pp Poly[tris(2-aminobutan-1-ol)copper(II) [hexakis-μ2-cyanido-κ12C:N-tetracopper(I)] bis(2-aminobutan-1-olato)aquacopper(II) monohydrate] By journals.iucr.org Published On :: 2024-08-30 The title structure, {[Cu(C4H11NO)3][Cu4(CN)6]·[Cu(C4H10NO)2(H2O)]·H2O}n, is made up of diperiodic honeycomb CuICN networks built from [Cu4(CN)6]2− units, together with two independent CuII complexes: six-coordinate [Cu(CH3CH2CH(NH2)CH2OH)3]2+ cations, and five-coordinate [Cu(CH3CH2CH(NH2)CH2O)2·H2O] neutral species. The two CuII complexes are not covalently bonded to the CuICN networks. Strong O—H⋯O hydrogen bonds link the CuII complexes into pairs and the pairs are hydrogen bonded into chains along the crystallographic b axis via the hydrate water molecule. In addition, O—H⋯(CN) and N—H⋯(CN) hydrogen bonds link the cations to the CuCN network. In the honeycomb polymeric moiety, all bridging cyanido ligands are disordered over two orientations, head-to-tail and tail-to-head, with occupancies for C and N atoms varying for each CN group. Full Article text
pp Crystal structures, electron spin resonance, and thermogravimetric analysis of three mixed-valence copper cyanide polymers By journals.iucr.org Published On :: 2024-05-01 The crystal structures of three mixed-valence copper cyanide alkanolamine polymers are presented, together with thermogravimetric analysis (TGA) and electron spin resonance (ESR) data. In all three structures, a CuII moiety on a crystallographic center of symmetry is coordinated by two alkanolamines and links two CuICN chains via cyanide bridging groups to form diperiodic sheets. The sheets are linked together by cuprophilic CuI–CuI interactions to form a three-dimensional network. In poly[bis(μ-3-aminopropanolato)tetra-μ-cyanido-dicopper(I)dicopper(II)], [Cu4(CN)4(C3H8NO)2]n, 1, propanolamine bases have lost their hydroxyl H atoms and coordinate as chelates to two CuII atoms to form a dimeric CuII moiety bridged by the O atoms of the bases with CuII atoms in square-planar coordination. The ESR spectrum is very broad, indicating exchange between the two CuII centers. In poly[bis(2-aminopropanol)tetra-μ-cyanido-dicopper(I)copper(II)], [Cu3(CN)4(C3H9NO)2]n, 2, and poly[bis(2-aminoethanol)tetra-μ-cyanido-dicopper(I)copper(II)], [Cu3(CN)4(CH7NO)2]n, 3, a single CuII atom links the CuICN chains together via CN bridges. The chelating alkanolamines are not ionized, and the OH groups form rather long bonds in the axial positions of the octahedrally coordinated CuII atoms. The coordination geometries of CuII in 2 and 3 are almost identical, except that the Cu—O distances are longer in 2 than in 3, which may explain their somewhat different ESR spectra. Thermal decomposition in 2 and 3, but not in 1, begins with the loss of HCN(g), and this can be correlated with the presence of OH protons on the ligands in 2 and 3, which are not present in 1. Full Article text
pp Applying 3D ED/MicroED workflows toward the next frontiers By journals.iucr.org Published On :: 2024-05-07 We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation. Full Article text
pp Supramolecular hydrogen-bonded networks formed from copper(II) carboxylate dimers By journals.iucr.org Published On :: 2024-05-22 The well-known copper carboxylate dimer, with four carboxylate ligands extending outwards towards the corners of a square, has been employed to generate a series of crystalline compounds. In particular, this work centres on the use of the 4-hydroxybenzoate anion (Hhba−) and its deprotonated phenolate form 4-oxidobenzoate (hba2−) to obtain complexes with the general formula [Cu2(Hhba)4–x(hba)xL2–y]x−, where L is an axial coligand (including solvent molecules), x = 0, 1 or 2, and y = 0 or 1. In some cases, short hydrogen bonds result in complexes which may be represented as [Cu2(Hhba)2(H0.5hba)2L2]−. The main focus of the investigation is on the formation of a variety of extended networks through hydrogen bonding and, in some crystals, coordinate bonds when bridging coligands (L) are employed. Crystals of [Cu2(Hhba)4(dioxane)2]·4(dioxane) consist of the expected Cu dimer with the Hhba− anions forming hydrogen bonds to 1,4-dioxane molecules which block network formation. In the case of crystals of composition [Et4N][Cu2(Hhba)2(H0.5hba)2(CH3OH)(H2O)]·2(dioxane), Li[Cu2(Hhba)2(H0.5hba)2(H2O)2]·3(dioxane)·4H2O and [Cu2(Hhba)2(H0.5hba)2(H0.5DABCO)2]·3CH3OH (DABCO is 1,4-diazabicyclo[2.2.2]octane), square-grid hydrogen-bonded networks are generated in which the complex serves as one type of 4-connecting node, whilst a second 4-connecting node is a hydrogen-bonding motif assembled from four phenol/phenolate groups. Another two-dimensional (2D) network based upon a related square-grid structure is formed in the case of [Et4N]2[Cu2(Hhba)2(hba)2(dioxane)2][Cu2(Hhba)4(dioxane)(H2O)]·CH3OH. In [Cu2(Hhba)4(H2O)2]·2(Et4NNO3), a square-grid structure is again apparent, but, in this case, a pair of nitrate anions, along with four phenolic groups and a pair of water molecules, combine to form a second type of 4-connecting node. When 1,8-bis(dimethylamino)naphthalene (bdn, `proton sponge') is used as a base, another square-grid network is generated, i.e. [Hbdn]2[Cu2(Hhba)2(hba)2(H2O)2]·3(dioxane)·H2O, but with only the copper dimer complex serving as a 4-connecting node. Complex three-dimensional networks are formed in [Cu2(Hhba)4(O-bipy)]·H2O and [Cu2(Hhba)4(O-bipy)2]·2(dioxane), where the potentially bridging 4,4'-bipyridine N,N'-dioxide (O-bipy) ligand is employed. Rare cases of mixed carboxylate copper dimer complexes were obtained in the cases of [Cu2(Hhba)3(OAc)(dioxane)]·3.5(dioxane) and [Cu2(Hhba)2(OAc)2(DABCO)2]·10(dioxane), with each structure possessing a 2D network structure. The final compound reported is a simple hydrogen-bonded chain of composition (H0.5DABCO)(H1.5hba), formed from the reaction of H2hba and DABCO. Full Article text
pp Synthesis, spectroscopic and crystallographic characterization of various cymantrenyl thioethers [Mn{C5HxBry(SMe)z}(PPh3)(CO)2] By journals.iucr.org Published On :: 2024-07-05 Starting from [Mn(C5H4Br)(PPh3)(CO)2] (1a), the cymantrenyl thioethers [Mn(C5H4SMe)(PPh3)(CO)2] (1b) and [Mn{C5H4–nBr(SMe)n}(PPh3)(CO)2] (n = 1 for compound 2, n = 2 for 3 and n = 3 for 4) were obtained, using either n-butyllithium (n-BuLi), lithium diisopropylamide (LDA) or lithium tetramethylpiperidide (LiTMP) as base, followed by electrophilic quenching with MeSSMe. Stepwise consecutive reaction of [Mn(C5Br5)(PPh3)(CO)2] with n-BuLi and MeSSMe led finally to [Mn{C5(SMe)5}(PPh3)(CO)2] (11), only the fifth complex to be reported containing a perthiolated cyclopentadienyl ring. The molecular and crystal structures of 1b, 3, 4 and 11 were determined and were studied for the occurrence of S⋯S and S⋯Br interactions. It turned out that although some interactions of this type occurred, they were of minor importance for the arrangement of the molecules in the crystal. Full Article text
