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
N-representable one-electron reduced density matrix reconstruction with frozen core electrons
An improved method of one-electron reduced density matrix reconstruction from structure factors and directional Compton profiles is tested on a urea crystal. Novel restrictions accounting for molecular symmetry and freezing of core electrons are introduced.
Acta Crystallographica Section B Acta Crystallographica Section B STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS |
research papers
Growth, crystal structure and IR luminescence of KSrY1–xErx(BO3)2
A series of novel KSrY1–xErx(BO3)2 (x = 0–1) phosphors, emitting near-infrared radiation, was synthesized by solid-state methods. A strong emission of Er3+ electron transition 4I13/2 → 4I15/2 was detected within the 1529–1549 nm range.
research papers
Crystal structure solution and high-temperature thermal expansion in NaZr2(PO4)3-type materials
The crystal structure in space group R3c in a high-temperature polymorph of SrZr4P6O24 and CaZr4P6O24 was solved with Fourier difference mapping. The thermal expansion tensors for several NaZr2P3O12-type materials were measured from 25 to 1500°C and crystallographic thermal expansion mechanisms investigated.
research papers
Attractive and repulsive forces in a crystal of [Rb(18-crown-6)][SbCl6] under high pressure
The structure of [Rb(18-crown-6)][SbCl6] is studied under high pressure. This sample serves as a compression model, demonstrating the influence of both attractive London dispersion forces and repulsive forces in the crystal affecting its behavior under extreme pressure.
research papers
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 |
research papers
research papers
research papers
Acta Crystallographica Section D Acta Crystallographica Section D STRUCTURAL BIOLOGY |
research papers
Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase
The crystal structures of europium(III)- and gadolinium(III)-bound phosphotriesterase are presented along with esterase activity data for the lanthanide-bound enzymes.
research papers
Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows
To simplify the cryo-electron tomography workflow and make this technique more accessible to all researchers, the Tomo Live software has been developed, which performs on-the-fly reconstruction of tilt series, enabling real-time data-quality monitoring, curation and export.
research papers
EMinsight: a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition
EMinsight is a Python-based tool for systematically mining metadata from single-particle analysis cryoEM experiments. The capture and analysis of metadata facilitates the assessment of instrument performance, provides concise reporting of experiment performance and sample quality by analysing preprocessing results, and gathers metadata for deposition. It is envisaged that this approach will benefit the microscope operator, facility managers, database developers and users.
Acta Crystallographica Section E Acta Crystallographica Section E CRYSTALLOGRAPHIC COMMUNICATIONS |
research communications (GM)
Lithium and sodium 3-(3,4-dihydroxyphenyl)propenoate hydrate
The Li cation in the crystal structure of the lithium salt LiC9H7O4·H2O shows a coordination number of four whereas the Na cation in the crystal structure of the sodium salt NaC9H7O4·H2O shows a coordination number of seven.
research communications (GO)
Crystal structure and Hirshfeld surface analysis of 6-imino-8-(4-methylphenyl)-1,3,4,6-tetrahydro-2H-pyrido[1,2-a]pyrimidine-7,9-dicarbonitrile
In the crystal, molecules are linked by N—H⋯N and C–H⋯N hydrogen bonds, forming a three-dimensional network. In addition, C—H⋯π interactions form layers parallel to the (100) plane. Thus, crystal-structure cohesion is ensured.
research communications (GO)
Crystal structure, Hirshfeld surface analysis, calculations of crystal voids, interaction energy and energy frameworks as well as density functional theory (DFT) calculations of 3-[2-(morpholin-4-yl)ethyl]-5,5-diphenylimidazolidine-2,4-dione
In the title molecule, the imidazolidine ring slightly deviates from planarity and the morpholine ring exhibits the usual chair conformation. In the crystal, N—H⋯O and C—H⋯O hydrogen bonds form helical chains of molecules extending parallel to the c axis that are connected by C—H⋯π(ring) interactions into a tri-periodic network.
research communications (GO)
Crystal structure and Hirshfeld surface analysis of 4,4′-dimethoxybiphenyl-3,3′,5,5′-tetracarboxylic acid dihydrate
The crystal structure is essentially stabilized by O—H⋯O bonds. Here, the carboxyl groups of neighbouring host molecules are connected by cyclic (8) synthons, leading to the formation of a three-dimensional network. The water molecules in turn form helical supramolecular strands running in the c-axis direction (chain-like water clusters). The second H atom of each water molecule provides a link to a methoxy O atom of the host molecule.
