forthcoming articles
The following articles are a selection of those recently accepted for publication in IUCr journals.
Acta Crystallographica Section A Acta Crystallographica Section A FOUNDATIONS AND ADVANCES |
research papers
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Unit-cell parameters determination from a set of independent electron diffraction zonal patterns
We present an algorithm for unit-cell determination from a set of randomly oriented electron diffraction patterns and demonstrate its performance for two known structures (copper perchlorophthalocyanine and lysozyme) and one as-yet uncharacterized structure.
research papers
A physical optics formulation of Bloch waves and its application to 4D STEM, 3D ED and inelastic scattering simulations
This article describes the re-formulation of Bloch waves using physical optics theory for more efficient simulation of large electron diffraction data sets.
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Crystallography of quasiperiodic moiré patterns in homophase twisted bilayers
The quasiperiodic nature of moiré patterns in homophase twisted bilayers is analyzed to understand the underlying basic periodicities and symmetries of homophase twisted bilayers built on any 2D structure.
Acta Crystallographica Section B Acta Crystallographica Section B STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS |
research papers
research papers
research papers
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Photoelasticity of crystals with the scheelite structure: quantum mechanical calculations
The methodology proposed combines the DFT calculations and photoelasticity caused by uniaxial compression of the crystal lattice, with particular emphasis on its anisotropy. It can be considered as part of optical engineering aimed at preliminary assessment of the photoelastic properties of crystal materials, thus assisting in their selection for synthesis and relevant applications.
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Crystal structure and doping in synthetic enstatite: an analysis of Li/Fe3+-doped single-crystal samples
Several Li+/Fe3+-doped Pbca orthoenstatite and Pbcn protoenstatite crystals were characterized revealing that varying levels of doping preferentially affect the pyroxene topologies.
research papers
research papers
Modulation of the modulated magnetic structure of an Ho i-MAX phase described by a magnetic (3+2)-dimensional superspace group
A rare complex incommensurate magnetic structure, an amplitude-modulated structure which itself is modulated, was determined in the Ho-based i-MAX phase (Mo2/3Ho1/3)2GaC. It represents a particularly distinctive case of a 2-k magnetic structure with no symmetry relation between the propagation vectors.
topical review
Crystallization induced by fungi and bacteria
The patterns of microbial crystallization are controlled by the chemical composition of biofilms associated with environmental exposure and the activity of microorganisms. The nutrition of microorganisms changes the oxalic acid and extracellular polymer substance content in the products of microbial metabolism, which significantly affects the medium pH promoting either the oxalate or carbonate crystallization.
research papers
SARAh – web representational analysis
The online software server SARAh—webRepresentational Analysis is introduced. The new suite of web apps carries out a range of calculations based on representation theory for the modelling of possible magnetic structures, their refinement from neutron scattering data and the analysis of other problems in condensed matter.
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Acta Crystallographica Section C Acta Crystallographica Section C STRUCTURAL CHEMISTRY |
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Synthesis and diverse crystal packing in o-, m- and p-bis(carbonylthioureido)benzenes containing bisferrocenes
Three bis(acylthiourea) positional isomers containing two ferrocenyl groups were synthesized and characterized by X-ray diffraction. Their various noncovalent interactions and crystal assemblies have been investigated.
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Conformational versatility among crystalline solids of L-phenylalanine derivatives
We present the synthesis and characterization of four new crystalline forms of a N-derivative of L-phenylalanine with 2-naphthaldehyde, where the compound adopts different unfolded and folded conformations depending on its charge state and the supramolecular environment. To characterize and classify such conformational differences, we propose the use of a dimensionless Shape Factor quantity defined as the Structural Aspect Ratio (SAR), which proves to be a simple but useful tool for this purpose, and its application could be extended to other conformational studies.
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Crystal structure of submicron-sized sulfur particles using 3D ED obtained in atmospheric conditions
The structure solution and refinement from three-dimensional electron diffraction (3D ED) data of elemental sulfur, known to sublimate in the vacuum of transmission electron microscopes, is enabled through the use of an environmental cell with a micro-electromechanical system. This work represents the first step in characterizing sulfur's transformation into lithium polysulfides using in-situ 3D ED.
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Fast event-based electron counting for small-molecule structure determination by MicroED
Fast readout event-based electron counting (EBEC) is a promising detection strategy to determine accurate ab initio structures of beam-sensitive small molecules by MicroED. A fast EBEC approach enhances the dynamic range of MicroED data by limiting the likelihood of coincidence loss (CL) – the undercounting of electrons due to their spatially and temporally unresolved arrival on a direct electron detector. As implemented by new counting detectors, fast EBEC allows structure-worthy data sets to be captured from individual small-molecule crystals in under a minute.