pp Synthesis of organotin(IV) heterocycles containing a xanthenyl group by a Barbier approach via ultrasound activation: synthesis, crystal structure and Hirshfeld surface analysis By journals.iucr.org Published On :: 2024-07-25 A series of organotin heterocycles of general formula [{Me2C(C6H3CH2)2O}SnR2] [R = methyl (Me, 4), n-butyl (n-Bu, 5), benzyl (Bn, 6) and phenyl (Ph, 7)] was easily synthesized by a Barbier-type reaction assisted by the sonochemical activation of metallic magnesium. The 119Sn{1H} NMR data for all four compounds confirm the presence of a central Sn atom in a four-coordinated environment in solution. Single-crystal X-ray diffraction studies for 17,17-dimethyl-7,7-diphenyl-15-oxa-7-stannatetracyclo[11.3.1.05,16.09,14]heptadeca-1,3,5(16),9(14),10,12-hexaene, [Sn(C6H5)2(C17H16O)], 7, at 100 and 295 K confirmed the formation of a mononuclear eight-membered heterocycle, with a conformation depicted as boat–chair, resulting in a weak Sn⋯O interaction. The Sn and O atoms are surrounded by hydrophobic C—H bonds. A Hirshfeld surface analysis of 7 showed that the eight-membered heterocycles are linked by weak C—H⋯π, π–π and H⋯H noncovalent interactions. The pairwise interaction energies showed that the cohesion between the heterocycles are mainly due to dispersion forces. Full Article text
pp Coordination structure and intermolecular interactions in copper(II) acetate complexes with 1,10-phenanthroline and 2,2'-bipyridine By journals.iucr.org Published On :: 2024-08-23 The crystal structures of two coordination compounds, (acetato-κO)(2,2'-bipyridine-κ2N,N')(1,10-phenanthroline-κ2N,N')copper(II) acetate hexahydrate, [Cu(C2H3O2)(C10H8N2)(C12H8N2)](C2H3O2)·6H2O or [Cu(bipy)(phen)Ac]Ac·6H2O, and (acetato-κO)bis(2,2'-bipyridine-κ2N,N')copper(II) acetate–acetic acid–water (1/1/3), [Cu(C2H3O2)(C10H8N2)2](C2H3O2)·C2H4O2·3H2O or [Cu(bipy)2Ac]Ac·HAc·3H2O, are reported and compared with the previously published structure of [Cu(phen)2Ac]Ac·7H2O (phen is 1,10-phenanthroline, bipy for 2,2'-bipyridine, ac is acetate and Hac is acetic acid). The geometry around the metal centre is pentacoordinated, but highly distorted in all three cases. The coordination number and the geometric distortion are both discussed in detail, and all complexes belong to the space group Poverline{1}. The analysis of the geometric parameters and the Hirshfeld surface properties dnorm and curvedness provide information about the metal–ligand interactions in these complexes and allow comparison with similar systems. Full Article text
pp A service-based approach to cryoEM facility processing pipelines at eBIC By journals.iucr.org Published On :: 2024-02-20 Electron cryo-microscopy image-processing workflows are typically composed of elements that may, broadly speaking, be categorized as high-throughput workloads which transition to high-performance workloads as preprocessed data are aggregated. The high-throughput elements are of particular importance in the context of live processing, where an optimal response is highly coupled to the temporal profile of the data collection. In other words, each movie should be processed as quickly as possible at the earliest opportunity. The high level of disconnected parallelization in the high-throughput problem directly allows a completely scalable solution across a distributed computer system, with the only technical obstacle being an efficient and reliable implementation. The cloud computing frameworks primarily developed for the deployment of high-availability web applications provide an environment with a number of appealing features for such high-throughput processing tasks. Here, an implementation of an early-stage processing pipeline for electron cryotomography experiments using a service-based architecture deployed on a Kubernetes cluster is discussed in order to demonstrate the benefits of this approach and how it may be extended to scenarios of considerably increased complexity. Full Article text
pp Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection By journals.iucr.org Published On :: 2024-06-04 The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields. Full Article text
pp Structural analysis of a ligand-triggered intermolecular disulfide switch in a major latex protein from opium poppy By journals.iucr.org Published On :: 2024-08-29 Several proteins from plant pathogenesis-related family 10 (PR10) are highly abundant in the latex of opium poppy and have recently been shown to play diverse and important roles in the biosynthesis of benzylisoquinoline alkaloids (BIAs). The recent determination of the first crystal structures of PR10-10 showed how large conformational changes in a surface loop and adjacent β-strand are coupled to the binding of BIA compounds to the central hydrophobic binding pocket. A more detailed analysis of these conformational changes is now reported to further clarify how ligand binding is coupled to the formation and cleavage of an intermolecular disulfide bond that is only sterically allowed when the BIA binding pocket is empty. To decouple ligand binding from disulfide-bond formation, each of the two highly conserved cysteine residues (Cys59 and Cys155) in PR10-10 was replaced with serine using site-directed mutagenesis. Crystal structures of the Cys59Ser mutant were determined in the presence of papaverine and in the absence of exogenous BIA compounds. A crystal structure of the Cys155Ser mutant was also determined in the absence of exogenous BIA compounds. All three of these crystal structures reveal conformations similar to that of wild-type PR10-10 with bound BIA compounds. In the absence of exogenous BIA compounds, the Cys59Ser and Cys155Ser mutants appear to bind an unidentified ligand or mixture of ligands that was presumably introduced during expression of the proteins in Escherichia coli. The analysis of conformational changes triggered by the binding of BIA compounds suggests a molecular mechanism coupling ligand binding to the disruption of an intermolecular disulfide bond. This mechanism may be involved in the regulation of biosynthetic reactions in plants and possibly other organisms. Full Article text
