Some reflections on symmetry: pitfalls of automation and some illustrative examples

An outline is given of some basic concepts and applications of symmetry in crystallography. Three specific examples of structure determinations are discussed, for which an understanding of these aspects of symmetry avoids mistakes that can readily be made by reliance on automatic procedures. Topics addressed include pseudo-symmetry, twinning, real and apparent disorder, chirality, and structure validation.

Crystal structure of 4,6-di­methyl-2-[(2,3,4,6-tetra-O-acetyl-β-D-galacto­pyranos­yl)sulfan­yl]pyrimidine

In the title com­pound, the S atom is attached equatorially to the sugar ring. The C—S bond lengths are unequal. In the crystal, a system of three weak hydrogen bonds, sharing an oxygen acceptor, links the mol­ecules to form chains propagating parallel to the b-axis direction.

An iridium complex with an unsupported Ir—Zn bond: di­iodido­(η⁵-penta­methyl­cyclo­penta­dien­yl)bis­(tri­methyl­phosphane)iridiumzinc(Ir—Zn) benzene hemisolvate

A mol­ecular compound with an unsupported Ir—Zn bond: [Cp*(PMe₃)₂Ir]-[ZnI₂] (Cp*=cyclo-C₅Me₅), is reported as its benzene solvate.

Crystal structure of benzo[h]quinoline-3-carbox­amide

A benzo­quinone com­pound was unintentionally synthesized by photocyclization and subsequent oxidation in air while attempting to transform the E isomer of a nicotinamide derivative to its Z isomer. The chemical and mol­ecular structures of the product was established crystallographically. The surprising synthesis, chromatographic purification and com­prehensive characterization of this com­pound including single crystal structural analysis are reported and its structure including crystal packing is discussed in detail.

Organically pillared layer framework of [Eu(NH₂–BDC)(ox)(H₃O)]

An organically pillared Eu^III–oxalate–carboxyl­ate framework structure with [Eu(NH₂—BDC)(ox)(H₃O)] topology is reported. The non-porous three-dimensional structure is constructed from two-dimensional layers of Eu^III–carboxyl­ate–oxalate, which are pillared by NH₂—BDC²⁻ pillars. The basic structural unit of the layer is an edge-sharing dimer of TPRS-{Eu^IIIO₉}, which is assembled through the ox²⁻ moiety. The intra­layer void is partially occupied by TPR-{Eu^IIIO₆} motifs.

Crystal structure and Hirshfeld surface analysis of poly[tris­(μ₄-benzene-1,4-di­carboxyl­ato)tetra­kis­(di­methyl­formamide)­trinickel(II)]: a two-dimensional coordination network

The structure of catena-[tris­(μ₄-benzene-1,4-di­carboxyl­ato)-tetra­kis­(μ₁– di­methyl­formamide-κ¹O)-trinickel(II)], C₃₆H₄₀N₄Ni₃O₁₆, has been determined in the monoclinic P2₁/n space group. The compound has a two-dimensional coordination network structure and it is of inter­est with respect to lithium-ion battery applications. Hirshfeld surface analysis was performed to characterize inter­planar inter­actions. The structure exhibits disorder of coordinated solvent mol­ecules.

Crystal structure of 1,4-bis­[5-(2-meth­oxy­phen­yl)-2H-tetra­zol-2-yl]butane

The diffraction data confirmed the title compound as the main isomer produced in a coupling reaction. The structure and Hirshfeld surface analysis of the formed di-tetra­zolyl chelate ligand are reported.

(μ-Di-tert-butyl­silanediolato)bis­[bis­(η⁵-cyclo­penta­dien­yl)methyl­zirconium]

The reaction of t-Bu₂Si(OH)₂ with two equivalents of Cp₂Zr(CH₃)₂ produces the t-Bu₂SiO₂-siloxide bridged dimer where one methyl group is retained per zirconium atom. The retention of one methyl group per metal center affords a site for further reactivity.

Crystal structure of 4-chloro-2-nitro­benzoic acid with 4-hy­droxy­quinoline: a disordered structure over two states of 4-chloro-2-nitro­benzoic acid–quinolin-4(1H)-one (1/1) and 4-hy­droxy­quinolinium 4-chloro-2-nitro­benzoate

The title compound was analysed as a disordered structure over two states, viz. co-crystal and salt, accompanied by a keto–enol tautomerization in the base mol­ecule. In the compound, the acid and base mol­ecules are linked by a short hydrogen bond [O⋯O = 2.4393 (15) Å], in which the H atom is disordered over two positions with equal occupancies.

Crystal structure and Hirshfeld surface analysis of a zinc xanthate complex containing the 2,2′-bi­pyridine ligand

The Zn^II ion lies on a crystallographic twofold axis and has distorted tetra­hedral coordination geometry. Two weak C—H⋯S intra­molecular hydrogen bonds exist between the bipyridyl and thiol groups. In the crystal, mol­ecules are linked by weak C—H⋯O and C—H⋯S hydrogen bonds, forming a three-dimensional supra­molecular architecture.

