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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o75.
Published online 2007 December 6. doi:  10.1107/S1600536807061739
PMCID: PMC2915032

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

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 [triangle]); Black et al. (1999 [triangle]); Etter (1990 [triangle]); Vogel (1996 [triangle]). For related structures, see: Xie et al. (1996 [triangle]); Weghorn et al. (1995 [triangle]).

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Object name is e-64-00o75-scheme1.jpg

Experimental

Crystal data

  • C30H28N2O4
  • M r = 480.54
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-00o75-efi1.jpg
  • 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
  • Δρmax = 0.46 e Å−3
  • Δρmin = −0.39 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

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

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+).

Refinement

H atoms were placed in idealized positions with C—H distances 0.95 - 0.99 Å and thereafter treated as riding. Uiso for H was assigned as 1.2 times Ueq of the attached C atoms (1.5 for methyl). A torsional parameter was refined for each methyl group.

Figures

Fig. 1.
Ellipsoids at the 50% level, with the asymmetric unit labeled. H atoms are represented with arbitrary radius.
Fig. 2.
View down the twofold axis, showing hydrogen bonding.

Crystal data

C30H28N2O4F000 = 1016
Mr = 480.54Dx = 1.283 Mg m3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 4869 reflections
a = 19.340 (2) Åθ = 2.5–33.1º
b = 9.8955 (10) ŵ = 0.09 mm1
c = 13.8495 (15) ÅT = 90 K
β = 110.217 (6)ºPrism, colorless
V = 2487.2 (5) Å30.30 × 0.22 × 0.15 mm
Z = 4

