Dimethyl 4,4′-dihy­droxy-3,3′-{[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octa­hydro-1H-1,3-benzimidazole-1,3-di­yl]bis­(methyl­ene)}dibenzoate

Augusto Rivera; Diego Quiroga; Jaime Ríos-Motta; Karla Fejfarová; Michal Dušek

doi:10.1107/S1600536811040906

. 2011 Oct 12;67(Pt 11):o2911–o2912. doi: 10.1107/S1600536811040906

Dimethyl 4,4′-dihydroxy-3,3′-{[(3aRS,7aRS)-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3-diyl]bis(methylene)}dibenzoate

Augusto Rivera ^a,^*, Diego Quiroga ^a, Jaime Ríos-Motta ^a, Karla Fejfarová ^b, Michal Dušek ^b

PMCID: PMC3247326 PMID: 22219944

Abstract

The title compound, C₂₅H₃₀N₂O₆, has the imidazolidine ring in an envelope conformation. There are two intramolecular O—H⋯N hydrogen-bond interactions with graph-set motif S(6). The cyclohexane ring adopts a slightly distorted chair conformation. One methyl carboxylate substituent forms a dihedral angle of 12.00 (5)° with the plane of the benzene ring, while the other methyl carboxylate group is almost coplanar, making a dihedral angle of 2.26 (9)°. In the crystal, pairs of intermolecular C—H⋯O hydrogen bonds form racemic dimers, corresponding to an R ₂ ²(18) graph-set motif. Further weak C—H⋯O interactions generate a chain running along the c axis.

Related literature

For related structures, see: Rivera et al. (2011a ▶,b ▶,c ▶). For the synthesis of the precursor, see: Murray-Rust & Riddell (1975 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶). For hydrogen-bond graph-set nomenclature, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C₂₅H₃₀N₂O₆
M _r = 454.5
Monoclinic,
a = 26.3472 (6) Å
b = 9.1432 (1) Å
c = 21.6585 (4) Å
β = 121.139 (3)°
V = 4465.7 (2) Å³
Z = 8
Cu Kα radiation
μ = 0.80 mm⁻¹
T = 120 K
0.41 × 0.23 × 0.16 mm

Data collection

Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ▶) T _min = 0.853, T _max = 1
17421 measured reflections
3970 independent reflections
3309 reflections with I > 3σ(I)
R _int = 0.028

Refinement

R[F ² > 2σ(F ²)] = 0.035
wR(F ²) = 0.097
S = 1.54
3970 reflections
304 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR2002 (Burla et al., 2003 ▶); program(s) used to refine structure: JANA2006 (Petříček et al., 2006 ▶); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ▶); software used to prepare material for publication: JANA2006.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811040906/bt5658sup1.cif

e-67-o2911-sup1.cif^{(23.1KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811040906/bt5658Isup2.hkl

e-67-o2911-Isup2.hkl^{(167.7KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811040906/bt5658Isup3.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
O3—H3⋯N1	0.90 (2)	1.80 (2)	2.6383 (18)	154.3 (16)
O6—H6⋯N2	0.87 (2)	1.88 (2)	2.6814 (18)	153.0 (18)
C2—H2⋯O1ⁱ	0.96	2.57	3.414 (2)	146
C4—H4b⋯O1ⁱ	0.96	2.58	3.353 (2)	137
C16—H16c⋯O6ⁱⁱ	0.96	2.59	3.350 (2)	136

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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 Praemium Academiae project of the Academy of Sciences of the Czech Republic. DQ acknowledges the Vicerrectoría Académica de la Universidad Nacional de Colombia for a fellowship.

supplementary crystallographic information

Comment

The synthesis of the title compound (I) represents an expansion of our previous work exploring the substituent effects on the solid state structures of di-Mannich bases (Rivera et al., 2011a,b,c). In the title compound (I), C₂₅H₃₀N₂O₆, the heterocyclc ring has a envelope conformation on C7 (Q(2) = 0.4439 (15) Å, φ = 296.59 (19)°). It is surprising, however, that of the 12 fused 1,3-disubstituted-(3aR,7aR/3aS,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole of this type studied to date by us, including the title compound, only two has an envelope conformation on aminalic carbon (NCH₂N); the other all have a twisted conformation on C—C bond joint to both rings. The molecular conformation is stabilized by two intramolecular O—H···N hydrogen-bond interaction with set graph motif S(6) (Bernstein,et al. 1995). The cyclohexane ring adopt a slightly distorted chair conformation (Cremer & Pople, 1975) with puckering parameters Q, θ and φ of 0.5834 (16) Å, 5.35 (16)°, 300.8 (17)°. In the molecule of the title compound (Fig. 1), bond lengths and angles are generally within normal ranges and comparable with those observed in related compounds (Rivera et al., 2011a,b,c). Whereas the first carbonyl group is coplanar with the phenyl ring [torsion angle C10—C11—C15—O1 of 1.3 (2)°], the second carbonyl group is slightly twisted out of the plane of the aromatic ring. The torsion angle C19—C20—C24—O4 amounts to -10.1 (2)°. Therefore, the differences in orientation likely arise as a result of steric considerations with respect to the crystal packing.

The crystal packing is dominated by non-conventional C—H···O hydrogen bond interactions, Table 1. In the racemic crystal of title compound, a pair of the enantiomers are bonded together with two intermolecular bifurcate hydrogen bonds (Figure 2), generating a R₂²(18) graph-set motifs (Bernstein,et al. 1995). So, O1 can form two bifurcate intermolecular hydrogen bonds with two hydrogen atoms, C2—H2···O1 [C···O = 3.414 (2) Å] and C4—H4b···O1 [C···O = 3.353 (2) Å], but the two hydrogen atoms are in the same molecule, which indicates that one molecule in the crystals can be connected with one neighboring molecule by two intermolecular C—H···O bifurcate hydrogen bonds. The racemic dimers are further connected by additional C16—H16c···O6 hydrogen bonds, forming a supramolecular chain along the c axis (Figure 3). Thus, the ability of O6—H6 hydroxyl group to act as a hydrogen bridge donor and acceptor is important for the formation of crystals packing of the title compound. However, this additional H-bonding does not influence the intramolecular O—H···N distance, which shows a typical O···N distances of 2.6814 (18) Å (Rivera et al., 2011a,b,c).

Experimental

A solution of methyl 4-hydroxybenzoate (304 mg, 2.00 mmol) in dioxane (3 ml) was added dropwise to (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), prepared following previously described procedures (Murray-Rust & Riddell, 1975). The mixture was refluxed for about 10 h. 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 20%, m.p. = 449–450 K). Single crystals of racemic (I) were grown from a chloroform: methanol solution by slow evaporation of the solvent at room temperature over a period of about 2 weeks.

¹H NMR (CDCl₃, 400 MHz): δ 1.30 (4H, m), 1.86 (2H, m), 2.06 (2H, m), 2.38 (2H, m), 3.53 (2H, s, NCH₂N), 3.54 (2H, d, ²J_H,H = 14.0 Hz, ArCH₂N), 4.20 (2H, d, ²J_H,H = 14.0 Hz, ArCH₂N), 3.84 (6H, s, CH₃), 6.83 (2H, d, ³J_H,H = 8.4 Hz), 7.68 (2H, s), 7.86 (2H, dd, ⁴J_H,H = 1.6 Hz, ³J_H,H = 8.4 Hz). ¹³C NMR (CDCl₃, 100 MHz): δ 23.9, 28.8, 51.8, 56.0, 69.1, 75.6, 116.2, 121.0, 121.3, 130.0, 131.2, 161.9, 166.8.