l The crystal structures determination and Hirshfeld surface analysis of N-(4-bromo-3-methoxyphenyl)- and N-{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}- derivatives of N-{[3-bromo-1-(phenylsulfonyl)-1H-indol- By journals.iucr.org Published On :: 2024-10-04 Two new phenylsulfonylindole derivatives, namely, N-{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}-N-(4-bromo-3-methoxyphenyl)benzenesulfonamide, C28H22Br2N2O5S2, (I), and N,N-bis{[3-bromo-1-(phenylsulfonyl)-1H-indol-2-yl]methyl}benzenesulfonamide, C36H27Br2N3O6S3, (II), reveal the impact of intramolecular π–π interactions of the indole moieties as a factor not only governing the conformation of N,N-bis(1H-indol-2-yl)methyl)amines, but also significantly influencing the crystal patterns. For I, the crystal packing is dominated by C—H⋯π and π–π bonding, with a particular significance of mutual indole–indole interactions. In the case of II, the molecules adopt short intramolecular π–π interactions between two nearly parallel indole ring systems [with the centroids of their pyrrole rings separated by 3.267 (2) Å] accompanied by a set of forced Br⋯O contacts. This provides suppression of similar interactions between the molecules, while the importance of weak C—H⋯O hydrogen bonding to the packing naturally increases. Short contacts of the latter type [C⋯O = 3.389 (6) Å] assemble pairs of molecules into centrosymmetric dimers with a cyclic R22(13) ring motif. These findings are consistent with the results of a Hirshfeld surface analysis and together they suggest a tool for modulating the supramolecular behavior of phenylsulfonylated indoles. Full Article text
l Synthesis and crystal structure of sodium (ethane-1,2-diyl)bis[(3-methoxypropyl)phosphinodithiolate] octahydrate By journals.iucr.org Published On :: 2024-10-08 The title compound, catena-poly[[triaquasodium]-di-μ-aqua-[triaquasodium]-μ-(ethane-1,2-diyl)bis[(3-methoxypropyl)phosphinodithiolato]], [Na2(C10H22O2P2S4)(H2O)8]n, crystallizes in the triclinic space group P1. The dianionic [CH3O(CH2)3P(=S)(S—)CH2CH2P(=S)(S—)(CH2)3OCH3]2− ligand fragments are joined by a dicationic [Na2(H2O)8]2+ cluster that includes the oxygen of the methoxypropyl unit of the ligand to form infinite chains. Full Article text
l Triclinic polymorph of bis[2-methyl-3-(pyridin-2-yl)imidazo[1,5-a]pyridin-2-ium] tetrachloridocadmium(II) By journals.iucr.org Published On :: 2024-10-04 The crystal structure of the title organic–inorganic hybrid salt, (C13H12N3)2[CdCl4], (I), has been reported with four molecules in the asymmetric unit in a monoclinic cell [Vassilyeva et al. (2021). RSC Advances, 11, 7713–7722]. While using two different aldehydes in the oxidative cyclization–condensation involving CH3NH2·HCl to prepare a new monovalent cation with the imidazo[1,5-a]pyridinium skeleton, a new polymorph was obtained for (I) in space group P1 and a unit cell with approximately half the volume of the monoclinic form. The structural configurations of the two crystallographically non-equivalent organic cations as well as the geometry of the moderately distorted tetrahedral CdCl42– dianion show minor changes. In the crystal, identically stacked cations and tetrachlorocadmate anions form separate columns parallel to the a axis. The loose packing of the anions leads to a minimal separation of approximately 9.53 Å between the metal atoms in the triclinic form versus 7.51 Å in the monoclinic one, indicating that the latter is packed slightly more densely. The two forms also differ by aromatic stacking motifs. Similar to the monoclinic polymorph, the triclinic one excited at 364 nm shows an intense unsymmetrical photoluminescent band with maximum at 403 nm and a full width at half maximum of 51 nm in the solid state. Full Article text
l Crystal structure of a hydrogen-bonded 2:1 co-crystal of 4-nitrophenol and 4,4'-bipyridine By journals.iucr.org Published On :: 2024-10-08 In the title compound, C10H8N2·2C6H5NO3, 4-nitrophenol and 4,4'-bipyridine crystallized together in a 2:1 ratio in the space group P21/n. There is a hydrogen-bonding interaction between the nitrogen atoms on the 4,4'-bipyridine molecule and the hydrogen atom on the hydroxyl group on the 4-nitrophenol, resulting in trimolecular units. This structure is a polymorph of a previously reported structure [Nayak & Pedireddi (2016). Cryst. Growth Des. 16, 5966–5975], which differs mainly due to a twist in the 4,4'-bipyridine molecule. Full Article text
l Synthesis, crystal structure and absolute configuration of (3aS,4R,5S,7aR)-7-(but-3-en-1-yn-1-yl)-2,2-dimethyl-3a,4,5,7a-tetrahydro-2H-1,3-benzodioxole-4,5-diol By journals.iucr.org Published On :: 2024-10-11 The absolute configuration of the title compound, C13H16O4, determined as 1S,2R,3S,4R based on the synthetic pathway, was confirmed by single-crystal X-ray diffraction. The molecule is a relevant intermediary for the synthesis of speciosins, epoxyquinoides or their analogues. The molecule contains fused five- and six-membered rings with two free hydroxyl groups and two protected as an isopropylidenedioxo ring. The packing is directed by hydrogen bonds that define double planes of molecules laying along the ab plane and van der Waals interactions between aliphatic chains that point outwards of the planes. Full Article text
l Crystal structures of two different multi-component crystals consisting of 1-(3,4-dimethoxybenzyl)-6,7-dimethoxyisoquinoline and fumaric acid By journals.iucr.org Published On :: 2024-10-11 Two different multi-component crystals consisting of papaverine [1-(3,4-dimethoxybenzyl)-6,7-dimethoxyisoquinoline, C20H21NO4] and fumaric acid [C4H4O4] were obtained. Single-crystal X-ray structure analysis revealed that one, C20H21NO4·1.5C4H4O4 (I), is a salt co-crystal composed of salt-forming and non-salt-forming molecules, and the other, C20H21NO4·0.5C4H4O4 (II), is a salt–co-crystal intermediate (i.e., in an intermediate state between a salt and a co-crystal). In this study, one state (crystal structure at 100 K) within the salt–co-crystal continuum is defined as the ‘intermediate’. Full Article text
