rat The crystal structure of (RS)-7-chloro-2-(2,5-dimethoxyphenyl)-2,3-dihydroquinazolin-4(1H)-one: two hydrogen bonds generate an elegant three-dimensional framework structure By scripts.iucr.org Published On :: 2019-05-21 In the title compound, C61H15ClN2O3, the heterocyclic ring adopts an envelope conformation, folded across the N⋯N line, with the 2,5-dimethoxyphenyl unit occupying a quasi-axial site. There are two N—H⋯O hydrogen bonds in the structure: one hydrogen bond links molecules related by a 41 screw axis to form a C(6) chain, and the other links inversion-related pairs of molecules to form an R22(8) ring. The ring motif links all of the chains into a continuous three-dimensional framework structure. Comparisons are made with the structures of some related compounds. Full Article text
rat Crystal structure and Hirshfeld surface analysis of tris(2,2'-bipyridine)nickel(II) bis(1,1,3,3-tetracyano-2-ethoxypropenide) dihydrate By scripts.iucr.org Published On :: 2019-05-24 The title compound, [Ni(C10H8N2)3](C9H5N4O)2·2H2O, crystallizes as a racemic mixture in the monoclinic space group C2/c. In the crystal, the 1,1,3,3-tetracyano-2-ethoxypropenide anions and the water molecules are linked by O—H⋯N hydrogen bonds, forming chains running along the [010] direction. The bpy ligands of the cation are linked to the chain via C—H⋯π(cation) interactions involving the CH3 group. The intermolecular interactions were investigated by Hirshfeld surface analysis and two-dimensional fingerprint plots. Full Article text
rat Crystal structure of methyl α-l-rhamnopyranosyl-(1→2)-α-l-rhamnopyranoside monohydrate By scripts.iucr.org Published On :: 2019-05-24 The title compound, C13H24O9·H2O, a structural model for part of bacterial O-antigen polysaccharides from Shigella flexneri and Escherichia coli, crystallizes with four independent disaccharide molecules and four water molecules in the asymmetric unit. The conformation at the glycosidic linkage joining the two rhamnosyl residues is described by the torsion angles φH of 39, 30, 37 and 37°, and ψH of −32, −35, −31 and −32°, which are the major conformation region known to be populated in an aqueous solution. The hexopyranose rings have the 1C4 chair conformation. In the crystal, the disaccharide and water molecules are associated through O—H⋯O hydrogen bonds, forming a layer parallel to the bc plane. The layers stack along the a axis via hydrophobic interactions between the methyl groups. Full Article text
rat Bis(4-acetoxy-N,N-dimethyltryptammonium) fumarate: a new crystalline form of psilacetin, an alternative to psilocybin as a psilocin prodrug By scripts.iucr.org Published On :: 2019-05-31 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]. Full Article text
rat Crystal structure of 3,14-diethyl-2,13-diaza-6,17-diazoniatricyclo[16.4.0.07,12]docosane dinitrate dihydrate from synchrotron X-ray data By scripts.iucr.org Published On :: 2019-05-31 The crystal structure of title salt, C22H46N42+·2NO3−·2H2O, has been determined using synchrotron radiation at 220 K. The structure determination reveals that protonation has occurred at diagonally opposite amine N atoms. The asymmetric unit contains half a centrosymmetric dication, one nitrate anion and one water molecule. The molecular dication, C22H46N42+, together with the nitrate anion and hydrate water molecule are involved in an extensive range of hydrogen bonds. The molecule is stabilized, as is the conformation of the dication, by forming intermolecular N—H⋯O, O—H⋯O, together with intramolecular N—H⋯N hydrogen bonds. Full Article text
rat Synthesis, characterization, and crystal structure of aquabis(4,4'-dimethoxy-2,2'-bipyridine)[μ-(2R,3R)-tartrato(4−)]dicopper(II) octahydrate By scripts.iucr.org Published On :: 2019-06-11 Typical electroless copper baths (ECBs), which are used to chemically deposit copper on printed circuit boards, consist of an aqueous alkali hydroxide solution, a copper(II) salt, formaldehyde as reducing agent, an l-(+)-tartrate as complexing agent, and a 2,2'-bipyridine derivative as stabilizer. Actual speciation and reactivity are, however, largely unknown. Herein, we report on the synthesis and crystal structure of aqua-1κO-bis(4,4'-dimethoxy-2,2'-bipyridine)-1κ2N,N';2κ2N,N'-[μ-(2R,3R)-2,3-dioxidosuccinato-1κ2O1,O2:2κ2O3,O4]dicopper(II) octahydrate, [Cu2(C12H12N2O2)2(C4H2O6)(H2O)]·8H2O, from an ECB mock-up. The title compound crystallizes in the Sohncke group P21 with one chiral dinuclear complex and eight molecules of hydrate water in the asymmetric unit. The expected retention of the tartrato ligand's absolute configuration was confirmed via determination of the absolute structure. The complex molecules exhibit an ansa-like structure with two planar, nearly parallel bipyridine ligands, each bound to a copper atom that is connected to the other by a bridging tartrato `handle'. The complex and water molecules give rise to a layered supramolecular structure dominated by alternating π stacks and hydrogen bonds. The understanding of structures ex situ is a first step on the way to prolonged stability and improved coating behavior of ECBs. Full Article text
rat Crystal structures of trans-diaqua(3-R-1,3,5,8,12-pentaazacyclotetradecane)copper(II) isophthalate hydrates (R = benzyl or pyridin-3-ylmethyl) By scripts.iucr.org Published On :: 2019-06-21 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. Full Article text
rat Crystal structure of bis[dihydrobis(pyrazol-1-yl)borato-κ2N2,N2'](1,10-phenanthroline-κ2N,N')zinc(II) By scripts.iucr.org Published On :: 2019-07-04 The asymmetric unit of the title compound, [Zn(C6H8N4B)2(C12H8N2)], comprises one half of a ZnII cation (site symmetry 2), one dihydrobis(pyrazol-1-yl)borate ligand in a general position, and one half of a phenanthroline ligand, the other half being completed by twofold rotation symmetry. The ZnII cation is coordinated in form of a slightly distorted octahedron by the N atoms of a phenanthroline ligand and by two pairs of N atoms of symmetry-related dihydrobis(pyrazol-1-yl)borate ligands. The discrete complexes are arranged into columns that elongate in the c-axis direction with a parallel alignment of the phenanthroline ligands, indicating weak π–π interactions. Full Article text
rat Crystal structure of poly[[[μ4-3-(1,2,4-triazol-4-yl)adamantane-1-carboxylato-κ5N1:N2:O1:O1,O1']silver(I)] dihydrate] By scripts.iucr.org Published On :: 2019-07-12 The heterobifunctional organic ligand, 3-(1,2,4-triazol-4-yl)adamantane-1-carboxylate (tr-ad-COO−), was employed for the synthesis of the title silver(I) coordination polymer, {[Ag(C13H16N3O2)]·2H2O}n, crystallizing in the rare orthorhombic C2221 space group. Alternation of the double μ2-1,2,4-triazole and μ2-η2:η1-COO− (chelating, bridging mode) bridges between AgI cations supports the formation of sinusoidal coordination chains. The AgI centers possess a distorted {N2O3} square-pyramidal arrangement with τ5 = 0.30. The angular organic linkers connect the chains into a tetragonal framework with small channels along the c-axis direction occupied by water molecules of crystallization, which are interlinked via O—H⋯O hydrogen bonds with carboxylate groups, leading to right- and left-handed helical dispositions. Full Article text