pp Comparison of two crystal polymorphs of NowGFP reveals a new conformational state trapped by crystal packing By journals.iucr.org Published On :: 2024-09-02 Crystal polymorphism serves as a strategy to study the conformational flexibility of proteins. However, the relationship between protein crystal packing and protein conformation often remains elusive. In this study, two distinct crystal forms of a green fluorescent protein variant, NowGFP, are compared: a previously identified monoclinic form (space group C2) and a newly discovered orthorhombic form (space group P212121). Comparative analysis reveals that both crystal forms exhibit nearly identical linear assemblies of NowGFP molecules interconnected through similar crystal contacts. However, a notable difference lies in the stacking of these assemblies: parallel in the monoclinic form and perpendicular in the orthorhombic form. This distinct mode of stacking leads to different crystal contacts and induces structural alteration in one of the two molecules within the asymmetric unit of the orthorhombic crystal form. This new conformational state captured by orthorhombic crystal packing exhibits two unique features: a conformational shift of the β-barrel scaffold and a restriction of pH-dependent shifts of the key residue Lys61, which is crucial for the pH-dependent spectral shift of this protein. These findings demonstrate a clear connection between crystal packing and alternative conformational states of proteins, providing insights into how structural variations influence the function of fluorescent proteins. Full Article text
pp Cocrystals of a coumarin derivative: an efficient approach towards anti-leishmanial cocrystals against MIL-resistant Leishmania tropica By journals.iucr.org Published On :: 2024-03-01 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. Pharmaceutical cocrystallization is an effective method to improve the physicochemical and biological properties of active pharmaceutical ingredients (APIs). Herein, we describe the cocrystallization of coumarin-3-carboxylic acid (CU, 1a; 2-oxobenzopyrane-3-carboxylic acid, C10H6O4) with five coformers [2-amino-3-bromopyridine (1b), 2-amino-5-(trifluoromethyl)-pyridine (1c), 2-amino-6-methylpyridine (1d), p-aminobenzoic acid (1e) and amitrole (1f)] in a 1:1 stoichiometric ratio via the neat grinding method. The cocrystals 2–6 obtained were characterized via single-crystal X-ray diffraction, powder X-ray diffraction, differential scanning calorimetry and thermogravimetric analysis, as well as Fourier transform infrared spectroscopy. Non-covalent interactions, such as van der Waals, hydrogen bonding, C—H⋯π and π⋯π interactions contribute significantly towards the packing of a crystal structure and alter the physicochemical and biological activity of CU. In this research, newly synthesized cocrystals were evaluated for their anti-leishmanial activity against the MIL-resistant L. tropica and cytotoxicity against the 3T3 (normal fibroblast) cell line. Among the non-cytotoxic cocrystals synthesized (2–6), CU:1b (2, IC50 = 61.83 ± 0.59 µM), CU:1c (3, 125.7 ± 1.15 µM) and CU:1d (4, 48.71 ± 0.75 µM) appeared to be potent anti-leishmanial agents and showed several-fold more anti-leishmanial potential than the tested standard drug (MIL, IC50 = 169.55 ± 0.078 µM). The results indicate that cocrystals 2–4 are promising anti-leishmanial agents which require further exploration. Full Article text
pp Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure By journals.iucr.org Published On :: 2024-04-11 An X-ray absorption spectroscopy (XAS) electrochemical cell was used to collect high-quality XAS measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. N-truncated Cu:Aβ peptide complexes contribute to oxidative stress and neurotoxicity in Alzheimer's patients' brains. However, the redox properties of copper in different Aβ peptide sequences are inconsistent. Therefore, the geometry of binding sites for the copper binding in Aβ4–8/12/16 was determined using novel advanced extended X-ray absorption fine structure (EXAFS) analysis. This enables these peptides to perform redox cycles in a manner that might produce toxicity in human brains. Fluorescence XAS measurements were corrected for systematic errors including defective-pixel data, monochromator glitches and dispersion of pixel spectra. Experimental uncertainties at each data point were measured explicitly from the point-wise variance of corrected pixel measurements. The copper-binding environments of Aβ4–8/12/16 were precisely determined by fitting XAS measurements with propagated experimental uncertainties, advanced analysis and hypothesis testing, providing a mechanism to pursue many similarly complex questions in bioscience. The low-temperature XAS measurements here determine that CuII is bound to the first amino acids in the high-affinity amino-terminal copper and nickel (ATCUN) binding motif with an oxygen in a tetragonal pyramid geometry in the Aβ4–8/12/16 peptides. Room-temperature XAS electrochemical-cell measurements observe metal reduction in the Aβ4–16 peptide. Robust investigations of XAS provide structural details of CuII binding with a very different bis-His motif and a water oxygen in a quasi-tetrahedral geometry. Oxidized XAS measurements of Aβ4–12/16 imply that both CuII and CuIII are accommodated in an ATCUN-like binding site. Hypotheses for these CuI, CuII and CuIII geometries were proven and disproven using the novel data and statistical analysis including F tests. Structural parameters were determined with an accuracy some tenfold better than literature claims of past work. A new protocol was also developed using EXAFS data analysis for monitoring radiation damage. This gives a template for advanced analysis of complex biosystems. Full Article text
pp RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures By journals.iucr.org Published On :: 2024-04-10 The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations. Full Article text
pp Structural characterization of TIR-domain signalosomes through a combination of structural biology approaches By journals.iucr.org Published On :: 2024-08-27 The TIR (Toll/interleukin-1 receptor) domain represents a vital structural element shared by proteins with roles in immunity signalling pathways across phyla (from humans and plants to bacteria). Decades of research have finally led to identifying the key features of the molecular basis of signalling by these domains, including the formation of open-ended (filamentous) assemblies (responsible for the signalling by cooperative assembly formation mechanism, SCAF) and enzymatic activities involving the cleavage of nucleotides. We present a historical perspective of the research that led to this understanding, highlighting the roles that different structural methods played in this process: X-ray crystallography (including serial crystallography), microED (micro-crystal electron diffraction), NMR (nuclear magnetic resonance) spectroscopy and cryo-EM (cryogenic electron microscopy) involving helical reconstruction and single-particle analysis. This perspective emphasizes the complementarity of different structural approaches. Full Article text
