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Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling

A new scaling program is presented with new features to support multi-sweep workflows and analysis within the DIALS software package.




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Crystal structure and Hirshfeld surface analysis of new polymorph of racemic 2-phenyl­butyramide

A new polymorph of the title compound, C10H13NO, was obtained by recrystallization of the commercial product from a water/ethanol mixture (1:1 v/v). Crystals of the previously reported racemic and homochiral forms of 2-phenyl­butyramide were grown from water–aceto­nitrile solution in 1:1 volume ratio [Khrustalev et al. (2014). Cryst. Growth Des. 14, 3360–3369]. While the previously reported racemic and enanti­opure forms of the title compound adopt very similar supra­molecular structures (hydrogen-bonded ribbons), the new racemic polymorph is stabilized by a single N—H⋯O hydrogen bond that links mol­ecules into chains along the c-axis direction with an anti­parallel (centrosymmetric) packing in the crystal. Hirshfeld mol­ecular surface analysis was employed to compare the inter­molecular inter­actions in the polymorphs of the title compound.




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Bis(4-acet­oxy-N,N-di­methyl­tryptammonium) fumarate: a new crystalline form of psilacetin, an alternative to psilocybin as a psilocin prodrug

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].




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A new form of NaMnAsO4

A new form of NaMnAsO4, sodium manganese(II) orthoarsenate, has been obtained under hydro­thermal conditions, and is referred to as the β-polymorph. In contrast to the previously reported ortho­rhom­bic α-polymorph that crystallizes in the olivine-type of structure and has one manganese(II) cation in a distorted octa­hedral coordination, the current β-polymorph contains two manganese(II) cations in [5]-coordination, inter­mediate between a square-pyramid and a trigonal bipyramid. In the crystal structure of β-NaMnAsO4, four [MnO5] polyhedra are linked through vertex- and edge-sharing into finite {Mn4O16} units strung into rows parallel to [100]. These units are linked through two distinct orthoarsenate groups into a framework structure with channels propagating parallel to the manganese oxide rows. Both unique sodium cations are situated inside the channels and exhibit coordination numbers of six and seven. β-NaMnAsO4 is isotypic with one form of NaCoPO4 and with NaCuAsO4.




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Synthesis and crystal structure of a new hybrid organic–inorganic material containing neutral mol­ecules, cations and hepta­molybdate anions

The title compound, hexa­kis­(2-methyl-1H-imidazol-3-ium) hepta­molybdate 2-methyl-1H-imidazole disolvate dihydrate, (C4H7N2)6[Mo7O24]·2C4H6N2·2H2O, was prepared from 2-methyl­imidazole and ammonium hepta­molybdate tetra­hydrate in acid solution. The [Mo7O24]6− hepta­molybdate cluster anion is accompanied by six protonated (C4H7N2)+ 2-methyl­imidazolium cations, two neutral C4H6N2 2-methyl­imidazole mol­ecules and two water mol­ecules of crystallization. The cluster consists of seven distorted MoO6 octa­hedra sharing edges or vertices. In the crystal, the components are linked by N—H⋯N, N—H⋯O, O—H⋯O, N—H⋯(O,O) and O—H⋯(O,O) hydrogen bonds, generating a three-dimensional network. Weak C—H⋯O inter­actions consolidate the packing.




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Two new glaserite-type orthovanadates: Rb2KDy(VO4)2 and Cs1.52K1.48Gd(VO4)2

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




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Crystal structures of two new isocoumarin derivatives: 8-amino-6-methyl-3,4-diphenyl-1H-isochromen-1-one and 8-amino-3,4-diethyl-6-methyl-1H-isochromen-1-one