rat Crystal structure of poly[[(μ3-hydroxido-κ3O:O:O)(μ3-selenato-κ3O1:O2:O3)tris[μ3-2-(1,2,4-triazol-4-yl)acetato-κ3N1:N2:O]tricopper(II)] dihydrate] By scripts.iucr.org Published On :: 2019-07-16 The title coordination polymer, {[Cu3(C4H4N3O9)3(SeO4)(OH)]·2H2O}n or ([Cu3(μ3-OH)(trgly)3(SeO4)]·2H2O), crystallizes in the monoclinic space group P21/c. The three independent Cu2+ cations adopt distorted square-pyramidal geometries with {O2N2+O} polyhedra. The three copper centres are bridged by a μ3-OH anion, leading to a triangular [Cu3(μ3-OH)] core. 2-(1,2,4-Triazol-4-yl)acetic acid (trgly-H) acts in a deprotonated form as a μ3-κ3N1:N2:O ligand. The three triazolyl groups bridge three copper centres of the hydroxo-cluster in an N1:N2 mode, thus supporting the triangular geometry. The [Cu3(μ3-OH)(tr)3] clusters serve as secondary building units (SBUs). Each SBU can be regarded as a six-connected node, which is linked to six neighbouring triangles through carboxylate groups, generating a two-dimensional uninodal (3,6) coordination network. The selenate anion is bound in a μ3-κ3O1:O2:O3 fashion to the trinuclear copper platform. The [Cu3(OH)(trgly)3(SeO4)] coordination layers and guest water molecules are linked together by numerous O—H⋯O and C—H⋯O hydrogen bonds, leading to a three-dimensional structure. Full Article text
rat Crystal structure and magnetic properties of bis[butyltris(1H-pyrazol-1-yl)borato]iron(II) By scripts.iucr.org Published On :: 2019-08-20 The asymmetric unit of the title compound, [Fe(C13H18BN6)2], contains two half independent complex molecules. In each complex, the FeII atom is located on an inversion center and is surrounded by two scorpionate ligand butyltris(1H-pyrazol-1-yl)borate molecules that coordinate to the iron(II) ion through the N atoms of the pyrazole groups. The two independent complex molecules differ essentially in the conformation of the butyl substituents. In the crystal, the complex molecules are linked by a series of C—H⋯π interactions, which generate a supramolecular three-dimensional structure. At 120 K, the average Fe—N bond distance is 1.969 Å, indicating the low-spin state of the iron(II) atom, which does not change upon heating, as demonstrated by high-temperature magnetic susceptibility measurements. Full Article text
rat The fumarate salts of the N-isopropyl-N-methyl derivatives of DMT and psilocin By scripts.iucr.org Published On :: 2019-08-16 The solid-state structures of the salts of two substituted tryptamines, namely N-isopropyl-N-methyltryptaminium (MiPT) fumarate {systematic name: [2-(1H-indol-3-yl)ethyl](methyl)propan-2-ylazanium 3-carboxyprop-2-enoate}, C14H21N2+·C4H3O4−, and 4-hydroxy-N-isopropyl-N-methyltryptaminium (4-HO-MiPT) fumarate monohydrate {systematic name: [2-(4-hydroxy-1H-indol-3-yl)ethyl](methyl)propan-2-ylazanium 3-carboxyprop-2-enoate monohydrate}, C14H21N2O+·C4H3O4−·H2O, are reported. Both salts possess a protonated tryptammonium cation and a 3-carboxyacrylate (hydrogen fumarate) anion in the asymmetric unit; the 4-HO-MiPT structure also contains a water molecule of crystallization. Both cations feature disorder of the side chain over two orientations, in a 0.630 (3):0.370 (3) ratio for MiPT and a 0.775 (5):0.225 (5) ratio for 4-HO-MiPT. In both extended structures, N—H⋯O and O—H⋯O hydrogen bonds generate infinite two-dimensional networks. Full Article text
rat Crystal structure of bis[2-(1H-benzimidazol-2-yl-κN3)aniline-κN]bis(nitrato-κO)cadmium(II) By scripts.iucr.org Published On :: 2019-09-12 In the title compound, [Cd(NO3)2(C13H11N3)2], the CdII atom lies on a twofold rotation axis and is coordinated by four N atoms and two O atoms, provided by two bidentate 2-(1H-benzimidazol-2-yl)aniline ligands, and two nitrato O atoms, forming a distorted octahedral geometry [range of bond angles around the Cd atom = 73.82 (2)–106.95 (8)°]. In the ligand, the dihedral angle between the aniline ring and the benzimidazole ring system is 30.43 (7)°. The discrete complex molecule is stabilized by an intramolecular N—H⋯O hydrogen bond. In the crystal, intermolecular N—H⋯O hydrogen bonds link the molecules, forming a three-dimensional network. Full Article text
rat Crystal structure, Hirshfeld surface analysis and physicochemical characterization of bis[4-(dimethylamino)pyridinium] di-μ-chlorido-bis[dichloridomercurate(II)] By scripts.iucr.org Published On :: 2019-10-03 The title molecular salt, (C7H11N2)2[Hg2Cl6], crystallizes with two 4-(dimethylamino)pyridinium cations (A and B) and two half hexachloridodimercurate(II) anions in the asymmetric unit. The organic cations exhibit essentially the same features with an almost planar pyridyl ring (r.m.s. deviations of 0.0028 and 0.0109 Å), which forms an inclined dihedral angle with the dimethyamino group [3.06 (1) and 1.61 (1)°, respectively]. The dimethylamino groups in the two cations are planar, and the C—N bond lengths are shorter than that in 4-(dimethylamino)pyridine. In the crystal, mixed cation–anion layers lying parallel to the (010) plane are formed through N—H⋯Cl hydrogen bonds and adjacent layers are linked by C—H⋯Cl hydrogen bonds, forming a three-dimensional network. The analyses of the calculated Hirshfeld surfaces confirm the relevance of the above intermolecular interactions, but also serve to further differentiate the weaker intermolecular interactions formed by the organic cations and inorganic anions, such as π–π and Cl⋯Cl interactions. The powder XRD data confirms the phase purity of the crystalline sample. Furthermore, the vibrational absorption bands were identified by IR spectroscopy and the optical properties were studied by using optical UV–visible absorption spectroscopy. Full Article text
rat Synthesis, crystal structure and Hirshfeld surface analysis of 4-[3-(4-hydroxyphenyl)-4,5-dihydro-1H-pyrazol-5-yl]-2-methoxyphenol monohydrate By scripts.iucr.org Published On :: 2019-10-03 In the title pyrazoline derivative, C16H16N2O3·H2O, the pyrazoline ring has an envelope conformation with the substituted sp2 C atom on the flap. The pyrazoline ring makes angles of 86.73 (12) and 13.44 (12)° with the trisubstituted and disubstituted benzene rings, respectively. In the crystal structure, the molecules are connected into chains running in the b-axis direction by O—H⋯N hydrogen bonding. Parallel chains interact through N—H⋯O hydrogen bonds and π–π stacking of the trisubstituted phenyl rings. The major contribution to the surface contacts are H⋯H contacts (44.3%) as concluded from a Hirshfeld surface analysis. Full Article text