pp Crossing length scales: X-ray approaches to studying the structure of biological materials By journals.iucr.org Published On :: 2024-08-28 Biological materials have outstanding properties. With ease, challenging mechanical, optical or electrical properties are realised from comparatively `humble' building blocks. The key strategy to realise these properties is through extensive hierarchical structuring of the material from the millimetre to the nanometre scale in 3D. Though hierarchical structuring in biological materials has long been recognized, the 3D characterization of such structures remains a challenge. To understand the behaviour of materials, multimodal and multi-scale characterization approaches are needed. In this review, we outline current X-ray analysis approaches using the structures of bone and shells as examples. We show how recent advances have aided our understanding of hierarchical structures and their functions, and how these could be exploited for future research directions. We also discuss current roadblocks including radiation damage, data quantity and sample preparation, as well as strategies to address them. Full Article text
pp Elastic and inelastic strain in submicron-thick ZnO epilayers grown on r-sapphire substrates by metal–organic vapour phase deposition By journals.iucr.org Published On :: 2024-02-13 A significant part of the present and future of optoelectronic devices lies on thin multilayer heterostructures. Their optical properties depend strongly on strain, being essential to the knowledge of the stress level to optimize the growth process. Here the structural and microstructural characteristics of sub-micron a-ZnO epilayers (12 to 770 nm) grown on r-sapphire by metal–organic chemical vapour deposition are studied. Morphological and structural studies have been made using scanning electron microscopy and high-resolution X-ray diffraction. Plastic unit-cell distortion and corresponding strain have been determined as a function of film thickness. A critical thickness has been observed as separating the non-elastic/elastic states with an experimental value of 150–200 nm. This behaviour has been confirmed from ultraviolet photoelectron spectroscopy, X-ray photoelectron spectroscopy and high-resolution transmission electron microscopy measurements. An equation that gives the balance of strains is proposed as an interesting method to experimentally determine this critical thickness. It is concluded that in the thinnest films an elongation of the Zn—O bond takes place and that the plastic strained ZnO films relax through nucleation of misfit dislocations, which is a consequence of three-dimensional surface morphology. Full Article text
pp Solvatomorphism in a series of copper(II) complexes with the 5-phenylimidazole/perchlorate system as ligands By journals.iucr.org Published On :: 2024-07-30 In the course of an investigation of the supramolecular behaviour of copper(II) complexes with the 5-phenylimidazole/perchlorate ligand system (`blend') remarkable solvatomorphism has been observed. By employing a variety of crystallization solvents (polar protic, polar/non-polar aprotic), a series of 12 crystalline solvatomorphs with the general formula [Cu(ClO4)2(LH)4]·x(solvent) have been obtained [LH = 5-phenylimidazole, x(solvent) = 3.3(H2O) (1), 2(methanol) (2), 2(ethanol) (3), 2(1-propanol) (4), 2(2-propanol) (5), 2(2-butanol) (6), 2(dimethylformamide) (7), 2(acetone) (8), 2(tetrahydrofurane) (9), 2(1,4-dioxane) (10), 2(ethyl acetate) (11) and 1(diethyl ether) (12)]. The structures have been solved using single-crystal X-ray diffraction and the complexes were characterized by thermal analysis and infrared spectroscopy. The solvatomorphs are isostructural (triclinic, P1), with the exception of compound 9 (monoclinic, P21/n). The supramolecular structures and the role of the various solvents is discussed. All potential hydrogen-bond functionalities, both of the [Cu(ClO4)2(LH)4] units and of the solvents, are utilized in the course of the crystallization process. The supramolecular assembly in all structures is directed by strong recurring Nimidazole–H⋯Operchlorate motifs leading to robust scaffolds composed of the [Cu(ClO4)2(LH)4] host complexes. The solvents are located in channels and, with the exception of the disordered waters in 1 and the diethyl ether in 12, participate in hydrogen-bonding formation with the [Cu(ClO4)2(LH)4] complexes, serving as both hydrogen-bond acceptors and donors (for the polar protic solvents in 2–6), or solely as hydrogen-bond acceptors (for the polar/non-polar aprotic solvents in 7–11), linking the complexes and contributing to the stability of the crystalline compounds. Full Article text
pp Importance of powder diffraction raw data archival in a curated database for materials science applications By journals.iucr.org Published On :: 2024-08-26 In recent years, there is a significant interest from the crystallographic and materials science communities to have access to raw diffraction data. The effort in archiving raw data for access by the user community is spearheaded by the International Union of Crystallography (IUCr) Committee on Data. In materials science, where powder diffraction is extensively used, the challenge in archiving raw data is different to that from single crystal data, owing to the very nature of the contributions involved. Powder diffraction (X-ray or neutron) data consist of contributions from the material under study as well as instrument specific parameters. Having raw powder diffraction data can be essential in cases of analysing materials with poor crystallinity, disorder, micro structure (size/strain) etc. Here, the initiative and progress made by the International Centre for Diffraction Data (ICDDR) in archiving powder X-ray diffraction raw data in the Powder Diffraction FileTM (PDFR) database is outlined. The upcoming 2025 release of the PDF-5+ database will have more than 20 800 raw powder diffraction patterns that are available for reference. Full Article text
pp Magnetic space groups versus representation analysis in the investigation of magnetic structures: the happy end of a strained relationship By journals.iucr.org Published On :: 2024-09-10 In recent decades, sustained theoretical and software developments have clearly established that representation analysis and magnetic symmetry groups are complementary concepts that should be used together in the investigation and description of magnetic structures. Historically, they were considered alternative approaches, but currently, magnetic space groups and magnetic superspace groups can be routinely used together with representation analysis, aided by state-of-the-art software tools. After exploring the historical antagonism between these two approaches, we emphasize the significant advancements made in understanding and formally describing magnetic structures by embracing their combined use. Full Article text
