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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890

June 2020 issue

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Cover illustration: Recent developments in all aspects of structure determination by X-ray diffraction have led to unprecedented automation and speed. A comprehensive overview of the perils associated with such automation is given, along with a series of tips and tricks for data collection, processing, structure solution, refinement and presentation. These serve as a handy guide for novices encountering non-routine structures and a timely reminder for experienced crystallographers. This paper is the third in a series derived from lectures at a recent microsymposium entitled `Teaching new dogs old tricks' presented at the 2019 ECM in Vienna. See: Linden [Acta Cryst. (2020). E76, 765-776].

research communications


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This article aims to encourage practitioners, young and seasoned, by enhancing their structure-determination toolboxes with a selection of tips and tricks on recognizing and handling aspects of data collection, structure modelling and refinement, and the interpretation of results.

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In the first reported crystal structure involving the potential ligand N,N′,N′′-tris­(2-pyridin­yl)-1,3,5-benzene­tricarboxamide, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules via their amide groups into slanted ladder-like chains. Only two of the three amide groups in the mol­ecule are involved in hydrogen bonding, which influences the degree of out-of-plane twisting at each amide group.

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In the structure of the title salt, second-order Jahn–Teller distortion of the coordination octa­hedra around V ions is reflected by coexistence of short V—O bonds and trans-positioned long V—F bonds, with four equatorial V—F distances being inter­mediate in magnitude. Hydrogen bonding of the anions is restricted to F-atom acceptors only, with particularly strong N–H⋯F inter­actions [N⋯F = 2.5072 (15) Å] established by axial and cis-positioned equatorial F atoms.

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The crystal structure of vanthoffite, Na6Mg(SO4)4, was redetermined and refined with anisotropic displacement parameters for all atoms. Here, for the first time, we give its detailed description.

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The new copper(II) complex [CuLCl2]2, where L is a product of Schiff base condensation between methyl­amine and 2-pyridine­carbaldehyde, is built of discrete centrosymmetric dimers.

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The title compound, 1-(2,5-di­meth­oxy­phen­yl)-2,2,6,6-tetra­methyl­piperidine, was synthesized as a side-product during the synthesis of the inter­mediate, methyl 3,6-dimeth­oxy-2-(2-meth­oxy-2-oxoeth­yl)benzoate, necessary for the total synthesis of the isocoumarin 5,8-dimeth­oxy-3-methyl-1H-isochromen-1-one.

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The asymmetric unit of the title compound contains two independent mol­ecules, consisting of perimidine and phenol units, which are linked through an N—H⋯O hydrogen bond. Intra­molecular O—H⋯N hydrogen bonds are observed in both independent mol­ecules.

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The cationic cyclo­metallated iridium(III) complex [Ir(C9H7N2)2(C12H8N2)](PF6) has been synthesized and crystallized by the inter-diffusion method. It contains an unknown number of solvent mol­ecules and has a different space-group symmetry (C2/c) structure than its solvatomorph (P21/c).

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The title compound exhibits exceptionally weak inter­molecular C—H⋯π hydrogen bonding of the ethynyl groups, with the corresponding H⋯π separations [2.91 (2) and 3.12 (2) Å] exceeding normal vdW distances. This bonding compliments distal contacts of the CH (aliphatic)⋯π type [H⋯π = 3.12 (2)–3.14 (2) Å] to sustain supra­molecular layers.

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The dihedral angle between the two aromatic rings of the title compound is 64.12 (14)°. The crystal structure is stabilized by a short Cl⋯H contact, C—Cl⋯π and van der Waals inter­actions.

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Febuxostat and ethanol mol­ecules are linked into an O—H⋯O and O—H⋯N bonded chain structure.

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The title complex, Cu(L)2 or [Cu(C15HF10O2)2], comprising one copper ion and two fully fluorinated ligands (L), was crystallized with 3,4-ethyl­ene­dioxy­thio­phene (EDOT, C6H6O2S) as a guest mol­ecule to give in a di­chloro­methane solution a unique co-crystal, Cu(L)2·3C6H6O2S.

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Three six-coordinate complexes of bis­(acetyl­acetonato)oxovanadium(IV) containing N-donating pyridyl ligands are reported. Both cis and trans isomers were isolated and characterized from these systems.

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The crystal structure of a new polymorph of CdTe2O5, designated as the β-form, contains 2[Te2O5]2– (100) layers with an undulating shape.

