journal
https://read.qxmd.com/read/38038991/stem-serialed-achieving-high-resolution-data-for-ab-initio-structure-determination-of-beam-sensitive-nanocrystalline-materials
#21
JOURNAL ARTICLE
Pascal Hogan-Lamarre, Yi Luo, Robert Bücker, R J Dwayne Miller, Xiaodong Zou
Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38019132/conformation-aggregation-interplay-in-the-simplest-aliphatic-ethers-probed-under-high-pressure
#22
JOURNAL ARTICLE
Natalia Sacharczuk, Anna Olejniczak, Maciej Bujak, Kamil Filip Dziubek, Andrzej Katrusiak, Marcin Podsiadło
The structures of the simplest symmetric primary ethers [(Cn H2n+1 )2 O, n = 1-3] determined under high pressure revealed their conformational preferences and intermolecular interactions. In three new polymorphs of diethyl ether (C2 H5 )2 O, high pressure promotes intermolecular CH...O contacts and enforces a conversion from the trans-trans conformer present in the α, β and γ phases to the trans-gauche conformer, which is higher in energy by 6.4 kJ mol-1 , in the δ phase...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/37990870/enhancing-hydrogen-positions-in-x-ray-structures-of-transition-metal-hydride-complexes-with-dynamic-quantum-crystallography
#23
JOURNAL ARTICLE
Magdalena Woińska, Anna A Hoser, Michał L Chodkiewicz, Krzysztof Woźniak
Hirshfeld atom refinement (HAR) is a method which enables the user to obtain more accurate positions of hydrogen atoms bonded to light chemical elements using X-ray data. When data quality permits, this method can be extended to hydrogen-bonded transition metals (TMs), as in hydride complexes. However, addressing hydrogen thermal motions with HAR, particularly in TM hydrides, presents a challenge. At the same time, proper description of thermal vibrations can be vital for determining hydrogen positions correctly...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/37962472/the-role-of-alkyl-chain-length-in-the-melt-and-solution-crystallization-of-paliperidone-aliphatic-prodrugs
#24
JOURNAL ARTICLE
An Chen, Peishan Cai, Yayun Peng, Minshan Guo, Yuan Su, Ting Cai
Fatty acid-derivative prodrugs have been utilized extensively to improve the physicochemical, biopharmaceutical and pharmacokinetic properties of active pharmaceutical ingredients. However, to our knowledge, the crystallization behavior of prodrugs modified with different fatty acids has not been explored. In the present work, a series of paliperidone aliphatic prodrugs with alkyl chain lengths ranging from C4 to C16 was investigated with respect to crystal structure, crystal morphology and crystallization kinetics...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/37962471/unravelling-the-components-of-diffuse-scattering-using-deep-learning
#25
JOURNAL ARTICLE
Chloe A Fuller, Lucas S P Rudden
Many technologically important material properties are underpinned by disorder and short-range structural correlations; therefore, elucidating structure-property relationships in functional materials requires understanding both the average and the local structures. The latter information is contained within diffuse scattering but is challenging to exploit, particularly in single-crystal systems. Separation of the diffuse scattering into its constituent components can greatly simplify analysis and allows for quantitative parameters describing the disorder to be extracted directly...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38446458/structural-dissection-of-two-redox-proteins-from-the-shipworm-symbiont-teredinibacter-turnerae
#26
JOURNAL ARTICLE
Badri S Rajagopal, Nick Yates, Jake Smith, Alessandro Paradisi, Catherine Tétard-Jones, William G T Willats, Susan Marcus, J Paul Knox, Mohd Firdaus-Raih, Bernard Henrissat, Gideon J Davies, Paul H Walton, Alison Parkin, Glyn R Hemsworth
The discovery of lytic polysaccharide monooxygenases (LPMOs), a family of copper-dependent enzymes that play a major role in polysaccharide degradation, has revealed the importance of oxidoreductases in the biological utilization of biomass. In fungi, a range of redox proteins have been implicated as working in harness with LPMOs to bring about polysaccharide oxidation. In bacteria, less is known about the interplay between redox proteins and LPMOs, or how the interaction between the two contributes to polysaccharide degradation...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38446457/transferable-hirshfeld-atom-model-for-rapid-evaluation-of-aspherical-atomic-form-factors
#27
JOURNAL ARTICLE
Michał Chodkiewicz, Leonid Patrikeev, Sylwia Pawlędzio, Krzysztof Woźniak
Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen-Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38446456/droplet-microfluidics-for-time-resolved-serial-crystallography
#28
JOURNAL ARTICLE
Jack Stubbs, Theo Hornsey, Niall Hanrahan, Luis Blay Esteban, Rachel Bolton, Martin Malý, Shibom Basu, Julien Orlans, Daniele de Sanctis, Jung Uk Shim, Patrick D Shaw Stewart, Allen M Orville, Ivo Tews, Jonathan West
Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here, we report the use of droplet miniaturization for the controlled production of uniform crystals, providing an avenue for controlled substrate addition and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3 µm crystals of lysozyme and 2 µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38446455/poetry-in-motion-catching-molecules-in-action
#29
JOURNAL ARTICLE
Edward N Baker
Researchers have long sought to `see' proteins and other macromolecules in motion, to better understand their functions. Technological developments, notably advances in serial crystallography, are now making these dreams a reality, heralding a new era of kinetic crystallography.