pp New copper carboxylate pyrene dimers: synthesis, crystal structure, Hirshfeld surface analysis and electrochemical characterization By journals.iucr.org Published On :: 2024-01-01 Two new copper dimers, namely, bis(dimethyl sulfoxide)tetrakis(μ-pyrene-1-carboxylato)dicopper(Cu—Cu), [Cu2(C17H9O2)4(C2H6OS)2] or [Cu2(pyr-COO−)4(DMSO)2] (1), and bis(dimethylformamide)tetrakis(μ-pyrene-1-carboxylato)dicopper(Cu—Cu), [Cu2(C17H9O2)4(C3H7NO)2] or [Cu2(pyr-COO−)4(DMF)2] (2) (pyr = pyrene), were synthesized from the reaction of pyrene-1-carboxylic acid, copper(II) nitrate and triethylamine from solvents DMSO and DMF, respectively. While 1 crystallized in the space group Poverline{1}, the crystal structure of 2 is in space group P21/n. The Cu atoms have octahedral geometries, with four oxygen atoms from carboxylate pyrene ligands occupying the equatorial positions, a solvent molecule coordinating at one of the axial positions, and a Cu⋯Cu contact in the opposite position. The packing in the crystal structures exhibits π–π stacking interactions and short contacts through the solvent molecules. The Hirshfeld surfaces and two-dimensional fingerprint plots were generated for both compounds to better understand the intermolecular interactions and the contribution of heteroatoms from the solvent ligands to the crystal packing. In addition, a Cu2+/Cu1+ quasi-reversible redox process was identified for compound 2 using cyclic voltammetry that accounts for a diffusion-controlled electron-donation process to the Cu dimer. Full Article text
pp Crystal structure and Hirshfeld-surface analysis of diaquabis(5-methyl-1H-1,2,4-triazole-3-carboxylato)copper(II) By journals.iucr.org Published On :: 2024-01-01 The title compound, [Cu(HL)2(H2O)2] or [Cu(C4H4N3O2)2(H2O)2], is a mononuclear octahedral CuII complex based on 5-methyl-1H-1,2,4-triazole-3-carboxylic acid (H2L). [Cu(HL)2(H2O)2] was synthesized by reaction of H2L with copper(II) nitrate hexahydrate (2:1 stoichiometric ratio) in water under ambient conditions to produce clear light-blue crystals. The central Cu atom exhibits an N2O4 coordination environment in an elongated octahedral geometry provided by two bidentate HL− anions in the equatorial plane and two water molecules in the axial positions. Hirshfeld surface analysis revealed that the most important contributions to the surface contacts are from H⋯O/O⋯H (33.1%), H⋯H (29.5%) and H⋯N/N⋯H (19.3%) interactions. Full Article text
pp Crystal structure of poly[hexa-μ-bromido-bis{2-[1-(pyridin-2-yl)ethylideneamino]ethanolato}tetracopper(II)] By journals.iucr.org Published On :: 2024-01-12 The reaction of the Schiff base 2-[1-(pyridin-2-yl)ethylideneamino]ethanol (HL), which is formed by reaction of 2-aminoethanol and 2-acetylpyridine with CuBr2 in ethanol results in the isolation of the new polymeric complex poly[hexa-μ-bromido-bis{2-[1-(pyridin-2-yl)ethylideneamino]ethanolato}tetracopper(II)], [Cu4Br6(C9H11N2O)2]n or [Cu4Br6L2]n. The asymmetric unit of the crystal structure of the polymeric [Cu4Br6L2]n complex is composed by four copper (II) cations, two monodeprotonated molecules of the ligand, and six bromide anions, which act as bridges. The ligand molecules act in a tridentate fashion through their azomethine nitrogen atoms, their pyridine nitrogen atoms, and their alcoholate O atoms. The crystal structure shows two types of geometries in the coordination polyhedrons around Cu2+ ions. Two copper cations are situated in a square-based pyramidal environment, while the two other copper cations adopt a tetrahedral geometry. Bromides anions acting as bridges between two metal ions connect the units, resulting in a tetranuclear polymer compound. Full Article text
pp Crystal structure and characterization of a new one-dimensional copper(II) coordination polymer containing a 4-aminobenzoic acid ligand By journals.iucr.org Published On :: 2024-02-20 A CuII coordination polymer, catena-poly[[[aquacopper(II)]-bis(μ-4-aminobenzoato)-κ2N:O;κ2O:N] monohydrate], {[Cu(pABA)2(H2O)]·H2O}n (pABA = p-aminobenzoate, C7H4NO2−), was synthesized and characterized. It exhibits a one-dimensional chain structure extended into a three-dimensional supramolecular assembly through hydrogen bonds and π–π interactions. While the twinned crystal shows a metrically orthorhombic lattice and an apparent space group Pbcm, the true symmetry is monoclinic (space group P2/c), with disordered Cu atoms and mixed roles of water molecules (aqua ligand/crystallization water). The luminescence spectrum of the complex shows an emission at 345 nm, cf. 349 nm for pABAH. Full Article text
pp Crystal structure of tetrakis(μ-2-hydroxy-3,5-diisopropylbenzoato)bis[(dimethyl sulfoxide)copper(II)] By journals.iucr.org Published On :: 2024-02-27 Metal complexes of 3,5-diisopropylsalicylate are reported to have anti-inflammatory and anti-convulsant activities. The title binuclear copper complex, [Cu2(C13H17O3)4(C2H6OS)2] or [Cu(II)2(3,5-DIPS)4(DMSO)2], contains two five-coordinate copper atoms that are bridged by four 3,5-diisopropylsalicylate ligands and capped by two axial dimethyl sulfoxide (DMSO) moieties. Each copper atom is attached to four oxygen atoms in an almost square-planar fashion, with the addition of a DMSO ligand in an apical position leading to a square-pyramidal arrangement. The hydroxy group of the diisopropylsalicylate ligands participates in intramolecular O—H⋯O hydrogen-bonding interactions. Full Article text
pp Crystal structure of tetraphenyl phosphate tetrakis[dimethyl (2,2,2-trichloroacetyl)phosphoramidato]lutetium(III), PPh4[LuL4] By journals.iucr.org Published On :: 2024-03-12 A lutetium(III) complex based on the anion of the ligand dimethyl (2,2,2-trichloroacetyl)phosphoramidate (HL) and tetraphenylphosphonium, of composition PPh4[LuL4] (L = CAPh = carbacylamidophosphate), or (C24H20)[Lu(C4H6Cl3NO4P)4], has been synthesized and structurally characterized. The X-ray diffraction study of the compound revealed that the lutetium ion is surrounded by four bis-chelating CAPh ligands, forming the complex anion [LuL4]− with a coordination number of 8[O] for LuIII, while PPh4+ serves as a counter-ion. The coordination geometry around the Lu3+ ion was determined to be a nearly perfect triangular dodecahedron. The complex crystallizes in the monoclinic crystal system, space group P21/c, with four molecules in the unit cell. Weak hydrogen bonds O⋯HC(Ph), Cl⋯HC(Ph) and N⋯HC(Ph) are formed between the cations and anions. For a comparative study, HL-based structures were retrieved from the Cambridge Structural Database (CSD) and their geometries and conformations are discussed. A Hirshfeld surface analysis was also performed. Full Article text
