Methyl (1H-pyrrol-2-ylcarbonyl­amino)acetate

Tang, G.H.; Li, D.D.; Zeng, X.C.; Dong, S.S.; Wang, Y.S.

doi:10.1107/S1600536808027451

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 64| Part 10| October 2008| Page o1867

doi:10.1107/S1600536808027451

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Methyl (1H-pyrrol-2-ylcarbonylamino)acetate

Gui Hong Tang,^a Dong Dong Li,^a Xiang Chao Zeng,^a ^* Shi Song Dong ^a and Yan Shuang Wang ^a

^aDepartment of Chemistry, Jinan University, Guangzhou, Guangdong 510632, People's Republic of China
^*Correspondence e-mail: xczeng@126.com

(Received 4 August 2008; accepted 26 August 2008; online 6 September 2008)

In the crystal structure of the title compound, C₈H₁₀N₂O₃, molecules are linked by N—H⋯O hydrogen bonds, forming ribbons of centrosymmetric dimers extending along the c axis.

Related literature

For related literature, see: Banwell et al. (2006 ); Bernstein et al. (1995 ); Faulkner (2002 ); Sosa et al. (2002 ); Zeng (2006 ); Zeng et al. (2007 ).

Experimental

Crystal data

C₈H₁₀N₂O₃
M_r = 182.18
Monoclinic, P 2₁ /n
a = 11.3398 (19) Å
b = 5.0732 (9) Å
c = 16.500 (3) Å
β = 108.060 (3)°
V = 902.5 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 173 (2) K
0.48 × 0.41 × 0.21 mm

Data collection

Bruker SMART 1K CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1997 ) T_min = 0.952, T_max = 0.979
4219 measured reflections
1576 independent reflections
1417 reflections with I > 2σ(I)
R_int = 0.033

Refinement

R[F² > 2σ(F²)] = 0.052
wR(F²) = 0.166
S = 1.10
1576 reflections
119 parameters
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.88	1.93	2.782 (2)	162
N2—H2⋯O2ⁱⁱ	0.88	2.09	2.9372 (19)	161
Symmetry codes: (i) -x+2, -y, -z+1; (ii) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 1999 ); cell refinement: SAINT-Plus (Bruker, 1999); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808027451/cf2214sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808027451/cf2214Isup2.hkl

checkCIF report

Comment top

Pyrrole derivatives are well known in many marine organisms (Faulkner, 2002). Some show important bioactivities, such as antitumor activity (Banwell et al., 2006) and protein kinase inhibiting activity (Sosa et al., 2002). This is the reason why they have attracted our interest. This study follows our previous studies on methyl 2-(4,5-dibromo-1H-pyrrole-2-carboxamido)propionate (Zeng et al., 2007) and 3-bromo-1-methyl-6,7-dihydropyrrolo[2,3-c]azepine- 4,8(1H,5H)-dione (Zeng, 2006).

In the crystal structure, molecules of the title compound are linked through N1—H1···O1ⁱ hydrogen bonds to form centrosymmetric dimers (Fig. 2) of graph-set motif R₂²(10) (Bernstein et al., 1995), which are linked by N2—H2···O2ⁱⁱ hydrogen bonds, generating ribbons extending along the c axis (also shown in Fig. 2). Bond lengths and angles are unexceptional.

Related literature top

For related literature, see: Banwell et al. (2006); Bernstein et al. (1995); Faulkner (2002); Sosa et al. (2002); Zeng (2006); Zeng et al. (2007).

Experimental top

The hydrochloric acid salt of glycine methyl ester (0.63 g, 5 mmol) and 2-trichloroacetylpyrrole (1.06 g, 5 mmol) were added to acetonitrile (12 ml), followed by the dropwise addition of triethylamine (1.4 ml). The mixture was stirred at room temperature for 10 h and then poured into water. After filtration, the precipitate was collected as a yellow solid. The impure product was dissolved in EtOH at room temperature. Light-yellow monoclinic crystals suitable for X-ray analysis (m.p. 420 K, 95.6% yield) grew over a period of one week when the solution was exposed to the air. CH&N elemental analysis. Calc. for C₈H₁₀N₂O₃: C 52.74, H 5.53, N 15.38%; found: C 52.78, H 5.59, N 15.49%.

Computing details top

Data collection: SMART (Bruker, 1999); cell refinement: SAINT-Plus (Bruker, 1999); data reduction: SAINT-Plus (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. Ribbons of dimers formed by hydrogen bonds (dashed lines).

