein-crystals
#12
Cecilia M Casadei, Karol Nass, Anton Barty, Mark S Hunter, Celestino Padeste, Ching-Ju Tsai, Sébastien Boutet, Marc Messerschmidt, Leonardo Sala, Garth J Williams, Dmitry Ozerov, Matthew Coleman, Xiao-Dan Li, Matthias Frank, Bill Pedrini
Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional crystals and suppressed in cryocooled samples. In previous work, diffraction data limited to a two-dimensional reciprocal-space slice were evaluated and it was demonstrated that the low intensity of the diffraction signal can be overcome by collecting highly redundant data, thus enhancing the achievable resolution...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713700/thresholding-of-cryo-em-density-maps-by-false-discovery-rate-control
#13
Maximilian Beckers, Arjen J Jakobi, Carsten Sachse
Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ . Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713699/a-bayesian-approach-to-beam-induced-motion-correction-in-cryo-em-single-particle-analysis
#14
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres
A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized...
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713698/interpreting-the-cryo-em-map
#15
Peter B Rosenthal
Beckers et al. [ IUCrJ (2019), 6 , 18-33] propose a general approach to visualization of cryo-EM maps. Their method overcomes some of the challenges inherent in the conventional approach for depicting maps using a single isosurface threshold.
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30713697/the-cryo-em-revolution-fueling-the-next-phase
#16
EDITORIAL
Sriram Subramaniam
Cryo-EM has seen unabated growth and adoption in the last three years. Continued support at institutional, regional and national levels is essential to sustain its evolution.
January 1, 2019: IUCrJ
https://read.qxmd.com/read/30443370/structure-based-mechanism-of-action-of-a-viral-poly-adp-ribose-polymerase-1-interacting-protein-facilitating-virus-replication
#17
Woo-Chang Chung, Junsoo Kim, Byung Chul Kim, Hye-Ri Kang, JongHyeon Son, Hosam Ki, Kwang Yeon Hwang, Moon Jung Song
Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA...
November 1, 2018: IUCrJ
https://read.qxmd.com/read/30443369/-deep-consensus-a-deep-learning-based-approach-for-particle-pruning-in-cryo-electron-microscopy
#18
Ruben Sanchez-Garcia, Joan Segura, David Maluenda, Jose Maria Carazo, Carlos Oscar S Sorzano
Single-particle cryo-electron microscopy (cryo-EM) has recently become a mainstream technique for the structural determination of macromolecules. Typical cryo-EM workflows collect hundreds of thousands of single-particle projections from thousands of micrographs using particle-picking algorithms. However, the number of false positives selected by these algorithms is large, so that a number of different 'cleaning steps' are necessary to decrease the false-positive ratio. Most commonly employed techniques for the pruning of false-positive particles are time-consuming and require user intervention...
November 1, 2018: IUCrJ
https://read.qxmd.com/read/30443368/crystal-structure-interaction-energies-and-experimental-electron-density-of-the-popular-drug-ketoprophen
#19
Sylwia Pawlędzio, Anna Makal, Damian Trzybiński, Krzysztof Woźniak
The crystal and molecular structure of the pure ( S )-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O-H⋯O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution...
November 1, 2018: IUCrJ
https://read.qxmd.com/read/30443367/committee-machine-that-votes-for-similarity-between-materials
#20
Duong-Nguyen Nguyen, Tien-Lam Pham, Viet-Cuong Nguyen, Tuan-Dung Ho, Truyen Tran, Keisuke Takahashi, Hieu-Chi Dam
A method has been developed to measure the similarity between materials, focusing on specific physical properties. The information obtained can be utilized to understand the underlying mechanisms and support the prediction of the physical properties of materials. The method consists of three steps: variable evaluation based on nonlinear regression, regression-based clustering, and similarity measurement with a committee machine constructed from the clustering results. Three data sets of well characterized crystalline materials represented by critical atomic predicting variables are used as test beds...
November 1, 2018: IUCrJ
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