checkCIF validation ALERTS: what they mean and how to respond

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.

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-carboxyl­ate

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.

Crystal structures of three 6-aryl-2-(4-chloro­benz­yl)-5-[(1H-indol-3-yl)meth­yl]imidazo[2,1-b][1,3,4]thia­diazo­les

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.

N,N′-Bis(pyridin-3-ylmeth­yl)ethanedi­amide monohydrate: crystal structure, Hirshfeld surface analysis and computational study

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.

Synthesis and crystal structure of catena-poly[[bis­[(2,2′;6′,2′′-terpyridine)­manganese(II)]-μ₄-penta­thio­dianti­monato] tetra­hydrate] showing a 1D MnSbS network

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.

Crystal structure of the coordination polymer catena-poly[[[(aceto­nitrile-κN)copper(I)]-μ₃-1,3-di­thiolane-κ³S:S:S′] hexa­fluoridophosphate]

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

Crystal and mol­ecular structures of a binuclear mixed ligand complex of silver(I) with thio­cyanate and 1H-1,2,4-triazole-5(4H)-thione

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

Two isostructural 3-(5-ar­yloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-(thio­phen-2-yl)prop-2-en-1-ones: disorder and supra­molecular assembly

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.

Crystal structure, Hirshfeld surface analysis and computational study of bis­(2-{[(2,6-di­chloro­benzyl­idene)hydrazinyl­idene]meth­yl}phenolato)cobalt(II) and of the copper(II) analogue

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

Crystal structure and Hirshfeld surface analysis of 4-{[(anthracen-9-yl)meth­yl]amino}­benzoic acid

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 (8) ring motif.

Syntheses and crystal structures of three [M(acac)₂(TMEDA)] complexes (M = Mn, Fe and Zn)

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.

Crystal structure and Hirshfeld surface analysis of (E)-3-(3-iodo­phen­yl)-1-(4-iodo­phen­yl)prop-2-en-1-one

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 para–para or meta–meta.

An unusually short inter­molecular N—H⋯N hydrogen bond in crystals of the hemi-hydro­chloride salt of 1-exo-acetamido­pyrrolizidine

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).

Synthesis and crystal structure of (1,8-naphth­yridine-κ²N,N′)[2-(1H-pyrazol-1-yl)phenyl-κ²N²,C¹]iridium(III) hexa­fluorido­phosphate di­chloro­methane monosolvate

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

Syntheses and crystal structures of 2,2,5-tri­methyl-1,3-dioxane-5-carb­oxy­lic acid and 2,2,5-tri­methyl-1,3-dioxane-5-carb­oxy­lic anhydride

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

Bis{4-[(2-hy­droxy-5-meth­oxy-3-nitro­benzyl­idene)amino]­phen­yl} ether

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.

Crystal structure, Hirshfeld surface analysis and DFT studies of 1-benzyl-3-[(1-benzyl-1H-1,2,3-triazol-5-yl)meth­yl]-2,3-di­hydro-1H-1,3-benzo­diazol-2-one monohydrate

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.

The 1:2 co-crystal formed between N,N′-bis­(pyridin-4-ylmeth­yl)ethanedi­amide and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study

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.

Crystal structure and Hirshfeld surface analysis of a copper(II) complex with ethyl­enedi­amine and non-coordinated benzoate

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%

Synthesis, crystal structure and Hirshfeld analysis of a crystalline compound comprising a 1/1 mixture of 1-[(1R,4S)- and 1-[(1S,4R)-1,7,7-tri­methyl-2-oxobi­cyclo[2.2.1]heptan-3-yl­idene]hydrazinecarbo­thio­amide

A racemic mixture of (R)- and (S)-camphor thio­semicarbazone, which crystallizes in the centrosymmetric space group C2/c, is reported.