Obtaining the best results: aspects of data collection, model finalization and inter­pretation of results in small-mol­ecule crystal-structure determination

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.

The missing crystal structure in the series of N,N′,N′′-tris­(pyridinyl)benzene-1,3,5-tricarbox­amides: the 2-pyridinyl derivative

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.

Crystal structure and Hirshfeld surface analysis of 4,4′-(propane-1,3-diyl)bis­(4H-1,2,4-triazol-1-ium) penta­fluorido­oxidovanadate(V)

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.

Redetermination and new description of the crystal structure of vanthoffite, Na₆Mg(SO₄)₄

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.

Crystal structure and characterization of a new copper(II) chloride dimer with meth­yl(pyridin-2-yl­methyl­idene)amine

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.

The crystal structure and Hirshfeld surface analysis of 1-(2,5-di­meth­oxy­phen­yl)-2,2,6,6-tetra­methyl­piperidine

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.

Crystal structure, Hirshfeld surface analysis and DFT studies of 2-(2,3-di­hydro-1H-perimidin-2-yl)phenol

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.

Synthesis and crystal structure of (1,10-phenanthroline-κ²N,N′)[2-(1H-pyrazol-1-yl)phenyl-κ²N²,C¹]iridium(III) hexa­fluorido­phosphate with an unknown number of solvent mol­ecules

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).

Crystal structure and Hirshfeld surface analysis of 1,3-diethynyladamantane

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.

Crystal structure and Hirshfeld surface analysis of 4-{2,2-di­chloro-1-[(E)-(4-fluoro­phen­yl)diazen­yl]ethen­yl}-N,N-di­methyl­aniline

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.

Febuxostat ethanol monosolvate

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

Co-crystal structure, Hirshfeld surface analysis and DFT studies of 3,4-ethyl­ene­dioxy­thio­phene solvated bis­[1,3-bis­(penta­fluoro­phen­yl)propane-1,3-dionato]copper(II)

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.

Crystal structures of a series of bis­(acetyl­aceto­nato)oxovanadium(IV) complexes containing N-donor pyridyl ligands

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.

The crystal structure of a new CdTe₂O₅ polymorph, isotypic with ∊-CaTe₂O₅

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

fac-Tri­aqua­(1,10-phenanthroline-κ²N,N′)(sulfato-κO)cobalt(II): crystal structure, Hirshfeld surface analysis and computational study

The Co^II 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.

Three 4-(4-fluoro­phen­yl)piperazin-1-ium salts containing organic anions: supra­molecular assembly in one, two and three dimensions

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

Synthesis and crystal structure of two manganese-based 12-metallacrown-4 complexes: Na₂(3-chloro­benzoate)₂[12-MC_{Mn(III)N(shi)}-4](DMF)₆ and MnNa(3-chloro­benzoate)₃[12-MC_{Mn(III)N(shi)}-4](DMF)(H₂O)₄·4DMF·0.72H₂O

The metallacrown (MC) complexes Na₂(3-chloro­benzoate)₂[12-MC_{Mn(III)N(shi)}-4](DMF)₆, 1, and MnNa(3-chloro­benzoate)₃[12-MC_{Mn(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 Mn^III 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 Mn^II ion and one Na⁺ ion in 2.

Mol­ecular and crystal structure, lattice energy and DFT calculations of two 2′-(nitro­benzo­yloxy)aceto­phenone isomers

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.

Crystal structures of two dis-symmetric di-Schiff base compounds: 2-({(E)-2-[(E)-2,6-di­chloro­benzyl­idene]hydrazin-1-yl­idene}meth­yl)-6-meth­oxy­phenol and 4-bromo-2-({(E)-2-[(E)-2,6-di­chloro­benzyl­idene]hydrazin-1-yl­idene}meth­yl)phenol

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.

Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N′-bis­[(pyridin-4-yl)meth­yl]ethanedi­amide and 3-chloro­benzoic acid

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.

In situ synthesis, crystal structures, topology and photoluminescent properties of poly[di-μ-aqua-di­aqua­[μ₃-4-(1H-tetra­zol-1-id-5-yl)benzoato-κ⁴O:O,O′:O′′]barium(II)] and poly[μ-aqua-di­aqua­[μ₃-4-(1H-tetra­zol-1-id-5-yl)benzoato-κ⁴O:O,O′:O′]strontium(II)]

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.