l Crystal structure of (μ2-7-{[bis(pyridin-2-ylmethyl)amino-1κ3N,N',N'']methyl}-5-chloroquinolin-8-olato-2κN;1:2κ2O)trichlorido-1κCl,2κ2Cl-dizinc(II) By journals.iucr.org Published On :: 2024-10-15 The title compound, [Zn2(C22H18ClN4O)Cl3], is a dinuclear zinc(II) complex with three chlorido ligands and one pentadentate ligand containing quinolin-8-olato and bis(pyridin-2-ylmethyl)amine groups. One of the two ZnII atom adopts a tetrahedral geometry and coordinates two chlorido ligands with chelate coordination of the N and O atoms of the quinolin-8-olato group in the ligand. The other ZnII atom adopts a distorted trigonal–bipyramidal geometry, and coordinates one chlorido-O atom of the quinolin-8-olato group and three N atoms of the bis(pyridin-2-ylmethyl)amine unit. In the crystal, two molecules are associated through a pair of intermolecular C—H⋯Cl hydrogen bonds, forming a dimer with an R22(12) ring motif. Another intermolecular C—H⋯Cl hydrogen bond forms a spiral C(8) chain running parallel to the [010] direction. The dimers are linked by these two intermolecular C—H⋯Cl hydrogen bonds, generating a ribbon sheet structure in ac plane. Two other intermolecular C—H⋯Cl hydrogen bonds form a C(7) chain along the c-axis direction and another C(7) chain generated by a d-glide plane. The molecules are cross-linked through the four intermolecular C—H⋯Cl hydrogen bonds to form a three-dimensional network. Full Article text
l Crystal structure of N,N',N''-tricyclopropylbenzene-1,3,5-tricarboxamide By journals.iucr.org Published On :: 2024-10-24 The title compound, C18H21N3O3, was prepared from 1,3,5-benzenetricarbonyl trichloride and cyclopropylamine. Its crystal structure was solved in the monoclinic space group P21/c. In the crystal, the three amide groups of the molecule are inclined at angles of 26.5 (1), 36.9 (1) and 37.8 (1)° with respect to the plane of the benzene ring. The molecules are linked by N—H⋯O hydrogen bonds, forming two-dimensional supramolecular aggregates that extend parallel to the crystallographic ab plane and are further connected by C—H⋯O contacts. As a result of the supramolecular interactions, a propeller-like conformation of the title molecule can be observed. Full Article text
l Crystal structure of catena-poly[[diaquadiimidazolecobalt(II)]-μ2-2,3,5,6-tetrabromobenzene-1,4-dicarboxylato] By journals.iucr.org Published On :: 2024-10-31 The asymmetric unit of the title compound, [Co(C8Br4O4)(C3H4N2)2(H2O)2]n or [Co(Br4bdc)(im)2(H2O)2]n, comprises half of CoII ion, tetrabromobenzenedicarboxylate (Br4bdc2−), imidazole (im) and a water molecule. The CoII ion exhibits a six-coordinated octahedral geometry with two oxygen atoms of the Br4bdc2− ligand, two oxygen atoms of the water molecules, and two nitrogen atoms of the im ligands. The carboxylate group is nearly perpendicular to the benzene ring and shows monodentate coordination to the CoII ion. The CoII ions are bridged by the Br4bdc2− ligand, forming a one-dimensional chain. The carboxylate group acts as an intermolecular hydrogen-bond acceptor toward the im ligand and a coordinated water molecule. The chains are connected by interchain N—H⋯O(carboxylate) and O—H(water)⋯O(carboxylate) hydrogen-bonding interactions and are not arranged in parallel but cross each other via interchain hydrogen bonding and π–π interactions, yielding a three-dimensional network. Full Article text
l Crystal structure, Hirshfeld surface analysis, and DFT and molecular docking studies of 6-cyanonaphthalen-2-yl 4-(benzyloxy)benzoate By journals.iucr.org Published On :: 2024-10-22 In the title compound, C25H17NO3, the torsion angle associated with the phenyl benzoate group is −173.7 (2)° and that for the benzyloxy group is −174.8 (2)° establishing an anti-type conformation. The dihedral angles between the ten-membered cyanonaphthalene ring and the aromatic ring of the phenyl benzoate and the benzyloxy fragments are 40.70 (10) and 87.51 (11)°, respectively, whereas the dihedral angle between the aromatic phenyl benzoate and the benzyloxy fragments is 72.30 (13)°. In the crystal, the molecules are linked by weak C—H⋯O interactions forming S(4) chains propagating parallel to [010]. The packing is consolidated by three C—H⋯π interactions and two π–π stacking interactions between the aromatic rings of naphthalene and phenyl benzoate with centroid-to-centroid distances of 3.9698 (15) and 3.8568 (15) Å, respectively. Intermolecular interactions were quantified using Hirshfeld surface analysis. The molecular structure was further optimized by density functional theory (DFT) at the B3LYP/6–311+ G(d,p) level, revealing that the energy gap between HOMO and LUMO is 3.17 eV. Molecular docking studies were carried out for the title compound as a ligand and SARS-Covid-2(PDB ID:7QF0) protein as a receptor giving a binding affinity of −9.5 kcal mol−1. Full Article text
l Crystal structure of an acetonitrile solvate of 2-(3,4,5-triphenylphenyl)acetic acid By journals.iucr.org Published On :: 2024-10-24 Crystal growth of 2-(3,4,5-triphenylphenyl)acetic acid (1) from acetonitrile yields a monosolvate, C26H20O2·CH3CN, of the space group P1. In the crystal, the title molecule adopts a conformation in which the three phenyl rings are arranged in a paddlewheel-like fashion around the central arene ring and the carboxyl residue is oriented nearly perpendicular to the plane of this benzene ring. Inversion-symmetric dimers of O—H⋯O-bonded molecules of 1 represent the basic supramolecular entities of the crystal structure. These dimeric molecular units are further linked by C—H⋯O=C bonds to form one-dimensional supramolecular aggregates running along the crystallographic [111] direction. Weak Caryl—H⋯N interactions occur between the molecules of 1 and acetonitrile. Full Article text
