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CRYSTALLOGRAPHIC
COMMUNICATIONS

Volume 80| Part 3

ISSN: 2056-9890

March 2024 issue

Cover illustration: Over the years, crystallography has established itself as the most powerful technique for understanding the structure of materials and rationalizing their properties and performance. Our discipline has been at the forefront of technological advances, from new and more intense radiation sources to new approaches to data collection under extreme conditions on smaller and increasingly more challenging samples. To keep up with those issues, it is necessary to encourage and support young and early-career scientists who are involved in crystallography. In this issue we highlight the history and activities of the German Young Crystallographers. Since its founding in 2013, the Young Crystallographers (YC) working group has rejuvenated the German Society for Crystallography by organizing meetings, hands-on experimental sessions at synchrotron beamlines, sessions on improving communication and presentation skills, a newsletter and presence on social media platforms, a prize for young scientists, a special issue on work done by young crystallographers, among other initiatives. The YC also foster collaboration with other YCs in Europe and around the world. The IUCr is enthusiastically supporting these efforts to guarantee the next generations of crystallographers will undertake the challenges that face our discipline in the future. It is hoped that this work will inspire young scientists in other countries. See: Meurer, Möbs, Nentwich, Weigel & Wöhrle [Acta Cryst. E80, 252–255].

AfCA collection

Synthesis and crystal structure of the adduct between 2-pyridylselenyl chloride and isobutyronitrile

A. W. Temesgen, A. A. Sapronov, A. S. Kubasov, A. S. Novikov, T. A. Le and A. G. Tskhovrebov

The reaction between 2-pyridylselenenyl chloride and isobutyronitrile results in the formation of the corresponding cationic pyridinium-fused 1,2,4-selenodiazole, namely, 3-(propan-2-yl)-1,2,4-[1,2,4]selenadiazolo[4,5-a]pyridin-4-ylium chloride, C₉H₁₁N₂Se⁺·Cl⁻, in high yield (89%). The bifurcated Se⋯Cl⁻⋯H—Cl chalcogen-hydrogen-bonding interactions were analysed by DFT followed by a topological analysis of the electron-density distribution.

CCDC reference: 2328546

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research communications

‘Young crystallographers’ rejuvenate crystallography in Germany

F. Meurer, J. Möbs, M. Nentwich, T. Weigel and J.-P. Wöhrle

The Young Crystallographers were founded in 2013 within the German Crystallographic Association and have revitalized the field of crystallography by establishing collaboration and support among early career researchers, organizing educational events, and promoting scientific contributions on national and international stages.

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Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-nitrophenyl)maleimide

M. Montoya-Garcia, H. Cortes-Hernandez, R. D'Vries and H. Valencia-Sanchez

The title compound crystallizes in the monoclinic system (space group P2₁/n) with two molecules in the asymmetric unit, which are linked by C—H⋯O hydrogen bonds. Hirshfeld surface analysis showed that the most significant contributions to the crystal packing are from H⋯O/O⋯H, H⋯C/C⋯H and H⋯H interactions. A DFT study was conducted using three different levels of theory.

CCDC reference: 2328386

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Crystal structure and Hirshfeld surface analysis of (Z)-N-{chloro[(4-ferrocenylphenyl)imino]methyl}-4-ferrocenylaniline N,N-dimethylformamide monosolvate

R. Sghyar, A. Bentama, A. Haoudi, A. Mazzah, J. T. Mague, T. Hökelek, E. M. EL Hadrami and N. K. Sebbar

The molecule of the title compound is twisted end to end so that the ferrocenyl groups are nearly perpendicular to one another. The central N/C/N unit is disordered. In the crystal, several C—H⋯π(ring) interactions lead to the formation of layers parallel to (010), which are connected by further C—H⋯π(ring) interactions.

CCDC reference: 2329443

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Structural characterization of a new samarium–sodium heterometallic coordination polymer

A. M. Hastings, A. Williams, R. G. Surbella III, A. E. Hixon and A. Arteaga

The crystal structure is reported of a new heterometallic samarium compound comprised of alternating Sm^III and Na^I metal centers bridged by o-vanillin ligands to create a helical chain.

