Coronavirus: the week explained - 10 April  The Guardian

Ancient underwater landslides help Brit scientists predict tsunamis  Metro.co.uk

Scientists Explain Why Earth’s Magnetic North Pole Is Drifting Away From Canada Towards Siberia  Mashable India

Explained: How coronavirus lockdown reduced Earth’s seismic noise levels  The Indian Express

Ancient underwater landslides help predict tsunami risk  Aberdeen Evening Express

Did the earth move for you? British Geological Survey has asked if Cumbrians felt an earth tremor last week  News & Star

The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is needed. Here, the crystal structure of PA5086 is reported at 1.90 Å resolution. A structural comparison of the three PldB immunity proteins showed vast divergences in their electrostatic potential surfaces. This interesting phenomenon provides an explanation of the stockpiling mechanism of T6SS immunity proteins.

The transmembrane intracellular lectin ER–Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosaccharides have revealed protein–protein and protein–sugar binding modes. In contrast, the polypeptide-recognition mechanism of MCFD2 remains largely unknown. Here, a 1.60 Å resolution crystal structure of the ERGIC-53CRD–MCFD2 complex is reported, along with three other crystal forms. Comparison of these structures with those previously reported reveal that MCFD2, but not ERGIC-53–CRD, exhibits significant conformational plasticity that may be relevant to its accommodation of various polypeptide ligands.

The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and l-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.

Solution structure of β-amylase 2 from Arabidopsis thaliana shows the role of the conserved N-terminus in enzyme tetramer formation.

The crystal and solution SAXS structures of a fragment of human leucocyte common antigen-related protein show that it is less flexible than the homologous proteins tyrosine phosphatase receptors δ and σ.

Structures of the immunodominant protein P46 from M. hyopneumoniae has been determined by X-ray crystallography and it is shown that P46 can bind a diversity of oligosaccharides, particularly xylose, which exhibits a very high affinity for this protein. Structures of a monoclonal antibody, both alone and in complex with P46, that was raised against M. hyopnemoniae cells and specifically recognizes P46 are also reported.

From the perspective of a young(ish) structural biologist who currently specialises in macromolecular X-ray crystallography, are the best years of crystallography over? Some evidence and hopefully thought-provoking analysis is presented here on the subject.

The paper reports the structure of a Δ1-pyrroline-2-carboxylate reductase from the archaeon Thermococcus litoralis, a key enzyme involved in the second step of trans-4-Hydroxy-L-proline metabolism, conserved in archaea, bacteria and humans.

The asymmetric unit of the title MOF, [Zn5(C14H5NO10S2)2(OH)2(H2O)10]n comprises three ZnII atoms, one of which is located on a centre of inversion, a tetra-negative carboxyl­ate ligand, one μ3-hydroxide and five water mol­ecules, each of which is coordinated. The ZnII atom, lying on a centre of inversion, is coordinated by trans sulfoxide-O atoms and four water mol­ecules in an octa­hedral geometry. Another ZnII atom is coordinated by two carboxyl­ate-O atoms, one hy­droxy-O, one sulfoxide-O and a water-O atom to define a distorted trigonal–bipyramidal geometry; a close Zn⋯O(carboxyl­ate) inter­action derived from an asymmetrically coordinating ligand (Zn—O = 1.95 and 3.07 Å) suggests a 5 + 1 coordination geometry. The third ZnII atom is coordinated in an octa­hedral fashion by two hy­droxy-O atoms, one carboxyl­ate-O, one sulfoxide-O and two water-O atoms, the latter being mutually cis. In all, the carboxyl­ate ligand binds six ZnII ions leading to a three-dimensional architecture. In the crystal, all acidic donors form hydrogen bonds to oxygen acceptors to contribute to the stability of the three-dimensional architecture.

In the mol­ecule of the title N,N'-disubstituted imidazol-2-yl­idene palladium(II) complex, [PdBr2(C21H24N4O)]·CH2Cl2, the palladium(II) atom adopts a slightly distorted square-planar coordination (r.m.s. deviation = 0.0145 Å), and the five-membered chelate ring is almost planar [maximum displacement = 0.015 (8) Å]. The mol­ecular conformation is enforced by intra­molecular C—H⋯Br hydrogen bonds. In the crystal, complex mol­ecules and di­chloro­methane mol­ecules are linked into a three-dimensional network by C—H⋯O and C—H⋯Br hydrogen bonds.