l Synthesis and crystal structure of 1,3,5-tris[(1H-benzotriazol-1-yl)methyl]-2,4,6-triethylbenzene By journals.iucr.org Published On :: 2024-10-31 In the crystal structure of the title compound, C33H33N9, the tripodal molecule exists in a conformation in which the substituents attached to the central arene ring are arranged in an alternating order above and below the ring plane. The three benzotriazolyl moieties are inclined at angles of 88.3 (1), 85.7 (1) and 82.1 (1)° with respect to the mean plane of the benzene ring. In the crystal, only weak molecular cross-linking involving C—H⋯N hydrogen bonds is observed. Full Article text
l Crystal structure of [Ni(OH2)6]Cl2·(18-crown-6)2·2H2O By journals.iucr.org Published On :: 2024-10-24 The crystal structure of the title compound, hexaaquanickel(II) dichloride–1,4,7,10,13,16-hexaoxacyclooctadecane–water (1/2/2), [Ni(H2O)6]Cl2·2C12H24O6·2H2O, is reported. The asymmetric unit contains half of the Ni(OH2)6 moiety with a formula of C12H32ClNi0.50O10 at 105 K and triclinic (P1) symmetry. The [Ni(OH2)6]2+ cation has close to ideal octahedral geometry with O—Ni—O bond angles that are within 3° of idealized values. The supramolecular structure includes hydrogen bonding between the water ligands, 18-crown-6 molecules, Cl− anions, and co-crystallized water solvent. Two crown ether molecules flank the [Ni(OH2)6]2+ molecule at the axial positions in a sandwich-like structure. The relatively symmetric hydrogen-bonding network is enabled by small Cl− counter-ions and likely influences the more idealized octahedral geometry of [Ni(OH2)6]2+. Full Article text
l Synthesis and structure of trans-2,5-dimethylpiperazine-1,4-diium dihydrogen diphosphate By journals.iucr.org Published On :: 2024-10-24 In the title salt, C6H16N22+ ·H2P2O72−, the complete dication is generated by a crystallographic centre of symmetry with the methyl groups in equatorial orientations. The complete dianion is generated by a crystallographic twofold axis with the central O atom lying on the axis: the P—O—P bond angle is 135.50 (12)°. In the crystal, the dihydrogen diphosphate anions are linked by O—H⋯O hydrogen bonds, generating (001) layers. The organic cations bond to the inorganic layers by way of N—H⋯O and C—H⋯O hydrogen bonds. A Hirshfeld surface analysis shows that the most important contributions for the crystal packing are from O⋯H/H⋯O (60.5%) and H⋯H (39.4%) contacts. Full Article text
l Structural multiplicity in a solvated hydrate of the antiretroviral protease inhibitor Lopinavir By journals.iucr.org Published On :: 2024-10-24 Lopinavir is a potent protease inhibitor that is used as a first-line pharmaceutical drug for the treatment of HIV. The multi-component solvated Lopinavir crystal, systematic name (2S)-N-[(2S,4S,5S)-5-[2-(2,6-dimethylphenoxy)acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl]-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide–ethane-1,2-diol–water (8/3/7) 8C37H48N4O5·3C2H6O2·7H2O, was prepared using evaporative methods. The crystalline material obtained from this experimental synthesis was characterized and elucidated by single-crystal X-ray diffraction (SC-XRD). The crystal structure is unusual in that the unit cell contains 18 molecules. The stoichiometric ratio of this crystal is eight Lopinavir molecules [8(C37H48N4O5)], three ethane-1,2-diol molecules [3(C2H6O2)] and seven water molecules [7(H2O)]. The crystal packing features both bi- and trifurcated hydrogen bonds between atoms. Full Article text
l Salts of 2-amino-5-iodopyridinium By journals.iucr.org Published On :: 2024-10-31 Reaction of 2-amino-5-iodopyridine (5IAP) with concentrated HBr at room temperature yielded 2-amino-5-iodopyridinium bromide, C5H6IN2+·Br− or (5IAPH)Br. The complex formed pale-yellow crystals, which exhibit significant hydrogen bonding between the amino and pyridinium N—H donors and bromide ion acceptors. Halogen bonding is also observed. Similarly, reaction of 5IAP with cobalt(II) chloride in mixed HCl/HBr in 1-propanol yielded 2-amino-5-iodopyridinium (2-amino-5-iodopyridine-κN1)bromido/chlorido(0.51/2.48)cobalt(II), (C5H6IN2)[CoBr0.51Cl2.48(C5H5IN2)] or (5-IAPH)[(5IAP)CoCl2.48Br0.51], as blue block-shaped crystals. Two of the three halide positions exhibit mixed occupancy [Cl/Br = 0.797 (5):0.203 (5) and 0.689 (6):0.311 (6)], while the third position is occupied solely by a chloride ion. Extensive hydrogen and halogen bonding is observed. Full Article text
l Synthesis, crystal structure and Hirshfeld surface analysis of 2-{4-[(2-chlorophenyl)methyl]-3-methyl-6-oxopyridazin-1-yl}-N-phenylacetamide By journals.iucr.org Published On :: 2024-10-31 In the title molecule, C20H18ClN3O2, the 2-chlorophenyl group is disordered to a small extent [occupancies 0.875 (2)/0.125 (2)]. The phenylacetamide moiety is nearly planar due to a weak, intramolecular C—H⋯O hydrogen bond. In the crystal, N—H⋯O hydrogen bonds and π-stacking interactions between pyridazine and phenyl rings form helical chains of molecules in the b-axis direction, which are linked by C—H⋯O hydrogen bonds and C—H⋯π(ring) interactions. A Hirshfeld surface analysis was performed, which showed that H⋯H, C⋯H/H⋯C and O⋯H/H⋯O interactions to dominate the intermolecular contacts in the crystal. Full Article text
l Crystal structures and photophysical properties of mono- and dinuclear ZnII complexes flanked by triethylammonium By journals.iucr.org Published On :: 2024-10-24 Two new zinc(II) complexes, triethylammonium dichlorido[2-(4-nitrophenyl)-4-phenylquinolin-8-olato]zinc(II), (C6H16N){Zn(C21H13N2O3)Cl2] (ZnOQ), and bis(triethylammonium) {2,2'-[1,4-phenylenebis(nitrilomethylidyne)]diphenolato}bis[dichloridozinc(II)], (C6H16N)2[Zn2(C20H14N2O2)Cl4] (ZnBS), were synthesized and their structures were determined using ESI–MS spectrometry, 1H NMR spectroscopy, and single-crystal X-ray diffraction. The results showed that the ligands 2-(4-nitrophenyl)-4-phenylquinolin-8-ol (HOQ) and N,N'-bis(2-hydroxybenzylidene)benzene-1,4-diamine (H2BS) were deprotonated by triethyl-amine, forming the counter-ion Et3NH+, which interacts via an N—H⋯O hydrogen bond with the ligand. The ZnII atoms have a distorted trigonal–pyramidal (ZnOQ) and distorted tetrahedral (ZnBS) geometries with a coordination number of four, coordinating with the ligands via N and O atoms. The N atoms coordinating with ZnII correspond to the heterocyclic nitrogen for the HOQ ligand, while for the H2BS ligand, it is the nitrogen of the imine (CH=N). The crystal packing of ZnOQ is characterized by C—H⋯π interactions, while that of ZnBS by C—H⋯Cl interactions. The emission spectra showed that ZnBS complex exhibits green fluorescence in the solid state with a small band-gap energy, and the ZnOQ complex does exhibit non-fluorescence. Full Article text
