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The crystal structure of 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine: a three-dimensional hydrogen-bonded framework, augmented by ?-? stacking inter-actions and I?N halogen bonds.

ABSTRACT: In 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine, C₁₅H₁₅IN₄O, the central piperazine ring adopts an almost perfect chair conformation with the pyrimidine substituent in an equatorial site. The planar amide unit makes a dihedral angle of 80.44?(7)° with the phenyl ring. A combination of C-H?O and C-H??(arene) hydrogen bonds links the mol-ecules into a complex three-dimensional network structure, augmented by a ?-? stacking inter-action and an I?N halogen bond, all involving different pairs of inversion-related mol-ecules. Comparisons are made with the structures of a number of related compounds.

SUBMITTER: Mahesha N

PROVIDER: S-EPMC6362664 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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The crystal structure of 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine: a three-dimensional hydrogen-bonded framework, augmented by π-π stacking inter-actions and I⋯N halogen bonds.

Mahesha Ninganayaka N Yathirajan Hemmige S HS Furuya Tetsundo T Akitsu Takashiro T Glidewell Christopher C

Acta crystallographica. Section E, Crystallographic communications 20190104 Pt 2

In 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine, C15H15IN4O, the central piperazine ring adopts an almost perfect chair conformation with the pyrimidine substituent in an equatorial site. The planar amide unit makes a dihedral angle of 80.44 (7)° with the phenyl ring. A combination of C-H⋯O and C-H⋯π(arene) hydrogen bonds links the mol-ecules into a complex three-dimensional network structure, augmented by a π-π stacking inter-action and an I⋯N halogen bond, ...[more]

PMID: 30800436

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Project description:The cis- and trans-isomers of 6-(3-(3,4-dichlorophenyl)-1,2,4-oxadiazol-5-yl)cyclohex-3-ene-1-carboxylic acid (cis-A and trans-A) were obtained by the reaction of 3,4-dichloro-N'-hydroxybenzimidamide and cis-1,2,3,6-tetrahydrophthalic anhydride. Cocrystals of cis-A with appropriate solvents (cis-A‧½(1,2-DCE), cis-A‧½(1,2-DBE), and cis-A‧½C6H14) were grown from 1,2-dichloroethane (1,2-DCE), 1,2-dibromoethane (1,2-DBE), and a n-hexane/CHCl3 mixture and then characterized by X-ray crystallography. In their structures, cis-A is self-assembled to give a hybrid 2D supramolecular organic framework (SOF) formed by the cooperative action of O-H⋯O hydrogen bonding, Cl⋯O halogen bonding, and π⋯π stacking. The self-assembled cis-A divides the space between the 2D SOF layers into infinite hollow tunnels incorporating solvent molecules. The energy contribution of each noncovalent interaction to the occurrence of the 2D SOF was verified by several theoretical approaches, including MEP and combined QTAIM and NCIplot analyses. The consideration of the theoretical data proved that hydrogen bonding (approx. -15.2 kcal/mol) is the most important interaction, followed by π⋯π stacking (approx. -11.1 kcal/mol); meanwhile, the contribution of halogen bonding (approx. -3.6 kcal/mol) is the smallest among these interactions. The structure of the isomeric compound trans-A does not exhibit a 2D SOF architecture. It is assembled by the combined action of hydrogen bonding and π⋯π stacking, without the involvement of halogen bonds. A comparison of the cis-A structures with that of trans-A indicated that halogen bonding, although it has the lowest energy in cis-A-based cocrystals, plays a significant role in the crystal design of the hybrid 2D SOF. The majority of the reported porous halogen-bonded organic frameworks were assembled via iodine and bromine-based contacts, while chlorine-based systems-which, in our case, are structure-directing-were unknown before this study.

Dataset Information

The crystal structure of 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine: a three-dimensional hydrogen-bonded framework, augmented by ?-? stacking inter-actions and I?N halogen bonds.

Publications

The crystal structure of 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine: a three-dimensional hydrogen-bonded framework, augmented by π-π stacking inter-actions and I⋯N halogen bonds.

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