Data collection

Nonius KappaCCD (with Oxford Cryostream) diffractometer3948 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.022
Monochromator: graphiteθmax = 33.2º
T = 90 Kθmin = 2.6º
ω scans with κ offsetsh = −29→29
Absorption correction: nonek = −15→15
28071 measured reflectionsl = −21→21
4748 independent reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.044H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.124  w = 1/[σ2(Fo2) + (0.067P)2 + 1.378P] where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max < 0.001
4748 reflectionsΔρmax = 0.46 e Å3
168 parametersΔρmin = −0.39 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
O10.38808 (4)0.18151 (7)0.63308 (5)0.01536 (14)
O20.45716 (4)0.03182 (7)0.58415 (5)0.01670 (14)
N10.46808 (4)0.21012 (7)0.43512 (5)0.01204 (14)
H1N0.4897 (7)0.1328 (14)0.4339 (10)0.014*
C10.43250 (5)0.24465 (9)0.50220 (6)0.01179 (15)
C20.40633 (5)0.37712 (9)0.48108 (6)0.01253 (15)
C30.42701 (5)0.42307 (8)0.39832 (6)0.01261 (15)
C40.46445 (5)0.31725 (8)0.37111 (6)0.01224 (15)
C50.49073 (5)0.31065 (9)0.28744 (6)0.01342 (15)
C60.42810 (5)0.14317 (8)0.57551 (6)0.01202 (15)
C70.36367 (5)0.45910 (9)0.53229 (7)0.01701 (17)
H7A0.39740.51870.58380.026*
H7B0.33890.39850.56600.026*
H7C0.32680.51370.48060.026*
C80.40864 (6)0.55667 (9)0.34548 (7)0.01793 (17)
H8A0.43580.56730.29790.027*
H8B0.42250.62920.39680.027*
H8C0.35560.56120.30710.027*
C90.37901 (5)0.07780 (9)0.70202 (7)0.01577 (16)
H9A0.42740.05530.75430.019*
H9B0.3584−0.00520.66270.019*
C100.32768 (5)0.13018 (9)0.75362 (6)0.01280 (15)
C110.26606 (5)0.20803 (9)0.70116 (7)0.01592 (16)
H110.25720.23370.63180.019*
C120.21747 (5)0.24831 (10)0.74984 (8)0.01892 (18)
H120.17610.30270.71410.023*
C130.22929 (6)0.20909 (11)0.85086 (8)0.0228 (2)
H130.19540.23460.88350.027*
C140.29082 (6)0.13248 (11)0.90349 (8)0.0235 (2)
H140.29920.10580.97250.028*
C150.34045 (5)0.09438 (10)0.85570 (7)0.01773 (17)
H150.38310.04380.89280.021*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0226 (3)0.0130 (3)0.0161 (3)0.0032 (2)0.0138 (2)0.0026 (2)
O20.0229 (3)0.0139 (3)0.0171 (3)0.0063 (2)0.0118 (2)0.0028 (2)
N10.0154 (3)0.0107 (3)0.0129 (3)0.0023 (2)0.0085 (2)0.0010 (2)
C10.0147 (3)0.0117 (3)0.0115 (3)0.0011 (3)0.0077 (3)−0.0001 (3)
C20.0151 (3)0.0117 (3)0.0128 (3)0.0017 (3)0.0074 (3)−0.0004 (3)
C30.0151 (4)0.0111 (3)0.0132 (3)0.0015 (3)0.0069 (3)0.0005 (3)
C40.0145 (3)0.0119 (3)0.0124 (3)0.0002 (3)0.0073 (3)0.0006 (3)
C50.0149 (4)0.0125 (3)0.0147 (3)0.0001 (3)0.0075 (3)0.0000 (3)
C60.0142 (3)0.0127 (3)0.0107 (3)0.0010 (3)0.0063 (3)0.0001 (3)
C70.0224 (4)0.0148 (4)0.0183 (4)0.0043 (3)0.0127 (3)−0.0008 (3)
C80.0241 (4)0.0128 (4)0.0192 (4)0.0035 (3)0.0105 (3)0.0038 (3)
C90.0220 (4)0.0145 (4)0.0152 (3)0.0034 (3)0.0119 (3)0.0038 (3)
C100.0159 (4)0.0120 (3)0.0128 (3)−0.0016 (3)0.0080 (3)−0.0005 (3)
C110.0158 (4)0.0180 (4)0.0145 (3)−0.0009 (3)0.0060 (3)−0.0004 (3)
C120.0155 (4)0.0186 (4)0.0248 (4)−0.0006 (3)0.0095 (3)−0.0019 (3)
C130.0274 (5)0.0211 (4)0.0285 (5)−0.0009 (4)0.0209 (4)−0.0028 (4)
C140.0351 (5)0.0238 (5)0.0190 (4)0.0027 (4)0.0188 (4)0.0021 (4)
C150.0240 (4)0.0169 (4)0.0150 (4)0.0026 (3)0.0101 (3)0.0020 (3)

Geometric parameters (Å, °)