March 1, 2024: IUCrJ
https://read.qxmd.com/read/37910142/a-new-polymorph-of-white-phosphorus-at-ambient-conditions
#30
JOURNAL ARTICLE
Regine Herbst-Irmer, Xiaobai Wang, Laura Haberstock, Ingo Köhne, Rainer Oswald, Jörg Behler, Dietmar Stalke
Phosphorus exists in several different allotropes: white, red, violet and black. For industrial and academic applications, white phosphorus is the most important. So far, three polymorphs of white phosphorus, all consisting of P4 tetrahedra, have been described. Among these, β-P4 crystallizes in the space group P1 and γ-P4 in the space group C2/m. α-P4 forms soft plastic crystals with a proposed structure in the cubic space group I43m with the lattice constant a = 18.51 (3) Å, consisting of 58 rotationally disordered tetrahedra and thus is similar to the structure of α-Mn...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37910141/thinner-than-a-knife-s-edge-3d-printed-liquid-sheet-jet-technology-for-solution-phase-xfel-experiments
#31
JOURNAL ARTICLE
Martin Trebbin
In this commentary, we explore the pioneering implementation of 3D-printed thin liquid sheet devices for advanced X-ray scattering and spectroscopy experiments at high-repetition rate XFELs.
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37903100/emergence-of-liquid-following-laser-melting-of-gold-thin-films
#32
JOURNAL ARTICLE
Ian K Robinson, Jack P Griffiths, Robert Koch, Tadesse A Assefa, Ana F Suzana, Yue Cao, Sungwon Kim, Dongjin Kim, Heemin Lee, Sunam Kim, Jae Hyuk Lee, Sang Youn Park, Intae Eom, JaeHyun Park, Daewoong Nam, Sangsoo Kim, Sae Hwan Chun, Hyojung Hyun, Kyung Sook Kim, Ming Lu, Changyong Song, Hyunjung Kim, Simon J L Billinge, Emil S Bozin
X-ray structural science is undergoing a revolution driven by the emergence of X-ray Free-electron Laser (XFEL) facilities. The structures of crystalline solids can now be studied on the picosecond time scale relevant to phonons, atomic vibrations which travel at acoustic velocities. In the work presented here, X-ray diffuse scattering is employed to characterize the time dependence of the liquid phase emerging from femtosecond laser-induced melting of polycrystalline gold thin films using an XFEL. In a previous analysis of Bragg peak profiles, we showed the supersonic disappearance of the solid phase and presented a model of pumped hot electrons carrying energy from the gold surface to scatter at internal grain boundaries...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37903099/a-transferable-quantum-mechanical-energy-model-for-intermolecular-interactions-using-a-single-empirical-parameter
#33
JOURNAL ARTICLE
Peter R Spackman, Mark A Spackman, Julian D Gale
The calculation of intermolecular interactions in molecular crystals using model energies provides a unified route to understanding the complex interplay of driving forces in crystallization, elastic properties and more. Presented here is a new single-parameter interaction energy model (CE-1p), extending the previous CrystalExplorer energy model and calibrated using density functional theory (DFT) calculations at the ωB97M-V/def2-QZVP level over 1157 intermolecular interactions from 147 crystal structures...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37870936/going-around-the-kok-cycle-of-the-water-oxidation-reaction-with-femtosecond-x-ray-crystallography
#34
JOURNAL ARTICLE
Asmit Bhowmick, Philipp S Simon, Isabel Bogacz, Rana Hussein, Miao Zhang, Hiroki Makita, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D Doyle, Mun Hon Cheah, Petko Chernev, Franklin D Fuller, Thomas Fransson, Roberto Alonso-Mori, Aaron S Brewster, Nicolas K Sauter, Uwe Bergmann, Holger Dobbek, Athina Zouni, Johannes Messinger, Jan Kern, Vittal K Yachandra, Junko Yano
The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4 Ca complex (Mn4 CaO5 ) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37860977/predicting-photoactivity-in-dithienylethene-crystalline-solids
#35
JOURNAL ARTICLE
Kristin M Hutchins
This commentary discusses the design of stimuli-responsive materials, specifically, light-responsive dithienylethene-based compounds. Recent progress in predicting photoactivity using a combination of theory and crystal structure landscape experiments is highlighted.