Synthesis, crystal structure and Hirshfeld surface analysis of di­ethyl 2,6-di­methyl-4-(thio­phen-3-yl)-1,4-di­hydro­pyridine-3,5-di­carboxyl­ate

In the title 1,4-di­hydro­pyridine derivative, the 1,4-di­hydro­pyridine ring makes an angle of 82.19 (13)° with the thio­phene ring. In the crystal, N—H⋯O and C—H⋯O hydrogen bonds as well as C—H⋯π inter­actions link the mol­ecules into a three-dimensional network.

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

A new polymorphic form of 3-acetyl-8-meth­oxy-2H-chromen-2-one is described and compared with the previously reported polymorph. In the crystal, hydrogen bonds, π–π inter­actions and anti­parallel C=O⋯C=O inter­actions give rise to a helical supra­molecular architecture

Crystal structure of [K(18-crown-6)]⁺₂[Pt(CN)₄]²⁻

K₂Pt(CN)₄ becomes soluble in di­chloro­methane upon addition of two equivalents of 18-crown-6. Crystals of [K(18-crown-6)]₂ [Pt(CN)₄] are obtained upon layering the di­chloro­methane solution with di­ethyl­ether. No Pt⋯Pt inter­actions are observed in the crystal.

Crystal structure of pyridinium tetra­iso­thio­cyanato­dipyridine­chromium(III) pyridine monosolvate

The crystal structure of the title compound consists of discrete negatively charged [Cr(NCS)₄(pyridine)₂]⁻ complexes that are charge balanced by pyridinium cations and contains additional pyridine solvent mol­ecules that are linked by weak C—H⋯S hydrogen bonding into a three-dimensional network.

Crystal structure, Hirshfeld surface analysis and DFT studies of 6-[(E)-2-(thio­phen-2-yl)ethenyl]-4,5-di­hydro­pyridazin-3(2H)-one

In the crystal, the mol­ecules are linked by N—H⋯O and C—H⋯O inter­actions, forming a three-dimensional network. The theoretical geometrical parameters are in good agreement with XRD results.

Crystal and mol­ecular structure of jatrophane diterpenoid (2R,3R,4S,5R,7S,8S,9S,13S,14S,15R)-2,3,8,9-tetra­acet­oxy-5,14-bis­(benzo­yloxy)-15-hy­droxy-7-(iso­butano­yloxy)jatropha-6(17),11(E)-diene

A jatrophane diterpenoid was isolated from the fructus of Euphorbia sororia and its structure and absolute configuration have been established by X-ray crystallographic analysis.

The varied structures of cobalt(II)–pyridine (py)–sulfate: [Co(SO₄)(py)₄]_n, [Co₂(SO₄)₂(py)₆]_n, and [Co₃(SO₄)₃(py)₁₁]_n

The crystal structures of two new forms of cobalt–pyridine–sulfate complexes are presented. The feature infinite chains of metal–pyridine units connected by bridging sulfate anions, which are distinct from the only previously reported structure of a cobalt–pyridine–sulfate compound.

Crystal structure of tris­[bis­(2,6-diiso­propyl­phen­yl) phosphato-κO]penta­kis­(methanol-κO)europium methanol monosolvate

The crystal structure of the complex {Eu[O₂P(O-2,6-ⁱPr₂C₆H₃)₂]₃(CH₃OH)₅}·CH₃OH, which exhibits intra- and inter­molecular O—H⋯O hydrogen bonding, and its luminescent properties have been studied.

Structure refinement of (NH₄)₃Al₂(PO₄)₃ prepared by ionothermal synthesis in phospho­nium based ionic liquids – a redetermination

The crystal structure of (NH₄)₃Al₂(PO₄)₃ was refined by powder XRD synchrotron data. (NH₄)₃Al₂(PO₄)₃ is a member of the structural family with formula A₃Al₂(PO₄)₃ where A is a group 1 element, of which the K and Rb forms are also known.

Crystal structure of dicarbon­yl[μ₂-methyl­enebis(di­phenyl­phosphane)-κ²P:P′][μ₂-2-(2,4,5-tri­methyl­phen­yl)-3-oxoprop-1-ene-1,3-di­yl](tri­phenyl­phosphane-κP)ironplatinum(Fe—Pt)–di­chloro­methane–toluene (1/1/2), [(OC)₂Fe(μ-dppm)(μ-C(=O)C(2,4,5-C₆H₂Me₃)=CH)Pt(PPh₃)]

The title compound, [(OC)₂Fe(μ-dppm)(μ-C(=O)C(2,4,5-C₆H₂Me₃)= CH)Pt(PPh₃)], represents an example of a diphosphane-bridged heterobimetallic dimetalla­cyclo­pentenone complex resulting from a bimetallic activation of 1-ethynyl-2,4,5-tri­methyl­benzene and a metal-coordinated carbonyl ligand.

