journal
https://read.qxmd.com/read/38427456/characterizing-self-assembled-structures-made-with-magnetic-janus-nanoparticles
#1
JOURNAL ARTICLE
Elizabeth Blackburn
Small-angle X-ray scattering has revealed how magnetic Janus particles pair up in solutions in small and large magnetic fields.
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38427455/cocrystals-of-a-coumarin-derivative-an-efficient-approach-towards-anti-leishmanial-cocrystals-against-mil-resistant-leishmania-tropica
#2
JOURNAL ARTICLE
Muhammad Shahbaz, Saba Farooq, M Iqbal Choudhary, Sammer Yousuf
Leishmaniasis is a neglected parasitic tropical disease with numerous clinical manifestations. One of the causative agents of cutaneous leishmaniasis (CL) is Leishmania tropica (L. tropica) known for causing ulcerative lesions on the skin. The adverse effects of the recommended available drugs, such as amphotericin B and pentavalent antimonial, and the emergence of drug resistance in parasites, mean the search for new safe and effective anti-leishmanial agents is crucial. Miltefosine (MIL) was the first recommended oral medication, but its use is now limited because of the rapid emergence of resistance...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38376913/persistence-of-atoms-in-molecules-there-is-room-beyond-electron-densities
#3
JOURNAL ARTICLE
María Menéndez-Herrero, Ángel Martín Pendás
Evidence that the electronic structure of atoms persists in molecules to a much greater extent than has been usually admitted is presented. This is achieved by resorting to N-electron real-space descriptors instead of one- or at most two-particle projections like the electron or exchange-correlation densities. Here, the 3N-dimensional maxima of the square of the wavefunction, the so-called Born maxima, are used. Since this technique is relatively unknown to the crystallographic community, a case-based approach is taken, revisiting first the Born maxima of atoms in their ground state and then some of their excited states...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38362918/structural-analysis-of-nanocrystals-by-pair-distribution-function-combining-electron-diffraction-with-crystal-tilting
#4
JOURNAL ARTICLE
Linshuo Guo, Shitao Wu, Zhengyang Zhou, Yanhang Ma
As an important characterization method, pair distribution function (PDF) has been extensively used in structural analysis of nanomaterials, providing key insights into the degree of crystallinity, atomic structure, local disorder etc. The collection of scattering signals with good statistics is necessary for a reliable structural analysis. However, current conventional electron diffraction experiments using PDF (ePDF) are limited in their ability to acquire continuous diffraction rings for large nanoparticles...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38358351/community-recommendations-on-cryoem-data-archiving-and-validation
#5
JOURNAL ARTICLE
Gerard J Kleywegt, Paul D Adams, Sarah J Butcher, Catherine L Lawson, Alexis Rohou, Peter B Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R Baldwin, John M Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I Croll, Radostin Danev, Sai J Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J Bernard Heymann, Juha T Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C Lander, Shee Mei Lok, Steven J Ludtke, Garib N Murshudov, Ryan Pye, Grigore D Pintilie, Jane S Richardson, Carsten Sachse, Osman Salih, Sjors H W Scheres, Gunnar F Schroeder, Carlos Oscar S Sorzano, Scott M Stagg, Zhe Wang, Rangana Warshamanage, John D Westbrook, Martyn D Winn, Jasmine Y Young, Stephen K Burley, Jeffrey C Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38327201/data-reduction-in-protein-serial-crystallography
#6
JOURNAL ARTICLE
Marina Galchenkova, Alexandra Tolstikova, Bjarne Klopprogge, Janina Sprenger, Dominik Oberthuer, Wolfgang Brehm, Thomas A White, Anton Barty, Henry N Chapman, Oleksandr Yefanov
Serial crystallography (SX) has become an established technique for protein structure determination, especially when dealing with small or radiation-sensitive crystals and investigating fast or irreversible protein dynamics. The advent of newly developed multi-megapixel X-ray area detectors, capable of capturing over 1000 images per second, has brought about substantial benefits. However, this advancement also entails a notable increase in the volume of collected data. Today, up to 2 PB of data per experiment could be easily obtained under efficient operating conditions...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38299376/the-prediction-of-single-molecule-magnet-properties-via-deep-learning