pp Synthesis, crystal structure and Hirshfeld surface analysis of bromidotetrakis[5-(prop-2-en-1-ylsulfanyl)-1,3,4-thiadiazol-2-amine-κN3]copper(II) bromide By journals.iucr.org Published On :: 2024-03-26 A novel cationic complex, bromidotetrakis[5-(prop-2-en-1-ylsulfanyl)-1,3,4-thiadiazol-2-amine-κN3]copper(II) bromide, [CuBr](C5H7N3S2)4Br, was synthesized. The complex crystallizes with fourfold molecular symmetry in the tetragonal space group P4/n. The CuII atom exhibits a square-pyramidal coordination geometry. The Cu atom is located centrally within the complex, being coordinated by four nitrogen atoms from four AAT molecules, while a bromine anion is located at the apex of the pyramid. The amino H atoms of AAT interact with bromine from the inner and outer spheres, forming a two-dimensional network in the [100] and [010] directions. Hirshfeld surface analysis reveals that 33.7% of the intermolecular interactions are from H⋯H contacts, 21.2% are from S⋯H/H⋯S contacts, 13.4% are from S⋯S contacts and 11.0% are from C⋯H/H⋯C, while other contributions are from Br⋯H/H⋯Br and N⋯H/H⋯N contacts. Full Article text
pp Crystal structure and Hirshfeld surface analysis of (1H-imidazole-κN3)[4-methyl-2-({[2-oxido-5-(2-phenyldiazen-1-yl)phenyl]methylidene}amino)pentanoate-κ3O,N,O']copper(II) By journals.iucr.org Published On :: 2024-04-11 The title copper(II) complex, [Cu(C18H19N3O3)(C3H4N2)], consists of a tridentate ligand synthesized from l-leucine and azobenzene-salicylaldehyde. One imidazole molecule is additionally coordinated to the copper(II) ion in the equatorial plane. The crystal structure features N—H⋯O hydrogen bonds. A Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H (52.0%) and C⋯H/H⋯C (17.9%) contacts. Full Article text
pp Crystal structure and Hirshfeld surface of a pentaaminecopper(II) complex with urea and chloride By journals.iucr.org Published On :: 2024-05-14 The reaction of copper(II) oxalate and hexamethylenetetramine in a deep eutectic solvent made of urea and choline chloride produced crystals of pentaaminecopper(II) dichloride–urea (1/1), [Cu(NH3)5]Cl2·CO(NH2)2, which was characterized by single-crystal X-ray diffraction. The complex contains discrete pentaaminecopper(II) units in a square-based pyramidal geometry. The overall structure of the multi-component crystal is dictated by hydrogen bonding between urea molecules and amine H atoms with chloride anions. Full Article text
pp Pyrazine-bridged polymetallic copper–iridium clusters By journals.iucr.org Published On :: 2024-07-27 Single crystals of the molecular compound, {Cu20Ir6Cl8(C21H24N2)6(C4H4N2)3]·3.18CH3OH or [({Cu10Ir3}Cl4(IMes)3(pyrazine))2(pyrazine)]·3.18CH3OH [where IMes is 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene], with a unique heterometallic cluster have been prepared and the structure revealed using single-crystal X-ray diffraction. The molecule is centrosymmetric with two {Cu10Ir3} cores bridged by a pyrazine ligand. The polymetallic cluster contains three stabilizing N-heterocyclic carbenes, four Cl ligands, and a non-bridging pyrazine ligand. Notably, the Cu—Ir core is arranged in an unusual shape containing 13 vertices, 22 faces, and 32 sides. The atoms within the tridecametallic cluster are arranged in four planes, with 2, 4, 4, 3 metals in each plane. Ir atoms are present in alternate planes with an Ir atom featuring in the peripheral bimetallic plane, and two Ir atoms featuring on opposite sides of the non-adjacent tetrametallic plane. The crystal contains two disordered methanol solvent molecules with an additional region of non-modelled electron density corrected for using the SQUEEZE routine in PLATON [Spek (2015). Acta Cryst. C71, 9–18]. The given chemical formula and other crystal data do not take into account the unmodelled methanol solvent molecule(s). Full Article text
pp Synthesis, crystal structure and Hirshfeld surface analysis of a new copper(II) complex based on diethyl 2,2'-(4H-1,2,4-triazole-3,5-diyl)diacetate By journals.iucr.org Published On :: 2024-08-30 The title compound, bis[μ-2,2'-(4H-1,2,4-triazole-3,5-diyl)diacetato]bis[diaquacopper(II)] dihydrate, [Cu2(C6H5N3O4)2(H2O)4]·2H2O, is a dinuclear octahedral CuII triazole-based complex. The central copper atoms are hexa-coordinated by two nitrogen atoms in the equatorial positions, two equatorial oxygen atoms of two carboxylate substituents in position 3 and 5 of the 1,2,4-triazole ring, and two axial oxygen atoms of two water molecules. Two additional solvent water molecules are linked to the title molecule by O—H⋯N and O⋯H—O hydrogen bonds. The crystal structure is built up from the parallel packing of discrete supramolecular chains running along the a-axis direction. Hirshfeld surface analysis suggests that the most important contributions to the surface contacts are from H⋯O/O⋯H (53.5%), H⋯H (28.1%), O⋯O (6.3%) and H⋯C/C⋯H (6.2%) interactions. The crystal studied was twinned by a twofold rotation around [100]. Full Article text
pp Crystal structure of a tris(2-aminoethyl)methane capped carbamoylmethylphosphine oxide compound By journals.iucr.org Published On :: 2024-08-30 The molecular structure of the tripodal carbamoylmethylphosphine oxide compound diethyl {[(5-[2-(diethoxyphosphoryl)acetamido]-3-{2-[2-(diethoxyphosphoryl)acetamido]ethyl}pentyl)carbamoyl]methyl}phosphonate, C25H52N3O12P3, features six intramolecular hydrogen-bonding interactions. The phosphonate groups have key bond lengths ranging from 1.4696 (12) to 1.4729 (12) Å (P=O), 1.5681 (11) to 1.5811 (12) Å (P—O) and 1.7881 (16) to 1.7936 (16) Å (P—C). Each amide group adopts a nearly perfect trans geometry, and the geometry around each phophorus atom resembles a slightly distorted tetrahedron. Full Article text
pp Synthesis and crystal structure of poly[[μ-chlorido-μ-(2,3-dimethylpyrazine)-copper(I)] ethanol hemisolvate], which shows a new isomeric CuCl(2,3-dimethylpyrazine) network By journals.iucr.org Published On :: 2024-09-24 Reaction of copper(I)chloride with 2,3-dimethylpyrazine in ethanol leads to the formation of the title compound, poly[[μ-chlorido-μ-(2,3-dimethylpyrazine)-copper(I)] ethanol hemisolvate], {[CuCl(C6H8N2)]·0.5C2H5OH}n or CuCl(2,3-dimethylpyrazine) ethanol hemisolvate. Its asymmetric unit consists of two crystallographically independent copper cations, two chloride anions and two 2,3-dimethylpyrazine ligands as well as one ethanol solvate molecule in general positions. The ethanol molecule is disordered and was refined using a split model. The methyl H atoms of the 2,3-dimethylpyrazine ligands are also disordered and were refined in two orientations rotated by 60° relative to each other. In the crystal structure, each copper cation is tetrahedrally coordinated by two N atoms of two bridging 2,3-dimethylpyrazine ligands and two μ-1,1-bridging chloride anions. Each of the two copper cations are linked by pairs of bridging chloride anions into dinuclear units that are further linked into layers via bridging 2,3-dimethylpyrazine coligands. These layers are stacked in such a way that channels are formed in which the disordered solvent molecules are located. The topology of this network is completely different from that observed in the two polymorphic modifications of CuCl(2,3-dimethylpyrazine) reported in the literature [Jess & Näther (2006). Inorg. Chem. 45, 7446–7454]. Powder X-ray diffraction measurements reveal that the title compound is unstable and transforms immediately into an unknown crystalline phase. Full Article text
