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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o3155.
Published online 2009 November 21. doi:  10.1107/S1600536809048867
PMCID: PMC2972134

Dimethyl 9-benzyl-3-cyano-9H-pyrrolo[1,2-a]benzimidazole-1,2-dicarboxyl­ate

Abstract

The title compound, C22H17N3O4, was prepared through 1,3-dipolar cyclo­addition: the dihedral angle between the benzimidazole and benzene rings is 80.93 (6)°. The crystal structure is stabilized by weak π–π inter­actions between the planar pyrrolobenzimidazole rings (r.m.s. deviation = 0.0293 Å) of neighbouring mol­ecules, forming chains along the c axis. The perpendicular distance is 3.47 (2) Å and the centroid–centroid distances are in the range of 3.590 (3)–3.944 (3) Å.

Related literature

For the use of 1,3-dipolar cyclo­addition reactions of azomethine ylides in the construction of five-membered nitro­gen heteroaromatic ring systems, see: Berry et al. (2007 [triangle]). For the applications of nitro­gen heteroaromatic ring systems, see: Ansari & Lal (2009 [triangle]); Shen et al. (2006 [triangle], 2008 [triangle]); Zhang et al. (2009 [triangle]). For the synthesis, see: Wang et al. (2000 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o3155-scheme1.jpg

Experimental

Crystal data

  • C22H17N3O4
  • M r = 387.39
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o3155-efi1.jpg
  • a = 9.8681 (15) Å
  • b = 24.766 (2) Å
  • c = 7.6551 (11) Å
  • β = 91.973 (3)°
  • V = 1869.7 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 291 K
  • 0.26 × 0.22 × 0.20 mm

Data collection

  • Bruker SMART APEX CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2000 [triangle]) T min = 0.97, T max = 0.98
  • 13898 measured reflections
  • 3615 independent reflections
  • 2699 reflections with I > 2σ(I)
  • R int = 0.057

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.125
  • S = 1.03
  • 3615 reflections
  • 264 parameters
  • H-atom parameters constrained
  • Δρmax = 0.19 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809048867/zq2016sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809048867/zq2016Isup2.hkl

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

Acknowledgments

We thank the Natural Science Foundation of Jiangsu Province of China (grant No. BK2008435) and the Natural Science Foundation of the Jiangsu Higher Education Insti­tutions of China (grant No. 07KJD150101) for financial support.

supplementary crystallographic information

Comment

1,3-Dipolar cycloadditions of azomethine ylides are one of the most powerful methods for the construction of five membered nitrogen heteroaromatic ring systems, both inter and intramolecularly (Berry et al., 2007). Nitrogen heteroaromatic ring systems, such as benzimidazoles and indolizines, can be utilized as not only a wide variety of biologically active and medicinally significant compounds (Zhang et al., 2009; Ansari et al., 2009), but also organic fluorescence probes (Shen et al., 2006; Shen et al., 2008). In our continuing studies in organic fluorescence probes, we synthesized the title compound (I), dimethyl 4-benzyl-1-cyano-4H-pyrrolo[1, 2 - a] benzimidazole-2,3-dicarboxylate, C22H17N3O4.

The crystal structure of (I) reveals that all the bond lengths and angles have normal values. There is one title compound molecule per asymmetric unit. Each molecule contains one pyrrolo-benzimidazole ring A and one benzyl ring B (Fig 1). The rings A and B are almost perpendicular, making a dihedral angle of 80.93 (6)°.

In the crystal structure there are weak π–π interactions between the planar pyrrolo-benzimidazole rings (r.m.s. deviation of 0.0293 Å) of neighbouring molecules. The perpendicular distance is 3.47 (2) Å and the distances Cg1—Cg2i and Cg2—Cg2iii are 3.590 (3) and 3.944 (3) Å, respectively. (Cg1 is the center of ring C7/C8/C9/C10/N1 and Cg2 is the center of ring C1/C2/C3/C4/C5/C6; i: 2 - x, 2 - y, 2 - z; iii: 2 - x, 2 - y, 1 - z). Through the π–π interactions one-dimensional chains are formed along c axis.