CCDC reference: 2329845

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[4-(2-Aminoethyl)morpholine-κ²N,N′]dibromidocadmium(II): synthesis, crystal structure and Hirshfeld surface analysis

B. Chidambaranathan, S. Sivaraj, P. Vijayamathubalan, S. Abraham Rajasekar and S. Selvakumar

The title coordination compound was synthesized upon complexation of 4-(2-aminoethyl)morpholine and cadmium(II) bromide tetrahydrate at 303 K. It crystallizes as a centrosymmetric dimer, with one cadmium atom, two bromine atoms and one N,N′-bidentate 4-(2-aminoethyl)morpholine ligand in the asymmetric unit.

CCDC reference: 2298040

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Crystal structure of diethylammonium dioxido{Z)-N-[(pyridin-2-yl)carbonylazanidyl]pyridine-2-carboximidato}vanadate(1−) monohydrate

B. Mondal

A new ionic dioxidovanadium(V) compound with an O,N,O donor ligand is reported. In the crystal, extensive hydrogen bonding is observed.

CCDC reference: 2294358

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Syntheses, characterizations, crystal structures and Hirshfeld surface analyses of methyl 4-[4-(difluoromethoxy)phenyl]-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, isopropyl 4-[4-(difluoromethoxy)phenyl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate and tert-butyl 4-[4-(difluoromethoxy)phenyl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate

S. Ö. Yıldırım, M. Akkurt, E. Pehlivanlar, G. Çetin, R. Şimşek, R. J. Butcher and A. Bhattarai

In the crystal structure of methyl 4-[4-(difluoromethoxy)phenyl]-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate (I), molecules are linked by N—H⋯O and C—H⋯O interactions, forming a tri-periodic network, while molecules of isopropyl 4-[4-(difluoromethoxy)phenyl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate (II) and tert-butyl 4-[4-(difluoromethoxy)phenyl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate (III) are linked by N—H⋯O, C—H⋯F and C—H⋯π interactions, forming layers parallel to (002).

CCDC references: 2331194; 2331193; 2331192

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Crystal structure of 4-(benzo[d]thiazol-2-yl)-1,2-dimethyl-1H-pyrazol-3(2H)-one

H. A. Elboshi, R. A. Azzam, G. H. Elgemeie and P. G. Jones

The ring systems of 4-(benzo[d]thiazol-2-yl)-1,2-dimethyl-1H-pyrazol-3(2H)-one are almost coplanar. In the three-dimensional packing, the carbonyl oxygen accepts four weak hydrogen bonds.

CCDC reference: 2331586

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Omadacycline dihydrate, C₂₉H₄₀N₄O₇·2H₂O, from X-ray powder diffraction data

J. A. Kaduk, N. C. Boaz, S. Gates-Rector, A. M. Gindhart and T. N. Blanton

The crystal structure of omadacycline dihydrate has been solved and refined using synchrotron X-ray powder diffraction data.

CCDC reference: 2332637

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Crystal structure of the sodium salt of mesotrione: a triketone herbicide

O. Bereziuk, K. Gubina, V. Trush and V. Ovchynnikov

The crystal structure of the sodium salt of mesotrione [2-(4-methylsulfonyl-2-nitrobenzoyl)cyclohexane-1,3-dione] is described. A one-dimensional polymer is formed by the coordination of all functional groups except the NO₂ group. The coordination number of the sodium atom in the compound is 5.

CCDC reference: 2072869

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Crystal structure and Hirshfeld surface analysis of 3-phenyl-1-{3-[(3-phenylquinoxalin-2-yl)oxy]propyl}-1,2-dihydroquinoxalin-2-one

N. Abad, J. T. Mague, A. Alsubari, E. M. Essassi, A. Y. A. Alzahrani and Y. Ramli

In the title compound, the quinoxaline units are distinctly non-planar and twisted end-to-end. In the crystal, C—H⋯O and C—H⋯N hydrogen bonds link the molecules into chains extending along the a-axis direction. The chains are linked through π-stacking interactions between inversion-related quinoxaline moieties.

