structure Crystal structure of a new phenyl(morpholino)methanethione derivative: 4-[(morpholin-4-yl)carbothioyl]benzoic acid By scripts.iucr.org Published On :: 2020-03-27 4-[(Morpholin-4-yl)carbothioyl]benzoic acid, C12H13NO3S, a novel phenyl(morpholino)methanethione derivative, crystallizes in the monoclinic space group P21/n. The morpholine ring adopts a chair conformation and the carboxylic acid group is bent out slightly from the benzene ring mean plane. The molecular geometry of the carboxylic group is characterized by similar C—O bond lengths [1.266 (2) and 1.268 (2) Å] as the carboxylate H atom is disordered over two positions. This molecular arrangement leads to the formation of dimers through strong and centrosymmetric low barrier O—H⋯O hydrogen bonds between the carboxylic groups. In addition to these intermolecular interactions, the crystal packing consists of two different molecular sheets with an angle between their mean planes of 64.4 (2)°. The cohesion between the different layers is ensured by C—H⋯S and C—H⋯O interactions. Full Article text
structure Crystal structure, Hirshfeld surface and frontier molecular orbital analysis of 10-benzyl-9-(3-ethoxy-4-hydroxyphenyl)-3,3,6,6-tetramethyl-3,4,6,7,9,10-hexahydroacridine-1,8(2H,5H)-dione By scripts.iucr.org Published On :: 2020-03-27 In the fused ring system of the title compound, C32H37NO4, the central dihydropyridine ring adopts a flattened boat conformation, the mean and maximum deviations of the dihydropyridine ring being 0.1429 (2) and 0.2621 (2) Å, respectively. The two cyclohexenone rings adopt envelope conformations with the tetrasubstituted C atoms as flap atoms. The benzene and phenyl rings form dihedral angles of 85.81 (2) and 88.90 (2)°, respectively, with the mean plane of the dihydropyridine ring. In the crystal, molecules are linked via an O—H⋯O hydrogen bond, forming a helical chain along the b-axis direction. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (65.2%), O⋯H/H⋯O (18.8%) and C⋯H/H⋯C (13.9%) contacts. Quantum chemical calculations for the frontier molecular orbitals were undertake to determine the chemical reactivity of the title compound. Full Article text
structure Crystal structure, Hirshfeld surface analysis and interaction energy, DFT and antibacterial activity studies of ethyl 2-[(2Z)-2-(2-chlorobenzylidene)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-4-yl]acetate By scripts.iucr.org Published On :: 2020-04-07 The title compound, C19H16ClNO3S, consists of chlorophenyl methylidene and dihydrobenzothiazine units linked to an acetate moiety, where the thiazine ring adopts a screw-boat conformation. In the crystal, two sets of weak C—HPh⋯ODbt (Ph = phenyl and Dbt = dihydrobenzothiazine) hydrogen bonds form layers of molecules parallel to the bc plane. The layers stack along the a-axis direction with intercalation of the ester chains. The crystal studied was a two component twin with a refined BASF of 0.34961 (5). The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (37.5%), H⋯C/C⋯H (24.6%) and H⋯O/O⋯H (16.7%) interactions. Hydrogen-bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, C—HPh⋯ODbt hydrogen bond energies are 38.3 and 30.3 kJ mol−1. 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. Moreover, the antibacterial activity of the title compound has been evaluated against gram-positive and gram-negative bacteria. Full Article text
structure Synthesis and crystal structure of a 6-chloronicotinate salt of a one-dimensional cationic nickel(II) coordination polymer with 4,4'-bipyridine By scripts.iucr.org Published On :: 2020-04-02 A 6-chloronicotinate (6-Clnic) salt of a one-dimensional cationic nickel(II) coordination polymer with 4,4'-bipyridine (4,4'-bpy), namely, catena-poly[[[tetraaquanickel(II)]-μ-4,4'-bipyridine-κ2N:N'] bis(6-chloronicotinate) tetrahydrate], {[Ni(C10H8N2)(H2O)4](C6H3ClNO2)2·4H2O}n or {[Ni(4,4'-bpy)(H2O)4](6-Clnic)2·4H2O}n, (1), was prepared by the reaction of nickel(II) sulfate heptahydrate, 6-chloronicotinic acid and 4,4'-bipyridine in a mixture of water and ethanol. The molecular structure of 1 comprises a one-dimensional polymeric {[Ni(4,4'-bpy)(H2O)4]2+}n cation, two 6-chloronicotinate anions and four water molecules of crystallization per repeating polymeric unit. The nickel(II) ion in the polymeric cation is octahedrally coordinated by four water molecule O atoms and by two 4,4'-bipyridine N atoms in the trans position. The 4,4'-bipyridine ligands act as bridges and, thus, connect the symmetry-related nickel(II) ions into an infinite one-dimensional polymeric chain extending along the b-axis direction. In the extended structure of 1, the polymeric chains of {[Ni(4,4'-bpy)(H2O)4]2+}n, the 6-chloronicotinate anions and the water molecules of crystallization are assembled into an infinite three-dimensional hydrogen-bonded network via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of the representative hydrogen-bonded ring motifs: tetrameric R24(8) and R44(10) loops, a dimeric R22(8) loop and a pentameric R45(16) loop. Full Article text
structure Crystal structures of (η4-cycloocta-1,5-diene)bis(1,3-dimethylimidazol-2-ylidene)iridium(I) iodide and (η4-cycloocta-1,5-diene)bis(1,3-diethylimidazol-2-ylidene)iridium(I) iodide By scripts.iucr.org Published On :: 2020-04-03 The title complexes, (η4-cycloocta-1,5-diene)bis(1,3-dimethylimidazol-2-ylidene)iridium(I) iodide, [Ir(C5H8N2)2(C8H12)]I, (1) and (η4-cycloocta-1,5-diene)bis(1,3-diethylimidazol-2-ylidene)iridium(I) iodide, [Ir(C7H12N2)2(C8H12)]I, (2), were prepared using a modified literature method. After carrying out the oxidative addition of the amino acid l-proline to [Ir(COD)(IMe)2]I in water and slowly cooling the reaction to room temperature, a suitable crystal of 1 was obtained and analyzed by single-crystal X-ray diffraction at 100 K. Although this crystal structure has previously been reported in the Pbam space group, it was highly disordered and precise atomic coordinates were not calculated. A single crystal of 2 was also obtained by heating the complex in water and letting it slowly cool to room temperature. Complex 1 was found to crystallize in the monoclinic space group C2/m, while 2 crystallizes in the orthorhombic space group Pccn, both with Z = 4. Full Article text