Acta Crystallographica Section D Acta Crystallographica Section D STRUCTURAL BIOLOGY |
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Reconsideration of the P-clusters in VFe proteins using the bond-valence method: towards their electron transfer and protonation
The oxidation of PN to P1+/P2+ clusters corresponds to coordination by the hydroxyl group of serine and the amide group of cysteine without electron and proton transfers.
Acta Crystallographica Section E Acta Crystallographica Section E CRYSTALLOGRAPHIC COMMUNICATIONS |
research communications (GO)
Synthesis and crystal structure of 2,2,2-trichloroethyl N-{4-[6-(1-hydroxyethyl)-1,2,4,5-tetrazin-3-yl]benzyl}carbamate
A 3,6-disubstituted 1,2,4,5-tetrazine was synthesized and characterized by single-crystal X-ray diffraction, revealing a complex hydrogen-bonded network with interactions between tetrazine N atoms and hydroxyl groups, thereby complementing the only scarcely explored features of tetrazines in the solid state.
research communications (GO)
Synthesis and structure of 2-oxo-2H-chromen-4-yl 4-bromobenzoate: work carried out as part of the CNRS AFRAMED project
In the title compound, the dihedral angle between the chromen-2-one ring system and the bromobenzene ring is 10.29 (6)°. In the crystal, the molecules are connected through C—H⋯O hydrogen bonds and π–π stacking interactions.
Acta Crystallographica Section F Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS |
research communications (RC)
Redox-dependent hydrogen-bond network rearrangement of ferredoxin-NADP+ reductase revealed by high-resolution X-ray and neutron crystallography
High-resolution X-ray and neutron crystallography reveal redox-dependent rearrangements in the hydrogen bond network of Ferredoxin-NADP+ reductase, highlighting structural changes around the FAD cofactor and shifts in water molecules that underpin its electron transfer mechanism. These findings provide valuable insights into the functional modulation of FNR.
research communications (RC)
Structure of Clostridium leptum carboxyspermidine decarboxylase and comparison to homologs prevalent within the human gut microbiome
A high-resolution structure of carboxyspermidine decarboxylase, a member of the PLP-dependent, β/α-barrel-fold, decarboxylase family is analyzed.
research communications (RC)
Structural insights into the role of the prosegment binding loop in a papain-superfamily cysteine protease from Treponema denticola
TDE0362 is an essential factor for the pathogenicity of T. denticola in oral bacterial disease. This work provides insights into the regulatory mechanism of TDE0362 and identifies putative substrate-binding interfaces which could be used to guide further research towards inhibition of this enzyme.
Journal of Applied Crystallography Journal of Applied Crystallography |
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Deep learning powered desmearing for small-angle scattering
We present a novel deep learning-based desmearing network (DSNet) that requires minimal simulation data for pre-training before fine-tuning. DSNet demonstrates excellent noise robustness and remarkable generalization performance, validated through both simulations and experiments.
research papers
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An extended thermal pressure equation of state for sodium fluoride
A PVT equation of state has been determined for sodium fluoride with a range of validity between 12 and 950 K in temperature and 0 and 25 GPa in pressure based on a fourth-order Birch–Murnaghan expression for isothermal compression and a Mie–Grüneisen–Debye model for thermal pressure.
research papers
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New robotic tools for multimodal non-destructive analysis and characterization of 2D and 3D objects
The forensic field requires versatile equipment for non-destructive characterization, analysis and inspection of 2D and 3D objects. The robotic scanner introduced here allows transmission X-ray imaging and mapping of individual photons with high-sensitivity and -resolution detectors. The broad capabilities of X-ray diffraction (XRD) imaging are now being complemented by X-ray fluorescence point analysis and mapping, multispectral macro imaging, and multispectral XRD analysis.
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Method of precise optical crystal alignment by tilting the diamond anvil cell
A novel method for precise crystal alignment in a diamond anvil cell has been developed. This method leverages Snell's law providing immediate visual feedback for alignment and offering exceptional accuracy (<0.02 mm) while being simple and fast, facilitating high-pressure diffraction experiments.
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An advanced approach combining solid-state NMR with powder diffraction applied to newly synthesized isothiouronium salts
The synthesis of new tetrafluoroborate and bromide salts of isothiouronium compounds is presented, followed by structural and spectroscopic studies, demonstrating that using solid-state NMR-derived intermolecular distances as a restriction can increase the likelihood of finding the crystal structure model when solving a crystal structure from powder diffraction data.
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Reciprocal-space mapping calculations of X-ray Laue diffraction in a crystal with thermomigration channels
In Laue geometry, based on two-dimensional recurrence relations of X-ray diffraction in a crystal with a complex elastic strain distribution, the method for calculating reciprocal-space maps has been developed.
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Integral X-ray diffuse scattering for studying irradiation-induced dislocation loops in single crystals
A computational and experimental investigation of integral X-ray diffuse scattering near Bragg reflections with a wide-open detector is presented for the case of small circular irradiation-induced dislocation loops in metals. The large wavevector asymptotic power-law falloff for such loops is determined computationally and incorporated into numerical and analytical integral X-ray diffuse scattering cross-section calculations. These calculations are shown to enable the experimental determination of the size distribution and concentrations of irradiation-induced dislocation loops in single-crystalline tungsten.