CCDC reference: 2332949

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Crystal structures of sulfonamide protected bicyclic guanidines: (S)-8-{[(tert-butyldimethylsilyl)oxy]methyl}-1-[(2,2,4,6,7-pentamethyl-2,3-dihydrobenzofuran-5-yl)sulfonyl]-1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidin-1-ium trifluoromethanesulfonate and (S)-8-(iodomethyl)-1-tosyl-1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidin-1-ium iodide

J. M. H. Alaboosh, S. P. Hill, B. M. Kariuki and J. E. Redman

The crystal structures of two sulfonamide-protected bicyclic guanidine salts are reported. The structures feature intramolecular N—H⋯O hydrogen bonding between the guanidinium group and the sulfonamide.

CCDC references: 2330294; 2330293

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Synthesis, characterization, and crystal structure of 2-(2-azidophenyl)-3-oxo-3H-indole 1-oxide

P. Dhote, S. Tothadi and C. V. Ramana

An attempt to explore the reactivity of the nitro group in the presence of gold catalysis in comparison to the azide group yielded intriguing results. Surprisingly, only the nitro group exhibited reactivity, ultimately giving rise to the formation of the title isatogen.

CCDC reference: 2303503

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Crystal structure of the tetraethylammonium salt of the non-steroidal anti-inflammatory drug nimesulide (polymorph II)

M. Rybczyńska and A. Sikorski

The crystal structure of the tetraethylammonium salt of the non-steroidal anti-inflammatory drug nimesulide (polymorph II), C₈H₂₀N⁺·C₁₃H₁₁N₂O₅S⁻, was determined using single-crystal X-ray diffraction. There are differences in the geometry of both the nimesulide anion and the tetraethylammonium cation in polymorphs I and II of the title compound.

CCDC reference: 2332021

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Synthesis and crystal structures of bis[1-oxopyridin-2-olato(1−)]bis(pentafluorophenyl)silicon(IV)–tetrahydrofuran–pentane (2/1/1), bis[1-oxopyridin-2-olato(1−)]bis(p-tolyl)silicon(IV), and dimesitylbis[1-oxopyridin-2-olato(1−)]silicon(IV)

B. M. Kraft, W. W. Brennessel, J. W. Andrews, M. T. Viggiani, N. F. Kittrell and M. T. Heckman

Three hexacoordinated bis(aryl)silicon(IV) complexes of 1-oxopyridin-2-one (OPO) are reported, each of which exhibit C/N site disorder in their pyridine rings. In (C₆F₅)₂Si(OPO)₂, the equal disorder ratios and solution NMR characterization together indicate the presence of a single totally asymmetric ON-trans-OC isomer. Unequal disorder ratios in p-tolyl₂Si(OPO)₂ and in mesityl₂Si(OPO)₂ indicate the presence of up to three isomers.

CCDC references: 2333179; 2333178; 2333177

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Crystal structure and Hirshfeld surface analysis of 4-oxo-3-phenyl-2-sulfanylidene-5-(thiophen-2-yl)-3,4,7,8,9,10-hexahydro-2H-pyrido[1,6-a:2,3-d′]dipyrimidine-6-carbonitrile

F. N. Naghiyev, V. N. Khrustalev, M. Akkurt, H. M. Mamedov, A. Bhattarai, A. N. Khalilov and İ. G. Mamedov

In the title compound, molecular pairs are linked by N—H⋯N hydrogen bonds along the c-axis direction and C—H⋯S and C—H⋯O hydrogen bonds along the b-axis direction, with $[R_{2}^{2}]$ (12) and $[R_{2}^{2}]$ (16) motifs, respectively, thus forming layers parallel to the (10 $[\overline{4}]$ ) plane. In addition, C=S⋯π and C≡N⋯π interactions between the layers ensure crystal cohesion.

CCDC reference: 2333770

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Crystal structure and characterization of a new one-dimensional copper(II) coordination polymer containing a 4-aminobenzoic acid ligand

A. Gogia, E. M. Novikov, I. A. Guzei, M. S. Fonari and T. V. Timofeeva

A new coordination polymer based on Cu^II and 4-aminobenzoic acid is isolated and characterized using single-crystal X-ray diffraction, FTIR and fluorescence spectroscopy, and thermal analysis.