Methyl (1H-pyrrol-2-ylcarbonylamino)acetate top

Crystal data top

C₈H₁₀N₂O₃	D_x = 1.341 Mg m⁻³
M_r = 182.18	Melting point: 420 K
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 11.3398 (19) Å	Cell parameters from 3468 reflections
b = 5.0732 (9) Å	θ = 2.6–27.0°
c = 16.500 (3) Å	µ = 0.10 mm⁻¹
β = 108.060 (3)°	T = 173 K
V = 902.5 (3) Å³	Block, light yellow
Z = 4	0.48 × 0.41 × 0.21 mm
F(000) = 384

Data collection top

Bruker SMART 1K CCD area-detector diffractometer	1576 independent reflections
Radiation source: fine-focus sealed tube	1417 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.033
ϕ and ω scans	θ_max = 25.0°, θ_min = 1.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)	h = −13→13
T_min = 0.952, T_max = 0.979	k = −6→5
4219 measured reflections	l = −16→19

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)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.166	H-atom parameters constrained
S = 1.10	w = 1/[σ²(F_o²) + (0.1092P)² + 0.2414P] where P = (F_o² + 2F_c²)/3
1576 reflections	(Δ/σ)_max = 0.001
119 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.31 e Å⁻³

Crystal data top

C₈H₁₀N₂O₃	V = 902.5 (3) Å³
M_r = 182.18	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 11.3398 (19) Å	µ = 0.10 mm⁻¹
b = 5.0732 (9) Å	T = 173 K
c = 16.500 (3) Å	0.48 × 0.41 × 0.21 mm
β = 108.060 (3)°

Data collection top

Bruker SMART 1K CCD area-detector diffractometer	1576 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)	1417 reflections with I > 2σ(I)
T_min = 0.952, T_max = 0.979	R_int = 0.033
4219 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.052	0 restraints
wR(F²) = 0.166	H-atom parameters constrained
S = 1.10	Δρ_max = 0.21 e Å⁻³
1576 reflections	Δρ_min = −0.31 e Å⁻³
119 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

	x	y	z	U_iso*/U_eq
O1	0.89632 (13)	0.2572 (2)	0.45357 (8)	0.0387 (4)
O2	0.63332 (13)	0.2895 (3)	0.31013 (8)	0.0391 (4)
N2	0.85781 (14)	0.5697 (3)	0.35256 (9)	0.0343 (4)
H2	0.8777	0.6472	0.3109	0.041*
O3	0.58657 (13)	0.4945 (3)	0.41547 (9)	0.0513 (5)
C3	1.06971 (17)	0.3350 (4)	0.29921 (12)	0.0364 (5)
H3	1.0414	0.4778	0.2608	0.044*
N1	1.08932 (14)	0.0465 (3)	0.40331 (10)	0.0343 (4)
H1	1.0773	−0.0386	0.4466	0.041*
C5	0.92253 (15)	0.3607 (3)	0.39334 (10)	0.0306 (5)
C6	0.75496 (17)	0.6645 (3)	0.37859 (12)	0.0352 (5)
H6A	0.7211	0.8266	0.3464	0.042*
H6B	0.7847	0.7099	0.4400	0.042*
C7	0.65395 (17)	0.4608 (3)	0.36324 (11)	0.0329 (5)
C4	1.02305 (17)	0.2601 (3)	0.36367 (11)	0.0313 (5)
C1	1.17634 (18)	−0.0142 (4)	0.36582 (13)	0.0394 (5)
H1A	1.2344	−0.1546	0.3817	0.047*
C2	1.16634 (18)	0.1618 (4)	0.30085 (13)	0.0413 (5)
H2A	1.2159	0.1652	0.2638	0.050*
C8	0.4845 (3)	0.3088 (6)	0.40341 (18)	0.0720 (9)
H8A	0.4282	0.3231	0.3450	0.108*
H8B	0.4391	0.3494	0.4437	0.108*
H8C	0.5174	0.1290	0.4135	0.108*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0451 (8)	0.0384 (8)	0.0386 (8)	0.0040 (6)	0.0217 (6)	0.0103 (5)
O2	0.0448 (8)	0.0368 (7)	0.0392 (8)	−0.0018 (6)	0.0180 (6)	−0.0094 (6)
N2	0.0403 (9)	0.0297 (8)	0.0388 (9)	0.0010 (6)	0.0207 (7)	0.0065 (6)
O3	0.0508 (9)	0.0644 (10)	0.0499 (9)	−0.0184 (7)	0.0319 (8)	−0.0247 (7)
C3	0.0388 (10)	0.0350 (10)	0.0387 (10)	−0.0025 (8)	0.0166 (8)	0.0063 (8)
N1	0.0376 (9)	0.0304 (8)	0.0385 (9)	−0.0018 (6)	0.0170 (7)	0.0044 (6)
C5	0.0330 (9)	0.0288 (10)	0.0315 (9)	−0.0055 (7)	0.0120 (8)	0.0008 (7)
C6	0.0423 (11)	0.0274 (9)	0.0394 (10)	0.0022 (7)	0.0178 (8)	−0.0003 (7)
C7	0.0383 (10)	0.0322 (9)	0.0304 (9)	0.0046 (7)	0.0141 (8)	−0.0008 (7)
C4	0.0341 (9)	0.0270 (9)	0.0337 (10)	−0.0042 (7)	0.0119 (8)	0.0006 (7)
C1	0.0368 (10)	0.0345 (10)	0.0502 (12)	0.0011 (8)	0.0184 (9)	0.0004 (8)
C2	0.0416 (11)	0.0416 (11)	0.0492 (12)	−0.0029 (8)	0.0265 (9)	0.0022 (9)
C8	0.0677 (16)	0.097 (2)	0.0690 (16)	−0.0400 (15)	0.0468 (14)	−0.0364 (15)

