1,1′-[(2,3,3a,4,5,6,7,7a-Octa­hydro-1H-1,3-benzimidazole-1,3-di­yl)bis­(methyl­ene)]bis­(1H-benzotriazole)

Augusto Rivera; Dency José Pacheco; Jaime Ríos-Motta; Michaela Pojarová; Michal Dušek

doi:10.1107/S160053681104044X

. 2011 Oct 29;67(Pt 11):o3071. doi: 10.1107/S160053681104044X

1,1′-[(2,3,3a,4,5,6,7,7a-Octahydro-1H-1,3-benzimidazole-1,3-diyl)bis(methylene)]bis(1H-benzotriazole)

Augusto Rivera ^a,^*, Dency José Pacheco ^a, Jaime Ríos-Motta ^a, Michaela Pojarová ^b, Michal Dušek ^b

PMCID: PMC3247461 PMID: 22220079

Abstract

The cyclohexane ring in the title compound, C₂₁H₂₄N₈, adopts a chair conformation and the five-membered heterocyclic ring to which it is fused adopts a twist conformation on their common C—C bond. The substituents on the N atoms of the central five-membered heterocycle are arranged trans with respect to the central ring. The terminal benzotriazole rings are oriented at angles of 74.66 (8) and 84.18 (8)° with respect to the mean plane of the central heterocycle. The angle between the two benzotriazole rings is 30.80 (9)°. The bond lengths and angles are within normal ranges; the largest deviation from expectation is for a long N—CH₂ bond length [1.476 (2) Å] as a consequence of an anomeric effect. In the crystal, molecules are connected by C—H⋯N hydrogen bonds.

Related literature

For general background to anomeric effects, see: Carey & Sundberg (2000 ▶). For related structures see: Rivera et al. (2011 ▶); Wang et al. (2008 ▶). For ring conformations, see: Cremer & Pople (1975 ▶). For standard bond lengths, see: Allen et al. (1987 ▶).

Experimental

Crystal data

C₂₁H₂₄N₈
M _r = 388.48
Monoclinic,
a = 11.9474 (2) Å
b = 5.9406 (1) Å
c = 27.3861 (4) Å
β = 90.861 (1)°
V = 1943.50 (5) Å³
Z = 4
Cu Kα radiation
μ = 0.68 mm⁻¹
T = 120 K
0.31 × 0.18 × 0.11 mm

Data collection

Oxford Diffraction Xcalibur Atlas Gemini ultra diffractometer
37999 measured reflections
3461 independent reflections
2990 reflections with I > 2σ(I)
R _int = 0.172

Refinement

R[F ² > 2σ(F ²)] = 0.052
wR(F ²) = 0.137
S = 1.06
3461 reflections
262 parameters
H-atom parameters constrained
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Data collection: CrysAlis PRO (Oxford Diffraction, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S160053681104044X/bh2381sup1.cif

e-67-o3071-sup1.cif^{(19.4KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681104044X/bh2381Isup2.hkl

e-67-o3071-Isup2.hkl^{(169.8KB, hkl)}

Supplementary material file. DOI: 10.1107/S160053681104044X/bh2381Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C7—H7b⋯N1ⁱ	0.97	2.38	3.301 (2)	159
C15—H15b⋯N7ⁱⁱ	0.97	2.62	3.504 (2)	151

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Symmetry codes: (i) Inline graphic ; (ii) .

Acknowledgments

We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de la Universidad Nacional de Colombia, for financial support of this work, as well as the Institutional research plan No. AVOZ10100521 of the Institute of Physics and the project Praemium Academiae of the Academy of Science of the Czech Republic.

supplementary crystallographic information

Comment

Among the most thoroughly studied stereoelectronic effects, the interactions between lone pairs have attracted much interest. These interactions between a non bonded electron pair and antibonding σ* sigma bonds usually play a feature role in the preferred conformations of such systems (Carey & Sundberg, 2000). The data of the crystal structure of the title compound indicate the occurrence of a n(N)→σ^*(C—N) electron delocalization, characteristic of the anomeric effect, as evidenced by the lengthened bond N6—C15 [1.476 (2) Å], shortened bond C15—N5 [1.433 (2)] and distorted C—N—C bond angles, C8—N5—C14 = 106.11 (13)°, C8—N5—C15 = 115.53 (13)°, and C14—N5—C15 = 118.03 (14)°. These results exhibit the same pattern of C—N shortened bond lengths that the crystal structure of 1,3-bis[(1H-benzotriazol-1-yl)methyl]-2,3-dihydro-1H-benzimidazole recently reported (Rivera et al., 2011). The structural parameters suggest an increase in p-character of nitrogen and reduction in N-pyramidality. The title compound was obtained by the reaction of racemic cyclic aminal (2R,7R,11S,16S)-1,8,10,17-tetraazapentacyclo-[8.8.1.1^8,17.0^2,7.0^11,16]icosane with two equivalents of benzotriazole. The molecular structure and atom-numbering scheme are shown in Fig. 1. The asymmetric unit comprises of one molecule of the title compound (Fig 1). The bond lengths (Allen et al., 1987) and angles are generally within normal ranges (Wang et al., 2008).

The cyclohexane ring adopts a chair conformation and the five-membered ring to which it is fused adopts a twist conformation on C9—C14 with Q(2) = 0.455 (2) Å and φ = 311.1 (2)° (Cremer & Pople, 1975) and a trans disubstitution. The benzotriazole rings (N1—N3/C1—C6; N6—N8/C16—C21) are essentially planar with the maximum deviations from planarity being 0.0220 (19) Å for atom C3 and -0.0161 (19) for atom C18. The central heterocyclic ring makes an angle of 74.66 (8)° and 84.18 (8)° with the planar benzotriazole rings. The angle between the two benzotriazole rings is 30.80 (9)°. The two exocyclic bonds of methylene carbon atoms occupy pseudo-axial positions.

The crystal structure contains an intermolecular C7—H7B···N1 hydrogen bond between one H atom of the N—CH₂—N group (aminal group) and one N atom of the benzotriazole ring of neighboring molecule linking adjacent molecules to form a one-dimensional chain running parallel to the b axis (Fig. 2), and further linked by weak C15—H15B···N intermolecular interactions. The distance of 3.4502 (9) Å between the centroids of the rings N1/N2/N3/C6/C1 related by the symmetry code (-x, 2 - y, -z) suggests a possible π–π interaction in the crystal.

Experimental

A solution of (2R,7R,11S,16S)-1,8,10,17-tetraazapentacyclo-[8.8.1.1^8,17.0^2,7.0^11,16]icosane (276 mg, 1.00 mmol) in dioxane (3 ml) and water (4 ml), previously prepared following described procedures, was added dropwise in a dioxane solution (3 ml) containing two equivalents of benzotriazole (238 mg, 2.00 mmol) in a two-necked round-bottomed flask. The mixture was stirred for about 6 h. and then the solvent was evaporated under reduced pressure until a sticky residue appeared. The product was purified by chromatography on a silica column, and subjected to gradient elution with benzene:ethyl acetate (yield 75%, m.p. = 424–425 K). Single crystals of the racemic title compound were grown from a chloroform solution by slow evaporation of the solvent at room temperature over a period of about 2 weeks.