rat Tetra-n-butylammonium orotate monohydrate: knowledge-based comparison of the results of accurate and lower-resolution analyses and a non-routine disorder refinement By scripts.iucr.org Published On :: 2019-10-08 The title hydrated molecular salt (systematic name: tetra-n-butylammonium 2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate monohydrate), C16H36N+·C5H3N2O4−·H2O, crystallizes with N—H⋯O and O—H⋯O hydrogen-bonded double-stranded antiparallel ribbons consisting of the hydrophilic orotate monoanions and water molecules, separated by the bulky hydrophobic cations. The hydrophobic and hydrophilic regions of the structure are joined by weaker non-classical C—H⋯O hydrogen bonds. An accurate structure analysis conducted at T = 100 K is compared to a lower-resolution less accurate determination using data measured at T = 295 K. The results of both analyses are evaluated using a knowledge-based approach, and it is found that the less accurate room-temperature structure analysis provides geometric data that are similar to those derived from the accurate low-temperature analysis, with both sets of results consistent with previously analyzed structures. A minor disorder of one methyl group in the cation at low temperature was found to be slightly more complex at room temperature; while still involving a minor fraction of the structure, the disorder at room temperature was found to require a non-routine treatment, which is described in detail. Full Article text
rat Bis[2-(4,5-diphenyl-1H-imidazol-2-yl)-4-nitrophenolato]copper(II) dihydrate: crystal structure and Hirshfeld surface analysis By scripts.iucr.org Published On :: 2019-10-22 The crystal and molecular structures of the title CuII complex, isolated as a dihydrate, [Cu(C21H14N3O3)2]·2H2O, reveals a highly distorted coordination geometry intermediate between square-planar and tetrahedral defined by an N2O2 donor set derived from two mono-anionic bidentate ligands. Furthermore, each six-membered chelate ring adopts an envelope conformation with the Cu atom being the flap. In the crystal, imidazolyl-amine-N—H⋯O(water), water-O—H⋯O(coordinated, nitro and water), phenyl-C—H⋯O(nitro) and π(imidazolyl)–π(nitrobenzene) [inter-centroid distances = 3.7452 (14) and 3.6647 (13) Å] contacts link the components into a supramolecular layer lying parallel to (101). The connections between layers forming a three-dimensional architecture are of the types nitrobenzene-C—H⋯O(nitro) and phenyl-C—H⋯π(phenyl). The distorted coordination geometry for the CuII atom is highlighted in an analysis of the Hirshfeld surface calculated for the metal centre alone. The significance of the intermolecular contacts is also revealed in a study of the calculated Hirshfeld surfaces; the dominant contacts in the crystal are H⋯H (41.0%), O⋯H/H⋯O (27.1%) and C⋯H/H⋯C (19.6%). Full Article text
rat The first structural characterization of the protonated azacyclam ligand in catena-poly[[[(perchlorato)copper(II)]-μ-3-(3-carboxypropyl)-1,5,8,12-tetraaza-3-azoniacyclotetradecane] bis(per& By scripts.iucr.org Published On :: 2019-10-22 The asymmetric unit of the title compound, catena-poly[[[(perchlorato-κO)copper(II)]-μ-3-(3-carboxypropyl)-1,5,8,12-tetraaza-3-azoniacyclotetradecane-κ4N1,N5,N8,N12] bis(perchlorate)], {[Cu(C13H30N5O2)(ClO4)](ClO4)2}n, (I), consists of a macrocyclic cation, one coordinated perchlorate anion and two perchlorate ions as counter-anions. The metal ion is coordinated in a tetragonally distorted octahedral geometry by the four secondary N atoms of the macrocyclic ligand, the mutually trans O atoms of the perchlorate anion and the carbonyl O atom of the protonated carboxylic acid group of a neighbouring cation. The average equatorial Cu—N bond lengths [2.01 (6) Å] are significantly shorter than the axial Cu—O bond lengths [2.379 (8) Å for carboxylate and average 2.62 (7) Å for disordered perchlorate]. The coordinated macrocyclic ligand in (I) adopts the most energetically favourable trans-III conformation with an equatorial orientation of the substituent at the protonated distal 3-position N atom in a six-membered chelate ring. The coordination of the carboxylic acid group of the cation to a neighbouring complex unit results in the formation of infinite chains running along the b-axis direction, which are crosslinked by N—H⋯O hydrogen bonds between the secondary amine groups of the macrocycle and O atoms of the perchlorate counter-anions to form sheets lying parallel to the (001) plane. Additionally, the extended structure of (I) is consolidated by numerous intra- and interchain C—H⋯O contacts. Full Article text
rat The `super acid' BF3H2O stabilized by 1,4-dioxane: new preparative aspects and the crystal structure of BF3H2O·C4H8O2 By scripts.iucr.org Published On :: 2019-10-31 Highly Brønsted-acidic boron trifluoride monohydrate, a widely used `super acid-catalyst', is a colourless fuming liquid that releases BF3 at room temperature. Compared to the liquid components, i.e. boron trifluoride monohydrate and 1,4-dioxane, their 1:1 adduct, BF3H2O·C4H8O2, is a solid with pronounced thermal stability (m.p. 401–403 K). The crystal structure of the long-time-stable easy-to-handle and weighable compound is reported along with new preparative aspects and the results of 1H, 11B, 13C and 19F spectroscopic investigations, particularly documenting its high Brønsted acidity in acetonitrile solution. The remarkable stability of solid BF3H2O·C4H8O2 is attributed to the chain structure established by O—H⋯O hydrogen bonds of exceptional strength {O2⋯H1—O1 [O⋯O = 2.534 (3) Å] and O1—H1⋯O3i [2.539 (3) Å] in the concatenating unit >O2⋯H1—O1—H2⋯O3i<}, taking into account the molecular (non-ionic) character of the structural moieties. Indirectly, this structural feature documents the outstanding acidification of the H2O molecule bound to BF3 and reflects the super acid nature of BF3H2O. In detail, the C22(7) zigzag chain system of hydrogen bonding in the title structure is characterized by the double hydrogen-bond donor and double (κO,κO') hydrogen-bond acceptor functionality of the aqua ligand and dioxane molecule, respectively, the almost equal strength of both hydrogen bonds, the approximatety linear arrangement of the dioxane O atoms and the two neighbouring water O atoms. Furthermore, the approximately planar arrangement of B, F and O atoms in sheets perpendicular to the c axis of the orthorhombic unit cell is a characteristic structural feature. Full Article text
