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Crystal structure of the co-crystalline adduct 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.1^3,8]dodecane (TATD)-4-iodo-phenol (1/2): supra-molecular assembly mediated by halogen and hydrogen bonding.

ABSTRACT: The asymmetric unit of the title co-crystalline adduct, 1,3,6,8-tetra-aza-tri-cyclo[4.4.1.1^3,8]dodecane (TATD)-4-iodo-phenol (1/2), C₈H₁₆N₄·2C₆H₅IO, comprises a half mol-ecule of the aminal cage polyamine plus a 4-iodo-phenol mol-ecule. A twofold rotation axis generates the other half of the adduct. The components are linked by two inter-molecular O-H⋯N hydrogen bonds. The adducts are further linked into a three-dimensional framework structure by a combination of N⋯I halogen bonds and weak non-conventional C-H⋯O and C-H⋯I hydrogen bonds.

SUBMITTER: Rivera A

PROVIDER: S-EPMC5683492 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Crystal structure of the co-crystalline adduct 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.13,8]dodecane (TATD)-4-iodo-phenol (1/2): supra-molecular assembly mediated by halogen and hydrogen bonding.

Rivera Augusto A Rojas Jicli José JJ Ríos-Motta Jaime J Bolte Michael M

Acta crystallographica. Section E, Crystallographic communications 20171020 Pt 11

The asymmetric unit of the title co-crystalline adduct, 1,3,6,8-tetra-aza-tri-cyclo[4.4.1.13,8]dodecane (TATD)-4-iodo-phenol (1/2), C8H16N4·2C6H5IO, comprises a half mol-ecule of the aminal cage polyamine plus a 4-iodo-phenol mol-ecule. A twofold rotation axis generates the other half of the adduct. The components are linked by two inter-molecular O-H⋯N hydrogen bonds. The adducts are further linked into a three-dimensional framew ...[more]

PMID: 29152352

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Crystal structure of the co-crystalline adduct 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.1(3,8)]dodecane (TATD)-4-bromo-phenol (1/2).

Project description:The structure of the 1:2 co-crystalline adduct C8H16N4·2C6H5BrO, (I), from the solid-state reaction of 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.1(3,8)]dodecane (TATD) and 4-bromo-phenol, has been determined. The asymmetric unit of the title co-crystalline adduct comprises a half mol-ecule of aminal cage polyamine plus a 4-bromo-phenol mol-ecule. A twofold rotation axis generates the other half of the adduct. The primary inter-species association in the title compound is through two inter-molecular O-H⋯N hydrogen bonds. In the crystal, the adducts are linked by weak non-conventional C-H⋯O and C-H⋯Br hydrogen bonds, giving a two-dimensional supra-molecular structure parallel to the bc plane.

| S-EPMC4420134 | biostudies-literature

Crystal structure of the co-crystalline adduct 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.1(3,8)]dodecane (TATD)-4-chloro-3,5-di-methyl-phenol (1/1).

Project description:In the crystal of the title co-crystalline adduct, C8H16N4·C8H9ClO, (I), prepared by solid-state reaction, the mol-ecules are linked by inter-molecular O-H⋯N hydrogen bonds, forming a D motif. The aza-adamantane structure in (I) is slightly distorted, with N-CH2-CH2-N torsion angles of 10.4 (3) and -9.0 (3)°. These values differ slightly from the corresponding torsion angles in the free aminal cage (0.0°) and in related co-crystalline adducts, which are not far from a planar geometry and consistent with a D 2d mol-ecular symmetry in the tetra-aza-tri-cyclo structure. The structures also differ in that there is a slight elongation of the N-C bond lengths about the N atom that accepts the hydrogen bond in (I) compared with the other N-C bond lengths. In the crystal, the two mol-ecules are not only linked by a classical O-H⋯N hydrogen bond but are further connected by weak C-H⋯π inter-actions, forming a two-dimensional supra-molecular network parallel to the bc plane.

| S-EPMC4518940 | biostudies-literature

First hydrogen-bonded adduct of sterically hindered 2-tert-butyl-4-methyl-phenol (TBMP) with 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.13,8]dodecane (TATD) via coupling of classical hydrogen bonds and C-H⋯π non-covalent inter-actions.

Project description:The title compound, C8H16N4·2C11H16O, was synthesized from the corres-ponding sterically crowded phenol by treatment with the aminal cage polyamine. Single-crystal X-ray diffraction structural analysis revealed the three-mol-ecule aggregate to crystallize in the monoclinic space group P2/c with one half of a 1,3,6,8-tetra-aztri-cyclo-[4.4.1.13,8]dodecane (TATD) mol-ecule and one 2-tert-butyl-4-methyl-phenol mol-ecule per asymmetric unit. The crystal structure features inter-molecular O-H⋯N and C-H⋯O hydrogen bonds, as well as inter-molecular C-H⋯π inter-actions.

| S-EPMC9431775 | biostudies-literature

Redetermination of 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.1(3,8)]dodeca-ne.

Project description:The structure of the title compound, C8H16N4, which consists of four fused seven-membered rings, has been redetermined at 173 K. This redetermination corrects the orientation of two H atoms, which were located at unrealistic positions in the original room-temperature study [Murray-Rust (1974 ▶). J. Chem. Soc. Perkin Trans. 2, pp. 1136-1141]. The complete mol-ecule is generated by -42m symmetry, with one quarter of a mol-ecule [one N atom (site symmetry m), two C atoms (one with site symmetry m and the other with site symmetry 2) and two H atoms] in the asymmetric unit. No directional inter-actions beyond van der Waals contacts are apparent in the crystal structure.

| S-EPMC3998434 | biostudies-literature

Crystal structure of the 1:2 co-crystal of 1,3,6,8-tetra-aza-tri-cyclo-[4.3.1.13,8]undecane (TATU) and 4-chloro-phenol (1/2).