The title compounds, 8-amino-6-methyl-3,4-diphenyl-1H-isochromen-1-one, C22H17NO2, (I), and 8-amino-3,4-diethyl-6-methyl-1H-isochromen-1-one, C14H17NO2, (II), are new isocoumarin derivatives in which the isochromene ring systems are planar. Compound II crystallizes with two independent mol­ecules (A and B) in the asymmetric unit. In I, the two phenyl rings are inclined to each other by 56.41 (7)° and to the mean plane of the 1H-isochromene ring system by 67.64 (6) and 44.92 (6)°. In both compounds, there is an intra­molecular N—H⋯O hydrogen bond present forming an S(6) ring motif. In the crystal of I, mol­ecules are linked by N—H⋯π inter­actions, forming chains along the b-axis direction. A C—H⋯π inter­action links the chains to form layers parallel to (100). The layers are then linked by a second C—H⋯π inter­action, forming a three-dimensional structure. In the crystal of II, the two independent mol­ecules (A and B) are linked by N—H⋯O hydrogen bonds, forming –A–B–A–B– chains along the [101] direction. The chains are linked into ribbons by C—H⋯π inter­actions involving inversion-related A mol­ecules. The latter are linked by offset π–π inter­actions [inter­centroid distances vary from 3.506 (1) to 3.870 (2) Å], forming a three-dimensional structure.




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Syntheses and crystal structures of a new family of hybrid perovskites: C5H14N2·ABr3·0.5H2O (A = K, Rb, Cs)

The syntheses and crystal structures of three hybrid perovskites, viz. poly[1-methyl­piperizine-1,4-diium [tri-μ-bromido-potassium] hemihydrate], {(C5H14N2)[KBr3]·0.5H2O}n, (I), poly[1-methyl­piperizine-1,4-diium [tri-μ-bromido-rubidium] hemihydrate], {(C5H14N2)[RbBr3]·0.5H2O}n, (II), and poly[1-methyl­piperizine-1,4-diium [tri-μ-bromido-caesium] hemihydrate], {(C5H14N2)[CsBr3]·0.5H2O}n, (III), are described. These isostructural (space group Amm2) phases contain a three-dimensional, corner-sharing network of distorted ABr6 octa­hedra (A = K, Rb, Cs) with the same topology as the classical perovskite structure. The doubly protonated C5H14N22+ cations occupy inter­stices bounded by eight octa­hedra and the water mol­ecules lie in square sites bounded by four octa­hedra. N—H⋯Br, N—H⋯(Br,Br), N—H⋯O and O—H⋯Br hydrogen bonds consolidate the structures.




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Crystal structure and Hirshfeld surface analysis of a new di­thio­glycoluril: 1,4-bis­(4-meth­oxy­phen­yl)-3a-methyl­tetra­hydro­imidazo[4,5-d]imidazole-2,5(1H,3H)-di­thione

In the title di­thio­glycoluril derivative, C19H20N4O3S2, there is a difference in the torsion angles between the thio­imidazole moiety and the meth­oxy­phenyl groups on either side of the mol­ecule [C—N—Car—Car = 116.9 (2) and −86.1 (3)°, respectively]. The N—C—N bond angle on one side of the di­thio­glycoluril moiety is slightly smaller compared to that on the opposite side, [110.9 (2)° cf. 112.0 (2)°], probably as a result of the steric effect of the methyl group. In the crystal, N—H⋯S hydrogen bonds link adjacent mol­ecules to form chains propagating along the c-axis direction. The chains are linked by C—H⋯S hydrogen bonds, forming layers parallel to the bc plane. The layers are then linked by C—H⋯π inter­actions, leading to the formation of a three-dimensional supra­molecular network. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to investigate the mol­ecular inter­actions in the crystal.