The mol­ecular structure of the title compound, C18H15ISi, which crystallizes in the space group C2/c, does not exhibit any unusual features. Two weak C—H⋯π inter­actions may help to consolidate the packing. The present structure is not isostructural with the known Ph3SiX (X = F, Cl or Br) compounds.

The asymmetric unit of the title compound (systematic name: 3,3,8,8-tetra­methyl-1,4,6,9-tetra­oxa-λ4-bora­spiro­[4.4]nonane-2,7-dione tetra­hydrate), C8H12BO6·4H2O, consists of half a bis­(2-methyl­lactato)borate mol­ecule and two water mol­ecules of solvation. In the crystal, O—H⋯O hydrogen bonds link the components into a three-dimensional network.

In the title compound, [Zn(C9H6O4)]n, the ZnII cations are coordinated in a tetra­hedral fashion by carboxyl­ate O-atom donors belonging to four 4-(carb­oxy­meth­yl) benzoate (4-cmb) ligands. Each 4-cmb ligand binds to four ZnII cations in an exo­tetra­dentate fashion to create a non-inter­penetrated [Zn(4-cmb)]n three-dimensional coordination polymer network with a new non-diamondoid 66 topology. The crystal studied was refined as an inversion twin.

In the title compound, C16H19NSe, the dihedral angle between the benzene rings is 66.49 (12) and a weak intra­molecular N—H⋯Se hydrogen bond generates an S(6) ring. In the crystal, weak N—H⋯N hydrogen bonds link the mol­ecules into [100] chains.

In the title compound, [Pd(C10H24N4)]I2·H2O, the PdII ion is four-coordinated in a slightly distorted square-planar coordination environment defined by four N atoms from a 1,4,8,11-tetra­aza­cyclo­tetra­decane ligand. The cationic complex, two I− anions and the solvent water mol­ecule are linked through inter­molecular hydrogen bonds into a three-dimensional network structure.

The title tetra­nuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex mol­ecules, A and B, in the asymmetric unit together with 1.5 mol­ecules of chloro­form. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex mol­ecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex mol­ecules are linked by a number of C—H⋯O hydrogen bonds within the layers and between the layers, forming a supra­molecular three-dimensional structure.

The synthesis and crystal structure of the title PtII complex, [Pt(C23H16N)Cl(CH3CN)], based on the C,N-chelating 2,4,6-tri­phenyl­pyridine as the primary ligand, is described. The central PtII atom is in a distorted square-planar coordination environment. In the crystal, mol­ecules are arranged via a metallophilic inter­action between platinum atoms with a Pt⋯Pt contact of 7.052 (2) Å. In addition, a π–π inter­action occurs.

The title magnesium complex, [Mg(C21H20NO2)2(C4H8O)]n, exhibits two N,O-bidentate 2-(di­methyl­amino)-α,α-di­phenyl­benzene­methano­late ligands, form­ing two six-membered chelate rings. The distorted square-pyramidal coordination sphere of the MgII atom is completed by the O atom of a tetra­hydro­furan ligand, with its O atom in the apical position. The O and N atoms are in a mutual trans arrangement. Except for two C—H⋯π inter­actions, no significant inter­molecular inter­actions are observed in the crystal.

The asymmetric unit of the title compound {systematic name: sodium [2-({2-[(1-carboxyl­ato-2-methyl-2-sulfanidylprop­yl)amino]­eth­yl}amino)-3-methyl-3-sulf­an­idyl­butano­ato-κ4S,N,N',S']indate(III) tetra­hydrate}, Na[In(C12H20N2O4S2)]·4H2O, contains four indate(III) complex anions {[In(d-ebp)]−; d-H4ebp = N,N'-ethyelenebis(d-penicillamine)], four sodium(I) cations and sixteen water mol­ecules. The indate(III) anions and sodium cations are alternately connected through coordination bonds between Na+ ions and the carboxyl­ate groups of the complex anions, forming an infinite sixfold right-handed helix along the c-axis direction. In the crystal, the helices are linked by O—H⋯O hydrogen bonds between water mol­ecules bound to Na+ ions and carboxyl­ate groups. The crystal studied was twinned via a twofold axis about [001].

