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
Universal simulation of absorption effects for X-ray diffraction in reflection geometry
A ray-tracing algorithm for the simulation of absorption effects for arbitrary rasterized samples is presented. The algorithm is used to analyze how the absorption correction is influenced by the lateral and vertical dimensions of the material distribution in a sample surface.
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Development of an innovative diffraction scattering theory of X-rays and electrons in imperfect crystals
The Liouville–Neumann-type series formalism is applied to solve the X-ray and electron boundary-value Cauchy problems formulated in the form of the matrix Volterra integral equation of the second kind. Using the two-stage resolvent solution of the second order, this approach is supported by straightforward calculation of the electron bright- and dark-field contrasts of the edge dislocation in a thick foil.
Acta Crystallographica Section B Acta Crystallographica Section B STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS |
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Polymorph sampling with coupling to extended variables: enhanced sampling of polymorph energy landscapes and free energy perturbation of polymorph ensembles
A design is tested for a polymorph search algorithm relevant for enhanced sampling of crystal structures based on the relation between internal molecular structure variables and corresponding crystal polymorphs as representative of the inherent vapor to crystal transitions that exist in nature. Molecules are represented as extended variables within a thermal reservoir. Unit-cell variables are generated using pseudo-random sampling incorporating a harmonic coupling to extended variables.
Acta Crystallographica Section C Acta Crystallographica Section C STRUCTURAL CHEMISTRY |
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Preferential crystallization of (±)-pinenyllithium·TMEDA
β-Pinene is remarkably more reactive toward butyllithium·TMEDA than α-pinene, rapidly yielding the allyllithium·TMEDA complex, which preferentially crystallizes in the racemic form even from 92% ee solutions. Pinenyllithium·TMEDA is monomeric, with structural features that avoid both the Li–[(allyl)–Li]n– and Li–[π–Li]n–π– modes of aggregation common to allyllithiums.
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Acta Crystallographica Section D Acta Crystallographica Section D STRUCTURAL BIOLOGY |
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Introduction of Capsules environment to support further growth of the SBGrid structural biology software collection
The integration of Capsules within the SBGrid software management platform marks a pivotal advancement in addressing the challenges of scientific software distribution, dependency management and computational reproducibility.
research papers
Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples
An n-helix tilt scheme for cryo-electron tomography of pillar-shaped samples is described and simulated, allowing the entire pillar volume to be reconstructed as a single unit. Three related tilt schemes to enable the collection of the most isotropic information across all spatial frequencies are also evaluated.
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High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms
Anomalous scattering and PanDDA were employed to determine the binding orientation(s) of novel planar and low-occupancy fragment hits containing sulfur and/or halogen atoms that bind to SARS-CoV-2 nsp1. This approach was validated for these challenging-to-fit fragments with an anomalous data-collection strategy designed to mitigate radiation-damage effects, which are known to particularly affect halogenated fragments due to their higher X-ray absorption cross sections.
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Crystal-packing analysis of translation initiation factor 2 reveals new details of its function
A comparative analysis of the known crystal structures of the archaeal translation initiation factor 2 from Sulfolobus solfataricus and its individual subunits is reported. This work confirms the leading role of switch 1 in the function of the γ subunit of translation initiation factor 2 and reveals some important new details of this process.
Acta Crystallographica Section E Acta Crystallographica Section E CRYSTALLOGRAPHIC COMMUNICATIONS |
research communications (GM)
Syntheses and crystal structures of the five- and sixfold coordinated complexes diisoselenocyanatotris(2-methylpyridine N-oxide)cobalt(II) and diisoselenocyanatotetrakis(2-methylpyridine N-oxide)cobalt(II)
The crystal structures of the title compounds, which arose from the same reaction, consist of discrete complexes in which the cobalt cations are either in a CoN2O3 trigonal–bipyramidal or a CoN2O4 octahedral coordination.
research communications (GO)
Crystal structure of Staudtienic acid, a diterpenoid from Staudtia kamerunensis Warb. (Myristicaceae)
This work presents the crystal structure of a natural diterpenoid, Staudtienic acid, isolated from the stem bark of Staudtia kamerunensis Warb (Myristicaceae). This work confirmed the results previously obtained from NOE spectroscopy.
research communications (GO)
The crystal structures and Hirshfeld surface analysis of three new bromo-substituted 3-methyl-1-(phenylsulfonyl)-1H-indole derivatives
The crystal structures of three new indole derivative are described. The supramolecular relations in the system were assessed with a Hirshfeld surface analysis and calculation of the interaction energies, which suggest a primary significance of π–π and C—H⋯π interactions involving the indole moieties.
research communications (GM)
Synthesis and crystal structure of the cluster (Et4N)[(Tp*)MoFe3S3(μ3-NSiMe3)(N3)3]
This type of heterometallic and heteroleptic single cubane cluster represents a typical example within the Mo–Fe–S cluster family, which may be a good reference for understanding the structure and function of the nitrogenase FeMo cofactor.