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The CoII atom in the title complex is octa­hedrally coordinated within an N2O4 donor set defined by two N-atom donors of the 1,10-phenanthroline ligand, sulfate-O and three aqua-O atoms, the latter occupying an octa­hedral face. In the crystal, supra­molecular layers parallel to (110) are sustained by aqua-O—H⋯O(sulfate) hydrogen bonding.

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Three salts containing the 4-(4-fluoro­phen­yl)piperazin-1-ium cation have been prepared and structurally characterized.

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The metallacrown (MC) complexes Na2(3-chloro­benzoate)2[12-MCMn(III)N(shi)-4](DMF)6, 1, and MnNa(3-chloro­benzoate)3[12-MCMn(III)N(shi)-4](DMF)(H2O)4·4DMF·0.72H2O, 2, where shi3− is salicyl­hydroximate and DMF is N,N-di­methyl­formamide, both have an overall square shape due to the presence of four ring MnIII ions and four shi3− ligands. The two MC complexes bind different cations in the central cavity of the mol­ecule: two Na+ ions in 1 and one MnII ion and one Na+ ion in 2.

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The two isomers 2′-(4-nitro­benzo­yloxy)aceto­phenone with para and ortho positions of the nitro substituent have been crystallized and studied. It is evident that the variation in the position of the nitro group causes a significant difference in the mol­ecular conformations.

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An E-configuration about the imine bond is found in both the title mol­ecules, which differ in their central C—N—N—C torsion angles. The main feature of the mol­ecular packing in both crystals is the formation of supra­molecular chains: the linear chains in (I) are consolidated by meth­oxy-C—H⋯O(meth­oxy) and chloro­benzene-C—Cl⋯π(chloro­benzene) inter­actions while the zigzag chains in (II) are sustained by Br⋯O secondary bonding inter­actions.

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In the title 1:2 co-crystal a three-mol­ecule aggregate, i.e. 4LH2.2(3-ClBA), is formed via carb­oxy­lic acid-O—H⋯N(pyrid­yl) hydrogen bonding. The three-mol­ecule aggregates are connected into a supra­molecular tape along [111] by amide-N—H⋯O(carbon­yl) hydrogen bonding.

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The crystal structures of two alkaline-earth-based coordination compounds containing bifunctional tetra­zole­carboxyl­ate ligands reveal a one-dimensional chain structure with the carboxyl­ate-tetra­zole anionic ligand. The structures of both compounds are dominated by hydrogen bonds involving water coordination ligands, with an underlying 3.6 − c network.

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Gefitinib, the anti­cancer drug, has been co-crystallized with azelaic acid to obtain a 1:1 co-crystal in the monoclinic P21/n space group containing one mol­ecule each of gefitinib and azelaic acid in the asymmetric unit. Both mol­ecules are associated with each other through N—H⋯O, O—H⋯N, C—H⋯O and C—H⋯F hydrogen bonds.

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The benzo­thia­zine moiety is folded along the N⋯S axis and a puckering analysis of the conformation of the heterocyclic ring was performed. The hexyl chain is mainly in an extended conformation. In the crystal, inversion dimers are formed by weak C—HMthn⋯OBnzthz hydrogen bonds and are linked into chains extending along the a-axis direction by weak C—HBnz⋯OBnzthz (Bnz = benzene, Bnzthz = benzo­thia­zine and Mthn = methine) hydrogen bonds.

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The title compounds were prepared from 1,3-di­phenyl­cyclo­penta­diene, pyrrolidine, and the corresponding aldehydes in an ethano­lic solution. Each compound crystallizes with one mol­ecule per asymmetric unit and exhibits the alternating short and long bond lengths typical of fulvenes. A network of C—H⋯C ring inter­actions as well as C—H⋯O inter­actions is observed, resulting in the compact packing found in each structure.

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Cs2Sr[Fe(CN)6] was synthesized. It is a potential phase to trap simultaneously caesium and strontium radionuclides. The crystal structure is isotypic with Cs2Sr[Mn(CN)6].

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The title compound is non-planar, subtending a dihedral angle of 82.38 (4)° between the plane of hy­droxy isophthalate-based ester and that of the benzo­nitrile moiety. The mol­ecule is bent at the ether linkage, with a Car­yl—O—Car­yl bond angle of 116.74 (11)°. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds and other weak inter­actions forming a supra­molecular framework.