In the title compound, [Pd(C7H3NO4)(C10H8N2)]·H2O, the PdII cation is four-coordinated in a distorted square-planar coordination geometry defined by the two N atoms of the 2,2'-bi­pyridine ligand, one O atom and one N atom from the pyridine-2,6-di­carboxyl­ate anion. The complex and solvent water mol­ecule are linked by inter­molecular hydrogen bonds. In the crystal, the complex mol­ecules are stacked in columns along the a axis.

The title compound, C25H22N2O2Se, crystallizes in the space group P21/c with one mol­ecule in the asymmetric unit. The compound was synthesized by the addition of phenyl­selenyl bromide to a cyanamide. The phenyl­selenyl portion and the cyano group, as well as the ketone functional group in the cyclo­hexa-2,5-dien-1-one portion of the structure, are disordered, with occupancy factors of 0.555 (14) and 0.445 (14).

In the title compound, C21H20BrNO4S, a key inter­mediate in the synthesis of the widely used β-lactamase inhibitor tazobactam, the five-membered thia­zolidine ring adopts an envelope conformation and the four-membered azetidine ring is in a distorted planar conformation. The crystal structure features C—H⋯O hydrogen bonds and a weak C—H⋯π inter­action.

The title hepta­nuclear alkoxido(oxido)vanadium(V) oxide cluster complex, [V7(C10H19O)O17(C18H24N2)3]·CH3CN, was obtained by the reaction of [V8O20(C18H24N2)4] with 4-tert-butyl­cyclo­hexa­nol (mixture of cis and trans) in a mixed CHCl3/CH3CN solvent. The complex has a V7O18N6 core with approximately Cs symmetry, which is composed of two VO4 tetra­hedra, two VO6 octa­hedra and three VO4N2 octa­hedra. In the crystal, these complexes are linked together by weak inter­molecular C—H⋯O hydrogen bonds between the 4,4'-di-tert-butyl-2,2'-bi­pyridine ligand and the V7O18N6 core, forming a one-dimensional network along the c-axis direction. Besides the complex, the asymmetric unit contains one CH3CN solvent mol­ecule. The contribution of other disordered solvent mol­ecules to the scattering was removed using the SQUEEZE option in PLATON [Spek (2015). Acta Cryst. C71, 9–18]. The unknown solvent mol­ecules are not considered in the chemical formula and other crystal data.

The solvated centrosymmmtric title compound, [Li2(C24H34O4P)2(C10H8N2)2]·2C7H8, was formed in the reaction between {Li[(2,6-iPr2C6H3-O)2POO](MeOH)3}(MeOH) and 2,2'-bi­pyridine (bipy) in toluene. The structure has monoclinic (P21/n) symmetry at 120 K and the asymmetric unit consists of half a complex mol­ecule and one mol­ecule of toluene solvent. The diaryl phosphate ligand demonstrates a μ-κO:κO'-bridging coordination mode and the 2,2'-bi­pyridine ligand is chelating to the Li+ cation, generating a distorted tetra­hedral LiN2O2 coordination polyhedron. The complex exhibits a unique dimeric Li2O4P2 core. One isopropyl group is disordered over two orientations in a 0.621 (4):0.379 (4) ratio. In the crystal, weak C—H⋯O and C—H⋯π inter­actions help to consolidate the packing. Catalytic systems based on the title complex and on the closely related complex {Li[(2,6-iPr2C6H3-O)2POO](MeOH)3}(MeOH) display activity in the ring-opening polymerization of ∊-caprolactone and l-dilactide.

The title binuclear CoIII complex, [Co2(C9H8BrNOS)2(C18H16Br2N2O2S2)]·C3H7NO, with a Schiff base ligand formed in situ from cyste­amine (2-amino­ethane­thiol) and 5-bromo­salicyl­aldehyde crystallizes in the space group P21. It was found that during the synthesis the ligand undergoes spontaneous oxidation, forming the new ligand H2L' having an S—S bond. Thus, the asymmetric unit consists of one Co2(L)2(L') mol­ecule and one DMF solvent mol­ecule. Each CoIII ion has a slightly distorted octa­hedral S2N2O2 coordination geometry. In the crystal, the components are linked into a three-dimensional network by several S⋯ Br, C⋯ Br, C—H⋯Br, short S⋯C (essentially shorter than the sum of the van der Waals radii for the atoms involved) contacts as well by weak C—H⋯O hydrogen bonds. The crystal studied was refined as an inversion twin.