l Crystal structure and Hirshfeld surface analysis of the salt 2-iodoethylammonium iodide – a possible side product upon synthesis of hybrid perovskites By journals.iucr.org Published On :: 2024-10-31 The title organic–inorganic hybrid salt, C2H7IN+·I−, is isotypic with its bromine analog, C2H7BrN+·Br− [Semenikhin et al. (2024). Acta Cryst. E80, 738–741]. Its asymmetric unit consists of one 2-iodoethylammonium cation and one iodide anion. The NH3+ group of the organic cation forms weak hydrogen bonds with four neighboring iodide anions, leading to the formation of supramolecular layers propagating parallel to the bc plane. Hirshfeld surface analysis reveals that the most important contribution to the crystal packing is from N—H⋯I interactions (63.8%). The crystal under investigation was twinned by a 180° rotation around [001]. Full Article text
l Crystal structure of bis{5-(4-chlorophenyl)-3-[6-(1H-pyrazol-1-yl)pyridin-2-yl]-1H-1,2,4-triazol-1-ido}nickel(II) methanol disolvate By journals.iucr.org Published On :: 2024-10-31 The unit cell of the title compound, [Ni(C16H10ClN6)2]·2CH3OH, consists of a neutral complex and two methanol molecules. In the complex, the two tridentate 2-(3-(4-chlorophenyl)-1H-1,2,4-triazol-5-yl)-6-(1H-pyrazol-1-yl)pyridine ligands coordinate to the central NiII ion through the N atoms of the pyrazole, pyridine and triazole groups, forming a pseudooctahedral coordination sphere. Neighbouring tapered molecules are linked through weak C—H(pz)⋯π(ph) interactions into monoperiodic chains, which are further linked through weak C—H⋯N/C interactions into diperiodic layers. The intermolecular contacts were quantified using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative contributions of the contacts to the crystal packing to be H⋯H 32.8%, C⋯H/H⋯C 27.5%, N⋯H/H⋯N 15.1%, and Cl⋯H/H⋯Cl 14.0%. The average Ni—N bond distance is 2.095 Å. Energy framework analysis at the HF/3–21 G theory level was performed to quantify the interaction energies in the crystal structure. Full Article text
l The cadmium oxidotellurates(IV) Cd5(TeO3)4(NO3)2 and Cd4Te5O14 By journals.iucr.org Published On :: 2024-11-05 Monoclinic single crystals of Cd5(TeO3)4(NO3)2 (space group P21/c), pentacadmium tetrakis[oxidotellurate(IV)] dinitrate, and of Cd4Te5O14 (space group C2/c), tetracadmium pentaoxidotellurate(IV), were obtained under the same hydrothermal conditions. Whereas the crystal structure of Cd5(TeO3)4(NO3)2 is distinctively layered, that of Cd4Te5O14 exhibits a tri-periodic framework. In Cd5(TeO3)4(NO3)2, the three CdII atoms have coordination numbers (CN) of 7, 6 and 6. The two types of [CdO6] and the [CdO7] polyhedra [bond lengths range from 2.179 (3) to 2.658 (2) Å] share corners and edges, resulting in layers extending parallel to (100). Both TeIV atoms are coordinated by three oxygen atoms in a trigonal–pyramidal shape. The oxygen atoms of the isolated [TeO3] groups [bond lengths range from 1.847 (3) to 1.886 (3) Å] all are part of the cadmium–oxygen layer. The electron lone pairs ψ of the TeIV atoms are directed away from the layer on both sides. The available interlayer space is co-occupied by the nitrate group, which is directly connected with two of its O atoms to the layer whereas the third O atom is solely bonded to the N atom and points towards the adjacent layer. In Cd4Te5O14, all three unique CdII atoms are coordinated by six oxygen atoms, considering Cd—O distances from 2.235 (2) to 2.539 (2) Å. By edge- and corner-sharing, the distorted [CdO6] polyhedra form an open framework that is partially filled with three different stereochemically active TeIV atoms. All of them exhibit a CN of 4, with Te—O bonds in a range from 1.859 (2) to 2.476 (2) Å. The corresponding [TeO4] units are linked to each other by corner- and edge-sharing, forming infinite helical 1∞[Te10O28] chains extending parallel to [203]. The connectivity in the chains can be described as (⋯–⋄–⋄=⋄–⋄–⋄–⋄–⋄=⋄–⋄–⋄–⋯)n where ‘⋄’ denotes a [TeO4] unit, ‘–’ a linkage via corners and ‘=’ a linkage via edges. Such a structural motif is unprecedented in the crystal chemistry of oxidotellurate(IV) compounds. Full Article text
l Crystal structure and Hirshfeld surface analysis of bis(benzoylacetonato)(ethanol)dioxidouranium(VI) By journals.iucr.org Published On :: 2024-11-05 A new uranium metal–organic complex salt, [U(C10H9O2)2O2(C2H6O)], with benzoyl acetone, namely, bis(benzoylacetonato)(ethanol)dioxidouranium(VI), was synthesized. The compound has monoclinic P21/n symmetry. The geometry of the seven-coordinate U atom is pentagonal bipyramidal, with the uranyl oxygen atoms in apical positions. In the complex, the ligands bind to the metal through oxygen atoms. Additional weak O—H⋯O contacts between the cations and anions consolidate the three-dimensional arrangement of the structure. On the Hirshfeld surface, the largest contributions come from the short contacts such as van der Waals forces, including H⋯H, O⋯H and C⋯H. Interactions including C⋯C and O⋯C contacts were also observed; however, their contribution to the overall cohesion of the crystal structure is minor. A packing analysis was performed to check the strength of the crystal packing. Full Article text