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The title compound is a two-dimensional coordination polymer with inter-layer connectivity provided by N—H⋯N hydrogen bonds.

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The main residue and the solvent mol­ecule aggregate to discrete pairs via a classical O—H⋯O hydrogen bond, while non-classical C—H⋯O inter­actions lead to the formation of an extended network.

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In the crystal, the mol­ecules are linked by weak C—H⋯π hydrogen bonds and very weak π–π stacking inter­actions. Two-dimensional fingerprint plots show that the largest contributions to the crystal cohesion come from H⋯H and C⋯H/H⋯C inter­actions.

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The crystal structures of 2-O-monooctyl isosorbide, 2-O-monodecyl isosorbide, 2-O-monododecyl isosorbide and 2-O-mono­tetra­decyl isosorbide are reported. All four compounds crystallize in the chiral space group P21.

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The title coordination polymer consists of parallel zigzag-like chains of [Ni(cyclam)]2+ cations bridged by the dianions of the acid in the axial positions of the trans-NiN4O2 coordination polyhedron. Polymeric chains propagating along the [101] direction are assembled into a three-dimensional network by O—H⋯O hydrogen bonds.

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The title di-substituted thio­urea has hy­droxy­lethyl and ethyl benzoate substituents bound to the same amine-N atom; overall the mol­ecule is twisted. Supra­molecular layers are formed in the crystal, with the mol­ecules connected by O—H⋯S and N—H⋯O(carbonyl, hydrox­yl) hydrogen bonds.

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In the title mol­ecule, which is based on a 1,4-distyryl-2,5-di­meth­oxy­benzene core with p-nitro-substituted terminal benzene rings, the dihedral angle between mean planes of the central fragment and the terminal phenyl ring is 16.46 (6)°. The crystal packing is stabilized by π–π inter­actions.

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In the title compound, the FeII ion is coordinated in a distorted octa­hedral [FeN4O2] environment by two di­cyano­aurate anions, two water mol­ecules and two partially protonated 1,2-di(4-pyrid­yl)ethyl­ene mol­ecules. Di­cyano­aurate anions bridge the FeII cations, forming infinite chains, which propagate along the a-axis direction. The chains are connected via aurophillic inter­actions with two non-coordinated di­cyano­aurate anions for each FeII ion.

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The crystal structures of [Li7(i-PrO)3(C4H10NO)3]2O (1) and [Na(i-PrOH)2(C8H18NO2)]2 (2) were determined at 100 K. In title compound 2, O—H⋯O hydrogen bonding can be observed which builds up the dimeric structure.

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In the fused ring of the title compound, C51H42O5, all of the five-membered rings are in an envelope conformation. The dihedral angle between the benzene rings attached to the fused ring is 74.66 (7)o.

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In the title compound, polymeric (100) sheets consisting of [Cd(SO4)(H2O)] units are linked by H2bmtz [H2bmtz is 3,6-bis­(pyrimidin-2-yl)-1,4-di­hydro-1,2,4,5-tetra­zine] into a three-dimensional structure.

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In the crystal structure, C—HMthphn⋯OMthphn (Mthphn = meth­oxy­phen­yl) hydrogen bonds form corrugated layers parallel to (100) that are connected along the a axis by C—H⋯π(ring) and π–π stacking inter­actions.

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The tetra-substituted pyrrolidine ring in the title compound has a twisted conformation about the central C—C bond with the N-bound ethyl­carboxyl­ate group in an equatorial position and the remaining substituents in axial positions. In the crystal, methyl- and methyl­ene-C—H⋯O(carbon­yl) inter­actions involving all four carbonyl-O atoms lead to supra­molecular double-layers.

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In the crystal, π-π stacking inter­actions and strong N—H⋯O and C—H⋯O hydrogen bonds link the cations and anions into layers parallel to the bc plane. The O⋯H/H⋯O inter­actions between the cation and anion are the major factor determining the crystal packing.

Research communications

Research communications are designed to help authors bring out the science behind their structure determinations. Authors are encouraged to report more than one structure in the same communication and also to include the results of investigations with other techniques. The Research communications format makes Acta E the natural home for structure determinations with interesting science to report.

Emerging Sources Citation Index

Acta E is included in the Emerging Sources Citation Index.

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