research communications (GO)
Structural characterization of the supramolecular complex between a tetraquinoxaline-based cavitand and benzonitrile
The 2:1 supramolecular complex between a tetraquinoxaline-based cavitand and benzonitrile as a guest has been studied through X-ray diffraction analysis. One of the benzonitrile molecules in engulfed inside the macrocycle.
research communications (GI)
research communications (GO)
Crystal structure of 1-(1,3-benzothiazol-2-yl)-3-(4-bromobenzoyl)thiourea
A thiourea derivative with two dissimilar functional groups was prepared and characterized. In the crystal, pairs of adjacent molecules interact via intermolecular hydrogen bonds of type C—H⋯N, C—H⋯S and N—H⋯S, resulting in molecular layers parallel to the ac plane.
research communications (GO)
Ethyl 2-[(2-oxo-2H-chromen-6-yl)oxy]acetate
Ethyl 2-[(2-oxo-2H-chromen-6-yl)oxy]acetate, a coumarin derivative, crystallizes in sheets, within which molecules are held by weak C—H⋯O hydrogen-bonding interactions and between which molecules interact by π–π stacking and additional C—H⋯O weak hydrogen bonds between ethyl acetoxy groups.
research communications (GO)
Structural multiplicity in a multi-component solvated crystal of the antiretroviral protease inhibitor Lopinavir
The multi-component solvated Lopinavir crystal was prepared using evaporative methods. The crystal structure is unusual in that although Lopinavir was crystallized in ethylene glycol (ethane-1,2-diol) alone, the unit cell contains four different components, totalling 18 molecules. The stoichiometric ratio of this crystal is eight lopinavir molecules, two ethane-1,2-diol molecules, one (E)-ethene-1,2-diol (C2H4O2) and seven water molecules.
Acta Crystallographica Section F Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS |
research communications (RC)
Cryo-EM structure and functional analysis of the chromatin remodeler RSF
RSF1 changes the chromatin-remodeling mode of SNF2h. The RSF complex does not have a nucleosome-recentering capacity and a `critical distance' exists during the action of RSF in vitro; this distance is about 24 base pairs. The RSF complex loosens parts of the nucleosome DNA and undergoes conformational change on linker DNA stimulation.
Journal of Applied Crystallography Journal of Applied Crystallography |
research papers
Demonstration of neutron time-of-flight diffraction with an event-mode imaging detector
This paper demonstrates for the first time an event-mode imaging based neutron diffraction detector system that employs a scintillator screen, an image intensifier, and a Timepix3 based camera. This highly configurable approach allows for large solid angle, low cost neutron diffraction setups and this work shows that the performance is comparable to the 3He detectors on a time-of-flight neutron diffraction beamline. Rietveld analysis for this type of data was enabled by implementing data reduction in the MAUD Rietveld code.
laboratory notes
A simple protocol for determining the zone axis direction from selected area electron diffraction spot patterns of cubic materials
Re-examination of the long-known Rn ratio method for indexing electron diffraction zone axis patterns of materials with cubic symmetry has revealed some unrecognized potential for lattice direction analysis and, in some cases, unambiguous identification of the Bravais lattice. A protocol has been developed which allows the identification of experimental spot patterns for the 15 most common lattice directions.
research papers
Updating Direct Methods II. Reduction of the structural complexity when triplet invariants are estimated via the Patterson map
A recently published probabilistic theory estimates triplet invariants by using the Patterson peaks as prior information. This paper is the first experimental test: we showed that the new estimates are so accurate that may be applied to macromolecules. Structural complexity and atomic data resolution are no more critical limits.
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A science-driven approach to optimize the design for a biological small-angle neutron scattering instrument
This work presents a time-of-flight small-angle neutron scattering instrument concept based on an optimization workflow using McStas simulations to explore the parameter space with a focus on instrument performance for a given scientific objective.
computer programs
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computer programs
Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III
The implementation is described of tools for rapid X-ray diffraction data processing and analysis for dynamic compression experiments using a diamond anvil cell.
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Quantitative selection of sample structures in small-angle scattering using Bayesian methods
We propose a Bayesian method for quantitatively selecting a mathematical model of a sample for small-angle scattering, and evaluate its performance through numerical experiments on artificial data of a sample containing a mixture of multiple spherical particles.
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A study of stress, composition and grain interaction gradients in energy-dispersive X-ray stress analysis on materials with cubic symmetry
The influence of various combinations of residual stress, composition and grain interaction gradients in polycrystalline materials with cubic symmetry on X-ray stress analysis by energy-dispersive diffraction is discussed on the basis of simulations for ferritic and austenitic steel.
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Journal of Synchrotron Radiation Journal of Synchrotron Radiation |
research papers
addenda and errata
research papers
Signal-to-noise and spatial resolution in in-line imaging. 1. Basic theory, numerical simulations and planar experimental images
Signal-to-noise ratio and spatial resolution are quantitatively analysed in the context of propagation based X-ray phase-contrast imaging. The performance of the method is shown to be determined by the Fresnel number and the ratio of the real decrement to the imaginary part of the refractive index of the imaged object.