structure Synthesis, crystal structure and Hirshfeld and thermal analysis of bis[benzyl 2-(heptan-4-ylidene)hydrazine-1-carboxylate-κ2N2,O]bis(thiocyanato)nickel(II) By scripts.iucr.org Published On :: 2020-04-07 The title centrosymmetric NiII complex, [Ni(NCS)2(C15H22N2O2)2], crystallizes with one half molecule in the asymmetric unit of the monoclinic unit cell. The complex adopts an octahedral coordination geometry with two mutually trans benzyl-2-(heptan-4-ylidene)hydrazine-1-carboxylate ligands in the equatorial plane with the axial positions occupied by N-bound thiocyanato ligands. The overall conformation of the molecule is also affected by two, inversion-related, intramolecular C—H⋯O hydrogen bonds. The crystal structure features N—H⋯S, C—H⋯S and C—H⋯N hydrogen bonds together with C—H⋯π contacts that stack the complexes along the b-axis direction. The packing was further explored by Hirshfeld surface analysis. The thermal properties of the complex were also investigated by simultaneous TGA–DTA analyses. Full Article text
structure Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of 2-(2,3-dihydro-1H-perimidin-2-yl)-6-methoxyphenol By scripts.iucr.org Published On :: 2020-04-03 The title compound, C18H16N2O2, consists of perimidine and methoxyphenol units, where the tricyclic perimidine unit contains a naphthalene ring system and a non-planar C4N2 ring adopting an envelope conformation with the NCN group hinged by 47.44 (7)° with respect to the best plane of the other five atoms. In the crystal, O—HPhnl⋯NPrmdn and N—HPrmdn⋯OPhnl (Phnl = phenol and Prmdn = perimidine) hydrogen bonds link the molecules into infinite chains along the b-axis direction. Weak C—H⋯π interactions may further stabilize the crystal structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (49.0%), H⋯C/C⋯H (35.8%) and H⋯O/O⋯H (12.0%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, the O—HPhnl⋯NPrmdn and N—HPrmdn⋯OPhnl hydrogen-bond energies are 58.4 and 38.0 kJ mol−1, respectively. 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
structure 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
structure Crystal structures of {1,1,1-tris[(salicylaldimino)methyl]ethane}gallium as both a pyridine solvate and an acetonitrile 0.75-solvate and {1,1,1-tris[(salicylaldimino)methyl]ethane}indium dichloro By scripts.iucr.org Published On :: 2020-04-03 The sexadentate ligand 1,1,1-tris[(salicylideneamino)methyl]ethane has been reported numerous times in its triply deprotonated form coordinated to transition metals and lanthanides, yet it has been rarely employed with main-group elements, including in substituted forms. Its structures with gallium and indium are reported as solvates, namely, ({[(2,2-bis{[(2-oxidobenzylidene)amino-κ2N,O]methyl}propyl)imino]methyl}phenololato-κ2N,O)gallium(III) pyridine monosolvate, [Ga(C26H24N3O3)]·C5H5N, the acetonitrile 0.75-solvate, [Ga(C26H24N3O3)]·0.75C2H3N, and ({[(2,2-bis{[(2-oxidobenzylidene)amino-κ2N,O]methyl}propyl)imino]methyl}phenololato-κ2N,O)indium(III) dichloromethane monosolvate, [In(C26H24N3O3)]·CH2Cl2. All three metal complexes are pseudo-octahedral and each structure contains multiple weak C—H⋯O and/or C—H⋯N intermolecular hydrogen-bonding interactions. The syntheses and additional characterization in the forms of melting points, high-resolution mass spectra, infra-red (IR) spectra, and 1H and 13C NMR spectra are also reported. Full Article text
structure Ni3Te2O2(PO4)2(OH)4, an open-framework structure isotypic with Co3Te2O2(PO4)2(OH)4 By scripts.iucr.org Published On :: 2020-04-03 Single crystals of Ni3(TeO(OH)2)2(PO4)2, trinickel(II) bis[(oxidodihydoxidotellurate(IV)] bis(phosphate),were obtained by hydrothermal synthesis at 483 K, starting from NiCO3·2Ni(OH)2, TeO2 and H3PO4 in a molar ratio of 1:2:2. The crystal structure of Ni3Te2O2(PO4)2(OH)4 is isotypic with that of Co3Te2O2(PO4)2(OH)4 [Zimmermann et al. (2011). J. Solid State Chem. 184, 3080–3084]. The asymmetric unit comprises two Ni (site symmetries overline{1}, 2/m) one Te (m), one P (m), five O (three m, two 1) and one H (1) sites. The tellurium(IV) atom shows a coordination number of five, with the corresponding [TeO3(OH)2] polyhedron having a distorted square-pyramidal shape. The two NiII atoms are both octahedrally coordinated but form different structural elements: one constitutes chains made up from edge-sharing [NiO6] octahedra extending parallel to [010], and the other isolated [NiO2(OH)4] octahedra. The two kinds of nickel/oxygen octahedra are connected by the [TeO3(OH)2] pyramids and the [PO4] tetrahedra through edge- and corner-sharing into a three-dimensional framework structure with channels extending parallel to [010]. Hydrogen bonds of medium strength between the hydroxy groups and one of the phosphate O atoms consolidate the packing. A quantitative structure comparison between Ni3Te2O2(PO4)2(OH)4 and Co3Te2O2(PO4)2(OH)4 is made. Full Article text
structure Crystal structure and Hirshfeld surface analysis of hexyl 1-hexyl-2-oxo-1,2-dihydroquinoline-4-carboxylate By scripts.iucr.org Published On :: 2020-04-09 The asymmetric unit of the title compound, C22H31NO3, comprises of one molecule. The molecule is not planar, with the carboxylate ester group inclined by 33.47 (4)° to the heterocyclic ring. Individual molecules are linked by aromaticC—H⋯Ocarbonyl hydrogen bonds into chains running parallel to [001]. Slipped π–π stacking interactions between quinoline moieties link these chains into layers extending parallel to (100). Hirshfeld surface analysis, two-dimensional fingerprint plots and molecular electrostatic potential surfaces were used to quantify the intermolecular interactions present in the crystal, indicating that the most important contributions for the crystal packing are from H⋯H (72%), O⋯H/H⋯O (14.5%) and C⋯H/H⋯C (5.6%) interactions. Full Article text
structure Synthesis, crystal structure, DFT calculations and Hirshfeld surface analysis of 3-butyl-2,6-bis(4-fluorophenyl)piperidin-4-one By scripts.iucr.org Published On :: 2020-04-09 The title compound, C21H23F2NO, consists of two fluorophenyl groups and one butyl group equatorially oriented on a piperidine ring, which adopts a chair conformation. The dihedral angle between the mean planes of the phenyl rings is 72.1 (1)°. In the crystal, N—H⋯O and weak C—H⋯F interactions, which form R22[14] motifs, link the molecules into infinite C(6) chains propagating along [001]. A weak C—H⋯π interaction is also observed. A Hirshfeld surface analysis of the crystal structure indicates that the most significant contributions to the crystal packing are from H⋯H (53.3%), H⋯C/C⋯H (19.1%), H⋯F/F⋯H (15.7%) and H⋯O/O⋯H (7.7%) contacts. Density functional theory geometry-optimized calculations were compared to the experimentally determined structure in the solid state and used to determine the HOMO–LUMO energy gap and compare it to the UV–vis experimental spectrum. Full Article text