l Synthesis and structure of pentakis(2-aminopyridinium) nonavanado(V)tellurate(VI) By journals.iucr.org Published On :: 2024-12-01 In the title compound, (C5H7N2)5[TeV9O28], the tellurium and vanadium atoms are statistically disordered over two of the ten metal-atom sites in the [TeV9O28]5– heteropolyanion. The anions stack along [100] and are extended into a three-dimensional supramolecular network through N—H⋯O and weak C—H⋯O hydrogen bonds involving the self-assembled 2-aminopyridinium pentamers, which are linked by C—H⋯π and π–π stacking interactions. The most important contributions to the Hirshfeld surface arise from O⋯H/H⋯O (54.8%), H⋯H (17.8%) and C⋯H/H⋯C (13.4%) contacts. Full Article text
l Multi-segment cooling design of a reflection mirror based on the finite-element method By journals.iucr.org Published On :: Through numerical optimization of cooling lengths and cooling groove positions for the first reflection mirror of a free-electron laser [OK?], the root mean square of the height error of the mirror's thermal deformation was minimized. The optimized mirror design effectively mitigated stray light and enhanced the peak intensity of the focus spot at the sample, thereby enhancing the optical performance of the high-heat-load mirror under high repetition rates at beamline FEL-II of the SHINE facility. Full Article text
l Hard X-ray single-shot spectrometer of PAL-XFEL By journals.iucr.org Published On :: A hard X-ray single-shot spectrometer comprising thin, bent Si crystals has been developed for the Pohang Accelerator Laboratory X-ray Free-Electron Laser (XFEL), for detailed analysis of ultrafast 4.5–17 keV XFEL pulses with a high spectral resolution. This instrument facilitates shot-to-shot spectral structure monitoring and optimization of the operating conditions of the XFEL owing to its ability to provide comprehensive data on the spectral properties and fluctuations of self-amplified spontaneous emission, monochromatic and seeded XFEL modes. Full Article text
l Reducing heat load density with asymmetric and inclined double-crystal monochromators: principles and requirements revisited By journals.iucr.org Published On :: The major principles and requirements of asymmetric and inclined double-crystal monochromators are re-examined and presented to guide their design and development for significantly reducing heat load density and gradient on the monochromators of fourth-generation synchrotron light sources and X-ray free-electron lasers. Full Article text
l Development of MHz X-ray phase contrast imaging at the European XFEL By journals.iucr.org Published On :: The development of instrumentation as well as applications for megahertz X-ray phase contrast imaging at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL are introduced here. Full Article text
l Review and experimental comparison of speckle-tracking algorithms for X-ray phase contrast imaging By journals.iucr.org Published On :: This review focuses on low-dose near-field X-ray speckle phase imaging in the differential mode introducing the existing algorithms with their specifications and comparing their performances under various experimental conditions. Full Article text
l The use of ethanol as contrast enhancer in Synchrotron X-ray phase-contrast imaging leads to heterogeneous myocardial tissue shrinkage: a case report By journals.iucr.org Published On :: In this work, we showed that the use of ethanol to increase image contrast when imaging cardiac tissue with synchrotron X-ray phase-contrast imaging (X-PCI) leads to heterogeneous tissue shrinkage, which has an impact on the 3D organization of the myocardium. Full Article text
l Development and testing of a dual-frequency, real-time hardware feedback system for the hard X-ray nanoprobe beamline of the SSRF By journals.iucr.org Published On :: we introduce a novel approach for a real-time dual-frequency feedback system, which has been firstly used at the hard X-ray nanoprobe beamline of SSRF. The BiBEST can then efficiently stabilize X-ray beam position and stability in parallel, making use of different optical systems in the beamline. Full Article text
l Enhancing the Efficiency of a Wavelength-Dispersive Spectrometer based upon a Slit-less Design Using a Single-Bounce Monocapillary By journals.iucr.org Published On :: A slit-less wavelength-dispersive spectrometer design using a single-bounce monocapillary that aligns the sample on the Rowland circle, enhancing photon throughput and maintaining resolution. The compact design supports flexibility and reconfiguration in facilities without complex beamline infrastructure, significantly improving detection efficiency. Full Article text
l Form factor of helical structures and twisted fibres By journals.iucr.org Published On :: 2023-11-07 A general formalism is presented for the isotropically averaged single-chain scattering function (form factor) of single, double, triple and higher-order helices, as well as twisted fibres consisting of concentric layers of strands. Form factors for double and triple helices with differently sized grooves have also been derived. The formulas include the longitudinal and transverse interference over the pitch and radius of the helices, respectively. The results may be useful for the analysis of small-angle scattering data of (bio)macromolecules or molecular assemblies exhibiting a helical arrangement. Full Article text
l The International Tables Symmetry Database By journals.iucr.org Published On :: 2023-11-29 The International Tables Symmetry Database (https://symmdb.iucr.org/), which is part of International Tables for Crystallography, is a collection of individual databases of crystallographic space-group and point-group information with associated programs. The programs let the user access and in some cases interactively visualize the data, and some also allow new data to be calculated `on the fly'. Together these databases and programs expand upon and complement the symmetry information provided in International Tables for Crystallography Volume A, Space-Group Symmetry, and Volume A1, Symmetry Relations between Space Groups. The Symmetry Database allows users to learn about and explore the space and point groups, and facilitates the study of group–subgroup relations between space groups, with applications in determining crystal-structure relationships, in studying phase transitions and in domain-structure analysis. The use of the International Tables Symmetry Database in all these areas is demonstrated using several examples. Full Article text