Project description:In the title compound, C7H14N4·2C6H5ClO, which crystallized with two crystallographically independent 4-chloro-phenol mol-ecules and one 1,3,6,8-tetra-aza-tri-cyclo-[4.3.1.13,8]undecane (TATU) mol-ecule in the asymmetric unit, the independent components are linked by two O-H⋯N hydrogen bonds. The hydrogen-bond acceptor sites are two non-equivalent N atoms from the aminal cage structure, and the tricyclic system distorts by changing the C-N bond lengths. In the crystal, these hydrogen-bonded aggregates are linked into chains along the c axis by C-H⋯N hydrogen bonds. The crystal structure also features C-H⋯π contacts.

| S-EPMC5095853 | biostudies-literature

2,7-Bis(2,6-diisopropyl-phen-yl)benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetra-one.

Project description:In the title compound, C(38)H(38)N(2)O(4), the 16 atoms comprising the four six-membered rings that are fused together are approximately coplanar (maximum r.m.s. deviation = 0.033?Å). The benzene rings at either ends are nearly perpendicular to the mean plane of the fused-ring system; one is aligned at 80.4?(1) ° and the other at 82.2?(1)°.

| S-EPMC3238844 | biostudies-other

Mechanochemical synthesis and crystal structure of a 1:2 co-crystal of 1,3,6,8-tetra-aza-tri-cyclo[4.3.1.13,8]undecane (TATU) and 4-chloro-3,5-dimethyl-phenol.

Project description:Solvent-free treatment of 1,3,6,8-tetra-aza-tri-cyclo-[4.3.1.13,8]undecano (TATU) with 4-chloro-3,5-di-methyl-phenol led to the formation of the title co-crystal, C7H14N4·2C8H9ClO. The asymmetric unit contains one aminal cage mol-ecule and two phenol mol-ecules linked via two O-H⋯N hydrogen bonds. In the aminal cage, the N-CH2-CH2-N unit is slightly distorted from a syn periplanar geometry. Aromatic π-π stacking between the benzene rings from two different neighbouring phenol mol-ecules [centroid-centroid distance = 4.0570 (11) Å] consolidates the crystal packing.

| S-EPMC5095854 | biostudies-literature

Crystal structure of the 1,3,6,8-tetra-aza-tri-cyclo[4.3.1.1(3,8)]undecane (TATU)-4-nitro-phenol (1/2) adduct: the role of anomeric effect in the formation of a second hydrogen-bond inter-action.

Project description:In the title ternary co-crystalline adduct, C7H14N4·2C6H5NO3, mol-ecules are linked by two inter-molecular O-H⋯N hydrogen bonds, forming a tricomponent aggregates in the asymmetric unit. The hydrogen-bond formation to one of the N atoms is enough to induce structural stereoelectronic effects in the normal donor→acceptor direction. In the title adduct, the two independent nitro-phenol mol-ecules are essentially planar, with maximum deviations of 0.0157 (13) and 0.0039 (13) Å. The dihedral angles between the planes of the nitro group and the attached benzene rings are 4.04 (17) and 5.79 (17)°. In the crystal, aggregates are connected by C-H⋯O hydrogen bonds, forming a supra-molecular dimer enclosing an R 6 (6)(32) ring motif. Additional C-H⋯O inter-molecular hydrogen-bonding inter-actions form a second supra-molecular inversion dimer with an R 2 (2)(10) motif. These units are linked via C-H⋯O and C-H⋯N hydrogen bonds, forming a three-dimensional network.

| S-EPMC4645038 | biostudies-literature

Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY.

Project description:Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (TyrB26) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-TyrB26]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (TyrB16, PheB24, PheB25, 3-I-TyrB26, and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-TyrB26]insulin analog (determined as an R6 zinc hexamer). Given that residues B24-B30 detach from the core on receptor binding, the environment of 3-I-TyrB26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a "micro-receptor" complex, we predict that 3-I-TyrB26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins.

| S-EPMC5207135 | biostudies-literature

Neutral Chiral Tetrakis-Iodo-Triazole Halogen-Bond Donor for Chiral Recognition and Enantioselective Catalysis.

Project description:Halogen bonding represents a powerful tool in the field of noncovalent interactions. However, applications in enantioselective recognition and catalysis remain almost nonexistent, due in part to the distinct features of halogen bonds, including long covalent and noncovalent bond distances and high directionality. Herein, this work presents a novel chiral tetrakis-iodo-triazole structure as a neutral halogen bond donor for both chiral anion-recognition and enantioinduction in ion-pair organocatalysis. NMR-titration studies revealed significant differences in anion affinity between the halogen bonding receptor and its hydrogen bonding parent. Selective recognition of chiral dicarboxylates and asymmetric induction in a benchmark organocatalytic reaction were demonstrated using the halogen bond donor. Inversions in the absolute sense of chiral recognition, enantioselectivity, and chiroptical properties relative to the related hydrogen donor were observed. Computational modeling suggested that these effects were the result of distinct anion-binding modes for the halogen- versus hydrogen-bond donors.

| S-EPMC7898328 | biostudies-literature