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Acta Crystallogr Sect E Struct Rep Online. 2008 October 1; 64(Pt 10): o1989.
Published online 2008 September 24. doi:  10.1107/S1600536808029929
PMCID: PMC2959273

Ethyl 3,5-dimethyl-1H-pyrrole-2-carboxyl­ate

Abstract

In the title compound, C9H13NO2, there are two independent mol­ecules per asymmetric unit. The mol­ecules are very similar and almost planar, with the ethoxy­carbonyl group anti to the pyrrole N atom. The two independent mol­ecules are joined into dimeric units by strong hydrogen bonds between NH groups and carbonyl O atoms.

Related literature

For general background, see: Bonnett (1995 [triangle], 2000 [triangle]). For related structures, see: Paixão et al. (2002 [triangle]), Ramos Silva et al. (2002 [triangle]); Sobral & Rocha Gonsalves (2001 [triangle]).

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Object name is e-64-o1989-scheme1.jpg

Experimental

Crystal data

  • C9H13NO2
  • M r = 167.20
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1989-efi1.jpg
  • a = 8.1357 (2) Å
  • b = 10.5568 (2) Å
  • c = 12.1428 (2) Å
  • α = 101.5451 (13)°
  • β = 97.8791 (14)°
  • γ = 110.4821 (14)°
  • V = 932.52 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 293 (2) K
  • 0.25 × 0.20 × 0.15 mm

Data collection

  • Bruker APEX CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2000 [triangle]) T min = 0.899, T max = 0.987
  • 20370 measured reflections
  • 4456 independent reflections
  • 2368 reflections with I > 2σ(I)
  • R int = 0.028

Refinement

  • R[F 2 > 2σ(F 2)] = 0.052
  • wR(F 2) = 0.182
  • S = 1.03
  • 4456 reflections
  • 223 parameters
  • H-atom parameters constrained
  • Δρmax = 0.20 e Å−3
  • Δρmin = −0.21 e Å−3

Data collection: SMART (Bruker, 2003 [triangle]); cell refinement: SAINT (Bruker, 2003 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEPII (Johnson, 1976 [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/S1600536808029929/bt2791sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808029929/bt2791Isup2.hkl

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

Acknowledgments

This work was supported by Fundação para a Ciência e a Tecnologia (FCT) under project POCI/AMB/55281/2004.

supplementary crystallographic information

Comment

Photodynamic therapy (PDT) is a developing method for the treatment of carcinomas and sarcomas. It consists in a selective absorption of a photosensitizer in a tumor, followed by irradiation with light of a selected wavelength, originating tumor necrosis. The fewer side effects of this therapeutic method when compared to chemotherapy and radiotherapy have prompted the search for new and more efficient photosensitizers, namely porphyrins (Bonnett, 1995, 2000). Pyrroles are building blocks for the synthesis of porphyrins and following our previous structural studies on pyrrole chemistry (Sobral & Rocha Gonsalves, 2001; Ramos Silva et al., 2002; Paixão et al., 2002) we present here the title compound ethyl 3,5-dimethyl-1H-pyrrole-2-carboxylate, (I), Fig. 1. There are two independent molecules per asymmetric unit. The two molecules are very similar and almost planar with the angle between molecular planes being 3.87 (5)°. The molecules show an eclipsed conformation, when viewed along the C1—C7 direction, with the ethoxycarbonylgroup anti to the pyrrole N atom. The molecules are grouped in dimers by strong hydrogen bonds between N—H groups and carbonyl O atoms (Fig.1, Table 1). The dimers stack in planes approximately 5 Å apart (Fig.2).

Experimental

The ethyl 3,5-dimethyl-1H-pyrrole-2-carboxylate was prepared by a Knorr-type reaction from the condensation of acetylacetone and ethyl oximinoacetoacetate.

Refinement

All H-atoms were positioned geometrically and refined using a riding model with C—H=0.93 Å, N—H=0.86 Å, Uiso(H)=1.2Ueq(C,N).

Figures

Fig. 1.
ORTEPII (Johnson, 1976) plot of the title compound. Displacement ellipsoids are drawn at the 50% level. The H-bonds are represented as dashed lines.
Fig. 2.
Packing diagram of the title compound.

