Dibenzyl 3,3′,4,4′-tetra­methyl-5,5′-(ethynedi­yl)bis­(pyrrole-2-carboxyl­ate)

Hillary K Tanui; Frank R Fronczek; M Graça H Vicente

doi:10.1107/S1600536807061739

. 2007 Dec 6;64(Pt 1):o75. doi: 10.1107/S1600536807061739

Dibenzyl 3,3′,4,4′-tetramethyl-5,5′-(ethynediyl)bis(pyrrole-2-carboxylate)

Hillary K Tanui ^a, Frank R Fronczek ^a,^*, M Graça H Vicente ^a

PMCID: PMC2915032 PMID: 21200952

Abstract

The title molecule, C₃₀H₂₈N₂O₄, has crystallographic twofold rotation symmetry, with the pyrrole planes forming a dihedral angle of 40.49 (4)°. The pyrrole N—H donor and adjacent ester carbonyl acceptor form R ₂ ²(10) hydrogen-bonded rings about inversion centers, leading to chains of hydrogen-bonded molecules along [001].

Related literature

For background literature, see: Chinchilla & Najera (2007 ▶); Black et al. (1999 ▶); Etter (1990 ▶); Vogel (1996 ▶). For related structures, see: Xie et al. (1996 ▶); Weghorn et al. (1995 ▶).

Experimental

Crystal data

C₃₀H₂₈N₂O₄
M _r = 480.54
Monoclinic,
a = 19.340 (2) Å
b = 9.8955 (10) Å
c = 13.8495 (15) Å
β = 110.217 (6)°
V = 2487.2 (5) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 90 K
0.30 × 0.22 × 0.15 mm

Data collection

Nonius KappaCCD diffractometer with Oxford Cryostream
Absorption correction: none
28071 measured reflections
4748 independent reflections
3948 reflections with I > 2σ(I)
R _int = 0.022

Refinement

R[F ² > 2σ(F ²)] = 0.044
wR(F ²) = 0.124
S = 1.03
4748 reflections
168 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.46 e Å⁻³
Δρ_min = −0.39 e Å⁻³

Data collection: COLLECT (Nonius, 2000 ▶); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997 ▶); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536807061739/dn2299sup1.cif

e-64-00o75-sup1.cif^{(16.9KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807061739/dn2299Isup2.hkl

e-64-00o75-Isup2.hkl^{(232.7KB, hkl)}

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
N1—H1N⋯O2ⁱ	0.875 (14)	1.987 (14)	2.8565 (10)	172.1 (12)

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Symmetry code: (i) Inline graphic .

Acknowledgments

The purchase of the diffractometer was made possible by grant No. LEQSF(1999–2000)-ENH-TR-13, administered by the Louisiana Board of Regents.

supplementary crystallographic information

Comment

Di(5-benzyloxycarbornyl-3,4-dimethyl-2-pyrrolyl)-ethyne (I) is an important intermediate in the synthesis of porphyrin analogues containing a two-carbon interpyrrolic bridge as in corrphycenes (Vogel, 1996). Compound (I) is also an interesting intermediate in the synthesis of dipyrroles with a two carbon bridge, which have shown selective binding properties to fluoride and other ions (Black et al. 1999). The title compound was prepared via an improved Sonogashira coupling reaction (Chinchilla & Najera, 2007), that took place between benzyl 5-iodo-3,4-dimethyl-1H-pyrrole-2-carboxylate and trimethylsilanyl-ethyne, in the presence of palladium(0) and copper(I) catalysts at room temperature. The exact experimental details are described below.

The structure of the title compound (I), which lies on a crystallographic twofold axis, is shown in Fig 1. The triple-bond distance is 1.2088 (17) Å, and the alkyne bridge is not quite linear, with C4—C5—C5ⁱ angle 175.61 (10)° (i = 1 - x, y, 1/2 - z). The pyrrole ring is essentially planar, its five atoms having a mean deviation 0.003 Å from their best plane, with maximum 0.0051 (7) Å for C4. The two pyrrole rings are not coplanar, but form a dihedral angle of 40.49 (4)°. The ester COO group lies nearly in the pyrrole plane, with N1—C1—C6—O2 torsion angle 3.67 (13)°.

The pyrrole N—H group and adjacent ester carbonyl form intermolecular hydrogen bonded rings about inversion centers, having graph-set notation (Etter, 1990) R₂²(10). Thus, each molecule engages in four hydrogen bonds with two other molecules, forming chains in the [0 0 1] direction, as shown in Fig. 2.

Experimental

To a 100 ml round bottom flask was added benzyl 5-iodo-3,4-dimethyl-1H-pyrrole-2-carboxylate (2.93 g, 10 mmol) followed by Pd(PPh)₂Cl₂ (0.7019 g, 0.1 mmol) and CuI (0.191 g 0.1 mmol). The flask was sealed and placed in a dry ice bath under N₂. Trimethylsilanyl-ethyne (0.6996 ml, 5 mmol), DBU (8.973 ml, 60 mmol) and water (0.072 ml, 40 molar equiv.) were dissolved in 30 ml of acetonitrile and added to the reaction flask. After the mixture froze in the dry ice bath, the flask was evacuated and N₂ gas added. The resulting reaction mixture was allowed to warm slowly to room temperature and was stirred until complete disappearance of the starting material by TLC. The reaction mixture was worked up by adding ethyl acetate (150 ml), and washing the organic layer three times with saline. The organic phase was dried over anhydrous sodium bicarbonate and concentrated under reduced pressure. The crude mixture was purified by flash column chromatography using hexane/ethyl acetate (5:1) for elution. The dipyrrole-ethyne (I) was obtained (0.755 g) in 54% yield and recrystallized from dichloromethane to afford colorless crystals. Spectroscopic analysis, ¹H NMR (250 MHz, CDCl₃, 293 K, δ): 11.99 (2H, s, NH), 7.47–7.32 (10H, m, Ar—H), 5.29 (4H, s, CH₂), 2.2 (6H, s, CH₃), 2.0 (6H, s, CH₃). MS (EI) m/z: 480.129 (M⁺).