rat Crystal structures of two coordination isomers of copper(II) 4-sulfobenzoic acid hexahydrate and two mixed silver/potassium 4-sulfobenzoic acid salts By scripts.iucr.org Published On :: 2019-10-31 A reaction of copper(II) carbonate and potassium 4-sulfobenzoic acid in water acidified with hydrochloric acid yielded two crystalline products. Tetraaquabis(4-carboxybenzenesulfonato)copper(II) dihydrate, [Cu(O3SC6H4CO2H)2(H2O)4]·2H2O, (I), crystallizes in the triclinic space group Poverline{1} with the Cu2+ ions located on centers of inversion. Each copper ion is coordinated to four water molecules in a square plane with two sulfonate O atoms in the apical positions of a Jahn–Teller-distorted octahedron. The carboxylate group is protonated and not involved in coordination to the metal ions. The complexes pack so as to create a layered structure with alternating inorganic and organic domains. The packing is reinforced by several O—H⋯O hydrogen bonds involving coordinated and non-coordinated water molecules, the carboxylic acid group and the sulfonate group. Hexaaquacopper(II) 4-carboxybenzenesulfonate, [Cu(H2O)6](O3SC6H4CO2H)2, (II), also crystallizes in the triclinic space group Poverline{1} with Jahn–Teller-distorted octahedral copper(II) aqua complexes on the centers of inversion. As in (I), the carboxylate group on the anion is protonated and the structure consists of alternating layers of inorganic cations and organic anions linked by O—H⋯O hydrogen bonds. A reaction of silver nitrate and potassium 4-sulfobenzoic acid in water also resulted in two distinct products that have been structurally characterized. An anhydrous silver potassium 4-carboxybenzenesulfonate salt, [Ag0.69K0.31](O3SC6H4CO2H), (III), crystallizes in the monoclinic space group C2/c. There are two independent metal sites, one fully occupied by silver ions and the other showing a 62% K+/38% Ag+ (fixed) ratio, refined in two slightly different positions. The coordination environments of the metal ions are composed primarily of sulfonate O atoms, with some participation by the non-protonated carboxylate O atoms in the disordered site. As in the copper compounds, the cations and anions cleanly segregate into alternating layers. A hydrated mixed silver potassium 4-carboxybenzenesulfonate salt dihydrate, [Ag0.20K0.80](O3SC6H4CO2H)·2H2O, (IV), crystallizes in the monoclinic space group P21/c with the Ag+ and K+ ions sharing one unique metal site coordinated by two water molecules and six sulfonate O atoms. The packing in (IV) follows the dominant motif of alternating inorganic and organic layers. The protonated carboxylate groups do not interact with the cations directly, but do participate in hydrogen bonds with the coordinated water molecules. (IV) is isostructural with pure potassium 4-sulfobenzoic acid dihydrate. Full Article text
rat Some reflections on symmetry: pitfalls of automation and some illustrative examples By scripts.iucr.org Published On :: 2019-11-08 In the context of increasing hardware and software automation in the process of crystal structure determination by X-ray diffraction, and based on conference sessions presenting some of the experience of senior crystallographers for the benefit of younger colleagues, an outline is given here of some basic concepts and applications of symmetry in crystallography. Three specific examples of structure determinations are discussed, for which an understanding of these aspects of symmetry avoids mistakes that can readily be made by reliance on automatic procedures. Topics addressed include pseudo-symmetry, twinning, real and apparent disorder, chirality, and structure validation. Full Article text
rat Crystal structure, Hirshfeld surface analysis and contact enrichment ratios of 1-(2,7-dimethylimidazo[1,2-a]pyridin-3-yl)-2-(1,3-dithiolan-2-ylidene)ethanone monohydrate By scripts.iucr.org Published On :: 2019-11-29 In the title hydrated hybrid compound C14H14N2OS2·H2O, the planar imidazo[1,2-a]pyridine ring system is linked to the 1,3-dithiolane moiety by an enone bridge. The atoms of the C—C bond in the 1,3-dithiolane ring are disordered over two positions with occupancies of 0.579 (14) and 0.421 (14) and both disordered rings adopt a half-chair conformation. The oxygen atom of the enone bridge is involved in a weak intramolecular C—H⋯O hydrogen bond, which generates an S(6) graph-set motif. In the crystal, the hybrid molecules are associated in R22(14) dimeric units by weak C—H⋯O interactions. O—H⋯O hydrogen bonds link the water molecules, forming infinite self-assembled chains along the b-axis direction to which the dimers are connected via O—H⋯N hydrogen bonding. Analysis of intermolecular contacts using Hirshfeld surface analysis and contact enrichment ratio descriptors indicate that hydrogen bonds induced by water molecules are the main driving force in the crystal packing formation. Full Article text
rat N,N'-Bis(pyridin-3-ylmethyl)ethanediamide monohydrate: crystal structure, Hirshfeld surface analysis and computational study By scripts.iucr.org Published On :: 2020-01-01 The molecular structure of the title bis-pyridyl substituted diamide hydrate, C14H14N4O2·H2O, features a central C2N2O2 residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methylene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intramolecular amide-N—H⋯O(carbonyl) hydrogen bonds are formed, each closing an S(5) loop. Supramolecular tapes are formed in the crystal via amide-N—H⋯O(carbonyl) hydrogen bonds and ten-membered {⋯HNC2O}2 synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water molecules via water-O—H⋯N(pyridyl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methylene-C—H⋯O(water) and methylene-C—H⋯π(pyridyl) interactions, give rise to a layer parallel to (10overline{1}); the layers stack without directional interactions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding interactions, and to the significant influence of the water molecule of crystallization upon the molecular packing. The analysis also indicates the contribution of methylene-C—H⋯O(carbonyl) and pyridyl-C—H⋯C(carbonyl) contacts to the stability of the inter-layer region. The calculated interaction energies are consistent with importance of significant electrostatic attractions in the crystal. Full Article text
rat Synthesis and crystal structure of catena-poly[[bis[(2,2';6',2''-terpyridine)manganese(II)]-μ4-pentathiodiantimonato] tetrahydrate] showing a 1D MnSbS network By scripts.iucr.org Published On :: 2020-01-01 The asymmetric unit of the title compound, {[Mn2Sb2S5(C15H11N3)2]·4H2O}n, consists of two crystallographically independent MnII ions, two unique terpyridine ligands, one [Sb2S5]4− anion and four solvent water molecules, all of which are located in general positions. The [Sb2S5]4− anion consists of two SbS3 units that share common corners. Each of the MnII ions is fivefold coordinated by two symmetry-related S atoms of [Sb2S5]4− anions and three N atoms of a terpyridine ligand within an irregular coordination. Each two anions are linked by two [Mn(terpyridine)]2+ cations into chains along the c-axis direction that consist of eight-membered Mn2Sb2S4 rings. These chains are further connected into a three-dimensional network by intermolecular O—H⋯O and O—H⋯S hydrogen bonds. The crystal investigated was twinned and therefore, a twin refinement using data in HKLF-5 [Sheldrick (2015). Acta Cryst. C71, 3–8] format was performed. Full Article text