l Time-resolved high-energy X-ray diffraction studies of ultrathin Ni ferrite films on MgO(001) By journals.iucr.org Published On :: 2023-11-29 Time-resolved high-energy X-ray diffraction was used during growth of ultrathin NixFe3−xO4 films with varying Ni content (0 ≤ x ≤ 1.5) deposited on MgO(001) substrates by reactive molecular beam epitaxy, providing an insight into the growth dynamics of these films. In order to obtain structural information, reciprocal-space maps were recorded and the temporal evolution of the Bragg peaks specific to the octahedral and tetrahedral lattice sites of the inverse spinel structure of NixFe3−xO4 was observed during growth of the films. A time delay, corresponding to a coverage of 1.2–1.8 nm, between the appearance of the Bragg reflections originating from octahedral sites and reflections originating exclusively from tetrahedral sites indicates that the ferrite films grow in two stages. In the initial growth phase, a rock salt interface layer is formed. Afterwards, a structural transition occurs and the films grow in an inverse spinel structure. The thickness of the initial rock salt phase was found to increase with Ni content and to be responsible for atypical strain in the thin films. Films with Ni contents x > 1 do not show a structural transition. These films remain in a (deficient) rock salt structure consisting of a mixed Ni–Fe oxide and do not form a spinel structure at all. They show an increased number of NiO clusters as detected by X-ray photoelectron spectroscopy of the valence band, accompanied by a significant roughening of the films. Full Article text
l Texture measurements on quartz single crystals to validate coordinate systems for neutron time-of-flight texture analysis By journals.iucr.org Published On :: 2023-11-24 In crystallographic texture analysis, ensuring that sample directions are preserved from experiment to the resulting orientation distribution is crucial to obtain physical meaning from diffraction data. This work details a procedure to ensure instrument and sample coordinates are consistent when analyzing diffraction data with a Rietveld refinement using the texture analysis software MAUD. A quartz crystal is measured on the HIPPO diffractometer at Los Alamos National Laboratory for this purpose. The methods described here can be applied to any diffraction instrument measuring orientation distributions in polycrystalline materials. Full Article text
l An electropneumatic cleaning device for piezo-actuator-driven picolitre-droplet dispensers By journals.iucr.org Published On :: 2024-02-01 Recently, we introduced the liquid application method for time-resolved analyses (LAMA). The time-consuming cleaning cycles required for the substrate solution exchange and storage of the sensitive droplet-dispenser nozzles present practical challenges. In this work, a dispenser cleaning system for the semi-automated cleaning of the piezo-actuator-driven picolitre-droplet dispensers required for LAMA is introduced to streamline typical workflows. Full Article text
l Van Vleck analysis of angularly distorted octahedra using VanVleckCalculator By journals.iucr.org Published On :: 2024-02-01 Van Vleck modes describe all possible displacements of octahedrally coordinated ligands about a core atom. They are a useful analytical tool for analysing the distortion of octahedra, particularly for first-order Jahn–Teller distortions, but determination of the Van Vleck modes of an octahedron is complicated by the presence of angular distortion of the octahedron. This problem is most commonly resolved by calculating the bond distortion modes (Q2, Q3) along the bond axes of the octahedron, disregarding the angular distortion and losing information on the octahedral shear modes (Q4, Q5 and Q6) in the process. In this paper, the validity of assuming bond lengths to be orthogonal in order to calculate the Van Vleck modes is discussed, and a method is described for calculating Van Vleck modes without disregarding the angular distortion. A Python package for doing this, VanVleckCalculator, is introduced and some examples of its use are given. Finally, it is shown that octahedral shear and angular distortion are often, but not always, correlated, and a parameter η is proposed as the shear fraction. It is demonstrated that η can be used to predict whether the values will be correlated when varying a tuning parameter such as temperature or pressure. Full Article text
l POMFinder: identifying polyoxometallate cluster structures from pair distribution function data using explainable machine learning By journals.iucr.org Published On :: 2024-02-01 Characterization of a material structure with pair distribution function (PDF) analysis typically involves refining a structure model against an experimental data set, but finding or constructing a suitable atomic model for PDF modelling can be an extremely labour-intensive task, requiring carefully browsing through large numbers of possible models. Presented here is POMFinder, a machine learning (ML) classifier that rapidly screens a database of structures, here polyoxometallate (POM) clusters, to identify candidate structures for PDF data modelling. The approach is shown to identify suitable POMs from experimental data, including in situ data collected with fast acquisition times. This automated approach has significant potential for identifying suitable models for structure refinement to extract quantitative structural parameters in materials chemistry research. POMFinder is open source and user friendly, making it accessible to those without prior ML knowledge. It is also demonstrated that POMFinder offers a promising modelling framework for combined modelling of multiple scattering techniques. Full Article text