pp 8-Hydroxyquinolinium trichlorido(pyridine-2,6-dicarboxylic acid-κ3O,N,O')copper(II) dihydrate By journals.iucr.org Published On :: 2024-09-24 The title compound, (C9H8NO)[CuCl3(C7H5NO4)]·2H2O, was prepared by reacting CuII acetate dihydrate, solid 8-hydroxyquinoline (8-HQ), and solid pyridine-2,6-dicarboxylic acid (H2pydc), in a 1:1:1 molar ratio, in an aqueous solution of dilute hydrochloric acid. The CuII atom exhibits a distorted CuO2NCl3 octahedral geometry, coordinating two oxygen atoms and one nitrogen atom from the tridentate H2pydc ligand and three chloride atoms; the nitrogen atom and one chloride atom occupy the axial positions with Cu—N and Cu—Cl bond lengths of 2.011 (2) Å and 2.2067 (9) Å, respectively. In the equatorial plane, the oxygen and chloride atoms are arranged in a cis configuration, with Cu—O bond lengths of 2.366 (2) and 2.424 (2) Å, and Cu—Cl bond lengths of 2.4190 (10) and 2.3688 (11) Å. The asymmetric unit contains 8-HQ+ as a counter-ion and two uncoordinated water molecules. The crystal structure features strong O—H⋯O and O—H⋯Cl hydrogen bonds as well as weak interactions including C—H⋯O, C—H⋯Cl, Cu—Cl⋯π, and π–π, which result in a three-dimensional network. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing involving the main residues are from H⋯Cl/Cl⋯H interactions, contributing 40.3% for the anion. Weak H⋯H contacts contribute 13.2% for the cation and 28.6% for the anion. Full Article text
pp The Pixel Anomaly Detection Tool: a user-friendly GUI for classifying detector frames using machine-learning approaches By journals.iucr.org Published On :: 2024-02-12 Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code. Full Article text
pp Convolutional neural network approach for the automated identification of in cellulo crystals By journals.iucr.org Published On :: 2024-02-23 In cellulo crystallization is a rare event in nature. Recent advances that have made use of heterologous overexpression can promote the intracellular formation of protein crystals, but new tools are required to detect and characterize these targets in the complex cell environment. The present work makes use of Mask R-CNN, a convolutional neural network (CNN)-based instance segmentation method, for the identification of either single or multi-shaped crystals growing in living insect cells, using conventional bright field images. The algorithm can be rapidly adapted to recognize different targets, with the aim of extracting relevant information to support a semi-automated screening pipeline, in order to aid the development of the intracellular protein crystallization approach. Full Article text
pp X-ray standing wave characterization of the strong metal–support interaction in Co/TiOx model catalysts By journals.iucr.org Published On :: 2024-03-31 The strong metal–support interaction (SMSI) is a phenomenon observed in supported metal catalyst systems in which reducible metal oxide supports can form overlayers over the surface of active metal nanoparticles (NPs) under a hydrogen (H2) environment at elevated temperatures. SMSI has been shown to affect catalyst performance in many reactions by changing the type and number of active sites on the catalyst surface. Laboratory methods for the analysis of SMSI at the nanoparticle-ensemble level are lacking and mostly based on indirect evidence, such as gas chemisorption. Here, we demonstrate the possibility to detect and characterize SMSIs in Co/TiOx model catalysts using the laboratory X-ray standing wave (XSW) technique for a large ensemble of NPs at the bulk scale. We designed a thermally stable MoNx/SiNx periodic multilayer to retain XSW generation after reduction with H2 gas at 600°C. The model catalyst system was synthesized here by deposition of a thin TiOx layer on top of the periodic multilayer, followed by Co NP deposition via spare ablation. A partial encapsulation of Co NPs by TiOx was identified by analyzing the change in Ti atomic distribution. This novel methodological approach can be extended to observe surface restructuring of model catalysts in situ at high temperature (up to 1000°C) and pressure (≤3 mbar), and can also be relevant for fundamental studies in the thermal stability of membranes, as well as metallurgy. Full Article text
pp Applications of the Clifford torus to material textures By journals.iucr.org Published On :: 2024-04-15 This paper introduces a new 2D representation of the orientation distribution function for an arbitrary material texture. The approach is based on the isometric square torus mapping of the Clifford torus, which allows for points on the unit quaternion hypersphere (each corresponding to a 3D orientation) to be represented in a periodic 2D square map. The combination of three such orthogonal mappings into a single RGB (red–green–blue) image provides a compact periodic representation of any set of orientations. Square torus representations of five different orientation sampling methods are compared and analyzed in terms of the Riesz s energies that quantify the uniformity of the samplings. The effect of crystallographic symmetry on the square torus map is analyzed in terms of the Rodrigues fundamental zones for the rotational symmetry groups. The paper concludes with example representations of important texture components in cubic and hexagonal materials. The new RGB representation provides a convenient and compact way of generating training data for the automated analysis of material textures by means of neural networks. Full Article text
pp Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images By journals.iucr.org Published On :: 2024-04-26 Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages (Dozor and DIALS), demonstrating that this is an appropriate framework to support future extensions and improvements. Full Article text