Experimental

Dimethyl 4-benzyl-1-cyano-4H-pyrrolo[1,2-a] benzimidazole-2,3-dicarboxylate was prepared through 1,3-dipolar cycloaddition according to a procedure described in the literature (Wang et al., 2000). Colorless crystals were obtained by recrystallization from a dichloromethane solution at room temperature.

Refinement

The H atoms were positioned geometrically and refined using a riding model (including free rotation about the ethanol C—C bond), with C—H = 0.93–0.97 Å and with Uiso(H) = 1.2 (1.5 for methyl groups) times Ueq(C).

Figures

Fig. 1.
A view of the title compound showing the atom-numbering scheme and displacement ellipsoids drawn at 50% probability level.
Fig. 2.
A view of the packing down b axis.
Fig. 3.
A view of the one-dimensional chains down b axis. Dashed lines indicate weak π–π interaction and all H atoms have been omitted for clarity (i: 2 - x, 2 - y, 2 - z; ii: x, y, 1 + z; iii: 2 - x, 2 - y, 1 - z).

Crystal data

C22H17N3O4F(000) = 808
Mr = 387.39Dx = 1.376 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1791 reflections
a = 9.8681 (15) Åθ = 2.6–25.2°
b = 24.766 (2) ŵ = 0.10 mm1
c = 7.6551 (11) ÅT = 291 K
β = 91.973 (3)°Block, colorless
V = 1869.7 (4) Å30.26 × 0.22 × 0.20 mm
Z = 4

Data collection

Bruker SMART APEX CCD diffractometer3615 independent reflections
Radiation source: sealed tube2699 reflections with I > 2σ(I)
graphiteRint = 0.057
phi and ω scansθmax = 26.0°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2000)h = −12→12
Tmin = 0.97, Tmax = 0.98k = −26→30
13898 measured reflectionsl = −9→9

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)] = 0.056Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.125H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.05P)2 + 0.66P] where P = (Fo2 + 2Fc2)/3
3615 reflections(Δ/σ)max < 0.001
264 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = −0.19 e Å3