research communications (GO)
Crystal structure and Hirshfeld surface analysis of 8-benzyl-1-[(4-methylphenyl)sulfonyl]-2,7,8,9-tetrahydro-1H-3,6:10,13-diepoxy-1,8-benzodiazacyclopentadecine ethanol hemisolvate
In the crystal, molecules are connected by C—H⋯O and O—H⋯O hydrogen bonds, forming a three-dimensional network. In addition, C—H⋯π interactions also strengthen the molecular packing.
research communications (GO)
Crystal structure of (S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone
The structure of (S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone has been determined to establish its absolute configuration in efforts to synthesize an anticancer drug candidate, parsaclisib.
Acta Crystallographica Section F Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS |
topical review
Journal of Applied Crystallography Journal of Applied Crystallography |
computer programs
iQual: a new computer program for qualitative phase analysis with efficient search–match capability
iQual is an innovative computer program that utilizes the optimized Crystal_db database, derived from the Crystallography Open Database, for efficient searching and matching of experimental X-ray diffraction patterns for qualitative phase analysis, employing a two-step approach and matrix operations for enhanced efficiency.
research papers
research papers
Energy storage properties influenced by relaxor ferroelectric properties dependent on the growth direction of epitaxial Bi2SiO5 thin films
Bi2SiO5 thin films that do not have a perovskite structure exhibit ferroelectric properties influenced by crystallinity due to the layered structure in which the Bi2O2 layer is formed. Bi2SiO5 thin films exhibited ferroelectric and energy storage characteristics influenced by various crystallinities on Nb-doped (111), (110) and (111) SrTiO3 substrates.
research papers
Structural and electronic properties of Mo-decorated graphene, reduced graphene and reduced graphene oxide: a DFT calculation
The possible energies of different active adsorption sites of Mo-doped symmetric reduced graphene (rG), Mo-decorated graphene, asymmetric reduced graphene and reduced graphene oxide (rGO) nanostructured have been calculated using density functional theory. Covalent interactions between Mo and rG/rGO structures resulted in adsorption bonding, enhancing electrical conductivity and making them ideal for eliminating pollutants.
research papers
A correction procedure for secondary scattering contributions from windows in small-angle X-ray scattering and ultra small angle X-ray scattering
The high scattering power of a sample at low angles may lead to significant secondary scattering contributions in the measured SAXS/USAXS patterns. A correction procedure is presented for the removal of the excess intensity and to improve the dynamic range of the measurement.
research papers
computer programs
iRing: a program for two-dimensional powder diffraction image integration with automatic calibration
iRing is a processing program that utilizes the Hough transform to automate peak finding and calibration, greatly improving the speed and ease of calibrating two-dimensional diffraction images collected by image detectors.
research papers
Laue microdiffraction on polycrystalline samples above 1500 K thanks to the QMAX-µLaue furnace
A unique X-ray Laue microdiffraction setup and alignment procedure allowing measurements of microstructure and strain field in polycrystalline specimens at temperatures as high as 1500 K has been developed at beamline BM32, ESRF, making use of a new version of the QMAX furnace.
research papers
computer programs
more ...
Journal of Synchrotron Radiation Journal of Synchrotron Radiation |
research papers
Modelling the power threshold and optimum thermal deformation of indirectly liquid nitrogen cryo-cooled Si monochromators
A robust theoretical analysis of thermal management of cryo-cooled Si monochromators in hard X-ray beamlines is developed. This universal theory has been validated by extensive finite element analysis studies, offering guidances to assess the heatload deformation quickly.
research papers
beamlines
Scattered high-energy synchrotron radiation at the KARA visible-light diagnostic beamline
High-energy scattered synchrotron radiation at the visible-light diagnostics beamline at KARA (Karlsruhe Research Accelerator) and consequences for the future design of beamlines and radiation shielding as accelerators, beamlines and methods/techniques develop are presented.
beamlines
A sub-100 nm thickness flat jet for extreme ultraviolet to soft X-ray absorption spectroscopy
In this article we report the commissioning of the liquid-flat-jet setup that is available from now on at the Elettra synchrotron and FERMI free electron laser. The setup will allow to perform (time resolved-) spectroscopy measurements in liquid environment in virtually any open-end beamline at Elettra and FERMI
research papers
High-pressure X-ray photon correlation spectroscopy at fourth-generation synchrotron sources
The development of an experimental setup to probe the dynamics of complex systems under high pressure in the GPa regime is presented. Feasibility is demonstrated on metallic systems both in glassy and super-cooled liquid states.
