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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

January 2020 issue

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Cover illustration: A checkCIF validation report lists as ALERTS not only potential errors or unusual findings, but also suggestions for improvement along with interesting information on the structure at hand. ALERTS come mostly as short single-line messages. Major ALERTS for issues are expected to be acted on before submission for publication or discussed in the associated paper and/or commented on in the CIF file. The validation report can be obtained either using the IUCr web-based checkCIF server or a locally installed version of PLATON/checkCIF. As recommended by the author, it is good practice to run checkCIF frequently during the crystal-structure determination and when interpreting the structure itself. This way pitfalls such as missed symmetry and/or twinning can be avoided. This publication is a mine of information on what the checkCIF ALERTS mean and how authors should respond to them. It is the second publication in this journal related to a recent microsymposium entitled `Teaching new dogs old tricks' given at the 2019 ECM in Vienna. See: Spek [Acta Cryst. (2020). E71, 1-11].

research communications


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This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them.

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The title compound, a new inhibitor of the Hepatitis B virus (HBV), was prepared via alkyl­ation of 3-(chloro­meth­yl)-5-(pentan-3-yl)-1,2,4-oxa­diazole in anhydrous dioxane in the presence of tri­ethyl­amine.

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In the crystals of three new 6-aryl-2-(4-chloro­benz­yl)-5-[(1H-indol-3-yl)meth­yl]imidazo[2,1-b][1,3,4]thia­diazo­les (where aryl is phenyl, 4-fluoro­phenyl or 4-bromo­phen­yl), the mol­ecules are linked by a combination of N—H⋯N and C—H⋯π inter­actions to form chains when the 6-aryl substituent is phenyl or 4-fluoro­phenyl and a three-dimensional framework when the 6-aryl group is 4-bromo­phenyl.

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The organic mol­ecule in the title bis-pyridyl-substituted di­amide hydrate has a U-shape as the 3-pyridyl rings lie to the same side of the central plane. In the crystal, two supra­molecular tapes, each sustained by amide-N—H⋯O(carbon­yl) hydrogen bonds and ten-membered {⋯HNC2O}2 synthons, are connected by a helical chain of hydrogen-bonded water mol­ecules.

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In the crystal structure of the title compound, two [Sb2S5 [anions built up of two SbS3 units sharing common corners with each linked by two [Mn(terpyridine)]2+ cations into chains that are further linked into a 3D network by inter­molecular O—H⋯O and O—H⋯S hydrogen bonding.

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The title one-dimensional ribbon-like coordination polymer results from the reaction of [Cu(MeCN)4][PF6] with 1,3-di­thiol­ane.

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The centrosymmetric binuclear complex features a tetra­hedral AgI centre within a S4 donor set. The three-dimensional mol­ecular packing is sustained by amine-NHS(thione), N—H⋯N(triazol­yl) and NHN(thio­cyanate) hydrogen bonds.

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In each of two isostructural 3-(5-ar­yloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-(thio­phen-2-yl)prop-2-en-1-ones, the thio­phene unit is disordered over two sets of atomic sites and a combination of C—H⋯N and C—H⋯O hydrogen bonds link the mol­ecules into sheets.

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Distinct coordination geometries are found in the crystals of the title CoII (trigonal bipyramidal) and CuII (square-planar) complexes, each defined by a N2S2 donor set derived from two chelating Schiff base anions.

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In mol­ecule of the title compound, the benzene ring is inclined to the mean plane of the anthracene ring system (r.m.s. deviation = 0.024 Å) by 75.21 (9)°. In the crystal, a classical carb­oxy­lic acid inversion dimer is formed enclosing an R_{2}^{2}(8) ring motif.

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Syntheses and crystal structures of three metal complexes [M(acac)2(TMEDA)] [M = Mn (1), Fe (2) and Zn (3)] with acetyl­acetonate and N,N,N′,N′-tetra­methyl­ethylenedi­amine are discussed.

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The title compound, C15H10I2O, is a halogenated chalcone formed from two iodine substituted rings, one para-substituted and the other meta-substituted, linked through a prop-2-en-1-one spacer. The crystal structure shows the mol­ecules contain halogen bonds which are always between equivalent iodine atoms, either parapara or metameta.

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In the crystal, two AcAP mol­ecules related by a crystallographic twofold axis link to H+ and Cl ions lying on the rotation axis, thereby forming N—H⋯N and N—H⋯Cl⋯H—N hydrogen bonds. The first of these has an unusually short N⋯N separation of 2.616 (2) Å: refinement of different models against the present data set could not distinguish between a symmetrical hydrogen bond (H atom lying on the twofold axis and equidistant from the N atoms) or static or dynamic disorder models (i.e. N—H⋯N + N⋯H—N).

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The coordination environment of the IrIII atom in the complex cation is pseudo-octa­hedral, with an N4C2 coordination set.

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The title compounds, C8H14O4 and C16H26O7, are precursors to dendrimers. The strong and weak hydrogen bonds in their extended structures are described.

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The mol­ecule of the title oxybis compound lies on a twofold rotational axis. The conformation of the title compound is discussed and compared to those of related structures. In the crystal, mol­ecules of the title compound are assembled into layers parallel to the ab plane through C—H⋯O hydrogen bonds.

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The di­hydro­benzo­diazole moiety is not quite planar while the whole mol­ecule adopts a U-shaped conformation in which there is a close approach of the two benzyl groups. Chains of alternating mol­ecules and lattice water extending along the normal to (301) are formed by O—H⋯O and O—H⋯N hydrogen bonds.

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The 4-pyridyl residues lie to either side of the central, planar C2N2O2 chromophore of the oxalamide mol­ecule which has a + anti-periplanar conformation. Conventional hydrogen-bonding inter­actions lead to supra­molecular tapes in the crystal.

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The asymmetric unit of the title compound contains two di­aqua­bis­(ethyl­enedi­amine)­copper(II) cations and four nitro­benzoate anions. These are connected into three-mol­ecule aggregates via N—H⋯O and O—H⋯O hydrogen bonds. The anions are disordered and modelled in two orientations. The major conformations have occupancies of 57, 59, 60 and 79%

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.

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