rat Crystal structure, Hirshfeld surface analysis and DFT studies of 1-benzyl-3-[(1-benzyl-1H-1,2,3-triazol-5-yl)methyl]-2,3-dihydro-1H-1,3-benzodiazol-2-one monohydrate By scripts.iucr.org Published On :: 2020-01-01 In the title molecule, C24H21N5O·H2O, the dihydrobenzodiazole moiety is not quite planar, while the whole molecule adopts a U-shaped conformation in which there is a close approach of the two benzyl groups. In the crystal, chains of alternating molecules and lattice water extending along [201] are formed by O—HUncoordW⋯ODhyr and O—HUncoordW⋯NTrz (UncoordW = uncoordinated water, Dhyr = dihydro and Trz = triazole) hydrogen bonds. The chains are connected into layers parallel to (010) by C—HTrz⋯OUncoordW hydrogen bonds with the dihydrobenzodiazole units in adjacent layers intercalating to form head-to-tail π-stacking [centroid-to-centroid distance = 3.5694 (11) Å] interactions between them, which generates the overall three-dimensional structure. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (52.1%), H⋯C/C⋯H (23.8%) and O⋯H/H⋯O (11.2%) interactions. Hydrogen-bonding and van der Waals interactions are the dominant interactions in the crystal packing. Density functional theory (DFT) optimized structures at the B3LYP/ 6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Full Article text
rat Crystal structure, DFT and Hirshfeld surface analysis of (E)-N'-[(1-chloro-3,4-dihydronaphthalen-2-yl)methylidene]benzohydrazide monohydrate By scripts.iucr.org Published On :: 2020-01-03 In the title compound, C18H15ClN2O·H2O, a benzohydrazide derivative, the dihedral angle between the mean plane of the dihydronaphthalene ring system and the phenyl ring is 17.1 (2)°. In the crystal, O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds link the benzohydrazide and water molecules, forming a layer parallel to the bc plane. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (45.7%) and H⋯C/C⋯H (20.2%) contacts. Full Article text
rat Crystal structure of di-μ-trihydro(pentafluorophenyl)borato-tetrakis(tetrahydrofuran)disodium By scripts.iucr.org Published On :: 2020-01-07 The title compound, [Na(μ-C6F5BH3)(C4H8O)2]2, represents a dimeric structure of sodium and organoborohydride, located about a centre of inversion. The Na⋯B distances of 2.7845 (19) and 2.7494 (18) Å were apparently longer than the Li⋯B distances (2.403–2.537 Å) of the lithium organotrihydroborates in the previous reports. Moreover, an interaction between the sodium atom and one fluorine atom on the 2-position of the benzene ring is observed [Na—F = 2.6373 (12) Å]. In the crystal, the dimeric molecules are stacked along the b-axis via a π–π interaction between the benzene rings. Full Article text
rat Crystal structure, spectroscopic characterization and Hirshfeld surface analysis of aquadichlorido{N-[(pyridin-2-yl)methylidene]aniline}copper(II) monohydrate By scripts.iucr.org Published On :: 2020-01-07 The reaction of N-phenyl-1-(pyridin-2-yl)methanimine with copper chloride dihydrate produced the title neutral complex, [CuCl2(C12H10N2)(H2O)]·H2O. The CuII ion is five-coordinated in a distorted square-pyramidal geometry, in which the two N atoms of the bidentate Schiff base, as well as one chloro and a water molecule, form the irregular base of the pyramidal structure. Meanwhile, the apical chloride ligand interacts through a strong hydrogen bond with a water molecule of crystallization. In the crystal, molecules are arranged in pairs, forming a stacking of symmetrical cyclic dimers that interact in turn through strong hydrogen bonds between the chloride ligands and both the coordinated and the crystallization water molecules. The molecular and electronic structures of the complex were also studied in detail using EPR (continuous and pulsed), FT–IR and Raman spectroscopy, as well as magnetization measurements. Likewise, Hirshfeld surface analysis was used to investigate the intermolecular interactions in the crystal packing. Full Article text
rat Crystal structure of the deuterated heptahydrate of potassium phosphate, K3PO4·7D2O By scripts.iucr.org Published On :: 2020-01-10 Deuterated potassium orthophosphate heptahydrate, K3PO4·7D2O, crystallizes in the Sohnke space group P21, and its absolute structure was determined from 2017 Friedel pairs [Flack parameter 0.004 (16)]. Each of the three crystallographically unique K+ cations is surrounded by six water molecules and one oxygen atom from the orthophosphate group, using a threshold for K—O bonds of 3.10 Å. The highly irregular coordination polyhedra are linked by corner- and edge-sharing into a three-dimensional network that is consolidated by an intricate network of O—D⋯O hydrogen bonds of medium strength. Full Article text
rat Crystal structure of strontium thiosulfate monohydrate By scripts.iucr.org Published On :: 2020-01-17 SrS2O3·H2O was obtained from an aqueous solution of Na2S2O3 and Sr(NO3)2 and crystallizes in space group Poverline{1} with all atoms at general positions. The Sr2+ ion exhibits an [8 + 1] coordination defined by two terminal S and six O atoms of thiosulfate ions, one of the latter at a longer distance, and by one O atom of a water molecule. Two thiosulfate anions act as bidentate, four as monodentate ligands. The structure consists of mainly ionically interacting layers lying parallel to the crystallographic ab plane. The layers are connected by O—H⋯S and O—H⋯O hydrogen bonds of moderate strength. Full Article text
rat Crystal structure of 2-methyl-1,2,3,4-tetrahydroisoquinoline trihydrate By scripts.iucr.org Published On :: 2020-02-06 The crystal structure of the title compound, C10H13N·3H2O, a heterocyclic amine, was determined in the presence of water. The compound co-crystallizes with three water molecules in the asymmetric unit, which leads to the formation of hydrogen bonding in the crystal. Full Article text
rat Tetraaqua[3-oxo-1,3-bis(pyridinium-2-yl)propan-1-olato]nickel(II) tribromide dihydrate By scripts.iucr.org Published On :: 2020-01-31 The crystal structure of the title compound, [Ni(C13H11N2O2)(H2O)4]Br3·2H2O, contains an octahedral NiII atom coordinated to the enol form of 1,3-dipyridylpropane-1,3-dione (dppo) and four water molecules. Both pyridyl rings on the ligand are protonated, forming pyridinium rings and creating an overall ligand charge of +1. The protonated nitrogen-containing rings are involved in hydrogen-bonding interactions with neighoring bromide anions. There are many additional hydrogen-bonding interactions involving coordinated water molecules on the NiII atom, bromide anions and hydration water molecules. Full Article text
