Methyl 1H-pyrrole-2-carboxyl­ate

Kerscher, T.; Mayer, P.; Klüfers, P.

doi:10.1107/S1600536809030906

organic compounds

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ISSN: 2056-9890

Volume 65| Part 9| September 2009| Page o2195

doi:10.1107/S1600536809030906

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Methyl 1H-pyrrole-2-carboxylate

Tobias Kerscher,^a Peter Mayer ^a and Peter Klüfers ^a ^*

^aDepartment Chemie und Biochemie, Ludwig-Maximilians-Universität, Butenandtstrasse 5–13, 81377 München, Germany
^*Correspondence e-mail: kluef@cup.uni-muenchen.de

(Received 30 July 2009; accepted 4 August 2009; online 19 August 2009)

The title compound, C₆H₇NO₂, is essentially planar with a dihedral angle of 3.6 (3)° between the pyrrole ring and the methoxycarbonyl O/C/O/C plane. In the crystal structure, the N atom is a hydrogen-bond donor to the carboxylate C=O O atom of the neighboring molecule. These intermolecular hydrogen bonds lead to the formation of helical chains along the b axis.

Related literature

For related structures, see: Kerscher, Klüfers, Kügel & Müller (2007 ); Kerscher, Klüfers & Kügel (2007 ). For graph-set analysis, see: Bernstein et al. (1995 ); Etter et al. (1990 ).

Experimental

Crystal data

C₆H₇NO₂
M_r = 125.13
Monoclinic, P 2₁ /c
a = 7.5346 (19) Å
b = 5.4598 (14) Å
c = 14.730 (4) Å
β = 100.55 (2)°
V = 595.7 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 200 K
0.38 × 0.16 × 0.06 mm

Data collection

Oxford Xcalibur KappaCCD diffractometer
Absorption correction: none
2591 measured reflections
1103 independent reflections
528 reflections with I > 2σ(I)
R_int = 0.112

Refinement

R[F² > 2σ(F²)] = 0.070
wR(F²) = 0.176
S = 0.95
1103 reflections
83 parameters
H-atom parameters constrained
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.26 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O2ⁱ	0.88	2.06	2.933 (4)	171
C4—H4⋯Cg1ⁱⁱ	0.95	2.63	3.401 (5)	139
Symmetry codes: (i) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ . Cg1 is the centroid of the pyrrole ring.

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 $[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 $[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996 ), ORTEP-3 (Farrugia, 1997 ) and Mercury (Macrae et al., 2006 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809030906/is2445sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809030906/is2445Isup2.hkl

checkCIF report

Comment top

The title compound was prepared, in the attempt to create new complexing ligands, as a byproduct. The compound is quite simular to other compounds already published by our group (Kerscher, Klüfers, Kügel & Müller, 2007; Kerscher, Klüfers & Kügel, 2007).

In the molecule, a formic acid methyl ester is in the 2 position of the pyrrole ring (Fig. 1). With a torsion angle for C2–C1–C5–O1 of only about 2.9°, the molecule is, with the exception of the H atoms of the methyl group, nearly planar. Because of this small torsion angle, the molecule is not C_s symmetric.

The hydrogen bonds of the nitrogen to the carboxylate oxygen lead to a chain like hydrogen bonding system which can be described according to graph-set analysis (Etter et al., 1990; Bernstein et al., 1995) with a C(5) descriptor on the unitary level [the rpluto program (Cambridge Crystallographic Data Centre, England) was used for the graph set analyses; one of these strands is shown in Fig. 2].

Considering contacts whose range falls below the sum of van der Waals radii by only about 0.1 Å, a set of weak C–H···π interactions leads to the formation of a second system of strands along [0 1 0] which can be described by a C(2) descriptor (see Fig. 3).

The two strand systems alternate, which means two hydrogen bonding strands are interconnected by a strand of weak C–H···π contacts (this situation is illustrated in Fig. 4) and vice versa, two strands made of weak C–H···π contacts are interconnected by hydrogen bonding strands. This bonding pattern leads to sheet like structures normal to [0 0 1].

The molecular packing of the title compound is shown in Figure 5.

Related literature top

For related structures, see: Kerscher, Klüfers, Kügel & Müller (2007); Kerscher, Klüfers & Kügel (2007). For graph-set analysis, see: Bernstein et al. (1995); Etter et al. (1990).