The title compound (systematic name: bis­{2-[4-(acet­yloxy)-1H-indol-3-yl]ethan-1-aminium} but-2-enedioate), 2C14H19N2O2+·C4H2O42−, has a single protonated psilacetin cation and one half of a fumarate dianion in the asymmetric unit. There are N—H⋯O hydrogen bonds between the ammonium H atoms and the fumarate O atoms, as well as N—H⋯O hydrogen bonds between the indole H atoms and the fumarate O atoms. The hydrogen bonds hold the ions together in infinite one-dimensional chains along [111].

The asymmetric units of the title compounds, trans-di­aqua­(3-benzyl-1,3,5,8,12-penta­aza­cyclo­tetra­decane-κ4N1,N5,N8,N12)copper(II) isophthalate monohydrate, [Cu(C16H29N5)(H2O)2](C8H4O4)·H2O, (I), and trans-di­aqua­[3-(pyridin-3-ylmeth­yl)-1,3,5,8,12-penta­aza­cyclo­tetra­decane-κ4N1,N5,N8,N12]copper(II) iso­phthalate 0.9-hydrate, [Cu(C15H28N6)(H2O)2](C8H4O4)·0.9H2O, (II) consist of one di­aqua macrocyclic cation, one di­carboxyl­ate anion and uncoordinated water mol­ecule(s). In each compound, the metal ion is coordinated by the four secondary N atoms of the macrocyclic ligand and the mutually trans O atoms of the water mol­ecules in a tetra­gonally distorted octa­hedral geometry. The average equatorial Cu—N bond lengths are significantly shorter than the average axial Cu—O bond lengths [2.020 (9) versus 2.495 (12) Å and 2.015 (4) versus 2.507 (7) Å for (I) and (II), respectively]. The coordinated macrocyclic ligand in the cations of both compounds adopts the most energetically favorable trans-III conformation. In the crystals, the complex cations and counter-anions are connected via hydrogen-bonding inter­actions between the N—H groups of the macrocycles and the O—H groups of coordinated water mol­ecules as the proton donors and the O atoms of the carboxyl­ate as the proton acceptors. Additionally, as a result of O—H⋯O hydrogen bonding with the coordinated and water mol­ecules of crystallization, the isophthalate dianions form layers lying parallel to the (overline{1}01) and (100) planes in (I) and (II), respectively.

Six different rare-earth oxyapatites, including Ca2RE8(SiO4)6O2 (RE = La, Nd, Sm, Eu, or Yb) and NaLa9(SiO4)6O2, were synthesized using solution-based processes followed by cold pressing and sinter­ing. The crystal structures of the synthesized oxyapatites were determined from powder X-ray diffraction (P-XRD) and their chemistries verified with electron probe microanalysis (EPMA). All the oxyapatites were isostructural within the hexa­gonal space group P63/m and showed similar unit-cell parameters. The isolated [SiO4]4− tetra­hedra in each crystal are linked by the cations at the 4f and 6h sites occupied by RE3+ and Ca2+ in Ca2RE8(SiO4)6O2 or La3+ and Na+ in NaLa9(SiO4)6O2. The lattice parameters, cell volumes, and densities of the synthesized oxyapatites fit well to the trendlines calculated from literature values.

In the crystal structure of the isostructural title compounds, namely {2,6-bis­[(di-tert-butyl­phosphan­yl)­oxy]-4-hy­droxy­phen­yl}chlorido­palladium(II), [Pd(C22H39O3P2)Cl], 1, and {2,6-bis­[(di-tert-butyl­phosphan­yl)­oxy]-4-hy­droxy­phen­yl}chlorido­platinum(II), [Pt(C22H39O3P2)Cl], 2, the metal centres are coordinated in a distorted square-planar fashion by the POCOP pincer fragment and the chloride ligand. Both complexes form strong hydrogen-bonded chain structures through an inter­action of the OH group in the 4-position of the aromatic POCOP backbone with the halide ligand.