Crystal structures of (E)-3-(4-hy­droxy­benzyl­idene)chroman-4-one and (E)-3-(3-hy­droxy­benzyl­idene)-2-phenyl­chroman-4-one

Two biologically active compounds were synthesized and their crystal structures were determined. The characteristic feature of both structures is mol­ecular layers in the crystal lattice formed via C—H⋯O and O—H⋯O inter­actions. The mol­ecular Hirshfeld surfaces analysis were explored with two-dimensional fingerprint plots for the title compounds and other known structures from the literature. Additionally, the lipophilicity parameters (logP) were determined and related to the C⋯H contact contribution in the Hirshfeld surface.

Synthesis, crystal structure and characterizations of di-μ-cyanido-1:2κ²N:C;2:3κ²C:N-bis­(4,7,13,16,21,24-hexa­oxa-1,10-di­aza­bicyclo­[8.8.8]hexacosa­ne)-1κ⁸N¹,N¹⁰,O⁴,O⁷,O¹³,O¹⁶,O²¹,O²⁴;3κ⁸N¹,N¹⁰,O⁴,O⁷,O¹³,O¹⁶,O²¹,O²⁴-[5,10,15,20-tetra­kis­(4-chloro­phen­yl)porphyrinato-2κ⁴N]-2-iron(II)-1,3-dipotassium(I) tetra­hydro­furan disolvate with an unknown solvent

In the title compound, the central Fe^II ion is coordinated by four pyrrole N atoms of the porphyrin core and two C atoms of the cyano groups in a slightly distorted octa­hedral coordination environment. The complex mol­ecule has a distorted porphyrin core.

Crystal structure, computational study and Hirshfeld surface analysis of ethyl (2S,3R)-3-(3-amino-1H-1,2,4-triazol-1-yl)-2-hy­droxy-3-phenyl­propano­ate

The mean planes of the phenyl and triazole rings are nearly perpendicular to one another as a result of the intra­molecular C—H⋯O and C—H⋯π(ring) inter­actions. In the crystal, layers parallel to (101) are generated by O—H⋯N, N—H⋯O and N—H⋯N hydrogen bonds. The layers are connected by inversion-related pairs of C—H⋯O hydrogen bonds.

Crystal structure, Hirshfeld surface analysis and DFT studies of 2-[5-(4-methyl­benz­yl)-6-oxo-3-phenyl-1,6-di­hydro­pyridazin-1-yl]acetic acid

In the title compound, the phenyl and pyridazine rings are inclined to each other by 10.55 (12)°, whereas the 4-methyl­benzyl ring is nearly orthogonal to the pyridazine ring with a dihedral angle of 72.97 (10)°.

(E)-3-{[(2-Bromo-3-methyl­phen­yl)imino]­meth­yl}benzene-1,2-diol: crystal structure and Hirshfeld surface analysis

In the title Schiff base derivative carrying a 2-bromo-3-methyl­phenyl group, the conformation about the C=N bond is E. In the crystal, O—H⋯O hydrogen-bond inter­actions consolidate the crystal packing. A Hirshfeld surface analysis and fingerprint plots were used to further investigate the inter­molecular inter­actions in the solid state.

Crystal structure, Hirshfeld surface analysis and contact enrichment ratios of 1-(2,7-di­methyl­imidazo[1,2-a]pyridin-3-yl)-2-(1,3-di­thio­lan-2-yl­idene)ethanone monohydrate

The synthesis of a hybrid mol­ecule is reported. The crystal structure of the monohydrate was investigated using Hirshfeld surface analysis and enrichment contact ratios. Hydrogen bonds induced by guest water mol­ecules are the main driving force in crystal packing formation.

Crystal structure, Hirshfeld surface analysis and inter­action energy and DFT studies of 1-methyl-3-(prop-2-yn-1-yl)-2,3-di­hydro-1H-1,3-benzo­diazol-2-one

The di­hydro­benzimidazol-2-one moiety is essentially planar with the prop-2-yn- 1-yl substituent rotated well out of this plane. In the crystal, C—H⋯π(ring) inter­actions and C—H⋯O hydrogen bonds form corrugated layers parallel to (10), which are associated through additional C—H⋯O hydrogen bonds and head-to-tail, slipped, π-stacking inter­actions between di­hydro­benzimidazol-2-one moieties

The crystal structure of the triclinic polymorph of 1,4-bis­([2,2′:6′,2′′-terpyridin]-4′-yl)benzene

A triclinic polymorph of 1,4-bis­([2,2′:6′,2′′-terpyridin]-4′-yl)benzene was obtained under solvothermal conditions.

Crystal structures and Hirshfeld surface analyses of (E)-N′-benzyl­idene-2-oxo-2H-chromene-3-carbo­hydrazide and the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimeth­oxybenzyl­idene)-2H-chromene-3-carbohydrazide: lattice energy and inter­molecular inter­action energy calculations for the former. Corrigendum

Erratum to Acta Cryst. (2019), E75, 1403–1410.