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

Abstract

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,

• a = 11.3398 (19) Å

• b = 5.0732 (9) Å

• c = 16.500 (3) Å

• β = 108.060 (3)°

• V = 902.5 (3) ų

• 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[F ² > 2σ(F ²)] = 0.052

• wR(F ²) = 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

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.

Supplementary Material

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

Enhanced figure: interactive version of Fig. 1

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) ; (ii) .

supplementary crystallographic information

Comment

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.

Experimental

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%.

Refinement

H atoms were positioned geometrically [C—H = 0.99Å for CH₂, 0.98Å for CH₃, 0.95Å for CH (aromatic), and N—H = 0.88 Å] and refined using a riding model, with U_iso = 1.2U_eq (1.5U_eq for the methyl group) of the parent atom.

Figures

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).

Crystal data

C8H10N2O3	Dx = 1.341 Mg m−3
Mr = 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

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

Refinement

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(Fo2) + (0.1092P)2 + 0.2414P] where P = (Fo2 + 2Fc2)/3
1576 reflections	(Δ/σ)max = 0.001
119 parameters	Δρmax = 0.21 e Å−3
0 restraints	Δρmin = −0.31 e Å−3

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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.