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IUCrJ

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https://www.readbyqxmd.com/read/30226220/response-to-comment-on-hydrogen-bonds-in-crystalline-d-alanine-diffraction-and-spectroscopic-evidence-for-differences-between-enantiomers
#1
COMMENT
Ezequiel A Belo, Jose E M Pereira, Paulo T C Freire, Dimitri N Argyriou, Juergen Eckert, Heloisa N Bordallo
A response is given to comments by Bürgi & Macchi [ IUCrJ (2018), 5 , 654-657] about Belo et al. [ IUCrJ (2018), 5 , 6-12.].
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224968/comments-on-hydrogen-bonds-in-crystalline-d-alanine-diffraction-and-spectroscopic-evidence-for-differences-between-enantiomers
#2
COMMENT
Hans-Beat Bürgi, Piero Macchi
The recent paper by Belo, Pereira, Freire, Argyriou, Eckert & Bordallo [(2018 ▸), IUCrJ , 5 , 6-12] reports observations that may lead one to think of very strong and visible consequences of the parity-violation energy difference between enantiomers of a molecule, namely alanine. If proved, this claim would have an enormous impact for research in structural chemistry. However, alternative, more realistic, explanations of their experiments have not been ruled out by the authors. Moreover, the theoretical calculations carried out to support the hypothesis are unable to differentiate between enantiomers (molecules or crystals)...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224967/exploring-the-simultaneous-%C3%AF-hole-%C3%AF-hole-bonding-characteristics-of-a-br%C3%A2-%C3%AF-interaction-in-an-ebselen-derivative-via-experimental-and-theoretical-electron-density-analysis
#3
Rahul Shukla, Nicolas Claiser, Mohamed Souhassou, Claude Lecomte, Shah Jaimin Balkrishna, Sangit Kumar, Deepak Chopra
In this study, the nature and characteristics of a short Br⋯π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[ d ][1,2]selenazol-3(2 H )-one, has been explored. The electronic nature of this Br⋯π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br⋯π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs)...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224966/bond-orders-for-intermolecular-interactions-in-crystals-charge-transfer-ionicity-and-the-effect-on-intramolecular-bonds
#4
Khidhir Alhameedi, Amir Karton, Dylan Jayatilaka, Sajesh P Thomas
The question of whether intermolecular interactions in crystals originate from localized atom⋯atom interactions or as a result of holistic molecule⋯molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby-Gould bond indices are reported for intermolecular 'σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224965/structural-basis-for-light-control-of-cell-development-revealed-by-crystal-structures-of-a-myxobacterial-phytochrome
#5
Nicole C Woitowich, Andrei S Halavaty, Patricia Waltz, Christopher Kupitz, Joseph Valera, Gregory Tracy, Kevin D Gallagher, Elin Claesson, Takanori Nakane, Suraj Pandey, Garrett Nelson, Rie Tanaka, Eriko Nango, Eiichi Mizohata, Shigeki Owada, Kensure Tono, Yasumasa Joti, Angela C Nugent, Hardik Patel, Ayesha Mapara, James Hopkins, Phu Duong, Dorina Bizhga, Svetlana E Kovaleva, Rachael St Peter, Cynthia N Hernandez, Wesley B Ozarowski, Shatabdi Roy-Chowdhuri, Jay-How Yang, Petra Edlund, Heikki Takala, Janne Ihalainen, Jennifer Brayshaw, Tyler Norwood, Ishwor Poudyal, Petra Fromme, John C H Spence, Keith Moffat, Sebastian Westenhoff, Marius Schmidt, Emina A Stojković
Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxo-bacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224964/twist-and-turn-a-revised-structural-view-on-the-unpaired-bubble-of-class-ii-cpd-photolyase-in-complex-with-damaged-dna
#6
Manuel Maestre-Reyna, Junpei Yamamoto, Wei-Cheng Huang, Ming-Daw Tsai, Lars-Oliver Essen, Yoshitaka Bessho
Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein-nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224963/the-hydrocarbon-bearing-clathrasil-chibaite-and-its-host-guest-structure-at-low-temperature
#7