#7
JOURNAL ARTICLE
Yuji Takiguchi, Daisuke Nakane, Takashiro Akitsu
This paper uses deep learning to present a proof-of-concept for data-driven chemistry in single-molecule magnets (SMMs). Previous discussions within SMM research have proposed links between molecular structures (crystal structures) and single-molecule magnetic properties; however, these have only interpreted the results. Therefore, this study introduces a data-driven approach to predict the properties of SMM structures using deep learning. The deep-learning model learns the structural features of the SMM molecules by extracting the single-molecule magnetic properties from the 3D coordinates presented in this paper...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38277167/crystal-structure-of-vancomycin-bound-to-the-resistance-determinant-d-alanine-d-serine
#8
JOURNAL ARTICLE
Jee Hoon Park, Rachel E Reviello, Patrick J Loll
Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a D-alanine-D-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either D-alanine-D-lactate or D-alanine-D-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38275161/the-curious-case-of-proton-migration-under-pressure-in-the-malonic-acid-and-4-4-bipyridine-cocrystal
#9
JOURNAL ARTICLE
Ewa Patyk-Kaźmierczak, Fernando Izquierdo-Ruiz, Alvaro Lobato, Michał Kaźmierczak, Ida Moszczyńska, Anna Olejniczak, J Manuel Recio
In the search for new active pharmaceutical ingredients, the precise control of the chemistry of cocrystals becomes essential. One crucial step within this chemistry is proton migration between cocrystal coformers to form a salt, usually anticipated by the empirical ΔpKa rule. Due to the effective role it plays in modifying intermolecular distances and interactions, pressure adds a new dimension to the ΔpKa rule. Still, this variable has been scarcely applied to induce proton-transfer reactions within these systems...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38214490/solving-protein-structures-by-combining-structure-prediction-molecular-replacement-and-direct-methods-aided-model-completion
#10
JOURNAL ARTICLE
Zengru Li, Haifu Fan, Wei Ding
Highly accurate protein structure prediction can generate accurate models of protein and protein-protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the more challenging cases such as multi-helical structures, multimeric structures and extremely large structures, both in the model preparation and in the completion steps, remains open for discussion. In this paper, a new strategy is proposed based on the framework of direct methods and dual-space iteration, which can greatly simplify the pre-processing steps of predicted models both in normal and in challenging cases...
March 1, 2024: IUCrJ
https://read.qxmd.com/read/38133556/orientational-analysis-of-atomic-pair-correlations-in-nanocrystalline-indium-oxide-thin-films
#11
JOURNAL ARTICLE
Justin M Hoffman, Niklas B Thompson, Olaf Borkiewicz, Xiang He, Samuel Amsterdam, Zhu Lin Xie, Aaron Taggart, Karen L Mulfort, Alex B F Martinson, Lin X Chen, Uta Ruett, David M Tiede
The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38131390/a-new-approach-for-serial-electron-diffraction-data-collection
#12
JOURNAL ARTICLE
Brent L Nannenga
A novel method is presented for serial electron diffraction data collection in electron crystallography, utilizing a scanning transmission electron microscope to rapidly obtain patterns with low radiation dose. This approach, demonstrated with zeolite samples, has the potential to provide highly automated and rapid structures from nanocrystalline materials.
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38131389/a-new-era-is-emerging-at-scientific-user-facilities
#13
JOURNAL ARTICLE
Dimitri Argyriou
Global scientific exchange has been profoundly perturbed by the COVID-19 pandemic, altering user travel behaviours and accelerating the use of remote access. Combined with the advent of artificial intelligence (AI), these trends together can change how large-scale user scientific facilities are used by the community and managed by operators.