structure Syntheses and crystal structures of two piperine derivatives By scripts.iucr.org Published On :: 2020-04-09 The title compounds, 5-(2H-1,3-benzodioxol-5-yl)-N-cyclohexylpenta-2,4-dienamide, C18H21NO3 (I), and 5-(2H-1,3-benzodioxol-5-yl)-1-(pyrrolidin-1-yl)penta-2,4-dien-1-one C16H17NO3 (II), are derivatives of piperine, which is known as a pungent component of pepper. Their geometrical parameters are similar to those of the three polymorphs of piperine, which indicate conjugation of electrons over the length of the molecules. The extended structure of (I) features N—H⋯O amide hydrogen bonds, which generate C(4) [010] chains. The crystal of (II) features aromatic π–π stacking, as for two of three known piperine polymorphs. Full Article text
structure 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
structure Crystal structure of trans-dichlorido(1,4,8,11-tetraazacyclotetradecane-κ4N)chromium(III) bis(formamide-κO)(1,4,8,11-tetraazacyclotetradecane-κ4N)chromium(III) bis[tetrach By scripts.iucr.org Published On :: 2020-04-09 The structure of the title compound, [CrCl2(C10H24N4)][Cr(HCONH2)2(C10H24N4)][ZnCl4]2 (C10H24N4 = 1,4,8,11-tetraazacyclotetradecane, cyclam; HCONH2 = formamide, fa), has been determined from synchrotron X-ray data. The asymmetric unit contains two independent halves of the [CrCl2(cyclam)]+ and [Cr(fa)(cyclam)]3+ cations, and one tetrachloridozincate anion. In each complex cation, the CrIII ion is coordinated by the four N atoms of the cyclam ligand in the equatorial plane and two Cl ligands or two O-bonded formamide molecules in a trans axial arrangement, displaying a distorted octahedral geometry with crystallographic inversion symmetry. The Cr—N(cyclam) bond lengths are in the range 2.061 (2) to 2.074 (2) Å, while the Cr—Cl and Cr—O(fa) bond distances are 2.3194 (7) and 1.9953 (19) Å, respectively. The macrocyclic cyclam moieties adopt the centrosymmetric trans-III conformation with six- and five-membered chelate rings in chair and gauche conformations. The crystal structure is stabilized by intermolecular hydrogen bonds involving the NH or CH groups of cyclam and the NH2 group of coordinated formamide as donors, and Cl atoms of the ZnCl42− anion as acceptors. Full Article text
structure Synthesis and crystal structure of ABW-type SrFe1.40V0.60O4 By scripts.iucr.org Published On :: 2020-04-17 Single crystals of SrFe1.40V0.60O4, strontium tetraoxidodi[ferrate(III)/vanadate(III)], have been obtained as a side product in the course of sinter experiments aimed at the synthesis of double perovskites in the system SrO–Fe2O3–V2O5. The crystal structure can be characterized by layers of six-membered rings of TO4-tetrahedra (T: FeIII, VIII) perpendicular to [100]. Stacking of the layers along [100] results in a three-dimensional framework enclosing tunnel-like cavities in which SrII cations are incorporated for charge compensation. The sequence of directedness of up (U) and down (D) pointing vertices of neighboring tetrahedra in a single six-membered ring is UUUDDD. The topology of the tetrahedral framework belongs to the zeolite-type ABW. Full Article text
structure Synthesis and crystal structures of tetrameric [2-(4,4-dimethyl-2-oxazolin-2-yl)anilido]sodium and tris[2-(4,4-dimethyl-2-oxazolin-2-yl)anilido]ytterbium(III) By scripts.iucr.org Published On :: 2020-04-21 Reaction of 2-(4,4-dimethyl-2-oxazolin-2-yl)aniline (H2-L1) with one equivalent of Na[N(SiMe3)2] in toluene afforded pale-yellow crystals of tetrameric poly[bis[μ3-2-(4,4-dimethyl-2-oxazolin-2-yl)anilinido][μ2-2-(4,4-dimethyl-2-oxazolin-2-yl)aniline]tetrasodium(I)], [Na4(C11H13N2O)4]n or [Na4(H-L1)4]n (2), in excellent yield. Subsequent reaction of [Na4(H-L1)4]n (2) with 1.33 equivalents of anhydrous YbCl3 in a 50:50 mixture of toluene–THF afforded yellow crystals of tris[2-(4,4-dimethyl-2-oxazolin-2-yl)anilinido]ytterbium(III), [Yb(C11H13N2O)3] or Yb(H-L1)3 (3) in moderate yield. Direct reaction of three equivalents of 2-(4',4'-dimethyl-2'-oxazolinyl)aniline (H2-L1) with Yb[N(SiMe3)2]3 in toluene resulted in elimination of hexamethyldisilazane, HN(SiMe3)2, and produced Yb(H-L1)3 (3) in excellent yield. The structure of 2 consists of tetrameric Na4(H-L1)4 subunits in which each Na+ cation is bound to two H-L1 bridging bidentate ligands and these subunits are connected into a polymeric chain by two of the four oxazoline O atoms bridging to Na+ cations in the adjacent tetramer. This results in two 4-coordinate and two 5-coordinate Na+ cations within each tetrameric unit. The structure of 3 consists of a distorted octahedron where the bite angle of ligand L1 ranges between 74.72 (11) and 77.79 (11) degrees. The oxazoline (and anilide) N atoms occupy meridional sites such that for one ligand an anilide nitrogen is trans to an oxazoline nitrogen while for the other two oxazoline N atoms are trans to each other. This results in a significantly longer Yb—N(oxazoline) distance [2.468 (3) Å] for the bond trans to the anilide compared to those for the oxazoline N atoms trans to one another [2.376 (3), 2.390 (3) Å]. Full Article text
structure Crystal structure of bis(1-mesityl-1H-imidazole-κN3)diphenylboron trifluoromethanesulfonate By scripts.iucr.org Published On :: 2020-04-21 The solid-state structure of bis(1-mesityl-1H-imidazole-κN3)diphenylboron trifluoromethanesulfonate, C36H38BN4+·CF3SO3− or (Ph2B(MesIm)2OTf), is reported. Bis(1-mesityl-1H-imidazole-κN3)diphenylboron (Ph2B(MesIm)2+) is a bulky ligand that crystallizes in the orthorhombic space group Pbcn. The asymmetric unit contains one Ph2B(MesIm)2+ cationic ligand and one trifluoromethanesulfonate anion that balances the positive charge of the ligand. The tetrahedral geometry around the boron center is distorted as a result of the steric bulk of the phenyl groups. Weak interactions, such as π–π stacking are present in the crystal structure. Full Article text