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Synthesis, characterization, crystal structure and supra­molecularity of ethyl (E)-2-cyano-3-(3-methyl­thio­phen-2-yl)acrylate and a new polymorph of ethyl (E)-2-cyano-3-(thio­phen-2-yl)acrylate

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




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New refinement of the crystal structure of Zn(NH3)2Cl2 at 100 K

The crystal structure of [ZnCl2(NH3)2], diamminedi­chlorido­zinc, was re-investigated at low temperature, revealing the positions of the hydrogen atoms and thus a deeper insight into the hydrogen-bonding scheme in the crystal packing. In comparison with previous crystal structure determinations [MacGillavry & Bijvoet (1936). Z. Kristallogr. 94, 249–255; Yamaguchi & Lindqvist (1981). Acta Chem. Scand. 35, 727–728], an improved precision of the structural parameters was achieved. In the crystal, tetra­hedral [Zn(NH3)2Cl2] units (point-group symmetry mm2) are linked through N—H⋯Cl hydrogen bonds into a three-dimensional network.




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The `super acid' BF3H2O stabilized by 1,4-dioxane: new preparative aspects and the crystal structure of BF3H2O·C4H8O2

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.




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Crystal structure of a new polymorph of 3-acetyl-8-meth­oxy-2H-chromen-2-one

A new polymorphic form of the title compound, C12H10O4, is described in the ortho­rhom­bic space group Pbca and Z = 8, as compared to polymorph I, which crystallizes in the monoclinic space group C2/c and Z = 8 [Li et al. (2012). Chin. J. Struct. Chem. 31, 1003–1007.]. In polymorph II, the coumarin ring system is almost planar (r.m.s. deviation = 0.00129 Å). In the crystal, mol­ecules are connected by Csp3—H⋯O and Car—H⋯O hydrogen bonds, forming mol­ecular sheets linked into zigzag shaped layers along the b-axis direction. The three-dimensional lattice is assembled through stacking of the zigzag layers by π–π inter­actions with a centroid-to-centroid distance of 3.600 (9) Å and anti­parallel C=O⋯C=O inter­actions with a distance of 3.1986 (17) Å, which give rise to a helical supra­molecular architecture.




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Crystal structure, Hirshfeld analysis and a mol­ecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo-2-{[5-(pentan-3-yl)-1,2,4-oxa­diazol-3-yl]meth­yl}-2H-1,2,6-thia­diazine-4-carboxyl­a

The title compound, C15H22N4O5S, was prepared via alkyl­ation of 3-(chloro­meth­yl)-5-(pentan-3-yl)-1,2,4-oxa­diazole in anhydrous dioxane in the presence of tri­ethyl­amine. The thia­diazine ring has an envelope conformation with the S atom displaced by 0.4883 (6) Å from the mean plane through the other five atoms. The planar 1,2,4-oxa­diazole ring is inclined to the mean plane of the thia­diazine ring by 77.45 (11)°. In the crystal, mol­ecules are linked by C—H⋯N hydrogen bonds, forming chains propagating along the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the inter­molecular contacts present in the crystal. Mol­ecular docking studies were use to evaluate the title compound as a potential system that inter­acts effectively with the capsid of the Hepatitis B virus (HBV), supported by an experimental in vitro HBV replication model.




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A new pseudopolymorph of perchlorinated neo­penta­silane: the benzene monosolvate Si(SiCl3)4·C6H6

A new pseudopolymorph of dodeca­chloro­penta­silane, namely a benzene monosolvate, Si5Cl12·C6H6, is described. There are two half mol­ecules of each kind in the asymmetric unit. Both Si5Cl12 mol­ecules are completed by crystallographic twofold symmetry. One of the benzene mol­ecules is located on a twofold rotation axis with two C—H groups located on this rotation axis. The second benzene mol­ecule has all atoms on a general position: it is disordered over two equally occupied orientations. No directional inter­actions beyond normal van der Waals contacts occur in the crystal.




