organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

aChemistry Department, University of Coimbra, P-3004-535 Coimbra, Portugal, and bCEMDRX, Physics Department, University of Coimbra, P-3004-516 Coimbra, Portugal
*Correspondence e-mail: manuela@pollux.fis.uc.pt

(Received 15 September 2008; accepted 17 September 2008; online 24 September 2008)

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[Bonnett, R. (1995). Chem. Soc. Rev. 24, 19-33.], 2000[Bonnett, R. (2000). Chemical Aspects of Photodynamic Therapy. Amsterdam: Gordon and Breach Science Publishers.]). For related structures, see: Paixão et al. (2002[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.]), Ramos Silva et al. (2002[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.]); Sobral & Rocha Gonsalves (2001[Sobral, A. J. F. N. & Rocha Gonsalves, A. M. d′A. (2001). J. Porphyrins Phthalocyanines, 5, 861-866.]).

[Scheme 1]

Experimental

Crystal data
  • C9H13NO2

  • Mr = 167.20

  • Triclinic, [P \overline 1]

  • 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[Sheldrick, G. M. (2000). SADABS. University of Göttingen, Germany.]) Tmin = 0.899, Tmax = 0.987

  • 20370 measured reflections

  • 4456 independent reflections

  • 2368 reflections with I > 2σ(I)

  • Rint = 0.028

Refinement
  • R[F2 > 2σ(F2)] = 0.052

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O4 0.86 2.02 2.857 (2) 166
N2—H2⋯O2 0.86 2.00 2.834 (2) 163

Data collection: SMART (Bruker, 2003[Bruker (2003). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2003[Bruker (2003). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEPII (Johnson, 1976[Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

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).

Related literature top

For related literature, see: Paixão et al. (2002), Ramos Silva et al. (2002); Sobral & Rocha Gonsalves (2001); Bonnett (1995, 2000).

Experimental top

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 top

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).

Computing details top

Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT (Bruker, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. Packing diagram of the title compound.
Ethyl 3,5-dimethyl-1H-pyrrole-2-carboxylate top
Crystal data top
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 top
Bruker APEX CCD area-detector
diffractometer
4456 independent reflections
Radiation source: fine-focus sealed tube2368 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.028
ϕ and ω scansθmax = 28.0°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2000)
h = 1010
Tmin = 0.899, Tmax = 0.987k = 1313
20370 measured reflectionsl = 1515
Refinement top
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 = 1.03 w = 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
Crystal data top
C9H13NO2γ = 110.4821 (14)°
Mr = 167.20V = 932.52 (4) Å3
Triclinic, P1Z = 4
a = 8.1357 (2) ÅMo Kα radiation
b = 10.5568 (2) ŵ = 0.08 mm1
c = 12.1428 (2) ÅT = 293 K
α = 101.5451 (13)°0.25 × 0.20 × 0.15 mm
β = 97.8791 (14)°
Data collection top
Bruker APEX CCD area-detector
diffractometer
4456 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2000)
2368 reflections with I > 2σ(I)
Tmin = 0.899, Tmax = 0.987Rint = 0.028
20370 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.182H-atom parameters constrained
S = 1.03Δρmax = 0.20 e Å3
4456 reflectionsΔρmin = 0.21 e Å3
223 parameters
Special details top

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) top
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)
H5A0.06530.09120.88910.112*
H5B0.19380.12180.97900.112*
H5C0.26170.06840.87560.112*
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)
N20.03335 (19)0.33131 (15)0.69754 (12)0.0514 (4)
H20.03410.34550.76350.062*
C100.0692 (3)0.43124 (19)0.65748 (16)0.0532 (5)
C110.1793 (3)0.3672 (2)0.54923 (17)0.0581 (5)
H110.22370.41200.50120.070*
C120.2140 (2)0.22325 (19)0.52282 (15)0.0511 (5)
C130.1210 (2)0.20295 (18)0.61697 (14)0.0470 (4)
C140.3308 (3)0.1161 (2)0.41335 (16)0.0666 (6)
H14A0.26760.06060.38290.100*
H14B0.36000.16280.35800.100*
H14C0.43970.05640.42900.100*
C150.0049 (3)0.58075 (19)0.72855 (18)0.0681 (6)
H15A0.06670.59100.78370.102*
H15B0.00180.64070.67910.102*
H15C0.12700.60630.76840.102*
C160.1000 (3)0.08222 (19)0.64427 (15)0.0525 (5)
C170.1825 (3)0.16323 (19)0.58381 (18)0.0635 (5)
H17A0.22230.17720.65380.076*
H17B0.05910.15650.59330.076*
C180.3012 (3)0.2831 (2)0.4826 (2)0.0777 (7)
H18A0.42260.28800.47340.116*
H18B0.29790.36910.49530.116*
H18C0.25930.26900.41410.116*
O30.19388 (17)0.03673 (13)0.56183 (10)0.0574 (4)
O40.0063 (2)0.08520 (14)0.73228 (12)0.0806 (5)
Atomic displacement parameters (Å2) top
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, º) top
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—C110.8 (2)
C4—N1—C1—C7179.58 (15)C13—N2—C10—C15178.44 (16)
N1—C1—C2—C30.4 (2)N2—C10—C11—C120.8 (2)
C7—C1—C2—C3179.57 (19)C15—C10—C11—C12178.28 (19)
N1—C1—C2—C6178.72 (18)C10—C11—C12—C130.6 (2)
C7—C1—C2—C60.4 (3)C10—C11—C12—C14179.03 (18)
C1—C2—C3—C40.4 (2)C11—C12—C13—N20.1 (2)
C6—C2—C3—C4178.74 (19)C14—C12—C13—N2179.49 (17)
C1—N1—C4—C30.0 (2)C11—C12—C13—C16179.8 (2)
C1—N1—C4—C5179.76 (16)C14—C12—C13—C160.6 (3)
C2—C3—C4—N10.3 (2)C10—N2—C13—C120.4 (2)
C2—C3—C4—C5179.4 (2)C10—N2—C13—C16179.68 (15)
N1—C1—C7—O21.0 (3)C12—C13—C16—O4177.7 (2)
C2—C1—C7—O2179.9 (2)N2—C13—C16—O42.2 (3)
N1—C1—C7—O1179.56 (14)C12—C13—C16—O31.7 (3)
C2—C1—C7—O10.5 (3)N2—C13—C16—O3178.41 (15)
O2—C7—O1—C80.4 (3)O4—C16—O3—C171.7 (3)
C1—C7—O1—C8178.98 (15)C13—C16—O3—C17178.86 (15)
C9—C8—O1—C7178.86 (15)C18—C17—O3—C16178.37 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O40.862.022.857 (2)166
N2—H2···O20.862.002.834 (2)163

Experimental details

Crystal data
Chemical formulaC9H13NO2
Mr167.20
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)8.1357 (2), 10.5568 (2), 12.1428 (2)
α, β, γ (°)101.5451 (13), 97.8791 (14), 110.4821 (14)
V3)932.52 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.25 × 0.20 × 0.15
Data collection
DiffractometerBruker APEX CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2000)
Tmin, Tmax0.899, 0.987
No. of measured, independent and
observed [I > 2σ(I)] reflections
20370, 4456, 2368
Rint0.028
(sin θ/λ)max1)0.660
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.182, 1.03
No. of reflections4456
No. of parameters223
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.20, 0.21

Computer programs: SMART (Bruker, 2003), SAINT (Bruker, 2003), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEPII (Johnson, 1976).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O40.86002.02002.857 (2)166.00
N2—H2···O20.86002.00002.834 (2)163.00
 

Acknowledgements

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

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