structure Synthesis and structure of ethyl 2-[(4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)sulfanyl]acetate By scripts.iucr.org Published On :: 2020-04-17 The title compound, C18H16N2O3S, was synthesized by reaction of 2-mercapto-3-phenylquinazolin-4(3H)-one with ethyl chloroacetate. The quinazoline ring forms a dihedral angle of 86.83 (5)° with the phenyl ring. The terminal methyl group is disordered by a rotation of about 60° in a 0.531 (13): 0.469 (13) ratio. In the crystal, C—H⋯O hydrogen-bonding interactions result in the formation of columns running in the [010] direction. Two parallel columns further interact by C—H⋯O hydrogen bonds. The most important contributions to the surface contacts are from H⋯H (48.4%), C⋯H/H⋯C (21.5%) and O⋯H/H⋯O (18.7%) interactions, as concluded from a Hirshfeld analysis. Full Article text
structure Functionalized 3-(5-aryloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-(4-substituted-phenyl)prop-2-en-1-ones: synthetic pathway, and the structures of six examples By scripts.iucr.org Published On :: 2020-04-21 Five examples each of 3-(5-aryloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-[4-(prop-2-yn-1-yloxy)phenyl]prop-2-en-1-ones and the corresponding 1-(4-azidophenyl)-3-(5-aryloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)prop-2-en-1-ones have been synthesized in a highly efficient manner, starting from a common source precursor, and structures have been determined for three examples of each type. In each of 3-[5-(2-chlorophenoxy)-3-methyl-1-phenyl-1H-pyrazol-4-yl]-1-[4-(prop-2-yn-1-yloxy)phenyl]prop-2-en-1-one, C28H21ClN2O3, (Ib), the isomeric 3-[5-(2-chlorophenoxy)-3-methyl-1-phenyl-1H-pyrazol-4-yl]-1-[4-(prop-2-yn-1-yloxy)phenyl]prop-2-en-1-one, (Ic), and 3-[3-methyl-5-(naphthalen-2-yloxy)-1-phenyl-1H-pyrazol-4-yl]-1-[4-(prop-2-ynyloxy)phenyl]prop-2-en-1-one, C32H24N2O3, (Ie), the molecules are linked into chains of rings, formed by two independent C—H⋯O hydrogen bonds in (Ib) and by a combination of C—H⋯O and C—H⋯π(arene) hydrogen bonds in each of (Ic) and (Ie). There are no direction-specific intermolecular interactions in the structure of 1-(4-azidophenyl)-3-[3-methyl-5-(2-methylphenoxy)-1-phenyl-1H-pyrazol-4-yl]prop-2-en-1-one, C26H21N5O2, (IIa). In 1-(4-azidophenyl)-3-[5-(2,4-dichlorophenoxy)-3-methyl-1-phenyl-1H-pyrazol-4-yl]prop-2-en-1-one, C25H17Cl2N5O2, (IId), the dichlorophenyl group is disordered over two sets of atomic sites having occupancies 0.55 (4) and 0.45 (4), and the molecules are linked by a single C—H⋯O hydrogen bond to form cyclic, centrosymmetric R22(20) dimers. Similar dimers are formed in 1-(4-azidophenyl)-3-[3-methyl-5-(naphthalen-2-yloxy)-1-phenyl-1H-pyrazol-4-yl]prop-2-en-1-one, C29H21N5O2, (IIe), but here the dimers are linked into a chain of rings by two independent C—H..π(arene) hydrogen bonds. Comparisons are made between the molecular conformations within both series of compounds. Full Article text
structure 2-[(2,4,6-Trimethylbenzene)sulfonyl]phthalazin-1(2H)-one: crystal structure, Hirshfeld surface analysis and computational study By scripts.iucr.org Published On :: 2020-04-21 The X-ray crystal structure of the title phthalazin-1-one derivative, C17H16N2O3S {systematic name: 2-[(2,4,6-trimethylbenzene)sulfonyl]-1,2-dihydrophthalazin-1-one}, features a tetrahedral sulfoxide-S atom, connected to phthalazin-1-one and mesityl residues. The dihedral angle [83.26 (4)°] between the organic substituents is consistent with the molecule having the shape of the letter V. In the crystal, phthalazinone-C6-C—H⋯O(sulfoxide) and π(phthalazinone-N2C4)–π(phthalazinone-C6) stacking [inter-centroid distance = 3.5474 (9) Å] contacts lead to a linear supramolecular tape along the a-axis direction; tapes assemble without directional interactions between them. The analysis of the calculated Hirshfeld surfaces confirm the importance of the C—H⋯O and π-stacking interactions but, also H⋯H and C—H⋯C contacts. The calculation of the interaction energies indicate the importance of dispersion terms with the greatest energies calculated for the C—H⋯O and π-stacking interactions. Full Article text
structure Crystal structure, Hirshfeld surface analysis and DFT studies of 6-bromo-3-(12-bromododecyl)-2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine By scripts.iucr.org Published On :: 2020-04-21 The title compound, C24H30Br2N4O2, consists of a 2-(4-nitrophenyl)-4H-imidazo[4,5-b]pyridine entity with a 12-bromododecyl substituent attached to the pyridine N atom. The middle eight-carbon portion of the side chain is planar to within 0.09 (1) Å and makes a dihedral angle of 21.9 (8)° with the mean plane of the imidazolopyridine moiety, giving the molecule a V-shape. In the crystal, the imidazolopyridine units are associated through slipped π–π stacking interactions together with weak C—HPyr⋯ONtr and C—HBrmdcyl⋯ONtr (Pyr = pyridine, Ntr = nitro and Brmdcyl = bromododecyl) hydrogen bonds. The 12-bromododecyl chains overlap with each other between the stacks. The terminal –CH2Br group of the side chain shows disorder over two resolved sites in a 0.902 (3):0.098 (3) ratio. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (48.1%), H⋯Br/Br⋯H (15.0%) and H⋯O/O⋯H (12.8%) interactions. The optimized molecular structure, using density functional theory at the B3LYP/ 6–311 G(d,p) level, is compared with the experimentally determined structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap. Full Article text
structure 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
structure Crystal structure and DFT computational studies of (E)-2,4-di-tert-butyl-6-{[3-(trifluoromethyl)benzyl]iminomethyl}phenol By scripts.iucr.org Published On :: 2020-04-24 The title compound, C23H28F3NO, is an ortho-hydroxy Schiff base compound, which adopts the enol–imine tautomeric form in the solid state. The molecular structure is not planar and the dihedral angle between the planes of the aromatic rings is 85.52 (10)°. The trifluoromethyl group shows rotational disorder over two sites, with occupancies of 0.798 (6) and 0.202 (6). An intramolecular O—H⋯N hydrogen bonding generates an S(6) ring motif. The crystal structure is consolidated by C—H⋯π interactions. The molecular structure was optimized via density functional theory (DFT) methods with the B3LYP functional and LanL2DZ basis set. The theoretical structure is in good agreement with the experimental data. The frontier orbitals and molecular electrostatic potential map were also examined by DFT computations. Full Article text