Geometric parameters (Å, º) top

O1—C5	1.239 (2)	N1—H1	0.880
O2—C7	1.204 (2)	C5—C4	1.465 (2)
N2—C5	1.345 (2)	C6—C7	1.505 (3)
N2—C6	1.444 (2)	C6—H6A	0.990
N2—H2	0.880	C6—H6B	0.990
O3—C7	1.328 (2)	C1—C2	1.373 (3)
O3—C8	1.458 (3)	C1—H1A	0.950
C3—C4	1.380 (2)	C2—H2A	0.950
C3—C2	1.398 (3)	C8—H8A	0.980
C3—H3	0.950	C8—H8B	0.980
N1—C1	1.353 (2)	C8—H8C	0.980
N1—C4	1.365 (2)

C5—N2—C6	118.64 (14)	O2—C7—O3	122.96 (17)
C5—N2—H2	120.7	O2—C7—C6	125.73 (17)
C6—N2—H2	120.7	O3—C7—C6	111.30 (15)
C7—O3—C8	114.87 (16)	N1—C4—C3	107.59 (16)
C4—C3—C2	107.31 (17)	N1—C4—C5	119.11 (15)
C4—C3—H3	126.3	C3—C4—C5	133.30 (17)
C2—C3—H3	126.3	N1—C1—C2	108.28 (17)
C1—N1—C4	109.46 (15)	N1—C1—H1A	125.9
C1—N1—H1	125.3	C2—C1—H1A	125.9
C4—N1—H1	125.3	C1—C2—C3	107.37 (17)
O1—C5—N2	120.38 (16)	C1—C2—H2A	126.3
O1—C5—C4	121.72 (16)	C3—C2—H2A	126.3
N2—C5—C4	117.89 (14)	O3—C8—H8A	109.5
N2—C6—C7	111.34 (14)	O3—C8—H8B	109.5
N2—C6—H6A	109.4	H8A—C8—H8B	109.5
C7—C6—H6A	109.4	O3—C8—H8C	109.5
N2—C6—H6B	109.4	H8A—C8—H8C	109.5
C7—C6—H6B	109.4	H8B—C8—H8C	109.5
H6A—C6—H6B	108.0

C6—N2—C5—O1	−2.1 (2)	C2—C3—C4—N1	−0.2 (2)
C6—N2—C5—C4	177.39 (15)	C2—C3—C4—C5	−179.42 (19)
C5—N2—C6—C7	−63.6 (2)	O1—C5—C4—N1	0.2 (3)
C8—O3—C7—O2	−0.4 (3)	N2—C5—C4—N1	−179.30 (14)
C8—O3—C7—C6	178.56 (19)	O1—C5—C4—C3	179.36 (19)
N2—C6—C7—O2	−26.5 (3)	N2—C5—C4—C3	−0.1 (3)
N2—C6—C7—O3	154.55 (16)	C4—N1—C1—C2	−0.1 (2)
C1—N1—C4—C3	0.2 (2)	N1—C1—C2—C3	0.0 (2)
C1—N1—C4—C5	179.57 (16)	C4—C3—C2—C1	0.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.88	1.93	2.782 (2)	162
N2—H2···O2ⁱⁱ	0.88	2.09	2.9372 (19)	161

Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+3/2, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₈H₁₀N₂O₃
M_r	182.18
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	173
a, b, c (Å)	11.3398 (19), 5.0732 (9), 16.500 (3)
β (°)	108.060 (3)
V (Å³)	902.5 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.48 × 0.41 × 0.21

Data collection
Diffractometer	Bruker SMART 1K CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1997)
T_min, T_max	0.952, 0.979
No. of measured, independent and observed [I > 2σ(I)] reflections	4219, 1576, 1417
R_int	0.033
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.052, 0.166, 1.10
No. of reflections	1576
No. of parameters	119
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.31

Computer programs: SMART (Bruker, 1999), SAINT-Plus (Bruker, 1999), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.88	1.93	2.782 (2)	162.1
N2—H2···O2ⁱⁱ	0.88	2.09	2.9372 (19)	161.2

Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+3/2, y+1/2, −z+1/2.

Acknowledgements

We thank the Natural Science Foundation of Guangdong Province, China (No. 06300581) for generously supporting this study.

References

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