Experimental top

The title compound was obtained by reaction of 228 mg (3.40 mmol) of pyrrole with 280 mg (1.70 mmol) phosgene imminium chloride in 6 ml of dry acetonitrile. After removal of the solvent, the remaining green solid was purified by column chromatoghraphy on silica with chloroform as eluent. Sublimation of fraction five yielded the title compound as colorless crystals.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996), ORTEP-3 (Farrugia, 1997) and Mercury 2.2 (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound with atom labels and anisotropic displacement ellipsoids (drawn at 50% probability level) for non-H atoms.
	Fig. 2. Strands formed by N–H···O hydrogen bonds along [0 1 0] in the crystal structure of the title compound, viewed along [1 0 0]. Symmetry codes: (i) -x, y + 1/2, 1/2 - z; (ii) x, y + 1, z; (iii) -x, y + 3/2, 1/2 - z.
	Fig. 3. Strands formed by C–H···π contacts along [0 1 0] in the crystal structure of the title compound, viewed along [0 0 1]. Symmetry codes: (i) 1 - x, y + 1/2, 1/2 - z; (ii) 1 - x, y - 1/2, z - 1/2; (iii) x, y - 1, z; (iv) 1 - x, y - 3/2, 1/2 - z; (v) x, y - 2, z.
	Fig. 4. The strands formed by hydrogen bonding in the crystal structure are interconnected by the strands formed by C–H···π contacts.
	Fig. 5. The packing of the title compound, viewed along [0 1 0].

Methyl 1H-pyrrole-2-carboxylate top

Crystal data top

C₆H₇NO₂	F(000) = 264
M_r = 125.13	D_x = 1.395 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1091 reflections
a = 7.5346 (19) Å	θ = 4.0–27.5°
b = 5.4598 (14) Å	µ = 0.11 mm⁻¹
c = 14.730 (4) Å	T = 200 K
β = 100.55 (2)°	Platelet, colourless
V = 595.7 (3) Å³	0.38 × 0.16 × 0.06 mm
Z = 4

Data collection top

Oxford Xcalibur KappaCCD diffractometer	528 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.112
Graphite monochromator	θ_max = 25.5°, θ_min = 4.0°
ω–scans	h = −9→9
2591 measured reflections	k = −6→6
1103 independent reflections	l = −17→17

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.070	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.176	H-atom parameters constrained
S = 0.95	w = 1/[σ²(F_o²) + (0.0745P)²] where P = (F_o² + 2F_c²)/3
1103 reflections	(Δ/σ)_max < 0.001
83 parameters	Δρ_max = 0.27 e Å⁻³
0 restraints	Δρ_min = −0.26 e Å⁻³

Crystal data top

C₆H₇NO₂	V = 595.7 (3) Å³
M_r = 125.13	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 7.5346 (19) Å	µ = 0.11 mm⁻¹
b = 5.4598 (14) Å	T = 200 K
c = 14.730 (4) Å	0.38 × 0.16 × 0.06 mm
β = 100.55 (2)°

Data collection top

Oxford Xcalibur KappaCCD diffractometer	528 reflections with I > 2σ(I)
2591 measured reflections	R_int = 0.112
1103 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.070	0 restraints
wR(F²) = 0.176	H-atom parameters constrained
S = 0.95	Δρ_max = 0.27 e Å⁻³
1103 reflections	Δρ_min = −0.26 e Å⁻³
83 parameters

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

	x	y	z	U_iso*/U_eq
O1	0.0203 (3)	0.7534 (4)	0.08955 (19)	0.0312 (8)
O2	−0.0644 (3)	0.4755 (5)	0.18723 (19)	0.0331 (8)
N1	0.2637 (4)	0.2221 (6)	0.1856 (2)	0.0286 (9)
H1	0.1960	0.1417	0.2183	0.034*
C1	0.2176 (5)	0.4370 (7)	0.1405 (3)	0.0248 (10)
C5	0.0452 (5)	0.5519 (7)	0.1425 (3)	0.0276 (10)
C6	−0.1459 (5)	0.8847 (7)	0.0877 (3)	0.0378 (12)
H6A	−0.2475	0.7701	0.0753	0.057*
H6B	−0.1594	1.0093	0.0391	0.057*
H6C	−0.1439	0.9640	0.1476	0.057*
C3	0.4923 (5)	0.3236 (7)	0.1182 (3)	0.0275 (10)
H3	0.6054	0.3212	0.0984	0.033*
C4	0.4295 (5)	0.1506 (7)	0.1726 (3)	0.0300 (10)
H4	0.4914	0.0065	0.1967	0.036*
C2	0.3585 (5)	0.5042 (7)	0.0975 (3)	0.0276 (10)
H2	0.3638	0.6461	0.0608	0.033*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0235 (16)	0.0309 (17)	0.0388 (19)	0.0084 (12)	0.0042 (12)	0.0051 (13)
O2	0.0241 (16)	0.0352 (17)	0.041 (2)	0.0013 (13)	0.0090 (14)	−0.0012 (14)
N1	0.025 (2)	0.0251 (19)	0.036 (2)	−0.0002 (15)	0.0059 (15)	−0.0020 (16)
C1	0.024 (2)	0.022 (2)	0.028 (2)	−0.0012 (18)	0.0041 (18)	−0.0015 (17)
C5	0.028 (2)	0.022 (2)	0.030 (2)	0.0005 (18)	−0.0009 (19)	−0.0072 (18)
C6	0.034 (3)	0.037 (3)	0.041 (3)	0.009 (2)	0.004 (2)	0.001 (2)
C3	0.026 (2)	0.031 (2)	0.026 (2)	0.0016 (18)	0.0079 (17)	−0.0016 (19)
C4	0.023 (2)	0.029 (2)	0.035 (3)	0.0024 (19)	−0.0013 (18)	−0.0029 (19)
C2	0.030 (2)	0.026 (2)	0.026 (3)	−0.0026 (19)	0.0051 (19)	0.0019 (19)