rat Poly[[tetradecakis(μ-propionato)heptabarium] propionic acid monosolvate tetrahydrate] By scripts.iucr.org Published On :: 2020-01-31 The title compound, {[Ba7(C3H5O2)14]·0.946C3H6O2·4H2O}n, is represented by a metal–organic framework structure that is held together by Ba—O—Ba bonds, as well as by O—H⋯O hydrogen bonds of moderate strength. The structure comprises of four independent Ba2+ cations (one of which is situated on a twofold rotation axis), seven independent propionate and two independent water molecules. The bond-valence sums of all the cations indicate a slight overbonding. There is also an occupationally, as well as a positionally disordered propionic acid molecule present in the structure. Its occupation is slightly lower than the full occupation while the disordered molecules occupy two positions related by a rotation about a twofold rotation axis. In addition, the methyl group in the symmetry-independent propionic acid molecule is also disordered, and occupies two positions. Each propionic acid molecule coordinates to just one cation from a pair of symmetry-equivalent Ba2+ sites and is simultaneously bonded by an O—H⋯Opropionate hydrogen bond. This means that on a microscopic scale, the coordination number of the corresponding Ba2+ site is either 9 or 10. The methyl as well as hydroxy hydrogen atoms of the disordered propionic acid molecule were not determined. Full Article text
rat Crystal structure of 1,4,8,11-tetramethyl-1,4,8,11-tetraazoniacyclotetradecane bis(perchlorate) dichloride from synchrotron X-ray data By scripts.iucr.org Published On :: 2020-02-11 The crystal structure of title salt, C14H36N44+·2ClO4−·2Cl−, has been determined using synchrotron radiation at 220 K. The structure determination reveals that protonation has occurred at all four amine N atoms. The asymmetric unit contains one half-cation (completed by crystallographic inversion symmetry), one perchlorate anion and one chloride anion. A distortion of the perchlorate anion is due to its involvement in hydrogen-bonding interactions with the cations. The crystal structure is consolidated by intermolecular hydrogen bonds involving the 1,4,8,11-tetramethyl-1,4,8,11-tetraazoniacyclotetradecane N—H and C—H groups as donor groups, and the O atoms of the perchlorate and chloride anion as acceptor groups, giving rise to a three-dimensional network. Full Article text
rat Crystal structures and comparisons of huntite aluminum borates REAl3(BO3)4 (RE = Tb, Dy and Ho) By scripts.iucr.org Published On :: 2020-02-14 Three huntite-type aluminoborates of stoichiometry REAl3(BO3)4 (RE = Tb, Dy and Ho), namely, terbium/dysprosium/holmium trialuminium tetrakis(borate), were synthesized by slow cooling within a K2Mo3O10 flux with spontaneous crystallization. The crystal structures were determined using single-crystal X-ray diffraction (SC-XRD) data. The synthesized borates are isostructural to the huntite [CaMg3(CO3)4] structure and crystallized within the trigonal R32 space group. The structural parameters were compared to literature data of other huntite REAl3(BO3)4 crystals within the R32 space group. All three borates fit well into the trends calculated from the literature data. The unit-cell parameters and volumes increase linearly with larger RE cations whereas the densities decrease. All of the crystals studied were refined as inversion twins. Full Article text
rat Syntheses and crystal structures of a new pyrazine dicarboxamide ligand, N2,N3-bis(quinolin-8-yl)pyrazine-2,3-dicarboxamide, and of a copper perchlorate binuclear complex By scripts.iucr.org Published On :: 2020-02-14 The title pyrazine dicarboxamide ligand, N2,N3-bis(quinolin-8-yl)pyrazine-2,3-dicarboxamide (H2L1), C24H16N6O2, has a twisted conformation with the outer quinoline groups being inclined to the central pyrazine ring by 9.00 (6) and 78.67 (5)°, and by 79.94 (4)° to each other. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming layers parallel to the (10overline{1}) plane, which are in turn linked by offset π–π interactions [intercentroid distances 3.4779 (9) and 3.6526 (8) Å], forming a supramolecular three-dimensional structure. Reaction of the ligand H2L1 with Cu(ClO4)2 in acetonitrile leads to the formation of the binuclear complex, [μ-(3-{hydroxy[(quinolin-8-yl)imino]methyl}pyrazin-2-yl)[(quinolin-8-yl)imino]methanolato]bis[diacetonitrilecopper(II)] tris(perchlorate) acetonitrile disolvate, [Cu2(C24H15N6O2)(CH3CN)4](ClO4)3·2CH3CN or [Cu2(HL1−)(CH3CN)4](ClO4)3·2CH3CN (I). In the cation of complex I, the ligand coordinates to the copper(II) atoms in a bis-tridentate fashion. A resonance-assisted O—H⋯O hydrogen bond is present in the ligand; the position of this H atom was located in a difference-Fourier map. Both copper(II) atoms are fivefold coordinate, being ligated by three N atoms of the ligand and by the N atoms of two acetonitrile molecules. The first copper atom has a perfect square-pyramidal geometry while the second copper atom has a distorted shape. In the crystal, the cation and perchlorate anions are linked by a number of C—H⋯O hydrogen bonds, forming a supramolecular three-dimensional structure. Full Article text
rat Crystal structure and Hirshfeld surface analysis of 3,6-bis(pyrimidin-2-yl)-1,4-dihydro-1,2,4,5-tetrazine dihydrate By scripts.iucr.org Published On :: 2020-03-03 In the title compound, C10H8N8·2H2O or H2bmtz·2H2O [bmtz = 3,6-bis(2'-pyrimidyl)-1,2,4,5-tetrazine], the asymmetric unit consists of one-half molecule of H2bmtz and one water molecule, the whole H2bmtz molecule being generated by a crystallographic twofold rotation axis passing through the middle point of the 1,4-dihydro-1,2,4,5-tetrazine moiety. In the crystal, N—H⋯O, N—H⋯N, O—H⋯O hydrogen bonds and aromatic π–π stacking interactions link the components into a three-dimensional supramolecular network. Hirshfeld surface analysis was used to further investigate the intermolecular interactions in the crystal structure. Full Article text
rat Crystal structure and photoluminescent properties of bis(4'-chloro-2,2':6',2''-terpyridyl)cobalt(II) dichloride tetrahydrate By scripts.iucr.org Published On :: 2020-03-05 In the title hydrated complex, [Co(C15H10ClN3)2]Cl2·4H2O, the complete dication is generated by overline{4} symmetry. The CoN6 moiety shows distortion from regular octahedral geometry with the trans bond angles of two N—Co—N units being 160.62 (9)°. In the crystal, O—H⋯Cl and C—H⋯O interactions link the components into (001) sheets. The title compound exhibits blue-light emission, as indicated by photoluminescence data, and a HOMO–LUMO energy separation of 2.23 eV was obtained from its diffuse reflectance spectrum. Full Article text