Crystal structure of a 1:1 co-crystal of the anti­cancer drug gefitinib with azelaic acid

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.

Crystal structure, Hirshfeld surface analysis and inter­action energy, DFT and anti­bacterial activity studies of (Z)-4-hexyl-2-(4-methyl­benzyl­idene)-2H-benzo[b][1,4]thia­zin-3(4H)-one

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—H_Mthn⋯O_Bnzthz hydrogen bonds and are linked into chains extending along the a-axis direction by weak C—H_Bnz⋯O_Bnzthz (Bnz = benzene, Bnzthz = benzo­thia­zine and Mthn = methine) hydrogen bonds.

Crystal structures of 6-cyclo­propyl-1,3-di­phenylfulvene and 6-(2,3-di­meth­oxy­naphth­yl)-1,3-di­phenylfulvene

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.

Crystal structure of dicaesium strontium hexa­cyanidoferrate(II), Cs₂Sr[Fe(CN)₆], from laboratory X-ray powder data

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].

Crystal structure and Hirshfeld surface analysis of di­ethyl 5-(2-cyano­phen­oxy)isophthalate

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 C_ar­yl—O—C_ar­yl 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.

Hydro­thermal synthesis and crystal structure of poly[bis­(μ₃-3,4-di­amino­benzoato)manganese], a layered coordination polymer

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

Stereochemistry of the methyl­idene-bridged quinazoline-iso­quinoline alkaloid 3-{[6,7-dimeth­oxy-1-(4-nitro­phen­yl)-1,2,3,4-tetra­hydro­isoquinolin-2-yl]methyl­idene}-1,2,3,9-tetra­hydro­pyrrolo­[2,1-b]quinazolin-9-one methanol monosolvate

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.

Crystal structure and Hirshfeld surface analysis of 4-(naphthalen-2-yl)-N-[(Z)-4-propoxybenzyl­idene]-1,3-thia­zol-2-amine

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.

2-O-Mono­alkyl isosorbide ethers with C8, C10, C12 and C14 chain lengths

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.

Crystal structure of the one-dimensional coordination polymer formed by the macrocyclic [Ni(cyclam)]²⁺ cation and the dianion of di­phenyl­silanediylbis(4-benzoic acid)

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.

2-[Carbamo­thio­yl(2-hy­droxy­eth­yl)amino]­ethyl benzoate: crystal structure, Hirshfeld surface analysis and computational study

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.

Mol­ecular and crystal structure, optical properties and DFT studies of 1,4-dimeth­oxy-2,5-bis­[2-(4-nitro­phen­yl)ethen­yl]benzene

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.

Crystal structure of catena-poly[[[di­aqua­[1,2-bis­(pyridin-4-yl)ethene]{4-[2-(pyridin-4-yl)ethen­yl]pyridinium}gold(I)iron(II)]-di-μ-cyanido] bis­[dicyanido­gold(I)] 1,2-bis­(pyridin-4-yl)ethene dihydrate]

In the title compound, the Fe^II 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 Fe^II 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 Fe^II ion.

Crystal structures of [Li₇(i-PrO)₃(C₄H₁₀NO)₃]₂O and [Na(i-PrOH)₂(C₈H₁₈NO₂)]₂

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.

Crystal structure of di­methyl 5-(4-ethyl­phen­yl)-4-[(4-ethyl­phen­yl)ethyn­yl]-6,11-di­phenyl-1,3,6,11-tetra­hydro-2H-6,11-ep­oxy­cyclo­penta­[a]anthracene-2,2-di­carboxyl­ate

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.

Crystal structure of a cadmium sulfate coordination polymer based on the 3,6-bis­(pyrimidin-2-yl)-1,4-di­hydro-1,2,4,5-tetra­zine ligand

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.

Crystal structure, Hirshfeld surface analysis, inter­action energy and DFT studies of 4-[(4-allyl-2-meth­oxy­phen­oxy)meth­yl]-1-(4-meth­oxy­phen­yl)-1H-1,2,3-triazole

In the crystal structure, C—H_Mthphn⋯O_Mthphn (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.

1-Ethyl 2-methyl 3,4-bis­(acet­yloxy)pyrrolidine-1,2-di­carboxyl­ate: crystal structure, Hirshfeld surface analysis and computational chemistry

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.

Crystal structure and Hirshfeld surface analysis of 4-bromo­anilinium nitrate

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.