Geometric parameters (Å, º) top

O1—C5	1.341 (4)	C6—H6A	0.9800
O1—C6	1.439 (4)	C6—H6B	0.9800
O2—C5	1.221 (5)	C6—H6C	0.9800
N1—C4	1.356 (5)	C3—C4	1.377 (5)
N1—C1	1.362 (5)	C3—C2	1.403 (5)
N1—H1	0.8800	C3—H3	0.9500
C1—C2	1.382 (5)	C4—H4	0.9500
C1—C5	1.447 (5)	C2—H2	0.9500

C5—O1—C6	116.6 (3)	O1—C6—H6C	109.5
C4—N1—C1	109.8 (3)	H6A—C6—H6C	109.5
C4—N1—H1	125.1	H6B—C6—H6C	109.5
C1—N1—H1	125.1	C4—C3—C2	107.4 (3)
N1—C1—C2	107.7 (3)	C4—C3—H3	126.3
N1—C1—C5	120.9 (3)	C2—C3—H3	126.3
C2—C1—C5	131.4 (4)	N1—C4—C3	108.0 (3)
O2—C5—O1	123.9 (4)	N1—C4—H4	126.0
O2—C5—C1	124.1 (4)	C3—C4—H4	126.0
O1—C5—C1	112.0 (4)	C1—C2—C3	107.2 (3)
O1—C6—H6A	109.5	C1—C2—H2	126.4
O1—C6—H6B	109.5	C3—C2—H2	126.4
H6A—C6—H6B	109.5

C4—N1—C1—C2	0.0 (4)	C2—C1—C5—O1	2.9 (6)
C4—N1—C1—C5	179.3 (3)	C1—N1—C4—C3	0.3 (4)
C6—O1—C5—O2	0.7 (5)	C2—C3—C4—N1	−0.4 (4)
C6—O1—C5—C1	−179.0 (3)	N1—C1—C2—C3	−0.2 (4)
N1—C1—C5—O2	4.1 (6)	C5—C1—C2—C3	−179.4 (4)
C2—C1—C5—O2	−176.8 (4)	C4—C3—C2—C1	0.4 (4)
N1—C1—C5—O1	−176.2 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.88	2.06	2.933 (4)	171
C4—H4···Cg1ⁱⁱ	0.95	2.63	3.401 (5)	139

Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x+1, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₆H₇NO₂
M_r	125.13
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	200
a, b, c (Å)	7.5346 (19), 5.4598 (14), 14.730 (4)
β (°)	100.55 (2)
V (Å³)	595.7 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.38 × 0.16 × 0.06

Data collection
Diffractometer	Oxford Xcalibur KappaCCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	2591, 1103, 528
R_int	0.112
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.070, 0.176, 0.95
No. of reflections	1103
No. of parameters	83
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.26

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEPIII (Burnett & Johnson, 1996), ORTEP-3 (Farrugia, 1997) and Mercury 2.2 (Macrae et al., 2006).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.88	2.06	2.933 (4)	171
C4—H4···Cg1ⁱⁱ	0.95	2.63	3.401 (5)	139

Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x+1, y−1/2, −z+1/2.

Acknowledgements

TK is indebted to the Hanns-Seidel Stiftung for a PhD grant funded by the German Bundesministerium für Bildung und Forschung.

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