structure Crystal structure and Hirshfeld surface analysis of 2-phenyl-1H-phenanthro[9,10-d]imidazol-3-ium benzoate By scripts.iucr.org Published On :: 2020-04-24 In the title compound, C21H15N2+·C7H5O2−, 2-phenyl-1H-phenanthro[9,10-d]imidazole and benzoic acid form an ion pair complex. The system is consolidated by hydrogen bonds along with π–π interactions and N—H⋯π interactions between the constituent units. For a better understanding of the crystal structure and intermolecular interactions, a Hirshfeld surface analysis was performed. Full Article text
structure Crystal structure and Hirshfeld surface analysis of 4-{[(anthracen-9-yl)methyl]amino}benzoic acid dimethylformamide monosolvate By scripts.iucr.org Published On :: 2020-04-24 The title compound, C22H17NO2·C3H7NO, was synthesized by condensation of an aromatic aldehyde with a secondary amine and subsequent reduction. It was crystallized from a dimethylformamide solution as a monosolvate, C22H17NO2·C3H7NO. The aromatic molecule is non-planar with a dihedral angle between the mean planes of the aniline moiety and the methyl anthracene moiety of 81.36 (8)°. The torsion angle of the Caryl—CH2—NH—Caryl backbone is 175.9 (2)°. The crystal structure exhibits a three-dimensional supramolecular network, resulting from hydrogen-bonding interactions between the carboxylic OH group and the solvent O atom as well as between the amine functionality and the O atom of the carboxylic group and additional C—H⋯π interactions. Hirshfeld surface analysis was performed to quantify the intermolecular interactions. Full Article text
structure The crystal structures of Fe-bearing MgCO3 sp2- and sp3-carbonates at 98 GPa from single-crystal X-ray diffraction using synchrotron radiation By scripts.iucr.org Published On :: 2020-04-21 The crystal structure of MgCO3-II has long been discussed in the literature where DFT-based model calculations predict a pressure-induced transition of the carbon atom from the sp2 to the sp3 type of bonding. We have now determined the crystal structure of iron-bearing MgCO3-II based on single-crystal X-ray diffraction measurements using synchrotron radiation. We laser-heated a synthetic (Mg0.85Fe0.15)CO3 single crystal at 2500 K and 98 GPa and observed the formation of a monoclinic phase with composition (Mg2.53Fe0.47)C3O9 in the space group C2/m that contains tetrahedrally coordinated carbon, where CO44− tetrahedra are linked by corner-sharing oxygen atoms to form three-membered C3O96− ring anions. The crystal structure of (Mg0.85Fe0.15)CO3 (magnesium iron carbonate) at 98 GPa and 300 K is reported here as well. In comparison with previous structure-prediction calculations and powder X-ray diffraction data, our structural data provide reliable information from experiments regarding atomic positions, bond lengths, and bond angles. Full Article text
structure Crystal structure and Hirshfeld surface analysis of 6-benzoyl-3,5-diphenylcyclohex-2-en-1-one By scripts.iucr.org Published On :: 2020-04-21 In the title compound, C25H20O2, the central cyclohexenone ring adopts an envelope conformation. The mean plane of the cyclohexenone ring makes dihedral angles of 87.66 (11) and 23.76 (12)°, respectively, with the two attached phenyl rings, while it is inclined by 69.55 (11)° to the phenyl ring of the benzoyl group. In the crystal, the molecules are linked by C—H⋯O and C—H⋯π interactions, forming a three-dimensional network. Full Article text
structure Synthesis and crystal structure of a pentacopper(II) 12-metallacrown-4: cis-diaquatetrakis(dimethylformamide-κO)manganese(II) tetrakis(μ3-N,2-dioxidobenzene-1-carboximidate)pentacopper(II) By scripts.iucr.org Published On :: 2020-04-30 The title compound, [Mn(C3H7NO)4(H2O)2][Cu5(C7H4NO3)4]·C3H7NO or cis-[Mn(H2O)2(DMF)4]{Cu[12-MCCu(II)N(shi)-4]}·DMF, where MC is metallacrown, shi3− is salicylhydroximate, and DMF is N,N-dimethylformamide, crystallizes in the monoclinic space group P21/n. Two crystallographically independent metallacrown anions are present in the structure, and both anions exhibit minor main molecule disorder by an approximate (non-crystallographic) 180° rotation with occupancy ratios of 0.9010 (9) to 0.0990 (9) for one anion and 0.9497 (8) to 0.0503 (8) for the other. Each pentacopper(II) metallacrown contains four CuII ions in the MC ring and a CuII ion captured in the central cavity. Each CuII ion is four-coordinate with a square-planar geometry. The anionic {Cu[12-MCCu(II)N(shi)-4]}2− is charged-balanced by the presence of a cis-[Mn(H2O)2(DMF)4]2+ cation located in the lattice. In addition, the octahedral MnII counter-cation is hydrogen bonded to both MC anions via the coordinated water molecules of the MnII ion. The water molecules form hydrogen bonds with the phenolate and carbonyl oxygen atoms of the shi3− ligands of the MCs. Full Article text
structure Crystal structure of lutetium aluminate (LUAM), Lu4Al2O9 By scripts.iucr.org Published On :: 2020-04-30 The crystal structure of the title compound containing lutetium, the last element in the lanthanide series, was determined using a single crystal prepared by heating a pressed pellet of a 2:1 molar ratio mixture of Lu2O3 and Al2O3 powders in an Ar atmosphere at 2173 K for 4 h. Lu4Al2O9 is isostructural with Eu4Al2O9 and composed of Al2O7 ditetrahedra and Lu-centered six- and sevenfold oxygen polyhedra. The unit-cell volume, 787.3 (3) Å3, is the smallest among the volumes of the rare-earth (RE) aluminates, RE4Al2O9. The crystal studied was refined as a two-component pseudo-merohedric twin. Full Article text
structure Synthesis, crystal structure and Hirshfeld surface analysis of N-(4-chlorophenyl)-5-cyclopropyl-1-(4-methoxyphenyl)-1H-1,2,3-triazole-4-carboxamide By scripts.iucr.org Published On :: 2020-04-30 The title compound, C19H17ClN4O2, was obtained via a two-step synthesis involving the enol-mediated click Dimroth reaction of 4-azidoanisole with methyl 3-cyclopropyl-3-oxopropanoate leading to the 5-cyclopropyl-1-(4-methoxyphenyl)-1H-1,2,3-triazole-4-carboxylic acid and subsequent acid amidation with 4-chloroaniline by 1,1'-carbonyldiimidazole (CDI). It crystallizes in space group P21/n, with one molecule in the asymmetric unit. In the extended structure, two molecules arranged in a near coplanar fashion relative to the triazole ring planes are interconnected by N—H⋯N and C—H⋯N hydrogen bonds into a homodimer. The formation of dimers is a consequence of the above interaction and the edge-to-face stacking of aromatic rings, which are turned by 58.0 (3)° relative to each other. The dimers are linked by C—H⋯O interactions into ribbons. DFT calculations demonstrate that the frontier molecular orbitals are well separated in energy and the HOMO is largely localized on the 4-chlorophenyl amide motif while the LUMO is associated with aryltriazole grouping. A Hirshfeld surface analysis was performed to further analyse the intermolecular interactions. Full Article text