rat Bis(4-hydroxy-N-isopropyl-N-methyltryptammonium) fumarate: a new crystalline form of miprocin By scripts.iucr.org Published On :: 2020-03-10 The title compound, bis(4-hydroxy-N-isopropyl-N-methyltryptammonium) (4-HO-MiPT) fumarate (systematic name: bis{[2-(4-hydroxy-1H-indol-3-yl)ethyl](methyl)propan-2-ylazanium} but-2-enedioate), 2C14H21N2O+·C4H2O42−, has a singly protonated tryptammonium cation and one half of a fumarate dianion in the asymmetric unit. The tryptammonium and fumarate ions are held together in one-dimensional chains by N—H⋯O and O—H⋯O hydrogen bonds. These chains are a combination of R42(20) rings, and C22(15) and C44(30) parallel chains along (110). They are further consolidated by N—H⋯π interactions. There are two two-component types of disorder impacting the tryptammonium fragment with a 0.753 (7):0.247 (7) occupancy ratio and one of the fumarate oxygen atoms with a 0.73 (8):0.27 (8) ratio. Full Article text
rat Silver(I) nitrate two-dimensional coordination polymers of two new pyrazinethiophane ligands: 5,7-dihydro-1H,3H-dithieno[3,4-b:3',4'-e]pyrazine and 3,4,8,10,11,13-hexahydro-1H,6H-bis([1,4]dithiocino)[6,7-b:6',7'-e By scripts.iucr.org Published On :: 2020-03-13 The two new pyrazineophanes, 5,7-dihydro-1H,3H-dithieno[3,4-b:3',4'-e]pyrazine, C8H8N2S2, L1, and 3,4,8,10,11,13-hexahydro-1H,6H-bis([1,4]dithiocino)[6,7-b:6',7'-e]pyrazine, C12H16N2S4, L2, both crystallize with half a molecule in the asymmetric unit; the whole molecules are generated by inversion symmetry. The molecule of L1, which is planar (r.m.s. deviation = 0.008 Å), consists of two sulfur atoms linked by a rigid tetra-2,3,5,6-methylenepyrazine unit, forming planar five-membered rings. The molecule of L2 is step-shaped and consists of two S–CH2–CH2–S chains linked by the central rigid tetra-2,3,5,6-methylenepyrazine unit, forming eight-membered rings that have twist-boat-chair configurations. In the crystals of both compounds, there are no significant intermolecular interactions present. The reaction of L1 with silver nitrate leads to the formation of a two-dimensional coordination polymer, poly[(μ-5,7-dihydro-1H,3H-dithieno[3,4-b;3',4'-e]pyrazine-κ2S:S')(μ-nitrato-κ2O:O')silver(I)], [Ag(NO3)(C8H8N2S2)]n, (I), with the nitrato anion bridging two equivalent silver atoms. The central pyrazine ring is situated about an inversion center and the silver atom lies on a twofold rotation axis that bisects the nitrato anion. The silver atom has a fourfold AgO2S2 coordination sphere with a distorted shape. The reaction of L2 with silver nitrate also leads to the formation of a two-dimensional coordination polymer, poly[[μ33,4,8,10,11,13-hexahydro-1H,6H-bis([1,4]dithiocino)[6,7-b;6',7'-e]pyrazine-κ3S:S':S''](nitrato-κO)silver(I)], [Ag(NO3)(C12H16N2S4)]n, (II), with the nitrate anion coordinating in a monodentate manner to the silver atom. The silver atom has a fourfold AgOS3 coordination sphere with a distorted shape. In the crystals of both complexes, the networks are linked by C—H⋯O hydrogen bonds, forming supramolecular frameworks. There are additional C—H⋯S contacts present in the supramolecular framework of II. Full Article text
rat Synthesis and crystal structures of two 1,3-di(alkyloxy)-2-(methylsulfanyl)imidazolium tetrafluoridoborates By scripts.iucr.org Published On :: 2020-03-17 Two salts were prepared by methylation of the respective imidazoline-2-thione at the sulfur atom, using Meerwein's salt (trimethyloxonium tetrafluoridoborate) in CH2Cl2. 1,3-Dimethoxy-2-(methylsulfanyl)imidazolium tetrafluoridoborate (1), C6H11N2O2S+·BF4−, displays a syn conformation of its two methoxy groups relative to each other whereas the two benzyloxy groups present in 1,3-dibenzyloxy-2-(methylsulfanyl)imidazolium tetrafluoridoborate (2), C18H19N2O2S+·BF4−, adopt an anti conformation. In the molecules of 1 and 2, the methylsulfanyl group is rotated out of the plane of the respective heterocyclic ring. In both crystal structures, intermolecular interactions are dominated by C—H⋯F—B contacts, leading to three-dimensional networks. The tetrafluoridoborate counter-ion of 2 is disordered over three orientations (occupancy ratio 0.42:0.34:0.24), which are related by rotation about one of the B—F bonds. Full Article text
rat Norpsilocin: freebase and fumarate salt By scripts.iucr.org Published On :: 2020-03-27 The solid-state structures of the naturally occurring psychoactive tryptamine norpsilocin {4-hydroxy-N-methyltryptamine (4-HO-NMT); systematic name: 3-[2-(methylamino)ethyl]-1H-indol-4-ol}, C11H14N2O, and its fumarate salt (4-hydroxy-N-methyltryptammonium fumarate; systematic name: bis{[2-(4-hydroxy-1H-indol-3-yl)ethyl]methylazanium} but-2-enedioate), C11H15N2O+·0.5C4H2O42−, are reported. The freebase of 4-HO-NMT has a single molecule in the asymmetric unit joined together by N—H⋯O and O—H⋯O hydrogen bonds in a two-dimensional network parallel to the (100) plane. The ethylamine arm of the tryptamine is modeled as a two-component disorder with a 0.895 (3) to 0.105 (3) occupancy ratio. The fumarate salt of 4-HO-NMT crystallizes with a tryptammonium cation and one half of a fumarate dianion in the asymmetric unit. The ions are joined together by N—H⋯O and O—H⋯O hydrogen bonds to form a three-dimensional framework, as well as π–π stacking between the six-membered rings of inversion-related indoles (symmetry operation: 2 − x, 1 − y, 2 – z). Full Article text
rat Dehydration synthesis and crystal structure of terbium oxychloride, TbOCl By scripts.iucr.org Published On :: 2020-04-03 Terbium oxychloride, TbOCl, was synthesized via the simple heat-treatment of TbCl3·6H2O and its structure was determined by refinement against X-ray powder diffraction data. TbOCl crystallizes with the matlockite (PbFCl) structure in the tetragonal space group P4/nmm and is composed of alternating (001) layers of (TbO)n and n Cl−. The unit-cell parameters, unit-cell volume, and density were compared to the literature data of other isostructural rare-earth oxychlorides in the same space group and showed good agreement when compared to the calculated trendlines. Full Article text
rat Crystal structure of N'-[4-(dimethylamino)benzylidene]furan-2-carbohydrazide monohydrate By scripts.iucr.org Published On :: 2020-04-09 The condensation of 2-furoic hydrazide and 4-dimethyl aminobenzaldehyde in ethanol yielded a yellow solid formulated as the title compound, C14H15N3O2·H2O. The crystal packing is stabilized by intermolecular O(water)—H⋯O,N(carbohydrazide) and N—H⋯O(water) hydrogen bonds, which form a two-dimensional network along the bc plane. Additional C—H⋯O interactions link the molecules into a three-dimensional network. The dihedral angle between the mean planes of the benzene and the furan ring is 34.47 (6)°. The carbohydrazide moiety, i.e., the C=N—N—C=O fragment and the benzene ring are almost coplanar, with an angle of 6.75 (9)° between their mean planes. Full Article text