l Operation model of a skew-symmetric split-crystal neutron interferometer By journals.iucr.org Published On :: 2024-02-01 The observation of neutron interference using a triple Laue interferometer formed by two separate crystals opens the way to the construction and operation of skew-symmetric interferometers with extended arm separation and length. The specifications necessary for their successful operation are investigated here: most importantly, how the manufacturing tolerance and crystal alignments impact the interference visibility. In contrast with previous studies, both incoherent sources and the three-dimensional operation of the interferometer are considered. It is found that, with a Gaussian Schell model of an incoherent source, the integrated density of the particles leaving the interferometer is the same as that yielded by a coherent Gaussian source having a radius equal to the coherence length. Full Article text
l ProLEED Studio: software for modeling low-energy electron diffraction patterns By journals.iucr.org Published On :: 2024-02-01 Low-energy electron diffraction patterns contain precise information about the structure of the surface studied. However, retrieving the real space lattice periodicity from complex diffraction patterns is challenging, especially when the modeled patterns originate from superlattices with large unit cells composed of several symmetry-equivalent domains without a simple relation to the substrate. This work presents ProLEED Studio software, built to provide simple, intuitive and precise modeling of low-energy electron diffraction patterns. The interactive graphical user interface allows real-time modeling of experimental diffraction patterns, change of depicted diffraction spot intensities, visualization of different diffraction domains, and manipulation of any lattice points or diffraction spots. The visualization of unit cells, lattice vectors, grids and scale bars as well as the possibility of exporting ready-to-publish models in bitmap and vector formats significantly simplifies the modeling process and publishing of results. Full Article text
l Fast nanoscale imaging of strain in a multi-segment heterostructured nanowire with 2D Bragg ptychography By journals.iucr.org Published On :: 2024-02-01 Developing semiconductor devices requires a fast and reliable source of strain information with high spatial resolution and strain sensitivity. This work investigates the strain in an axially heterostructured 180 nm-diameter GaInP nanowire with InP segments of varying lengths down to 9 nm, simultaneously probing both materials. Scanning X-ray diffraction (XRD) is compared with Bragg projection ptychography (BPP), a fast single-projection method. BPP offers a sufficient spatial resolution to reveal fine details within the largest segments, unlike scanning XRD. The spatial resolution affects the quantitative accuracy of the strain maps, where BPP shows much-improved agreement with an elastic 3D finite element model compared with scanning XRD. The sensitivity of BPP to small deviations from the Bragg condition is systematically investigated. The experimental confirmation of the model suggests that the large lattice mismatch of 1.52% is accommodated without defects. Full Article text
l Using XAS to monitor radiation damage in real time and post-analysis, and investigation of systematic errors of fluorescence XAS for Cu-bound amyloid-β By journals.iucr.org Published On :: 2024-02-01 X-ray absorption spectroscopy (XAS) is a promising technique for determining structural information from sensitive biological samples, but high-accuracy X-ray absorption fine structure (XAFS) requires corrections of systematic errors in experimental data. Low-temperature XAS and room-temperature X-ray absorption spectro-electrochemical (XAS-EC) measurements of N-truncated amyloid-β samples were collected and corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumber (k). A new protocol was developed using extended X-ray absorption fine structure (EXAFS) data analysis for monitoring radiation damage in real time and post-analysis. The reliability of the structural determinations and consistency were validated using the XAS measurement experimental uncertainty. The correction of detector pixel efficiencies improved the fitting χ2 by 12%. An improvement of about 2.5% of the structural fitting was obtained after dead-time corrections. Normalization allowed the elimination of 90% of the monochromator glitches. The remaining glitches were manually removed. The dispersion of spectra due to self-absorption was corrected. Standard errors of experimental measurements were propagated from pointwise variance of the spectra after systematic corrections. Calculated uncertainties were used in structural refinements for obtaining precise and reliable values of structural parameters including atomic bond lengths and thermal parameters. This has permitted hypothesis testing. Full Article text
l BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis By journals.iucr.org Published On :: 2024-02-01 BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI; updated automated Guinier fitting and Dmax finding algorithms; automated series (e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares (REGALS); creation of electron-density reconstructions using electron density via solution scattering (DENSS); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program. Full Article text