Crystal data

C9H13NO2Z = 4
Mr = 167.20F(000) = 360
Triclinic, P1Dx = 1.191 Mg m3
a = 8.1357 (2) ÅMo Kα radiation, λ = 0.71073 Å
b = 10.5568 (2) ÅCell parameters from 3873 reflections
c = 12.1428 (2) Åθ = 2.4–23.9°
α = 101.5451 (13)°µ = 0.08 mm1
β = 97.8791 (14)°T = 293 K
γ = 110.4821 (14)°Prism, colourless
V = 932.52 (4) Å30.25 × 0.20 × 0.15 mm

Data collection

Bruker APEX CCD area-detector diffractometer4456 independent reflections
Radiation source: fine-focus sealed tube2368 reflections with I > 2σ(I)
graphiteRint = 0.028
[var phi] and ω scansθmax = 28.0°, θmin = 1.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)h = −10→10
Tmin = 0.899, Tmax = 0.987k = −13→13
20370 measured reflectionsl = −15→15

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.182H-atom parameters constrained
S = 1.03w = 1/[σ2(Fo2) + (0.0939P)2 + 0.0508P] where P = (Fo2 + 2Fc2)/3
4456 reflections(Δ/σ)max < 0.001
223 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = −0.21 e Å3

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
N10.2122 (2)0.18401 (15)0.96119 (12)0.0526 (4)
H10.14720.16890.89410.063*
C10.2894 (2)0.31179 (18)1.04326 (14)0.0483 (4)
C20.3837 (3)0.29357 (19)1.13867 (15)0.0535 (5)
C30.3587 (3)0.1515 (2)1.11083 (17)0.0620 (5)
H30.40600.10831.15890.074*
C40.2537 (3)0.08658 (19)1.00165 (17)0.0561 (5)
C50.1877 (3)−0.0621 (2)0.92988 (19)0.0745 (6)
H5A0.0653−0.09120.88910.112*
H5B0.1938−0.12180.97900.112*
H5C0.2617−0.06840.87560.112*
C60.4927 (3)0.4029 (2)1.24868 (16)0.0700 (6)
H6A0.59410.47161.23310.105*
H6B0.53460.35941.30240.105*
H6C0.41930.44761.28100.105*
C70.2626 (2)0.43124 (19)1.01696 (15)0.0497 (4)
C80.3246 (3)0.67311 (19)1.08651 (16)0.0598 (5)
H8A0.19870.65981.07440.072*
H8B0.36850.69561.01960.072*
C90.4325 (3)0.7891 (2)1.19379 (19)0.0736 (6)
H9A0.39010.76421.25950.110*
H9B0.41910.87421.18690.110*
H9C0.55730.80301.20350.110*
O10.34589 (17)0.54785 (12)1.10374 (10)0.0571 (4)
O20.1739 (2)0.42886 (14)0.92727 (11)0.0697 (4)
N2−0.03335 (19)0.33131 (15)0.69754 (12)0.0514 (4)
H20.03410.34550.76350.062*
C10−0.0692 (3)0.43124 (19)0.65748 (16)0.0532 (5)
C11−0.1793 (3)0.3672 (2)0.54923 (17)0.0581 (5)
H11−0.22370.41200.50120.070*
C12−0.2140 (2)0.22325 (19)0.52282 (15)0.0511 (5)
C13−0.1210 (2)0.20295 (18)0.61697 (14)0.0470 (4)
C14−0.3308 (3)0.1161 (2)0.41335 (16)0.0666 (6)