research papers
Increased spatial coherence length from an asymmetric crystal reflection at grazing exit
A multiple crystal diffraction arrangement with a final asymmetric crystal diffracting at grazing exit was found to yield a 76% longer spatial coherence length compared with that for a beam directly exiting a double-crystal monochromator.
beamlines
VerSoX B07-B: a high-throughput XPS and ambient pressure NEXAFS beamline at Diamond Light Source
This manuscript describes a new beamline for soft X-ray spectroscopy – VerSoX B07-B – at Diamond Light Source, UK. The beamline is designed to accommodate a wide range of sample environments and measurement conditions ranging from ultrahigh vacuum to in situ liquid studies.
beamlines
research papers
Efficient end-to-end simulation of time-dependent coherent X-ray scattering experiments
End-to-end simulation of time-dependent partially coherent X-ray scattering experiments is demonstrated with SRW code. A coherent-mode decomposition and GPU acceleration recently implemented in the code make such simulations feasible and efficient for a typical XPCS experiment at a storage ring light source. This enables more detailed tests and optimization of experimental configurations and data processing prior to beam time as well as understanding experimental data.
research papers
more ...
research papers
The ABC toxin complex from Yersinia entomophaga can package three different cytotoxic components expressed from distinct genetic loci in an unfolded state: the structures of both shell and cargo
A cytotoxin encoded by an `orphan' genetic locus in the insect pathogen Yersinia entomophaga is shown to be a functional part of an ABC toxin complex, and the structures of both the RHS-repeat-containing `shell' and the free toxin alone are determined by X-ray crystallography. The structure of the toxin indicates that it most likely functions by directly modifying actin in the target cell.
research papers
Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure
X-ray absorption spectroscopy-electrochemical cell was used to collect high-quality X-ray absorption spectroscopy measurements of N-truncated Cu:amyloid-β samples under near-physiological conditions. The geometry of binding sites for the copper binding in Aβ(4–8/12/16) and the ability of these peptides to perform redox cycles in a manner that might produce toxicity in human brains were determined.
research papers
Dynamical refinement with multipolar electron scattering factors
Transferable aspherical atom model dynamical refinement on precession electron diffraction data for 1-methyluracil crystals offers superior performance compared with the independent atom model and reveals that the quality of 3D electron diffraction data and dynamical refinement is already sufficient to detect minute variations of the electrostatic potential caused by bonding and intermolecular interactions.
IUCrData IUCrData |
data reports (HM)
Poly[(μ-2,3-diethyl-7,8-dimethylquinoxaline-κ2N:N)(2,3-diethyl-7,8-dimethylquinoxaline-κN)-μ-nitrato-κ2O:O′-nitrato-κ2O,O′-disilver(I)]
The structure of the title compound, [Ag2(NO3)2(C14H18N2)2]n, contains subtle differences in ligand, metal, and counter-anion coordination. One quinoxaline ligand uses one of its quinoxaline N atoms to bond to one silver cation. That silver cation is bound to a second quinoxaline which, in turn, is bound to a second silver atom, thereby using both of its quinoxaline N atoms. A nitrate group bonds with one of its O atoms to the first silver and uses the same oxygen to bond to a silver atom (related by symmetry to the second), thereby forming an extended network. The second nitrate group on the other silver bonds via two nitrate O atoms; one silver cation therefore has a coordination number of three whereas the second has a coordination number of four.
data reports (HM)
trans-Dibromidotetrakis(5-methyl-1H-pyrazole-κN2)manganese(II)
The title compound was synthesized using Mn(CO)5Br. The manganese atom is situated on a crystallographic inversion center. The supramolecular architecture is characterized by several intermolecular C—H⋯N, N—H⋯Br and C—H⋯π interactions.
data reports (HO)
data reports (HM)
2-Ferrocenyl-2-[(2-ferrocenylethenyl)(morpholin-4-yl)methyl]-1,3-dithiolane
The structure of 2-ferrocenyl-2-[(2-ferrocenylethenyl)(morpholin-4-yl)methyl]-1,3-dithiolane, is described. In the crystal, cyclopentadienyl-C—H⋯O(morpholinyl) interactions feature within helical chains parallel to the c-axis direction. The chains are connected by methylene- and cyclopentadienyl-C—H⋯O(cyclopentadienyl) interactions.
data reports (HO)
data reports (HO)