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Journal of Synchrotron Radiation Journal of Synchrotron Radiation |
research papers
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Deep learning-based spatio-temporal fusion for high-fidelity ultra-high-speed x-ray radiography
We develop and evaluate a deep learning-based algorithm that demonstrates the potential to reconstruct simultaneously high resolution, high frame-rate x-ray image sequences with high fidelity through spatio-temporal fusion. Our experimental evaluation shows that our method can significantly improve the accuracy of the reconstruction, achieving an average peak signal-to-noise ratio (PSNR) of more than 35 dB on two representative x-ray image sequences with input data streams of 4 times lower spatial resolution and 20 times lower frame rate, respectively.
beamlines
The current status and future prospects of the Synchrotron Radiation Protein Crystallography Core Facility at NSRRC: a focus on the TPS 05A, TPS 07A and TLS 15A1 beamlines
The SPXF has revolutionized structural biology research through its advanced light sources, enabling crucial breakthroughs in disease research. The facility's integration of automation and cutting-edge techniques provides world-class resources for global researchers.
computer programs
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Image registration for accurate electrode deformation analysis in operando microscopy of battery materials
We applied advanced image-processing techniques, including fast Fourier Transform analysis, image registration and optical flow, to mitigate artifacts caused by system instabilities and accurately track battery electrode deformations during operation. This approach improves the reliability of high-resolution operando imaging, providing deeper insights into battery degradation and enhancing our understanding of chemomechanical interactions in battery performance.
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Macromolecular crystallography from an industrial perspective – the impact of synchrotron radiation on structure-based drug discovery
Structure-based drug design has been a critical component of drug discovery for over 30 years, contributing to numerous approved drugs. The paper discusses the approach taken by AstraZeneca (Sweden) to synchrotron data collection for supporting a large portfolio of drug discovery projects and provides examples to demonstrate the continued importance of experimental structures.
research papers
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Probing soft X-ray induced photoreduction of a model Mn-complex at cryogenic conditions
This controlled radiation damage study at different temperatures allows the approaches to measuring radiation-damage-free/limited spectra from redox-sensitive metalloenzymes and metal complexes in the soft X-ray regime at synchrotrons to be refined.
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New online beam intensity synchronous monitoring system in scanning transmission X-ray microscopy
A new online beam intensity synchronous monitoring system has been designed which can precisely and synchronously monitor X-ray beam intensity variations. This can be used to remove noise due to electron injection from STXM images, thereby markedly improving the quality of STXM imaging.
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Compensation for the source drift of a free-electron laser beamline by adjusting the fixed-focus constant of the grating monochromator
A method for compensating for the source drift of a free-electron laser beamline by adjusting the Cff value of a grating monochromator is introduced.
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The nature of halogen bonding: insights from interacting quantum atoms and source function studies
Interacting quantum atoms and source function studies on a series of halogen-bonded complexes between substituted pyridines and X2 or XCN molecules (X = I, Br) focus on the combined role played by the X and N interacting pairs and their local environment.
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Understanding the selectivity of nonsteroidal anti-inflammatory drugs for cyclooxygenases using quantum crystallography and electrostatic interaction energy
This study employs quantum crystallography to elucidate the selectivity of NSAIDs, including ibuprofen, flurbiprofen, meloxicam and celecoxib, for cyclooxygenase-1 and cyclooxygenase-2 enzymes by analyzing binding energy and electrostatic interactions. The findings reveal key structural determinants of NSAID selectivity, providing valuable insights for the rational design of safer and more effective anti-inflammatory drugs.
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Single-shot X-ray imaging of two-dimensional strain fields in colloidal crystals
We used the Bragg coherence diffraction imaging method at the Coherent Scattering and Imaging endstation of the Shanghai Soft X-ray Free Electron Laser Facility to characterize colloidal crystals. This method successfully reproduced the static shape of crystals and we observed the defect structure of colloidal samples.
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Accounting for electron beam-induced warping of molecular nanocrystals in MicroED structure determination
Here we identify and characterize the warping of molecular crystal lattices induced by electron beam exposure during microcrystal electron diffraction (MicroED/3DED) data collection. We find changes to consensus crystal lattice orientation that are often dramatic, and appear ubiquitous in small organic molecule crystals. This evidence highlights the relevance of crystal bending or warping as a consequence of radiation-induced damage on molecular specimens, and points to it as a fundamental source of error in MicroED/3DED data collection and structure determination.
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Experimental electronic structure of copper complexes with biphenyldiimino dithioether – model of blue copper proteins
Differences in the electronic structures of Cu(I) and Cu(II) coordination compounds with the same ligand as model structures for blue copper proteins were studied.
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