Reductive cyclization of 1,3,5-triphenyl- and 3-(2-meth­oxy­phen­yl)-1,5-di­phenyl­pentane-1,5-diones by zinc in acetic acid medium leads to the formation of 1,2,4-tri­phenyl­cyclo­pentane-1,2-diol [1,2,4-Ph3C5H5-1,2-(OH)2, C23H22O2, (I)] and 4-(2-meth­oxy­phen­yl)-1,2-di­phenyl­cyclo­pentane-1,2-diol [4-(2-MeOC6H4)-1,2-Ph2C5H5-1,2-(OH)2, C24H24O3, (II)]. Their single crystals have been obtained by crystallization from a THF/hexane solvent mixture. Diols (I) and (II) crystallize in ortho­rhom­bic (Pbca) and triclinic (Poverline{1}) space groups, respectively, at 150 K. Their asymmetric units comprise one [in the case of (I)] and three [in the case of (II)] crystallographically independent mol­ecules of the achiral (1R,2S,4r)-diol isomer. Each hydroxyl group is involved in one intra­molecular and one inter­molecular O—H⋯O hydrogen bond, forming one-dimensional chains. Compounds (I) and (II) have been used successfully as precatalyst activators for the ring-opening polymerization of ∊-caprolactone.

The crystal structures of dirubidium potassium dysprosium bis­(vanadate), Rb2KDy(VO4)2, and caesium potassium gadolinium bis­(vanadate), Cs1.52K1.48Gd(VO4)2, were solved from single-crystal X-ray diffraction data. Both compounds, synthesized by the reactive flux method, crystallize in the space group Poverline{3}m1 with the glaserite structure type. VO4 tetra­hedra are linked to DyO6 or GdO6 octa­hedra by common vertices to form sheets stacking along the c axis. The large twelve-coordinate Cs+ or Rb+ cations are sandwiched between these layers in tunnels along the a and b axes, while the K+ cations, surrounded by ten oxygen atoms, are localized in cavities.

The title mol­ecule crystallizes as a di­methyl­formamide monosolvate, C19H14N2O6S2·C3H7NO. The mol­ecule was expected to adopt mirror symmetry but slightly different conformational characteristics of the condensed benzo­thia­zine ring lead to point group symmetry 1. In the crystal, mol­ecules form two types of stacking dimers with distances of 3.464 (2) Å and 3.528 (2) Å between π-systems. As a result, columns extending parallel to [100] are formed, which are connected to inter­mediate di­methyl­formamide solvent mol­ecules by C—H⋯O inter­actions.

The title compound, C31H30N2S2O6, possesses crystallographically imposed twofold symmetry with the two C atoms of the central benzene ring and the C atom of its methyl substituent lying on the twofold rotation axis. The two dansyl groups are twisted away from the plane of methyl­phenyl bridging unit in opposite directions. The three-dimensional arrangement in the crystal is mainly stabilized by weak hydrogen bonds between the sulfonyl oxygen atoms and the hydrogen atoms from the N-methyl groups. Stacking of the dansyl group is not observed. From the DFT calculations, the HOMO–LUMO energy gap was found to be 2.99 eV and indicates n→π* and π→π* transitions within the mol­ecule.

The asymmetric unit of the title 1:1 solvate, C14H14N4O2·C6H6 [systematic name of the oxalamide mol­ecule: N,N'-bis­(pyridin-4-ylmeth­yl)ethanedi­amide], comprises a half mol­ecule of each constituent as each is disposed about a centre of inversion. In the oxalamide mol­ecule, the central C2N2O2 atoms are planar (r.m.s. deviation = 0.0006 Å). An intra­molecular amide-N—H⋯O(amide) hydrogen bond is evident, which gives rise to an S(5) loop. Overall, the mol­ecule adopts an anti­periplanar disposition of the pyridyl rings, and an orthogonal relationship is evident between the central plane and each terminal pyridyl ring [dihedral angle = 86.89 (3)°]. In the crystal, supra­molecular layers parallel to (10overline{2}) are generated owing the formation of amide-N—H⋯N(pyrid­yl) hydrogen bonds. The layers stack encompassing benzene mol­ecules which provide the links between layers via methyl­ene-C—H⋯π(benzene) and benzene-C—H⋯π(pyrid­yl) inter­actions. The specified contacts are indicated in an analysis of the calculated Hirshfeld surfaces. The energy of stabilization provided by the conventional hydrogen bonding (approximately 40 kJ mol−1; electrostatic forces) is just over double that by the C—H⋯π contacts (dispersion forces).

The asymmetric unit of the title compound, C12H22N+·CH3O3S−, consists of three (3,5-di­methyl­adamantan-1-yl)ammonium cations, C12H22N+, and three methane­sulfonate anions, CH3O3S−. In the crystal, the cations and anions associate via N—H⋯O hydrogen bonds into layers, parallel to the (001) plane, which include large supra­molecular hydrogen-bonded rings.