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The crystal structures and Hirshfeld surface analyses of a cadmium(II) and a zinc(II) mononuclear complex of the new tetrakis-substituted pyrazine ligand N,N',N'',N'''-[pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene)]tetra­kis

The whole mol­ecule of the cadmium(II) complex, di­iodido­{N,N',N'',N'''-[pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene)]tetra­kis­(N-methyl­aniline)-κ3N2,N1,N6}cadmium(II), [CdI2(C36H40N6)], (I), of the ligand N,N',N'',N'''-[pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene)]tetra­kis­(N-methyl­aniline) (L), is generated by a twofold rotation symmetry; the twofold axis bis­ects the cadmium atom and the nitro­gen atoms of the pyrazine ring. The ligand coordinates in a mono-tridentate manner and the cadmium atom has a fivefold CdN3I2 coordination environment with a distorted shape. In the zinc(II) complex, dichlorido{N,N',N'',N'''-[pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene)]tetra­kis­(N-methyl­aniline)-κ3N2,N1,N6}zinc(II) di­chloro­methane 0.6-solvate, [ZnCl2(C36H40N6)]·0.6CH2Cl2, (II), ligand L also coordinates in a mono-tridentate manner and the zinc atom has a fivefold ZnN3Cl2 coordination environment with a distorted shape. It crystallized as a partial di­chloro­methane solvate. In the crystal of I, the complex mol­ecules are linked by weak C—H⋯I contacts, forming ribbons propagating along [100]. In the crystal of II, the complex mol­ecules are linked by a series of C—H⋯π inter­actions, forming layers lying parallel to the (1overline{1}1) plane. In the crystals of both compounds there are metal–halide⋯π(pyrazine) contacts present. The Hirshfeld analyses confirm the importance of the C—H⋯halide contacts in the crystal packing of both compounds.




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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

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.




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Crystal structures and Hirshfeld surface analyses of two new tetra­kis-substituted pyrazines and a degredation product

The two new tetra­kis-substituted pyrazines, 1,1',1'',1'''-(pyrazine-2,3,5,6-tetra­yl) tetra­kis­(N,N-di­methyl­methanamine), C16H32N6, (I) and N,N',N'',N'''-[pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene)]tetra­kis­(N-methyl­aniline), C36H40N6, (II), both crystallize with half a mol­ecule in the asymmetric unit; the whole mol­ecules are generated by inversion symmetry. There are weak intra­molecular C—H⋯N hydrogen bonds present in both mol­ecules and in (II) the pendant N-methyl­aniline rings are linked by a C—H⋯π inter­action. The degredation product, N,N'-[(6-phenyl-6,7-di­hydro-5H-pyrrolo­[3,4-b]pyrazine-2,3-di­yl)bis(methyl­ene)]bis­(N-methyl­aniline), C28H29N5, (III), was obtained several times by reacting (II) with different metal salts. Here, the 6-phenyl ring is almost coplanar with the planar pyrrolo­[3,4-b]pyrazine unit (r.m.s. deviation = 0.029 Å), with a dihedral angle of 4.41 (10)° between them. The two N-meth­yl­aniline rings are inclined to the planar pyrrolo­[3,4-b]pyrazine unit by 88.26 (10) and 89.71 (10)°, and to each other by 72.56 (13)°. There are also weak intra­molecular C—H⋯N hydrogen bonds present involving the pyrazine ring and the two N-methyl­aniline groups. In the crystal of (I), there are no significant inter­molecular contacts present, while in (II) mol­ecules are linked by a pair of C—H⋯π inter­actions, forming chains along the c-axis direction. In the crystal of (III), mol­ecules are linked by two pairs of C—H⋯π inter­actions, forming inversion dimers, which in turn are linked by offset π–π inter­actions [inter­centroid distance = 3.8492 (19) Å], forming ribbons along the b-axis direction.




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Bis(4-hy­droxy-N-isopropyl-N-methyl­trypt­ammo­nium) fumarate: a new crystalline form of miprocin

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.




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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

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.




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Crystal structure of a new phen­yl(morpholino)methane­thione derivative: 4-[(morpholin-4-yl)carbothioyl]benzoic acid

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.