structure SVAT4: a computer program for visualization and analysis of crystal structures By scripts.iucr.org Published On :: 2020-05-05 SVAT4 is a computer program for interactive visualization of three-dimensional crystal structures, including chemical bonds and magnetic moments. A wide range of functions, e.g. revealing atomic layers and polyhedral clusters, are available for further structural analysis. Atomic sizes, colors, appearance, view directions and view modes (orthographic or perspective views) are adjustable. Customized work for the visualization and analysis can be saved and then reloaded. SVAT4 provides a template to simplify the process of preparation of a new data file. SVAT4 can generate high-quality images for publication and animations for presentations. The usability of SVAT4 is broadened by a software suite for simulation and analysis of electron diffraction patterns. Full Article text
structure CrystalCMP: automatic comparison of molecular structures By scripts.iucr.org Published On :: 2020-04-23 This article describes new developments in the CrystalCMP software. In particular, an automatic procedure for comparison of molecular packing is presented. The key components are an automated procedure for fragment selection and the replacement of the angle calculation by root-mean-square deviation of atomic positions. The procedure was tested on a large data set taken from the Cambridge Structural Database (CSD) and the results of all the comparisons were saved as an HTML page, which is freely available on the web. The analysis of the results allowed estimation of the threshold for identification of identical packing and allowed duplicates and entries with potentially incorrect space groups to be found in the CSD. Full Article text
structure Screening topological materials with a CsCl-type structure in crystallographic databases By scripts.iucr.org Published On :: 2019-06-13 CsCl-type materials have many outstanding characteristics, i.e. simple in structure, ease of synthesis and good stability at room temperature, thus are an excellent choice for designing functional materials. Using high-throughput first-principles calculations, a large number of topological semimetals/metals (TMs) were designed from CsCl-type materials found in crystallographic databases and their crystal and electronic structures have been studied. The CsCl-type TMs in this work show rich topological character, ranging from triple nodal points, type-I nodal lines and critical-type nodal lines, to hybrid nodal lines. The TMs identified show clean topological band structures near the Fermi level, which are suitable for experimental investigations and future applications. This work provides a rich data set of TMs with a CsCl-type structure. Full Article text
structure 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
structure Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder By scripts.iucr.org Published On :: 2019-06-20 Ependymin was first discovered as a predominant protein in brain extracellular fluid in fish and was suggested to be involved in functions mostly related to learning and memory. Orthologous proteins to ependymin called ependymin-related proteins (EPDRs) have been found to exist in various tissues from sea urchins to humans, yet their functional role remains to be revealed. In this study, the structures of EPDR1 from frog, mouse and human were determined and analyzed. All of the EPDR1s fold into a dimer using a monomeric subunit that is mostly made up of two stacking antiparallel β-sheets with a curvature on one side, resulting in the formation of a deep hydrophobic pocket. All six of the cysteine residues in the monomeric subunit participate in the formation of three intramolecular disulfide bonds. Other interesting features of EPDR1 include two asparagine residues with glycosylation and a Ca2+-binding site. The EPDR1 fold is very similar to the folds of bacterial VioE and LolA/LolB, which also use a similar hydrophobic pocket for their respective functions as a hydrophobic substrate-binding enzyme and a lipoprotein carrier, respectively. A further fatty-acid binding assay using EPDR1 suggests that it indeed binds to fatty acids, presumably via this pocket. Additional interactome analysis of EPDR1 showed that EPDR1 interacts with insulin-like growth factor 2 receptor and flotillin proteins, which are known to be involved in protein and vesicle translocation. Full Article text
structure Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination By scripts.iucr.org Published On :: 2019-07-12 Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal–organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool. Full Article text
structure Symmetry-mode analysis for intuitive observation of structure–property relationships in the lead-free antiferroelectric (1−x)AgNbO3–xLiTaO3 By scripts.iucr.org Published On :: 2019-06-21 Functional materials are of critical importance to electronic and smart devices. A deep understanding of the structure–property relationship is essential for designing new materials. In this work, instead of utilizing conventional atomic coordinates, a symmetry-mode approach is successfully used to conduct structure refinement of the neutron powder diffraction data of (1−x)AgNbO3–xLiTaO3 (0 ≤ x ≤ 0.09) ceramics. This provides rich structural information that not only clarifies the controversial symmetry assigned to pure AgNbO3 but also explains well the detailed structural evolution of (1−x)AgNbO3–xLiTaO3 (0 ≤ x ≤ 0.09) ceramics, and builds a comprehensive and straightforward relationship between structural distortion and electrical properties. It is concluded that there are four relatively large-amplitude major modes that dominate the distorted Pmc21 structure of pure AgNbO3, namely a Λ3 antiferroelectric mode, a T4+ a−a−c0 octahedral tilting mode, an H2 a0a0c+/a0a0c− octahedral tilting mode and a Γ4− ferroelectric mode. The H2 and Λ3 modes become progressively inactive with increasing x and their destabilization is the driving force behind the composition-driven phase transition between the Pmc21 and R3c phases. This structural variation is consistent with the trend observed in the measured temperature-dependent dielectric properties and polarization–electric field (P-E) hysteresis loops. The mode crystallography applied in this study provides a strategy for optimizing related properties by tuning the amplitudes of the corresponding modes in these novel AgNbO3-based (anti)ferroelectric materials. Full Article text