Three new isotypic heteropolynuclear complexes, namely penta­aqua­carbonato­penta­kis­(glycinehydroxamato)nitrato­penta­copper(II)lanthanide(III) x-hydrate, [LnCu5(GlyHA)5(CO3)(NO3)(H2O)5]·xH2O (GlyHA2− is glycine­hydrox­amate, N-hy­droxy­glycinamidate or amino­aceto­hydroxamate, C2H4N2O22−), with lanthanide(III) (LnIII) = gadolinium (Gd, 1, x = 3.5), dysprosium (Dy, 2, x = 3.28) and holmium (Ho, 3, x = 3.445), within a 15-metallacrown-5 class were obtained on reaction of lanthanide(III) nitrate, copper(II) acetate and sodium glycinehydroxamate. Complexes 1–3 contain five copper(II) ions and five bridging GlyHA2− anions, forming a [CuGlyHA]5 metallamacrocyclic core. The LnIII ions are coordinated to the metallamacrocycle through five O-donor hydroxamates. The electroneutrality of complexes 1–3 is achieved by a bidentate carbonate anion coordinated to the LnIII ion and a monodentate nitrate anion coordinated apically to one of the copper(II) ions of the metallamacrocycle. The lattice parameters of complexes 1–3 are similar to those previously reported for an EuIII–CuII 15-metallacrown-5 complex with glycine­hydroxamate of proposed composition [EuCu5(GlyHA)5(OH)(NO3)2(H2O)4]·3.5H2O [Stemmler et al. (1999). Inorg. Chem. 38, 2807–2817]. High-quality X-ray data obtained for 1–3 have allowed a re-evaluation of the X-ray data solution proposed earlier for the EuCu5 complex and suggest that the formula is actually [EuCu5(GlyHA)5(CO3)(NO3)(H2O)5]·3.5H2O.

The isostructural title compounds, poly[piperazin-1-ium [di-μ-bromido-caesium]], {(C4H11N2)[CsBr2]}n, and poly[piperazin-1-ium [di-μ-bromido-rubidium]], {(C4H11N2)[RbBr2]}n, contain singly-protonated piperazin-1-ium cations and unusual ABr6 (A = Cs or Rb) trigonal prisms. The prisms are linked into a distinctive `curtain wall' arrangement propagating in the (010) plane by face and edge sharing. In each case, a network of N—H⋯N, N—H⋯Br and N—H⋯(Br,Br) hydrogen bonds consolidates the structure.

Bidentate and tridentate coordination of a 2,4-di-tert-butyl-substituted bridging amine bis­(phenolate) ligand to a palladium(II) center are observed within the same crystal structure, namely di­chlorido­({6,6'-[(ethane-1,2-diylbis(methyl­aza­nedi­yl)]bis­(methyl­ene)}bis­(2,4-di-tert-butyl­phenol))palladium(II) chlorido­(2,4-di-tert-butyl-6-{[(2-{[(3,5-di-tert-butyl-2-hy­droxy­phen­yl)meth­yl](meth­yl)amino}­eth­yl)(meth­yl)amino]­meth­yl}phenolato)palladium(II) methanol 1.685-solvate 0.315-hydrate, [PdCl2(C34H56N2O2)][PdCl(C34H55N2O2)]·1.685CH3OH·0.315H2O. Both complexes exhibit a square-planar geometry, with unbound phenol moieties participating in inter­molecular hydrogen bonding with co-crystallized water and methanol. The presence of both κ2 and κ3 coordination modes arising from the same solution suggest a dynamic process in which phenol donors may coordinate or dissociate from the metal center, and offers insight into catalyst speciation throughout Pd-mediated processes. The unit cell contains di­chlorido­({6,6'-[(ethane-1,2-diylbis(methyl­aza­nedi­yl)]bis­(methyl­ene)}bis­(2,4-di-tert-butyl­phenol))palladium(II), {(L2)PdCl2}, and chlorido­(2,4-di-tert-butyl-6-{[(2-{[(3,5-di-tert-butyl-2-hy­droxy­phen­yl)meth­yl](methyl)amino}eth­yl)(meth­yl)amino]­meth­yl}phenolato)palladium(II), {(L2X)PdCl}, mol­ecules as well as fractional water and methanol solvent mol­ecules.