K S Scheidl, H S Effenberger, T Yagi, K Momma, Ronald Miletich
The natural sII-type clathrasil chibaite [chemical formula SiO2 ·( M 12 , M 16 ), where M x denotes a guest mol-ecule] was investigated using single-crystal X-ray diffraction and Raman spectroscopy in the temperature range from 273 to 83 K. The O atoms of the structure at room temperature, which globally conforms to space group [ V = 7348.9 (17) Å3 , a = 19.4420 (15) Å], have anomalous anisotropic displacement parameters indicating a static or dynamic disorder. With decreasing temperature, the crystal structure shows a continuous symmetry-lowering transformation accompanied by twinning...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224962/homology-based-loop-modeling-yields-more-complete-crystallographic-protein-structures
#8
Bart van Beusekom, Krista Joosten, Maarten L Hekkelman, Robbie P Joosten, Anastassis Perrakis
Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and 'graft' these regions of interest...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224961/rapid-sample-delivery-for-megahertz-serial-crystallography-at-x-ray-fels
#9
Max O Wiedorn, Salah Awel, Andrew J Morgan, Kartik Ayyer, Yaroslav Gevorkov, Holger Fleckenstein, Nils Roth, Luigi Adriano, Richard Bean, Kenneth R Beyerlein, Joe Chen, Jesse Coe, Francisco Cruz-Mazo, Tomas Ekeberg, Rita Graceffa, Michael Heymann, Daniel A Horke, Juraj Knoška, Valerio Mariani, Reza Nazari, Dominik Oberthür, Amit K Samanta, Raymond G Sierra, Claudiu A Stan, Oleksandr Yefanov, Dimitrios Rompotis, Jonathan Correa, Benjamin Erk, Rolf Treusch, Joachim Schulz, Brenda G Hogue, Alfonso M Gañán-Calvo, Petra Fromme, Jochen Küpper, Andrei V Rode, Saša Bajt, Richard A Kirian, Henry N Chapman
Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224960/controlled-usage-of-h-d-exchange-to-circumvent-concomitant-polymorphs-of-roy
#10
Jacqueline Falk, Detlef Hofmann, Klaus Merz
The hypothesis that H/D exchange affects the structural formation of organic compounds in the solid state is supported by a deeper understanding of the altering polymorphism of ROY (a substance striking for its high number of polymorphic forms) through deuteration. Therefore, ROY was deuterated at its amine function, which leads to a seemingly small yet effective modification of the hydrogen-bond strength. In contrast to the crystallization of the non-deuterated ROY in methanol or ethanol, which leads to the simultaneous formation of two forms (OP and Y polymorphs), so-called concomitant polymorphs, the crystallization of d 1 -ROY leads to the selective formation of the Y polymorph exclusively...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224959/double-role-of-metalloporphyrins-in-catalytic-bioinspired-supramolecular-metal-organic-frameworks-smofs
#11
Arkaitz Fidalgo-Marijuan, Eder Amayuelas, Gotzone Barandika, Edurne S Larrea, Begoña Bazán, Miren Karmele Urtiaga, Marta Iglesias, María Isabel Arriortua
Heterogeneous catalysts are of great interest in many industrial processes for environmental reasons and, during recent years, a great effort has been devoted to obtain metal-organic frameworks (MOFs) with improved catalytic behaviour. Few supramolecular metal-organic frameworks (SMOFs) are stable under ambient conditions and those with anchored catalysts exhibit favourable properties. However, this paper presents an innovative approach that consists of using metal nodes as both structural synthons and catalysts...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224958/solving-protein-structure-from-sparse-serial-microcrystal-diffraction-data-at-a-storage-ring-synchrotron-source
#12
Ti-Yen Lan, Jennifer L Wierman, Mark W Tate, Hugh T Philipp, Jose M Martin-Garcia, Lan Zhu, David Kissick, Petra Fromme, Robert F Fischetti, Wei Liu, Veit Elser, Sol M Gruner
In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224957/do-the-basic-crystal-chemistry-principles-agree-with-a-plethora-of-recent-quantum-chemistry-data
#13
Elena Levi, Doron Aurbach, Carlo Gatti