H14A−0.26760.06060.38290.100*
H14B−0.36000.16280.35800.100*
H14C−0.43970.05640.42900.100*
C150.0049 (3)0.58075 (19)0.72855 (18)0.0681 (6)
H15A−0.06670.59100.78370.102*
H15B0.00180.64070.67910.102*
H15C0.12700.60630.76840.102*
C16−0.1000 (3)0.08222 (19)0.64427 (15)0.0525 (5)
C17−0.1825 (3)−0.16323 (19)0.58381 (18)0.0635 (5)
H17A−0.2223−0.17720.65380.076*
H17B−0.0591−0.15650.59330.076*
C18−0.3012 (3)−0.2831 (2)0.4826 (2)0.0777 (7)
H18A−0.4226−0.28800.47340.116*
H18B−0.2979−0.36910.49530.116*
H18C−0.2593−0.26900.41410.116*
O3−0.19388 (17)−0.03673 (13)0.56183 (10)0.0574 (4)
O4−0.0063 (2)0.08520 (14)0.73228 (12)0.0806 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0640 (10)0.0477 (9)0.0397 (8)0.0212 (8)0.0025 (7)0.0053 (7)
C10.0532 (10)0.0434 (10)0.0407 (9)0.0155 (8)0.0037 (8)0.0055 (8)
C20.0575 (11)0.0533 (11)0.0445 (10)0.0198 (9)0.0041 (8)0.0099 (8)
C30.0759 (14)0.0568 (12)0.0565 (12)0.0307 (11)0.0067 (10)0.0189 (10)
C40.0674 (12)0.0478 (11)0.0552 (11)0.0256 (9)0.0123 (9)0.0133 (9)
C50.0935 (16)0.0467 (12)0.0772 (15)0.0282 (11)0.0119 (12)0.0069 (10)
C60.0797 (15)0.0690 (14)0.0472 (11)0.0236 (11)−0.0088 (10)0.0103 (10)
C70.0534 (11)0.0470 (11)0.0408 (10)0.0160 (8)0.0037 (8)0.0059 (8)
C80.0741 (13)0.0482 (11)0.0566 (12)0.0256 (10)0.0108 (10)0.0124 (9)
C90.0911 (16)0.0509 (12)0.0669 (14)0.0229 (11)0.0142 (12)0.0014 (10)
O10.0726 (9)0.0436 (7)0.0455 (7)0.0207 (6)−0.0015 (6)0.0050 (6)
O20.0918 (11)0.0559 (8)0.0498 (8)0.0314 (8)−0.0130 (7)0.0039 (6)
N20.0561 (9)0.0459 (9)0.0428 (8)0.0157 (7)0.0011 (7)0.0061 (7)
C100.0583 (11)0.0456 (11)0.0535 (11)0.0191 (9)0.0097 (9)0.0126 (9)
C110.0639 (12)0.0531 (12)0.0538 (11)0.0222 (9)0.0002 (9)0.0166 (9)
C120.0511 (10)0.0515 (11)0.0439 (10)0.0166 (9)0.0035 (8)0.0089 (8)
C130.0496 (10)0.0423 (10)0.0403 (9)0.0133 (8)0.0035 (8)0.0050 (7)
C140.0691 (13)0.0649 (13)0.0491 (11)0.0186 (11)−0.0086 (10)0.0081 (10)
C150.0796 (15)0.0451 (12)0.0702 (13)0.0218 (10)0.0066 (11)0.0068 (10)
C160.0580 (11)0.0476 (11)0.0426 (10)0.0169 (9)0.0017 (9)0.0050 (8)
C170.0701 (13)0.0484 (12)0.0643 (13)0.0226 (10)0.0037 (10)0.0073 (10)
C180.0850 (16)0.0475 (12)0.0825 (16)0.0204 (11)0.0047 (12)−0.0019 (11)
O30.0664 (8)0.0428 (7)0.0508 (8)0.0179 (6)−0.0027 (6)0.0029 (6)
O40.1088 (12)0.0548 (9)0.0572 (9)0.0290 (8)−0.0237 (8)0.0037 (7)