Six new 1-aroyl-4-(4-meth­oxy­phen­yl)piperazines have been prepared, using coupling reactions between benzoic acids and N-(4-meth­oxy­phen­yl)piperazine. There are no significant hydrogen bonds in the structure of 1-benzoyl-4-(4-meth­oxy­phen­yl)piperazine, C18H20N2O2, (I). The mol­ecules of 1-(2-fluoro­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H19FN2O2, (II), are linked by two C—H⋯O hydrogen bonds to form chains of rings, which are linked into sheets by an aromatic π–π stacking inter­action. 1-(2-Chloro­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H19ClN2O2, (III), 1-(2-bromo­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H19BrN2O2, (IV), and 1-(2-iodo­benzo­yl)-4-(4-meth­oxyphen­yl)piperazine, C18H19IN2O2, (V), are isomorphous, but in (III) the aroyl ring is disordered over two sets of atomic sites having occupancies of 0.942 (2) and 0.058 (2). In each of (III)–(V), a combination of two C—H⋯π(arene) hydrogen bonds links the mol­ecules into sheets. A single O—H⋯O hydrogen bond links the mol­ecules of 1-(2-hy­droxy­benzo­yl)-4-(4-meth­oxy­phen­yl)piperazine, C18H20N2O3, (VI), into simple chains. Comparisons are made with the structures of some related compounds.

The sterically hindered silicon compound 2-methyl-1,1,2,3,3-penta­phenyl-2-sila­propane, C33H30Si (I), was prepared via the reaction of two equivalents of di­phenyl­methyl­lithium (benzhydryllithium) and di­chloro­methyl­phenyl­silane. This bis­benzhydryl-substituted silicon compound was then reacted with tri­fluoro­methane­sulfonic acid, followed by hydrolysis with water to give the silanol 2-methyl-1,1,3,3-tetra­phenyl-2-silapropan-2-ol, C27H26OSi (II). Key geometric features for I are the Si—C bond lengths that range from 1.867 (2) to 1.914 (2) Å and a τ4 descriptor for fourfold coordination around the Si atom of 0.97 (indicating a nearly perfect tetra­hedron). Key geometric features for compound II include Si—C bond lengths that range from 1.835 (4) to 1.905 (3) Å, a Si—O bond length of 1.665 (3) Å, and a τ4 descriptor for fourfold coordination around the Si atom of 0.96. In compound II, there is an intra­molecular C—H⋯O hydrogen bond present. In the crystal of I, mol­ecules are linked by two pairs of C—H⋯π inter­actions, forming dimers that are linked into ribbons propagating along the b-axis direction. In the crystal of II, mol­ecules are linked by C—H⋯π and O—H⋯π inter­actions that result in the formation of ribbons that run along the a-axis direction.

Lapachol acetate [systematic name: 3-(3-methyl­but-2-en­yl)-1,4-dioxonaph­thalen-2-yl acetate], C17H16O4, was prepared using a modified high-yield procedure and its crystal structure is reported for the first time 80 years after its first synthesis. The full spectroscopic characterization of the mol­ecule is reported. The mol­ecular conformation shows little difference with other lapachol derivatives and lapachol itself. The packing is directed by inter­molecular π–π and C—H⋯O inter­actions, as described by Hirshfeld surface analysis. The former inter­actions make the largest contributions to the total packing energy in a ratio of 2:1 with respect to the latter.

The synthesis, crystal structure and structural motif of two thio­phene-based cyano­acrylate derivatives, namely, ethyl (E)-2-cyano-3-(3-methyl­thio­phen-2-yl)acrylate (1), C11H11NO2S, and ethyl (E)-2-cyano-3-(thio­phen-2-yl)acrylate (2), C10H9NO2S, are reported. Derivative 1 crystallized with two independent molecules in the asymmetric unit, and derivative 2 represents a new monoclinic (C2/m) polymorph. The mol­ecular conformations of 1 and the two polymorphs of 2 are very similar, as all non-H atoms are planar except for the methyl of the ethyl groups. The inter­molecular inter­actions and crystal packing of 1 and 2 are described and compared with that of the reported monoclinic (C2/m) polymorph of derivative 2 [Castro Agudelo et al. (2017). Acta Cryst. E73, 1287–1289].