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A new small-angle X-ray scattering model for polymer spherulites with a limited lateral size of the lamellar crystals

As is well known, polymers commonly form lamellar crystals, and these assemble further into lamellar stacks and spherulites during quiescent crystallization. Fifty years ago, Vonk and Kortleve constructed the classical small-angle X-ray scattering theory (SAXS) for a lamellar system, in which it was assumed that the lamellar stack had an infinite lateral size [Vonk & Kortleve (1967), Kolloid Z. Z. Polym. 220, 19–24]. Under this assumption, only crystal planes satisfying the Bragg condition can form strong scattering, and the scattering from the lamellar stack arises from the difference between the scattering intensities in the amorphous and crystalline layers, induced by the incident X-ray beam. This assumption is now deemed unreasonable. In a real polymer spherulite, the lamellar crystal commonly has dimensions of only a few hundred nanometres. At such a limited lateral size, lamellar stacks in a broad orientation have similar scattering, so interference between these lamellar stacks must be considered. Scattering from lamellar stacks parallel to the incident X-ray beam also needs to be considered when total reflection occurs. In this study, various scattering contributions from lamellar stacks in a spherulite are determined. It is found that, for a limited lateral size, the scattering induced by the incident X-ray beam is not the main origin of SAXS. It forms double peaks, which are not observed in real scattering because of destructive interference between the lamellar stacks. The scattering induced by the evanescent wave is the main origin. It can form a similar interference pattern to that observed in a real SAXS measurement: a Guinier region in the small-q range, a signal region in the intermediate-q range and a Porod region in the high-q range. It is estimated that, to avoid destructive interference, the lateral size needs to be greater than 11 µm, which cannot be satisfied in a real lamellar system. Therefore, SAXS in a real polymer system arises largely from the scattering induced by the evanescent wave. Evidence for the existence of the evanescent wave was identified in the scattering of isotactic polypropyl­ene. This study corrects a long-term misunderstanding of SAXS in a polymer lamellar system.




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DeepRes: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps

In this article, a method is presented to estimate a new local quality measure for 3D cryoEM maps that adopts the form of a `local resolution' type of information. The algorithm (DeepRes) is based on deep-learning 3D feature detection. DeepRes is fully automatic and parameter-free, and avoids the issues of most current methods, such as their insensitivity to enhancements owing to B-factor sharpening (unless the 3D mask is changed), among others, which is an issue that has been virtually neglected in the cryoEM field until now. In this way, DeepRes can be applied to any map, detecting subtle changes in local quality after applying enhancement processes such as isotropic filters or substantially more complex procedures, such as model-based local sharpening, non-model-based methods or denoising, that may be very difficult to follow using current methods. It performs as a human observer expects. The comparison with traditional local resolution indicators is also addressed.




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New zeolite-like RUB-5 and its related hydrous layer silicate RUB-6 structurally characterized by electron microscopy

This study made use of a recently developed combination of advanced methods to reveal the atomic structure of a disordered nanocrystalline zeolite using exit wave reconstruction, automated diffraction tomography, disorder modelling and diffraction pattern simulation. By applying these methods, it was possible to determine the so far unknown structures of the hydrous layer silicate RUB-6 and the related zeolite-like material RUB-5. The structures of RUB-5 and RUB-6 contain the same dense layer-like building units (LLBUs). In the case of RUB-5, these building units are interconnected via additional SiO4/2 tetrahedra, giving rise to a framework structure with a 2D pore system consisting of intersecting 8-ring channels. In contrast, RUB-6 contains these LLBUs as separate silicate layers terminated by silanol/sil­oxy groups. Both RUB-6 and RUB-5 show stacking disorder with intergrowths of different polymorphs. The unique structure of RUB-6, together with the possibility for an interlayer expansion reaction to form RUB-5, make it a promising candidate for interlayer expansion with various metal sources to include catalytically active reaction centres.