The main descriptors of chemical bonding such as bond order (BO) and electron density at the bond critical point, ρc , are customarily used to understand the crystal and electronic structure of materials, as well as to predict their reactivity and stability. They can be obtained in the framework of crystal chemistry and quantum chemistry approaches, which are mostly applied as alternatives to each other. This paper verifies the convergence of the two approaches by analyzing a plethora of quantum chemistry data available in the literature...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224956/considerations-for-three-dimensional-image-reconstruction-from-experimental-data-in-coherent-diffractive-imaging
#14
Ida V Lundholm, Jonas A Sellberg, Tomas Ekeberg, Max F Hantke, Kenta Okamoto, Gijs van der Schot, Jakob Andreasson, Anton Barty, Johan Bielecki, Petr Bruza, Max Bucher, Sebastian Carron, Benedikt J Daurer, Ken Ferguson, Dirk Hasse, Jacek Krzywinski, Daniel S D Larsson, Andrew Morgan, Kerstin Mühlig, Maria Müller, Carl Nettelblad, Alberto Pietrini, Hemanth K N Reddy, Daniela Rupp, Mario Sauppe, Marvin Seibert, Martin Svenda, Michelle Swiggers, Nicusor Timneanu, Anatoli Ulmer, Daniel Westphal, Garth Williams, Alessandro Zani, Gyula Faigel, Henry N Chapman, Thomas Möller, Christoph Bostedt, Janos Hajdu, Tais Gorkhover, Filipe R N C Maia
Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224955/-de-novo-protein-structure-determination-by-heavy-atom-soaking-in-lipidic-cubic-phase-and-siras-phasing-using-serial-synchrotron-crystallography
#15
S Botha, D Baitan, K E J Jungnickel, D Oberthür, C Schmidt, S Stern, M O Wiedorn, M Perbandt, H N Chapman, C Betzel
During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported...
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30224954/atomic-level-three-dimensional-structure-of-individual-particles-with-xfels
#16
Changyong Song
Progress in single-particle three-dimensional imaging is discussed, with advances in both data-collection and data-handling techniques described.
September 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30004094/response-to-comment-on-protein-crystal-lattices-are-dynamic-assemblies-the-role-of-conformational-entropy-in-the-protein-condensed-phase
#17
COMMENT
Margarita Dimova, Yancho D Devedjiev
A response is given to Nespolo's comment [ IUCrJ (2018), 5 , https://doi.org/10.1107/S2052252518006267] about the usage of the the term 'crystal lattice' in Dimova & Devedjiev [ IUCrJ (2018), 5 , 130-140].
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002853/erratum-grazing-incidence-small-angle-x-ray-scattering-gisaxs-on-small-periodic-targets-using-large-beams-erratum
#18
Mika Pflüger, Victor Soltwisch, Jürgen Probst, Frank Scholze, Michael Krumrey
[This corrects the article DOI: 10.1107/S2052252517006297.].
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002852/comment-on-the-article-protein-crystal-lattices-are-dynamic-assemblies-the-role-of-conformational-entropy-in-the-protein-condensed-phase
#19
COMMENT
Massimo Nespolo
A comment is given on Dimova & Devedjiev [ IUCrJ (2018), 5 , 130-140].
July 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30002851/identification-of-a-tyrosine-switch-in-copper-haem-nitrite-reductases
#20
Jianshu Dong, Daisuke Sasaki, Robert R Eady, Svetlana V Antonyuk, S Samar Hasnain
There are few cases where tyrosine has been shown to be involved in catalysis or the control of catalysis despite its ability to carry out chemistry at much higher potentials (1 V versus NHE). Here, it is shown that a tyrosine that blocks the hydrophobic substrate-entry channel in copper-haem nitrite reductases can be activated like a switch by the treatment of crystals of Ralstonia pickettii nitrite reductase ( Rp NiR) with nitric oxide (NO) (-0.8 ± 0.2 V). Treatment with NO results in an opening of the channel originating from the rotation of Tyr323 away from AspCAT 97...
July 1, 2018: IUCrJ
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