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38131388/the-interoperability-of-crystallographic-data-and-databases
#14
JOURNAL ARTICLE
Alice Brink, Ian Bruno, John Helliwell, Brian McMahon
Interoperability of crystallographic data with other disciplines is essential for the smooth and rapid progress of structure-based science in the computer age. Within crystallography and closely related subject areas, there is already a high level of conformance to the generally accepted FAIR principles (that data be findable, accessible, interoperable and reusable) through the adoption of common information exchange protocols by databases, publishers, instrument vendors, experimental facilities and software authors...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38099813/orientational-ordering-and-assembly-of-silica-nickel-janus-particles-in-a-magnetic-field
#15
JOURNAL ARTICLE
Gouranga Manna, Thomas Zinn, Lewis Sharpnack, Theyencheri Narayanan
The orientation ordering and assembly behavior of silica-nickel Janus particles in a static external magnetic field were probed by ultra small-angle X-ray scattering (USAXS). Even in a weak applied field, the net magnetic moments of the individual particles aligned in the direction of the field, as indicated by the anisotropy in the recorded USAXS patterns. X-ray photon correlation spectroscopy (XPCS) measurements on these suspensions revealed that the corresponding particle dynamics are primarily Brownian diffusion [Zinn, Sharpnack & Narayanan (2023)...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38096040/what-is-isostructurality-questions-on-the-definition
#16
JOURNAL ARTICLE
Petra Bombicz
Investigation of isostructurality leads to a deeper understanding of close-packing principles and contributes to the ability of crystal engineering. A given packing motif may tolerate small molecular changes within a limit. Slight alterations of a crystal packing arrangement are carried out in order to fine-tune the structural and macroscopic properties, keeping the balance of the spatial requirements and electrostatic effects of the altered molecules in the crystals, preserving their isostructurality. Even so, the definition of isostructurality is not explicit about several issues...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38096039/c-spam-an-open-source-time-resolved-specimen-vitrification-device-with-light-activated-molecules
#17
JOURNAL ARTICLE
Alejandra Montaño Romero, Calli Bonin, Edward C Twomey
Molecular structures can be determined in vitro and in situ with cryo-electron microscopy (cryo-EM). Specimen preparation is a major obstacle in cryo-EM. Typical sample preparation is orders of magnitude slower than biological processes. Time-resolved cryo-EM (TR-cryo-EM) can capture short-lived states. Here, Cryo-EM sample preparation with light-activated molecules (C-SPAM) is presented, an open-source, photochemistry-coupled device for TR-cryo-EM that enables millisecond resolution and tunable timescales across broad biological applications...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38096038/refining-short-range-order-parameters-from-the-three-dimensional-diffuse-scattering-in-single-crystal-electron-diffraction-data
#18
JOURNAL ARTICLE
Romy Poppe, Nikolaj Roth, Reinhard B Neder, Lukas Palatinus, Bo Brummerstedt Iversen, Joke Hadermann
Our study compares short-range order parameters refined from the diffuse scattering in single-crystal X-ray and single-crystal electron diffraction data. Nb0.84 CoSb was chosen as a reference material. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms were refined from the diffuse scattering using a Monte Carlo refinement in DISCUS. The difference between the Sb and Co displacements refined from the diffuse scattering and the Sb and Co displacements refined from the Bragg reflections in single-crystal X-ray diffraction data is 0...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38096037/dynamic-x-ray-speckle-tracking-imaging-with-high-accuracy-phase-retrieval-based-on-deep-learning
#19
JOURNAL ARTICLE
Fucheng Yu, Kang Du, Xiaolu Ju, Feixiang Wang, Ke Li, Can Chen, Guohao Du, Biao Deng, Honglan Xie, Tiqiao Xiao
Speckle-tracking X-ray imaging is an attractive candidate for dynamic X-ray imaging owing to its flexible setup and simultaneous yields of phase, transmission and scattering images. However, traditional speckle-tracking imaging methods suffer from phase distortion at locations with abrupt changes in density, which is always the case for real samples, limiting the applications of the speckle-tracking X-ray imaging method. In this paper, we report a deep-learning based method which can achieve dynamic X-ray speckle-tracking imaging with high-accuracy phase retrieval...
January 1, 2024: IUCrJ
https://read.qxmd.com/read/38096036/structure-determination-using-high-order-spatial-correlations-in-single-particle-x-ray-scattering
#20
JOURNAL ARTICLE
Wenyang Zhao, Osamu Miyashita, Miki Nakano, Florence Tama
Single-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct the 3D diffraction intensity volume and subsequently the sample's density model. While most approaches perform 3D reconstruction via determining the orientation of each diffraction pattern, a correlation-based approach utilizes the averaged spatial correlations of diffraction intensities over all patterns, making it well suited for processing experimental data with a poor signal-to-noise ratio of individual patterns...
January 1, 2024: IUCrJ
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