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37860976/structural-snapshots-of-mycobacterium-tuberculosis-enolase-reveal-dual-mode-of-2pg-binding-and-its-implication-in-enzyme-catalysis
#36
JOURNAL ARTICLE
Mohammed Ahmad, Bhavya Jha, Sucharita Bose, Satish Tiwari, Abhisek Dwivedy, Deepshikha Kar, Ravikant Pal, Richard Mariadasse, Tanya Parish, Jeyaraman Jeyakanthan, Kutti R Vinothkumar, Bichitra Kumar Biswal
Enolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phosphoglycerate (2PG) to phosphoenolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The underlying mechanism of the 2PG to PEP conversion has been studied in great detail in previous work, however that of the reverse reaction remains to be explored. Here we present structural snapshots of Mycobacterium tuberculosis (Mtb) enolase in apo, PEP-bound and two 2PG-bound forms as it catalyzes the conversion of PEP to 2PG...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37830774/kilohertz-serial-crystallography-with-the-jungfrau-detector-at-a-fourth-generation-synchrotron-source
#37
JOURNAL ARTICLE
Filip Leonarski, Jie Nan, Zdenek Matej, Quentin Bertrand, Antonia Furrer, Ishkhan Gorgisyan, Monika Bjelčić, Michal Kepa, Hannah Glover, Viktoria Hinger, Thomas Eriksson, Aleksander Cehovin, Mikel Eguiraun, Piero Gasparotto, Aldo Mozzanica, Tobias Weinert, Ana Gonzalez, Jörg Standfuss, Meitian Wang, Thomas Ursby, Florian Dworkowski
Serial and time-resolved macromolecular crystallography are on the rise. However, beam time at X-ray free-electron lasers is limited and most third-generation synchrotron-based macromolecular crystallography beamlines do not offer the necessary infrastructure yet. Here, a new setup is demonstrated, based on the JUNGFRAU detector and Jungfraujoch data-acquisition system, that enables collection of kilohertz serial crystallography data at fourth-generation synchrotrons. More importantly, it is shown that this setup is capable of collecting multiple-time-point time-resolved protein dynamics at kilohertz rates, allowing the probing of microsecond to second dynamics at synchrotrons in a fraction of the time needed previously...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37815488/single-crystal-quality-data-from-polycrystalline-samples-finding-the-needle-in-the-haystack
#38
JOURNAL ARTICLE
Joseph Charles Bear, Nikitas Terzoudis, Jeremy Karl Cockcroft
Multi-grain crystallography, traditionally performed at synchrotron sources in association with high-pressure studies, has new relevance with respect to laboratory single-crystal X-ray diffraction, in which crystals can be grown rapidly in situ, and a preliminary dataset analysed and solved in a matter of minutes. Subsequently, a full-sphere of IUCr-quality data can then be collected in a few hours. To demonstrate the applicability of laboratory multi-grain crystallography with Cu Kα X-rays, co-crystals of hexafluorobenzene and pyrrole were grown rapidly by cooling a 1:1 liquid mixture in an X-ray capillary on the diffractometer...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37782462/a-phenomenological-model-of-the-x-ray-pulse-statistics-of-a-high-repetition-rate-x-ray-free-electron-laser
#39
JOURNAL ARTICLE
Trey W Guest, Richard Bean, Raimund Kammering, Grant van Riessen, Adrian P Mancuso, Brian Abbey
Many coherent imaging applications that utilize ultrafast X-ray free-electron laser (XFEL) radiation pulses are highly sensitive to fluctuations in the shot-to-shot statistical properties of the source. Understanding and modelling these fluctuations are key to successful experiment planning and necessary to maximize the potential of XFEL facilities. Current models of XFEL radiation and their shot-to-shot statistics are based on theoretical descriptions of the source and are limited in their ability to capture the shot-to-shot intensity fluctuations observed experimentally...
November 1, 2023: IUCrJ
https://read.qxmd.com/read/37772598/observing-femtosecond-orbital-dynamics-in-ultrafast-ge-melting-with-time-resolved-resonant-x-ray-scattering
#40
JOURNAL ARTICLE
Heemin Lee, Je Young Ahn, Sae Hwan Chun, Do Hyung Cho, Daeho Sung, Chulho Jung, Jaeyong Shin, Junha Hwang, Sung Soo Ha, Hoyoung Jang, Byeong Gwan Cho, Sunam Kim, Jaeku Park, Daewoong Nam, Intae Eom, Ji Hoon Shim, Do Young Noh, Yungok Ihm, Changyong Song
Photoinduced nonequilibrium phase transitions have stimulated interest in the dynamic interactions between electrons and crystalline ions, which have long been overlooked within the Born-Oppenheimer approximation. Ultrafast melting before lattice thermalization prompted researchers to revisit this issue to understand ultrafast photoinduced weakening of the crystal bonding. However, the absence of direct evidence demonstrating the role of orbital dynamics in lattice disorder leaves it elusive. By performing time-resolved resonant X-ray scattering with an X-ray free-electron laser, we directly monitored the ultrafast dynamics of bonding orbitals of Ge to drive photoinduced melting...
November 1, 2023: IUCrJ
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