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Roentgenoscopy of laser-induced projectile impact testing
Laser-induced projectile impact testing (LIPIT) based on X-ray white-light imaging is presented. This study confirms the potential of LIPIT based on synchrotron in situ imaging, which allows the recording of the trajectories of high-speed particles inside a material and the material's impact response in real time.
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The effect of transport apertures on relay-imaged, sharp-edged laser profiles in photoinjectors and the impact on electron beam properties
Wavefront propagation studies show that apertures in the laser injection path into photoinjector electron guns result in spatial ripples in relay-imaged cut-Gaussian profiles. The effect on electron beam properties depends on the extent to which space charge washes out the corresponding ripples in the emitted electron bunch, but could significantly negatively impact on the quality of the electron bunch.
letters to the editor
The HEPS Synchrotron unleashes new medical frontiers
The High Energy Photon Source (HEPS) in Beijing achieved a beam energy of 6GeV, positioning it as the world's brightest fourth-generation synchrotron with the smallest emittance. This milestone enables groundbreaking advances in health sciences and various research fields, promising new insights into biological and quantum processes.
research papers
Automated spectrometer alignment via machine learning
In this study, we showcase the application of a machine learning approach for the automated alignment of a soft X-ray spectrometer. Our method has been validated with experimental data at the beamline and significantly reduces the alignment time from approximately one hour to just a few minutes.
research papers
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Soft X-ray wavefront sensing at an ellipsoidal mirror shell
Phase retrieval at an axisymmetric ellipsoidal mirror is demonstrated with soft X-rays (277 eV), completed by a reconstruction of the focus as well as figure and alignment error of the mirror. Based on simple measurements of the cross-focal, three-dimensional intensity distribution, an intuitive algorithm is proposed which combines the advantages of high resolution, sensitivity and reliability even under difficult conditions like a low source flux or weak spatial coherence.
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Statistical optimization of guest uptake in crystalline sponges: grading structural outcomes
A statistical design of experiments approach applied to crystalline sponge analysis enables greater understanding of experimental influences and the development of a novel molecular structure quality grading system.
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Structural insight into piezo-solvatochromism of Reichardt's dye
This work employs the preference of compounds to crystallize at high-pressure in the form of solvates to explore the solvation process and piezo-solvatochromic effects of Reichardt's dye, ET(1). Its solute–solvent interactions affect the optical properties of the dye in various solvents as shown by X-ray diffraction and UV–Vis spectroscopy, revealing applications in nonlinear optoelectronics and molecular pressure sensor development.
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topical review
Chromic soft crystals based on luminescent platinum(II) complexes
Platinum(II) complexes exhibit intense luminescence based on their molecular arrangement and chromic luminescence, which is a color change in response to gentle stimuli such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively control the chromic phenomenon of platinum(II) complexes.
IUCrData IUCrData |
data reports (HM)
(4-Butyl-1-ethyl-1,2,4-triazol-5-ylidene)[(1,2,5,6-η)-cycloocta-1,5-diene](triphenylphosphane)iridium(I) tetrafluoridoborate
The title triazole-based N-heterocyclic carbene iridium(I) cationic complex with a tetrafluoridoborate counter-anion, crystallizes with two cations and two anions in the asymmetric unit. In the extended structure, non-classical C–H⋯F hydrogen bonds, one of which is notably short (H⋯F = 2.21 Å), link the cations and anions.
data reports (HM)
(2,5-Dimethylimidazole){N,N′,N′′,N′′′-[porphyrin-5,10,15,20-tetrayltetra(2,1-phenylene)]tetrakis(pyridine-3-carboxamide)}manganese(II) chlorobenzene disolvate
In the title compound, the central MnII ion is coordinated by four pyrrole N atoms of the porphyrin core in the basal sites and one N atom of the 2,5-dimethylimidazole ligand in the apical site. Two chlorobenzene solvent molecules are also present in the asymmetric unit.
data reports (HM)
Chlorido[5,10,15,20-tetrakis(quinoline-7-carboxamido)porphinato]iron(III)
The porphyrin macrocycle shows a characteristic ruffled-shape distortion. The central FeIII cation (site symmetry 2) is coordinated in a fivefold manner, with four pyrrole N atoms of the porphyrin core in the basal sites and one Cl atom (site symmetry 2) in the apical position.
data reports (HO)
data reports (HM)
Poly[[{μ2-5-[(dimethylamino)(thioxo)methoxy]benzene-1,3-dicarboxylato-κ4O1,O1′:O3,O3′}(μ2-4,4′-dipyridylamine-κ2N4:N4′)cobalt(II)] dimethylformamide hemisolvate monohydrate]
The crystal structure of the title compound shows a layered arrangement parallel to the bc plane where [CoO4N2] octahedra are linked by dmtb2– and dpa ligands.
data reports (HI)
data reports (HM)
data reports (HO)
(S)-2-Carboxyethyl L-cysteinyl sulfone
The molecule is a zwitterion, with a protonated α-amino group and a deprotonated α-carboxyl group. Within the crystal, the molecules are linked by a system of hydrogen bonds formed by both the protonated and deprotonated carboxylic groups, and the protonated ammonium group.
data reports (HO)
data reports (HM)
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