rat Structure of a push–pull olefin prepared by ynamine hydroboration with a borandiol ester By scripts.iucr.org Published On :: 2020-04-21 N-[(Z)-2-(2H-1,3,2-Benzodioxaborol-2-yl)-2-phenylethenyl]-N-(propan-2-yl)aniline, C23H22BNO2, contains a C=C bond that is conjugated with a donor and an acceptor group. An analysis that included similar push–pull olefins revealed that bond lengths in their B—C=C—N core units correlate with the perceived acceptor and donor strength of the groups. The two phenyl groups in the molecule are rotated with respect to the plane that contains the BCCN atoms, and are close enough for significant π-stacking. Definite characterization of the title compound demonstrates, for the first time in a reliable way, that hydroboration of ynamines with borandiol esters is feasible. Compared to olefin hydroboration with borane, the ynamine substrate is activated enough to undergo reaction with the less active hydroboration reagent catecholborane. Full Article text
rat Optimization of crystallization of biological macromolecules using dialysis combined with temperature control By scripts.iucr.org Published On :: 2020-05-05 A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone – which is the optimal location for slow and ordered crystal expansion – by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant–concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination. Full Article text
rat Equatorial aberration of powder diffraction data collected with an Si strip X-ray detector by a continuous-scan integration method By scripts.iucr.org Published On :: 2020-05-05 Exact and approximate mathematical formulas of equatorial aberration for powder diffraction data collected with an Si strip X-ray detector in continuous-scan integration mode are presented. An approximate formula is applied to treat the experimental data measured with a commercial powder diffractometer. Full Article text
rat A thermal-gradient approach to variable-temperature measurements resolved in space By scripts.iucr.org Published On :: 2020-04-23 Temperature is a ubiquitous environmental variable used to explore materials structure, properties and reactivity. This article reports a new paradigm for variable-temperature measurements that varies the temperature continuously across a sample such that temperature is measured as a function of sample position and not time. The gradient approach offers advantages over conventional variable-temperature studies, in which temperature is scanned during a series measurement, in that it improves the efficiency with which a series of temperatures can be probed and it allows the sample evolution at multiple temperatures to be measured in parallel to resolve kinetic and thermodynamic effects. Applied to treat samples at a continuum of temperatures prior to measurements at ambient temperature, the gradient approach enables parametric studies of recovered systems, eliminating temperature-dependent structural and chemical variations to simplify interpretation of the data. The implementation of spatially resolved variable-temperature measurements presented here is based on a gradient-heater design that uses a 3D-printed ceramic template to guide the variable pitch of the wire in a resistively heated wire-wound heater element. The configuration of the gradient heater was refined on the basis of thermal modelling. Applications of the gradient heater to quantify thermal-expansion behaviour, to map metastable polymorphs recovered to ambient temperature, and to monitor the time- and temperature-dependent phase evolution in a complex solid-state reaction are demonstrated. Full Article text
rat Accurate high-resolution single-crystal diffraction data from a Pilatus3 X CdTe detector By scripts.iucr.org Published On :: 2020-04-23 Hybrid photon-counting detectors are widely established at third-generation synchrotron facilities and the specifications of the Pilatus3 X CdTe were quickly recognized as highly promising in charge-density investigations. This is mainly attributable to the detection efficiency in the high-energy X-ray regime, in combination with a dynamic range and noise level that should overcome the perpetual problem of detecting strong and weak data simultaneously. These benefits, however, come at the expense of a persistent problem for high diffracted beam flux, which is particularly problematic in single-crystal diffraction of materials with strong scattering power and sharp diffraction peaks. Here, an in-depth examination of data collected on an inorganic material, FeSb2, and an organic semiconductor, rubrene, revealed systematic differences in strong intensities for different incoming beam fluxes, and the implemented detector intensity corrections were found to be inadequate. Only significant beam attenuation for the collection of strong reflections was able to circumvent this systematic error. All data were collected on a bending-magnet beamline at a third-generation synchrotron radiation facility, so undulator and wiggler beamlines and fourth-generation synchrotrons will be even more prone to this error. On the other hand, the low background now allows for an accurate measurement of very weak intensities, and it is shown that it is possible to extract structure factors of exceptional quality using standard crystallographic software for data processing (SAINT-Plus, SADABS and SORTAV), although special attention has to be paid to the estimation of the background. This study resulted in electron-density models of substantially higher accuracy and precision compared with a previous investigation, thus for the first time fulfilling the promise of photon-counting detectors for very accurate structure factor measurements. Full Article text
rat Cryo-EM structure of Neurospora crassa respiratory complex IV By scripts.iucr.org Published On :: 2019-06-26 In fungi, the mitochondrial respiratory chain complexes (complexes I–IV) are responsible for oxidative phosphorylation, as in higher eukaryotes. Cryo-EM was used to identify a 200 kDa membrane protein from Neurospora crassa in lipid nanodiscs as cytochrome c oxidase (complex IV) and its structure was determined at 5.5 Å resolution. The map closely resembles the cryo-EM structure of complex IV from Saccharomyces cerevisiae. Its ten subunits are conserved in S. cerevisiae and Bos taurus, but other transmembrane subunits are missing. The different structure of the Cox5a subunit is typical for fungal complex IV and may affect the interaction with complex III in a respiratory supercomplex. Additional density was found between the matrix domains of the Cox4 and Cox5a subunits that appears to be specific to N. crassa. Full Article text