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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-

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.




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Synthesis and crystal structure of sodium (ethane-1,2-di­yl)bis­[(3-meth­oxy­prop­yl)phosphinodi­thiol­ate] octa­hydrate

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.




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Triclinic polymorph of bis­[2-methyl-3-(pyridin-2-yl)imidazo[1,5-a]pyridin-2-ium] tetra­chloridocadmium(II)

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.




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Crystal structure of a hydrogen-bonded 2:1 co-crystal of 4-nitro­phenol and 4,4'-bi­pyridine

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.




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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

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.




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Crystal structures of two different multi-component crystals consisting of 1-(3,4-di­meth­oxy­benz­yl)-6,7-di­meth­oxy­iso­quinoline and fumaric acid

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’.




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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)

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.




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Crystal structure of N,N',N''-tri­cyclo­prop­ylbenzene-1,3,5-tricarboxamide

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.




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Crystal structure of catena-poly[[di­aqua­di­imida­zole­cobalt(II)]-μ2-2,3,5,6-tetra­bromo­benzene-1,4-di­carboxyl­ato]

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.




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Crystal structure, Hirshfeld surface analysis, and DFT and mol­ecular docking studies of 6-cyanona­phthalen-2-yl 4-(benz­yloxy)benzoate

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.




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Crystal structure of an aceto­nitrile solvate of 2-(3,4,5-triphen­ylphen­yl)acetic acid

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.




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Synthesis and crystal structure of 1,3,5-tris­[(1H-benzotriazol-1-yl)meth­yl]-2,4,6-tri­ethyl­benzene

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.




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Crystal structure of [Ni(OH2)6]Cl2·(18-crown-6)2·2H2O

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+.




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Synthesis and structure of trans-2,5-di­methyl­piperazine-1,4-diium di­hydrogen diphosphate

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.




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Structural multiplicity in a solvated hydrate of the anti­retroviral protease inhibitor Lopinavir

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.




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Salts of 2-amino-5-iodo­pyridinium

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.




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Synthesis, crystal structure and Hirshfeld surface analysis of 2-{4-[(2-chloro­phen­yl)meth­yl]-3-methyl-6-oxopyridazin-1-yl}-N-phenyl­acetamide

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.




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Crystal structures and photophysical properties of mono- and dinuclear ZnII complexes flanked by tri­ethyl­ammonium

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.




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Crystal structure and Hirshfeld surface analysis of the salt 2-iodo­ethyl­ammonium iodide – a possible side product upon synthesis of hybrid perovskites

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].




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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

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.




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The cadmium oxidotellurates(IV) Cd5(TeO3)4(NO3)2 and Cd4Te5O14

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.




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Crystal structure and Hirshfeld surface analysis of bis­(benzoyl­acetonato)(ethanol)dioxidouranium(VI)

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.




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Synthesis and structure of penta­kis­(2-aminopyridinium) nona­vanado(V)tellurate(VI)

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.




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Multi-segment cooling design of a reflection mirror based on the finite-element method

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.




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Hard X-ray single-shot spectrometer of PAL-XFEL

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.




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Reducing heat load density with asymmetric and inclined double-crystal monochromators: principles and requirements revisited

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.




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Development of MHz X-ray phase contrast imaging at the European XFEL

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.




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Review and experimental comparison of speckle-tracking algorithms for X-ray phase contrast imaging

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.




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The use of ethanol as contrast enhancer in Synchrotron X-ray phase-contrast imaging leads to heterogeneous myocardial tissue shrinkage: a case report

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.




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Development and testing of a dual-frequency, real-time hardware feedback system for the hard X-ray nanoprobe beamline of the SSRF

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.




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Enhancing the Efficiency of a Wavelength-Dispersive Spectrometer based upon a Slit-less Design Using a Single-Bounce Monocapillary

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.




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Form factor of helical structures and twisted fibres

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.




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The International Tables Symmetry Database

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.




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Time-resolved high-energy X-ray diffraction studies of ultrathin Ni ferrite films on MgO(001)

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.




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Texture measurements on quartz single crystals to validate coordinate systems for neutron time-of-flight texture analysis

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.




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An electropneumatic cleaning device for piezo-actuator-driven picolitre-droplet dispensers

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.




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Van Vleck analysis of angularly distorted octahedra using VanVleckCalculator

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.




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POMFinder: identifying polyoxometallate cluster structures from pair distribution function data using explainable machine learning

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.




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Operation model of a skew-symmetric split-crystal neutron interferometer

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.




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ProLEED Studio: software for modeling low-energy electron diffraction patterns

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.




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Fast nanoscale imaging of strain in a multi-segment heterostructured nanowire with 2D Bragg ptychography

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.




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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

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.




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BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis

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.




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Refinement of X-ray and electron diffraction crystal structures using analytical Fourier transforms of Slater-type atomic wavefunctions in Olex2

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.




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A simple solution to the Rietveld refinement recipe problem

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.




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INSIGHT: in situ heuristic tool for the efficient reduction of grazing-incidence X-ray scattering data

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.




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Time-resolved AUSAXS at BL28XU at SPring-8

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.




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The Pixel Anomaly Detection Tool: a user-friendly GUI for classifying detector frames using machine-learning approaches

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.




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Crystals in the community and the classroom

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.




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A note on the Hendrickson–Lattman phase probability distribution and its equivalence to the generalized von Mises distribution

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.