pp Tracking copper nanofiller evolution in polysiloxane during processing into SiOC ceramic By journals.iucr.org Published On :: 2024-06-18 Polymer-derived ceramics (PDCs) remain at the forefront of research for a variety of applications including ultra-high-temperature ceramics, energy storage and functional coatings. Despite their wide use, questions remain about the complex structural transition from polymer to ceramic and how local structure influences the final microstructure and resulting properties. This is further complicated when nanofillers are introduced to tailor structural and functional properties, as nanoparticle surfaces can interact with the matrix and influence the resulting structure. The inclusion of crystalline nanofiller produces a mixed crystalline–amorphous composite, which poses characterization challenges. With this study, we aim to address these challenges with a local-scale structural study that probes changes in a polysiloxane matrix with incorporated copper nanofiller. Composites were processed at three unique temperatures to capture mixing, pyrolysis and initial crystallization stages for the pre-ceramic polymer. We observed the evolution of the nanofiller with electron microscopy and applied synchrotron X-ray diffraction with differential pair distribution function (d-PDF) analysis to monitor changes in the matrix's local structure and interactions with the nanofiller. The application of the d-PDF to PDC materials is novel and informs future studies to understand interfacial interactions between nanofiller and matrix throughout PDC processing. Full Article text
pp Subperiodic groups, line groups and their applications By journals.iucr.org Published On :: 2024-05-31 Understanding the symmetries described by subperiodic groups – frieze, rod and layer groups – has been instrumental in predicting various properties (band structures, optical absorption, Raman spectra, diffraction patterns, topological properties etc.) of `low-dimensional' crystals. This knowledge is crucial in the tailored design of materials for specific applications across electronics, photonics and materials engineering. However, there are materials that have the property of being periodic only in one direction and whose symmetry cannot be described by the subperiodic rod groups. Describing the symmetry of these materials necessitates the application of line group theory. This paper gives an overview of subperiodic groups while briefly introducing line groups in order to acquaint the crystallographic community with these symmetries and direct them to pertinent literature. Since line groups are generally not subperiodic, they have thus far remained outside the realm of symmetries traditionally considered in crystallography, although there are numerous `one-dimensional' crystals (i.e. monoperiodic structures) possessing line group symmetry. Full Article text
pp Application of laboratory micro X-ray fluorescence devices for X-ray topography By journals.iucr.org Published On :: 2024-05-17 It is demonstrated that high-resolution energy-dispersive X-ray fluorescence mapping devices based on a micro-focused beam are not restricted to high-speed analyses of element distributions or to the detection of different grains, twins and subgrains in crystalline materials but can also be used for the detection of dislocations in high-quality single crystals. Si single crystals with low dislocation densities were selected as model materials to visualize the position of dislocations by the spatially resolved measurement of Bragg-peak intensity fluctuations. These originate from the most distorted planes caused by the stress fields of dislocations. The results obtained by this approach are compared with laboratory-based Lang X-ray topographs. The presented methodology yields comparable results and it is of particular interest in the field of crystal growth, where fast chemical and microstructural characterization feedback loops are indispensable for short and efficient development times. The beam divergence was reduced via an aperture management system to facilitate the visualization of dislocations for virtually as-grown, non-polished and non-planar samples with a very pronounced surface profile. Full Article text
pp Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications By journals.iucr.org Published On :: 2024-09-17 X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0, which is available to download from https://12idb.xray.aps.anl.gov/solx.html. Full Article text
pp Determination of the average crystallite size and the crystallite size distribution: the envelope function approach EnvACS By journals.iucr.org Published On :: 2024-09-17 A procedure is presented to exactly obtain the apparent average crystallite size (ACS) of powder samples using standard in-house powder diffraction experiments without any restriction originating from the Scherrer equation. Additionally, the crystallite size distribution within the sample can be evaluated. To achieve this, powder diffractograms are background corrected and long-range radial distribution functions G(r) up to 300 nm are calculated from the diffraction data. The envelope function fenv of G(r) is approximated by a procedure determining the absolute maxima of G(r) in a certain interval (r range). Fitting of an ACS distribution envelope function to this approximation gives the ACS and its distribution. The method is tested on diffractograms of LaB6 standard reference materials measured with different wavelengths to demonstrate the validity of the approach and to clarify the influence of the wavelength used. The latter results in a general description of the maximum observable average crystallite size, which depends on the instrument and wavelength used. The crystallite site distribution is compared with particle size distributions based on transmission electron microscopy investigations, providing an approximation of the average number of crystallites per particle. Full Article text
pp Pinhole small-angle neutron scattering based approach for desmearing slit ultra-small-angle neutron scattering data By journals.iucr.org Published On :: 2024-09-25 Presented here is an effective approach to desmearing slit ultra-small-angle neutron scattering (USANS) data, based on complementary small-angle neutron scattering (SANS) measurements, leading to a seamless merging of these data sets. The study focuses on the methodological aspects of desmearing USANS data, which can then be presented in the conventional manner of SANS, enabling a broader pool of data analysis methods. The key innovation lies in the use of smeared SANS data for extrapolating slit USANS, offering a self-consistent integrand function for desmearing with Lake's iterative method. The proposed approach is validated through experimental data on porous anodized aluminium oxide membranes, showcasing its applicability and benefits. The findings emphasize the importance of accurate desmearing for merging USANS and SANS data in the crossover q region, which is particularly crucial for complex scattering patterns. Full Article text
pp Foreword to the special virtual issue on X-ray spectroscopy to understand functional materials: instrumentation, applications, data analysis By journals.iucr.org Published On :: 2024-10-21 Full Article text
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