structure Cryo-EM structure of the CFA/I pilus rod By scripts.iucr.org Published On :: 2019-07-09 Enterotoxigenic Escherichia coli (ETEC) are common agents of diarrhea for travelers and a major cause of mortality in children in developing countries. To attach to intestinal cells ETEC express colonization factors, among them CFA/I, which are the most prevalent factors and are the archetypical representative of class 5 pili. The helical quaternary structure of CFA/I can be unwound under tensile force and it has been shown that this mechanical property helps bacteria to withstand shear forces from fluid motion. We report in this work the CFA/I pilus structure at 4.3 Å resolution from electron cryomicroscopy (cryo-EM) data, and report details of the donor strand complementation. The CfaB pilins modeled into the cryo-EM map allow us to identify the buried surface area between subunits, and these regions are correlated to quaternary structural stability in class 5 and chaperone–usher pili. In addition, from the model built using the EM structure we also predicted that residue 13 (proline) of the N-terminal β-strand could have a major impact on the filament's structural stability. Therefore, we used optical tweezers to measure and compare the stability of the quaternary structure of wild type CFA/I and a point-mutated CFA/I with a propensity for unwinding. We found that pili with this mutated CFA/I require a lower force to unwind, supporting our hypothesis that Pro13 is important for structural stability. The high-resolution CFA/I pilus structure presented in this work and the analysis of structural stability will be useful for the development of novel antimicrobial drugs that target adhesion pili needed for initial attachment and sustained adhesion of ETEC. Full Article text
structure Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography By scripts.iucr.org Published On :: 2019-06-23 Copper-containing nitrite reductases (CuNiRs) that convert NO2− to NO via a CuCAT–His–Cys–CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD−, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2− a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed. Full Article text
structure High-throughput structures of protein–ligand complexes at room temperature using serial femtosecond crystallography By scripts.iucr.org Published On :: 2019-10-10 High-throughput X-ray crystal structures of protein–ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein–ligand complexes using SFX. Full Article text
structure Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase By scripts.iucr.org Published On :: 2019-10-24 Indanomycin is biosynthesized by a hybrid nonribosomal peptide synthase/polyketide synthase (NRPS/PKS) followed by a number of `tailoring' steps to form the two ring systems that are present in the mature product. It had previously been hypothesized that the indane ring of indanomycin was formed by the action of IdmH using a Diels–Alder reaction. Here, the crystal structure of a selenomethionine-labelled truncated form of IdmH (IdmH-Δ99–107) was solved using single-wavelength anomalous dispersion (SAD) phasing. This truncated variant allows consistent and easy crystallization, but importantly the structure was used as a search model in molecular replacement, allowing the full-length IdmH structure to be determined to 2.7 Å resolution. IdmH is a homodimer, with the individual protomers consisting of an α+β barrel. Each protomer contains a deep hydrophobic pocket which is proposed to constitute the active site of the enzyme. To investigate the reaction catalysed by IdmH, 88% of the backbone NMR resonances were assigned, and using chemical shift perturbation of [15N]-labelled IdmH it was demonstrated that indanomycin binds in the active-site pocket. Finally, combined quantum mechanical/molecular mechanical (QM/MM) modelling of the IdmH reaction shows that the active site of the enzyme provides an appropriate environment to promote indane-ring formation, supporting the assignment of IdmH as the key Diels–Alderase catalysing the final step in the biosynthesis of indanomycin through a similar mechanism to other recently characterized Diels–Alderases involved in polyketide-tailoring reactions. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at https://proteopedia.org/w/Journal:IUCrJ:S2052252519012399. Full Article text
structure Toward G protein-coupled receptor structure-based drug design using X-ray lasers By scripts.iucr.org Published On :: 2019-10-24 Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins. Full Article text
structure Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases By scripts.iucr.org Published On :: 2020-01-01 Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54–Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1'. Moreover, residue Cys23 within a conserved cysteine–glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1' to S6'. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms. Full Article text
structure Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data By scripts.iucr.org Published On :: 2020-01-01 With the emergence of X-ray free-electron lasers, it is possible to investigate the structure of nanoscale samples by employing coherent diffractive imaging in the X-ray spectral regime. In this work, we developed a refinement method for structure reconstruction applicable to low-quality coherent diffraction data. The method is based on the gradient search method and considers the missing region of a diffraction pattern and the small number of detected photons. We introduced an initial estimate of the structure in the method to improve the convergence. The present method is applied to an experimental diffraction pattern of an Xe cluster obtained in an X-ray scattering experiment at the SPring-8 Angstrom Compact free-electron LAser (SACLA) facility. It is found that the electron density is successfully reconstructed from the diffraction pattern with a large missing region, with a good initial estimate of the structure. The diffraction pattern calculated from the reconstructed electron density reproduced the observed diffraction pattern well, including the characteristic intensity modulation in each ring. Our refinement method enables structure reconstruction from diffraction patterns under difficulties such as missing areas and low diffraction intensity, and it is potentially applicable to the structure determination of samples that have low scattering power. Full Article text