Geometric parameters (Å, °)

N1—C41.346 (2)N2—C101.348 (2)
N1—C11.380 (2)N2—C131.380 (2)
N1—H10.8600N2—H20.8600
C1—C21.384 (2)C10—C111.373 (3)
C1—C71.440 (2)C10—C151.498 (2)
C2—C31.404 (3)C11—C121.405 (2)
C2—C61.498 (3)C11—H110.9300
C3—C41.369 (3)C12—C131.378 (2)
C3—H30.9300C12—C141.500 (2)
C4—C51.498 (3)C13—C161.438 (3)
C5—H5A0.9600C14—H14A0.9600
C5—H5B0.9600C14—H14B0.9600
C5—H5C0.9600C14—H14C0.9600
C6—H6A0.9600C15—H15A0.9600
C6—H6B0.9600C15—H15B0.9600
C6—H6C0.9600C15—H15C0.9600
C7—O21.212 (2)C16—O41.213 (2)
C7—O11.336 (2)C16—O31.333 (2)
C8—O11.443 (2)C17—O31.444 (2)
C8—C91.504 (3)C17—C181.497 (3)
C8—H8A0.9700C17—H17A0.9700
C8—H8B0.9700C17—H17B0.9700
C9—H9A0.9600C18—H18A0.9600
C9—H9B0.9600C18—H18B0.9600
C9—H9C0.9600C18—H18C0.9600
C4—N1—C1109.98 (15)C10—N2—C13109.89 (15)
C4—N1—H1125.0C10—N2—H2125.1
C1—N1—H1125.0C13—N2—H2125.1
N1—C1—C2107.62 (15)N2—C10—C11107.26 (16)
N1—C1—C7119.00 (15)N2—C10—C15121.47 (17)
C2—C1—C7133.38 (16)C11—C10—C15131.26 (18)
C1—C2—C3105.90 (16)C10—C11—C12108.90 (17)
C1—C2—C6127.36 (17)C10—C11—H11125.6
C3—C2—C6126.73 (17)C12—C11—H11125.6
C4—C3—C2109.18 (17)C13—C12—C11106.15 (16)
C4—C3—H3125.4C13—C12—C14128.26 (17)
C2—C3—H3125.4C11—C12—C14125.59 (17)
N1—C4—C3107.32 (16)C12—C13—N2107.79 (15)
N1—C4—C5121.31 (18)C12—C13—C16133.95 (16)
C3—C4—C5131.37 (19)N2—C13—C16118.26 (15)
C4—C5—H5A109.5C12—C14—H14A109.5
C4—C5—H5B109.5C12—C14—H14B109.5
H5A—C5—H5B109.5H14A—C14—H14B109.5
C4—C5—H5C109.5C12—C14—H14C109.5
H5A—C5—H5C109.5H14A—C14—H14C109.5
H5B—C5—H5C109.5H14B—C14—H14C109.5
C2—C6—H6A109.5C10—C15—H15A109.5
C2—C6—H6B109.5C10—C15—H15B109.5
H6A—C6—H6B109.5H15A—C15—H15B109.5
C2—C6—H6C109.5C10—C15—H15C109.5
H6A—C6—H6C109.5H15A—C15—H15C109.5
H6B—C6—H6C109.5H15B—C15—H15C109.5
O2—C7—O1122.56 (16)O4—C16—O3121.97 (17)
O2—C7—C1124.92 (16)O4—C16—C13124.71 (16)
O1—C7—C1112.52 (15)O3—C16—C13113.32 (15)
O1—C8—C9106.73 (15)O3—C17—C18107.56 (16)
O1—C8—H8A110.4O3—C17—H17A110.2
C9—C8—H8A110.4C18—C17—H17A110.2
O1—C8—H8B110.4O3—C17—H17B110.2
C9—C8—H8B110.4C18—C17—H17B110.2
H8A—C8—H8B108.6H17A—C17—H17B108.5
C8—C9—H9A109.5C17—C18—H18A109.5
C8—C9—H9B109.5C17—C18—H18B109.5
H9A—C9—H9B109.5H18A—C18—H18B109.5
C8—C9—H9C109.5C17—C18—H18C109.5
H9A—C9—H9C109.5H18A—C18—H18C109.5
H9B—C9—H9C109.5H18B—C18—H18C109.5
C7—O1—C8116.76 (13)C16—O3—C17116.64 (14)
C4—N1—C1—C20.3 (2)C13—N2—C10—C11−0.8 (2)
C4—N1—C1—C7179.58 (15)C13—N2—C10—C15178.44 (16)
N1—C1—C2—C3−0.4 (2)N2—C10—C11—C120.8 (2)
C7—C1—C2—C3−179.57 (19)C15—C10—C11—C12−178.28 (19)
N1—C1—C2—C6178.72 (18)C10—C11—C12—C13−0.6 (2)
C7—C1—C2—C6−0.4 (3)C10—C11—C12—C14179.03 (18)
C1—C2—C3—C40.4 (2)C11—C12—C13—N20.1 (2)
C6—C2—C3—C4−178.74 (19)C14—C12—C13—N2−179.49 (17)
C1—N1—C4—C30.0 (2)C11—C12—C13—C16−179.8 (2)
C1—N1—C4—C5−179.76 (16)C14—C12—C13—C160.6 (3)
C2—C3—C4—N1−0.3 (2)C10—N2—C13—C120.4 (2)
C2—C3—C4—C5179.4 (2)C10—N2—C13—C16−179.68 (15)
N1—C1—C7—O21.0 (3)C12—C13—C16—O4177.7 (2)
C2—C1—C7—O2−179.9 (2)N2—C13—C16—O4−2.2 (3)
N1—C1—C7—O1−179.56 (14)C12—C13—C16—O3−1.7 (3)
C2—C1—C7—O1−0.5 (3)N2—C13—C16—O3178.41 (15)
O2—C7—O1—C80.4 (3)O4—C16—O3—C171.7 (3)
C1—C7—O1—C8−178.98 (15)C13—C16—O3—C17−178.86 (15)
C9—C8—O1—C7−178.86 (15)C18—C17—O3—C16178.37 (16)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O40.862.022.857 (2)166.
N2—H2···O20.862.002.834 (2)163.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT2791).

References

  • Bonnett, R. (1995). Chem. Soc. Rev.24, 19–33.
  • Bonnett, R. (2000). Chemical Aspects of Photodynamic Therapy Amsterdam: Gordon and Breach Science Publishers.
  • Bruker (2003). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Johnson, C. K. (1976). ORTEPII Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.
  • Paixão, J. A., Ramos Silva, M., Matos Beja, A., Sobral, A. J. F. N., Lopes, S. H. & Rocha Gonsalves, A. M. d′A. (2002). Acta Cryst. C58, o721–o723. [PubMed]
  • Ramos Silva, M., Matos Beja, A., Paixão, J. A., Sobral, A. J. F. N., Lopes, S. H. & Rocha Gonsalves, A. M. d′A. (2002). Acta Cryst. C58, o572–o574. [PubMed]
  • Sheldrick, G. M. (2000). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Sobral, A. J. F. N. & Rocha Gonsalves, A. M. d′A. (2001). J. Porphyrins Phthalocyanines, 5, 861–866.

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