l Refinement of X-ray and electron diffraction crystal structures using analytical Fourier transforms of Slater-type atomic wavefunctions in Olex2 By journals.iucr.org Published On :: 2024-02-01 An implementation of Slater-type spherical scattering factors for X-ray and electron diffraction for elements in the range Z = 1–103 is presented within the software Olex2. Both high- and low-angle Fourier behaviour of atomic electron density and electrostatic potential can thus be addressed, in contrast to the limited flexibility of the four Gaussian plus constant descriptions which are currently the most widely used method for calculating atomic scattering factors during refinement. The implementation presented here accommodates the increasing complexity of the electronic structure of heavier elements by using complete atomic wavefunctions without any interpolation between precalculated tables or intermediate fitting functions. Atomic wavefunctions for singly charged ions are implemented and made accessible, and these show drastic changes in electron diffraction scattering factors compared with the neutral atom. A comparison between the two different spherical models of neutral atoms is presented as an example for four different kinds of X-ray and two electron diffraction structures, and comparisons of refinement results using the existing diffraction data are discussed. A systematic but slight improvement in R values and residual densities can be observed when using the new scattering factors, and this is discussed relative to effects on the atomic displacement parameters and atomic positions, which are prominent near the heavier elements in a structure. Full Article text
l A simple solution to the Rietveld refinement recipe problem By journals.iucr.org Published On :: 2024-02-01 Rietveld refinements are widely used for many purposes in the physical sciences. Conducting a Rietveld refinement typically requires expert input because correct results may require that parameters be added to the fit in the proper order. This order will depend on the nature of the data and the initial parameter values. A mechanism for computing the next parameter to add to the refinement is shown. The fitting function is evaluated with the current parameter value set and each parameter incremented and decremented by a small offset. This provides the partial derivatives with respect to each parameter, along with information to discriminate meaningful values from numerical computational errors. The implementation of this mechanism in the open-source GSAS-II program is discussed. This new method is discussed as an important step towards the development of automated Rietveld refinement technology. Full Article text
l INSIGHT: in situ heuristic tool for the efficient reduction of grazing-incidence X-ray scattering data By journals.iucr.org Published On :: 2024-02-12 INSIGHT is a Python-based software tool for processing and reducing 2D grazing-incidence wide- and small-angle X-ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel-wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time-resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one-step solution to reduce, process, analyze and export findings of large in situ and operando data sets. Full Article text
l Time-resolved AUSAXS at BL28XU at SPring-8 By journals.iucr.org Published On :: 2024-02-01 An anomalous ultra-small-angle X-ray scattering (AUSAXS) system has been constructed at BL28XU at SPring-8 for time-resolved AUSAXS experiments. The path length was extended to 9.1 m and a minimum of q = 0.0069 nm−1 was attained. Scattering profiles at 0.0069 to 0.3 nm−1 were successfully obtained at 17 different X-ray energies in 30 s using the BL28XU optical setup, which enables adjustment of the energy of the incident X-rays quickly without the beam position drifting. Time-resolved measurements were conducted to investigate changes in the structure of zinc compounds in poly(styrene-ran-butadiene) rubber during vulcanization. A change in energy dependence of the scattered intensity with time was found during vulcanization, suggesting the transformation of zinc in the reaction. Full Article text
l 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
l Crystals in the community and the classroom By journals.iucr.org Published On :: 2024-02-01 The growing pressure on school curricula has meant crystals and the science of crystallography have been cut from or made optional for many educational programs. This omission is a serious disservice to the history and understanding of modern sciences, given that crystallography underpins many of the greatest advancements in science over the past century, is a critical component of many modern research papers and patents, and has 29 Nobel Prizes awarded in the field. This contribution describes a simple activity to target classroom and public engagement with crystallography, using marshmallows or equivalent sweets/candy to represent atoms and cocktail sticks to represent bonds, together with examples of how crystals are studied and how they are useful. Though it has a simple basis, this activity can be extended in numerous ways to reflect the aims of the demonstrator, and a few of these are described. Full Article text
l A note on the Hendrickson–Lattman phase probability distribution and its equivalence to the generalized von Mises distribution By journals.iucr.org Published On :: 2024-02-16 Hendrickson & Lattman [Acta Cryst. (1970), B26, 136–143] introduced a method for representing crystallographic phase probabilities defined on the unit circle. Their approach could model the bimodal phase probability distributions that can result from experimental phase determination procedures. It also provided simple and highly effective means to combine independent sources of phase information. The present work discusses the equivalence of the Hendrickson–Lattman distribution and the generalized von Mises distribution of order two, which has been studied in the statistical literature. Recognizing this connection allows the Hendrickson–Lattman distribution to be expressed in an alternative form which is easier to interpret, as it involves the location and concentration parameters of the component von Mises distributions. It also allows clarification of the conditions for bimodality and access to a simplified analytical method for evaluating the trigonometric moments of the distribution, the first of which is required for computing the best Fourier synthesis in the presence of phase, but not amplitude, uncertainty. Full Article text