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Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling

In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collections. Scaling corrects for effects such as changes in sample illumination, absorption and, to some extent, global radiation damage that cause the measured intensities of symmetry-equivalent observations to differ throughout a data set. This necessarily requires a prior evaluation of the point-group symmetry of the crystal. This paper describes and evaluates the scaling algorithms implemented within the DIALS data-processing package and demonstrates the effectiveness and key features of the implementation on example macromolecular crystallographic rotation data. In particular, the scaling algorithms enable new workflows for the scaling of multi-crystal or multi-sweep data sets, providing the analysis required to support current trends towards collecting data from ever-smaller samples. In addition, the implementation of a free-set validation method is discussed, which allows the quantification of the suitability of scaling-model and algorithm choices.




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New attempt to combine scanning electron microscopy and small-angle scattering in reciprocal space

An attempt has been made to combine small-angle scattering of X-rays or neutrons with scanning electron microscopy in reciprocal space, in order to establish a structural analysis method covering a wide range of sizes from micro- to macro-scales.




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A new ZnII metallocryptand with unprecedented diflexure helix induced by V-shaped di­imidazole building blocks

A new ZnII metallocryptand is presented, with an unprecedented diflexure helix.




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A new monoclinic structure type for ternary gallide MgCoGa2

The crystal structure of MgCoGa2 (magnesium cobalt digallide) was solved by direct methods and refined in two space groups as P21/c (standard choice) and P21/n (non-standard choice). The refined lattice parameters for the standard choice are a = 5.1505 (2), b = 7.2571 (2), c = 8.0264 (3) Å and β = 125.571 (3)°, and for the non-standard choice are a = 5.1505 (2), b = 7.2571 (2), c = 6.5464 (2) Å and β = 94.217 (3)°. All parameters for MgCoGa2 refined to R1 = 0.027 and wR2 = 0.042 using 594 reflections. The crystal structure peculiarities of this compound are discussed. Particular attention has been given to relationships with other similar structures, such as YPd2Si and Fe3C. Crystallographic analysis, together with linear muffin-tin orbital electronic structure calculations, reveals the presence of three-dimensional polyatomic nets with partial covalent bonding between the Ga atoms.




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Brand New & Trying To Learn




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New research reveals our galaxy is much larger than we thought

New measurements show that the Milky Way is bigger and more massive than previous data suggested, putting us on equal footing with our neighbor. Specifically, the Milky Way is 15 percent larger in size and contains 50 percent more mass. That is the cosmic equivalent of a 5-foot-5, 140-pound man suddenly bulking up to the size of a 6-foot-3, 210-pound NFL linebacker.

The post New research reveals our galaxy is much larger than we thought appeared first on Smithsonian Insider.




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Smithsonian Scientist Discovers Two New Bat Species Hiding in Museum Collections for More Than 150 Years

While studying bats recently at the Academy of Natural Sciences in Philadelphia, Smithsonian mammalogist Kristofer Helgen discovered a new species of flying fox bat from […]

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New species of giant rat discovered in crater of volcano in Papua New Guinea

A Smithsonian Institution biologist, working with the Natural History Unit of the British Broadcasting Corp., has discovered a new species of giant rat on a film-making expedition to a remote rainforest in New Guinea.

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The Smithsonian’s National Air and Space Museum opens new Public Observatory on the Mall in Washington, D.C.

The Smithsonian’s National Air and Space Museum has opened a new Public Observatory that contains a 16-inch, 3,000-pound Boller and Chivens telescope, on loan from the Smithsonian Astrophysical Observatory. Through this powerful telescope, museum visitors can now observe the sun (with a special filter), the moon and the brighter stars and planets, such as Venus, Jupiter and Saturn, during daylight hours. Funding for the project was provided by the National Science Foundation.

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Females are giants in newly discovered species of golden orb weaver spider

Native to Africa and Madagascar, females of the species have a body length of 1.5 inches and a leg span of 4 to 5 inches. Males are tiny in comparison.

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Telescope array finds new evidence that exploding stars are sources of cosmic rays

Nearly 100 years ago, scientists detected the first signs of cosmic rays—subatomic particles (mostly protons) that zip through space at nearly the speed of light. […]

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