structure Synthesis, structure, magnetic and half-metallic properties of Co2−xRuxMnSi (x = 0, 0.25, 0.5, 0.75, 1) compounds By scripts.iucr.org Published On :: 2020-01-01 A series of Co2−xRuxMnSi (x = 0, 0.25, 0.5, 0.75, 1) Heusler compounds were successfully synthesized. The heat-treatment conditions were crucial to make the materials form a single phase with a Heusler structure. With increasing Ru content, the half-metallic gap, lattice parameters and magnetization are continuously adjustable in a wide range. The Co2−xRuxMnSi (x = 0, 0.25) compounds are rigorous half-metals and show a T3 dependence of resistance at low temperature. The Co2−xRuxMnSi (x = 0.5, 0.75, 1) Heusler compounds are the nearly half-metallic materials and show a semiconductive dependence of resistance at low temperature. The experimental magnetization is consistent with that in theory and follows the Slater–Pauling rule. The Curie temperature is higher than 750 K for all Co2−xRuxMnSi Heusler compounds. Full Article text
structure fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins By scripts.iucr.org Published On :: 2020-01-17 The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software. Full Article text
structure Isomorphism: `molecular similarity to crystal structure similarity' in multicomponent forms of analgesic drugs tolfenamic and mefenamic acid By scripts.iucr.org Published On :: 2020-01-07 The non-steroidal anti-inflammatory drugs mefenamic acid (MFA) and tolfenamic acid (TFA) have a close resemblance in their molecular scaffold, whereby a methyl group in MFA is substituted by a chloro group in TFA. The present study demonstrates the isomorphous nature of these compounds in a series of their multicomponent solids. Furthermore, the unique nature of MFA and TFA has been demonstrated while excavating their alternate solid forms in that, by varying the drug (MFA or TFA) to coformer [4-dimethylaminopyridine (DMAP)] stoichiometric ratio, both drugs have produced three different types of multicomponent crystals, viz. salt (1:1; API to coformer ratio), salt hydrate (1:1:1) and cocrystal salt (2:1). Interestingly, as anticipated from the close similarity of TFA and MFA structures, these multicomponent solids have shown an isomorphous relation. A thorough characterization and structural investigation of the new multicomponent forms of MFA and TFA revealed their similarity in terms of space group and structural packing with isomorphic nature among the pairs. Herein, the experimental results are generalized in a broader perspective for predictably identifying any possible new forms of comparable compounds by mapping their crystal structure landscapes. The utility of such an approach is evident from the identification of polymorph VI of TFA from hetero-seeding with isomorphous MFA form I from acetone–methanol (1:1) solution. That aside, a pseudopolymorph of TFA with dimethylformamide (DMF) was obtained, which also has some structural similarity to that of the solvate MFA:DMF. These new isostructural pairs are discussed in the context of solid form screening using structural landscape similarity. Full Article text
structure Extraordinary structural complexity of ilmajokite: a multilevel hierarchical framework structure of natural origin By scripts.iucr.org Published On :: 2020-01-01 The crystal structure of ilmajokite, a rare Na-K-Ba-Ce-titanosilicate from the Khibiny mountains, Kola peninsula, Russia, has been solved using single-crystal X-ray diffraction data. The crystal structure is based on a 3D titanosilicate framework consisting of trigonal prismatic titanosilicate (TPTS) clusters centered by Ce3+ in [9]-coordination. Four adjacent TPTS clusters are linked into four-membered rings within the (010) plane and connected via ribbons parallel to 101. The ribbons are organized into layers parallel to (010) and modulated along the a axis with a modulation wavelength of csinβ = 32.91 Å and an amplitude of ∼b/2 = 13.89 Å. The layers are linked by additional silicate tetrahedra. Na+, K+, Ba2+ and H2O groups occur in the framework cavities and have different occupancies and coordination environments. The crystal structure of ilmajokite can be separated into eight hierarchical levels: atoms, coordination polyhedra, TPTS clusters, rings, ribbons, layers, the framework and the whole structure. The information-based analysis allows estimation of the complexity of the structure as 8.468 bits per atom and 11990.129 bits per cell. According to this analysis, ilmajokite is the third-most complex mineral known to date after ewingite and morrisonite, and is the most complex mineral framework structure, comparable in complexity to paulingite-(Ca) (11 590.532 bits per cell). Full Article text
structure Crystal twinning of bicontinuous cubic structures By scripts.iucr.org Published On :: 2020-02-01 Bicontinuous cubic structures in soft matter consist of two intertwining labyrinths separated by a partitioning layer. Combining experiments, numerical modelling and techniques in differential geometry, we investigate twinning defects in bicontinuous cubic structures. We first demonstrate that a twin boundary is most likely to occur at a plane that cuts the partitioning layer almost perpendicularly, so that the perturbation caused by twinning remains minimal. This principle can be used as a criterion to identify potential twin boundaries, as demonstrated through detailed investigations of mesoporous silica crystals characterized by diamond and gyroid surfaces. We then discuss that a twin boundary can result from a stacking fault in the arrangement of inter-lamellar attachments at an early stage of structure formation. It is further shown that enhanced curvature fluctuations near the twin boundary would cost energy because of geometrical frustration, which would be eased by a crystal distortion that is experimentally observed. Full Article text