O1—C61.3436 (10)C8—H8A0.9800
O1—C91.4530 (10)C8—H8B0.9800
O2—C61.2240 (10)C8—H8C0.9800
N1—C41.3680 (11)C9—C101.5018 (12)
N1—C11.3767 (10)C9—H9A0.9900
N1—H1N0.875 (14)C9—H9B0.9900
C1—C21.3992 (12)C10—C111.3940 (12)
C1—C61.4514 (11)C10—C151.3941 (12)
C2—C31.4133 (11)C11—C121.3910 (13)
C2—C71.4987 (12)C11—H110.9500
C3—C41.3969 (12)C12—C131.3925 (15)
C3—C81.4932 (12)C12—H120.9500
C4—C51.4185 (12)C13—C141.3866 (16)
C5—C5i1.2088 (17)C13—H130.9500
C7—H7A0.9800C14—C151.3931 (13)
C7—H7B0.9800C14—H140.9500
C7—H7C0.9800C15—H150.9500
C6—O1—C9114.55 (7)H8A—C8—H8B109.5
C4—N1—C1108.62 (7)C3—C8—H8C109.5
C4—N1—H1N125.7 (8)H8A—C8—H8C109.5
C1—N1—H1N125.7 (8)H8B—C8—H8C109.5
N1—C1—C2108.70 (7)O1—C9—C10108.58 (7)
N1—C1—C6117.66 (7)O1—C9—H9A110.0
C2—C1—C6133.63 (7)C10—C9—H9A110.0
C1—C2—C3106.71 (7)O1—C9—H9B110.0
C1—C2—C7128.81 (8)C10—C9—H9B110.0
C3—C2—C7124.47 (8)H9A—C9—H9B108.4
C4—C3—C2107.22 (7)C11—C10—C15119.27 (8)
C4—C3—C8126.09 (8)C11—C10—C9121.96 (7)
C2—C3—C8126.60 (8)C15—C10—C9118.70 (8)
N1—C4—C3108.75 (7)C12—C11—C10120.32 (8)
N1—C4—C5122.75 (8)C12—C11—H11119.8
C3—C4—C5128.34 (8)C10—C11—H11119.8
C5i—C5—C4175.61 (10)C11—C12—C13120.22 (9)
O2—C6—O1122.38 (8)C11—C12—H12119.9
O2—C6—C1123.73 (8)C13—C12—H12119.9
O1—C6—C1113.89 (7)C14—C13—C12119.58 (9)
C2—C7—H7A109.5C14—C13—H13120.2
C2—C7—H7B109.5C12—C13—H13120.2
H7A—C7—H7B109.5C13—C14—C15120.35 (9)
C2—C7—H7C109.5C13—C14—H14119.8
H7A—C7—H7C109.5C15—C14—H14119.8
H7B—C7—H7C109.5C14—C15—C10120.22 (9)
C3—C8—H8A109.5C14—C15—H15119.9
C3—C8—H8B109.5C10—C15—H15119.9
C4—N1—C1—C2−0.61 (10)C9—O1—C6—C1176.08 (7)
C4—N1—C1—C6178.33 (7)N1—C1—C6—O23.67 (13)
N1—C1—C2—C30.08 (10)C2—C1—C6—O2−177.72 (9)
C6—C1—C2—C3−178.63 (9)N1—C1—C6—O1−175.51 (7)
N1—C1—C2—C7179.36 (9)C2—C1—C6—O13.10 (14)
C6—C1—C2—C70.65 (16)C6—O1—C9—C10−174.76 (7)
C1—C2—C3—C40.47 (10)O1—C9—C10—C1138.88 (11)
C7—C2—C3—C4−178.85 (8)O1—C9—C10—C15−144.09 (8)
C1—C2—C3—C8177.24 (9)C15—C10—C11—C12−0.68 (14)
C7—C2—C3—C8−2.09 (14)C9—C10—C11—C12176.33 (9)
C1—N1—C4—C30.92 (10)C10—C11—C12—C13−1.15 (14)
C1—N1—C4—C5−174.76 (8)C11—C12—C13—C141.62 (16)
C2—C3—C4—N1−0.86 (10)C12—C13—C14—C15−0.25 (16)
C8—C3—C4—N1−177.64 (8)C13—C14—C15—C10−1.59 (16)
C2—C3—C4—C5174.51 (8)C11—C10—C15—C142.04 (14)
C8—C3—C4—C5−2.28 (15)C9—C10—C15—C14−175.07 (9)
C9—O1—C6—O2−3.12 (12)

Symmetry codes: (i) −x+1, y, −z+1/2.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···O2ii0.875 (14)1.987 (14)2.8565 (10)172.1 (12)

Symmetry codes: (ii) −x+1, −y, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2299).

References

  • Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst.32, 115–119.
  • Black, C. B., Andrioletti, B., Try, A. C., Ruiperez, C. & Sessler, J. L. (1999). J. Am. Chem. Soc.121, 10438–10439.
  • Chinchilla, R. & Najera, C. (2007). Chem. Rev.107, 874–922. [PubMed]
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  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
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  • Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.
  • Sheldrick, G. M. (1997). SHELXL97 University of Göttingen, Germany. [PubMed]
  • Vogel, E. (1996). Pure Appl. Chem.68, 1355–1360.
  • Weghorn, S. J., Lynch, V. & Sessler, J. L. (1995). Tetrahedron Lett.36, 4713–4716.
  • Xie, H., Lee, D. A., Wallace, D. M., Senge, O. M. & Smith, K. M. (1996). J. Org. Chem.61, 8508–8517.

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