CCDC reference: 2332153

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Crystal structure of tetrakis(μ-2-hydroxy-3,5-diisopropylbenzoato)bis[(dimethyl sulfoxide)copper(II)]

D. G. Shlian, R. H. Summers, K. Martinez and R. K. Upmacis

A solution of 2-hydroxy-3,5-bis(1-methylethyl)benzoic acid copper(II) hydrate (C₂₆H₃₄CuO₆·xH₂O), also known as copper(II) 3,5-diisopropylsalicylate hydrate, in dimethyl sulfoxide (DMSO) affords crystals of tetrakis-3,5-diisopropylsalicylatobis-dimethylsulfoxidodicopper(II), [Cu(II)₂(3,5-DIPS)₄(DMSO)₂], upon evaporation. The structure has an empirical formula of [Cu₂(C₁₃H₁₇O₃)₄(C₂H₆OS)₂] and consists of a centrosymmetric binuclear copper complex surrounded by four 3,5-diisopropylsalicylate ligands. Each copper atom is attached to four oxygen atoms in an almost square-planar fashion, with the addition of a DMSO ligand in an apical position leading to a square-pyramidal arrangement.

CCDC reference: 2333981

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Crystal structure of 1-{4-[bis(4-methylphenyl)amino]phenyl}ethene-1,2,2-tricarbonitrile

M. M. Bader and P.-T. Pham

The title compound crystallizes in the centrosymmetric orthorhombic space group Pbca, with 8 molecules in the unit cell. The main feature noticeable in the structure is the impact of the tricyanovinyl (TCV) group in forcing partial planarity of the portion of the molecule carrying the TCV group and directing the molecular packing in the solid state, resulting in the formation of π-stacks of dimers within the unit cell.

CCDC reference: 2202337

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issue contents

March 2024 issue

AfCA collection

Synthesis and crystal structure of the adduct between 2-pyridylselenyl chloride and isobutyronitrile

research communications

‘Young crystallographers’ rejuvenate crystallography in Germany

Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-nitrophenyl)maleimide

Crystal structure and Hirshfeld surface analysis of (Z)-N-{chloro[(4-ferrocenylphenyl)imino]methyl}-4-ferrocenylaniline N,N-dimethylformamide monosolvate

Structural characterization of a new samarium–sodium heterometallic coordination polymer

[4-(2-Aminoethyl)morpholine-κ²N,N′]dibromidocadmium(II): synthesis, crystal structure and Hirshfeld surface analysis

Crystal structure of diethylammonium dioxido{Z)-N-[(pyridin-2-yl)carbonylazanidyl]pyridine-2-carboximidato}vanadate(1−) monohydrate

Crystal structure of 4-(benzo[d]thiazol-2-yl)-1,2-dimethyl-1H-pyrazol-3(2H)-one

Omadacycline dihydrate, C₂₉H₄₀N₄O₇·2H₂O, from X-ray powder diffraction data

Crystal structure of the sodium salt of mesotrione: a triketone herbicide

Crystal structure and Hirshfeld surface analysis of 3-phenyl-1-{3-[(3-phenylquinoxalin-2-yl)oxy]propyl}-1,2-dihydroquinoxalin-2-one

Synthesis, characterization, and crystal structure of 2-(2-azidophenyl)-3-oxo-3H-indole 1-oxide

Crystal structure of the tetraethylammonium salt of the non-steroidal anti-inflammatory drug nimesulide (polymorph II)

Synthesis and crystal structures of bis[1-oxopyridin-2-olato(1−)]bis(pentafluorophenyl)silicon(IV)–tetrahydrofuran–pentane (2/1/1), bis[1-oxopyridin-2-olato(1−)]bis(p-tolyl)silicon(IV), and dimesitylbis[1-oxopyridin-2-olato(1−)]silicon(IV)

Crystal structure and Hirshfeld surface analysis of 4-oxo-3-phenyl-2-sulfanylidene-5-(thiophen-2-yl)-3,4,7,8,9,10-hexahydro-2H-pyrido[1,6-a:2,3-d′]dipyrimidine-6-carbonitrile

Crystal structure and characterization of a new one-dimensional copper(II) coordination polymer containing a 4-aminobenzoic acid ligand

Crystal structure of tetrakis(μ-2-hydroxy-3,5-diisopropylbenzoato)bis[(dimethyl sulfoxide)copper(II)]

Crystal structure of 1-{4-[bis(4-methylphenyl)amino]phenyl}ethene-1,2,2-tricarbonitrile

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