Special details

Experimental. 1H-NMR (CDCl3, 400 MHz) δ: 3.81 (s, 3H, –COOCH3), 4.00 (s, 3H, –COOCH3), 5.92 (s, 2H, –CH2Ph), 7.20–7.41 (m, 8H, ArH), 8.07 (d, 1H, J = 7.9 Hz, ArH)
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. Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)-0.0001(0.0049) x + 11.1526(0.0083)y + 6.8309(0.0017) z = 16.2473 (0.0105)* 0.0370 (0.0017) C1 * 0.0187 (0.0017) C2 * -0.0329 (0.0017) C3 * -0.0312 (0.0019) C4 * -0.0132 (0.0017) C5 * 0.0115 (0.0017) C6 * 0.0056 (0.0017) C7 * -0.0396 (0.0016) C8 * -0.0420 (0.0016) C9 * 0.0128 (0.0016) C10 * 0.0392 (0.0015) N1 * 0.0341 (0.0015) N2Rms deviation of fitted atoms = 0.02937.9901(0.0063)x + 10.7417(0.0233)y - 3.2379(0.0071)z = 12.8495 (0.0190)Angle to previous plane (with approximate e.s.d.) = 80.93 (0.06)* 0.0109 (0.0016) C13 * -0.0131 (0.0017) C14 * 0.0058 (0.0018) C15 * 0.0036 (0.0019) C16 * -0.0055 (0.0019) C17 * -0.0016 (0.0017) C18Rms deviation of fitted atoms = 0.0078
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
C11.0019 (2)1.00932 (8)0.7360 (3)0.0272 (4)
C21.0476 (2)1.05587 (9)0.6574 (3)0.0342 (5)
H21.13941.06340.64810.041*
C30.9480 (3)1.09034 (10)0.5935 (3)0.0403 (6)
H30.97271.12190.53670.048*
C40.8095 (2)1.07867 (9)0.6128 (3)0.0387 (6)
H40.74501.10330.57100.046*
C50.7662 (2)1.03148 (10)0.6925 (3)0.0359 (5)
H50.67461.02390.70420.043*
C60.8651 (2)0.99690 (9)0.7526 (3)0.0283 (5)
C70.9829 (2)0.92732 (8)0.8653 (3)0.0252 (4)
C81.0572 (2)0.88306 (9)0.9310 (3)0.0283 (5)
C91.1957 (2)0.89723 (9)0.9075 (3)0.0301 (5)
C101.2040 (2)0.94775 (9)0.8330 (3)0.0288 (5)
C111.3184 (2)0.97791 (9)0.7903 (3)0.0333 (5)
C120.7257 (2)0.91558 (10)0.8516 (3)0.0326 (5)
H12A0.65090.94020.86920.039*
H12B0.73250.89130.95090.039*
C130.69949 (19)0.88336 (9)0.6848 (3)0.0292 (5)
C140.6168 (2)0.90361 (10)0.5555 (3)0.0394 (6)
H140.57470.93680.57060.047*
C150.5946 (3)0.87514 (11)0.4004 (3)0.0463 (7)
H150.54030.88980.31080.056*
C160.6539 (3)0.82453 (12)0.3795 (3)0.0493 (7)
H160.63820.80550.27610.059*
C170.7340 (3)0.80288 (12)0.5082 (3)0.0466 (6)
H170.77290.76900.49440.056*
C180.7576 (2)0.83240 (10)0.6629 (3)0.0411 (6)
H180.81250.81790.75210.049*
C191.0032 (2)0.83746 (9)1.0316 (3)0.0336 (5)
C201.0629 (3)0.76423 (12)1.2133 (4)0.0577 (8)
H20A1.00480.77781.30130.087*
H20B1.14200.74821.26820.087*
H20C1.01500.73761.14410.087*
C211.3202 (2)0.86405 (10)0.9391 (3)0.0376 (5)
C221.4343 (3)0.78357 (12)0.8747 (4)0.0528 (7)
H22A1.50760.79610.80610.079*
H22B1.41020.74750.84000.079*
H22C1.46190.78380.99620.079*
N11.07206 (16)0.96508 (7)0.8086 (2)0.0243 (4)
N20.85368 (17)0.94658 (7)0.8381 (2)0.0278 (4)
N31.41453 (19)1.00265 (9)0.7614 (3)0.0411 (5)
O11.10343 (16)0.80841 (7)1.1015 (2)0.0403 (4)
O20.88636 (17)0.82715 (7)1.0552 (2)0.0449 (5)
O31.31742 (17)0.81903 (7)0.8471 (2)0.0451 (5)
O41.4114 (2)0.87751 (9)1.0281 (3)0.0648 (6)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0323 (11)0.0244 (11)0.0247 (10)−0.0022 (9)−0.0037 (8)−0.0041 (8)
C20.0466 (13)0.0273 (12)0.0285 (11)−0.0057 (10)0.0002 (10)−0.0019 (9)
C30.0513 (15)0.0310 (13)0.0385 (13)0.0007 (11)0.0013 (11)−0.0045 (10)
C40.0433 (14)0.0249 (12)0.0473 (14)0.0040 (10)−0.0059 (11)−0.0014 (10)
C50.0323 (12)0.0352 (13)0.0399 (13)0.0041 (10)−0.0055 (10)−0.0037 (10)
C60.0274 (10)0.0230 (11)0.0343 (11)0.0022 (9)−0.0014 (9)−0.0041 (9)
C70.0232 (10)0.0269 (11)0.0254 (10)−0.0068 (8)0.0006 (8)−0.0034 (8)
C80.0264 (10)0.0329 (12)0.0257 (10)−0.0025 (9)0.0022 (8)−0.0034 (9)
C90.0301 (11)0.0342 (13)0.0255 (10)−0.0010 (9)−0.0045 (9)−0.0033 (9)
C100.0238 (10)0.0337 (13)0.0284 (10)0.0024 (9)−0.0040 (8)−0.0013 (9)
C110.0260 (11)0.0289 (12)0.0448 (13)0.0028 (9)−0.0003 (10)−0.0014 (10)
C120.0189 (10)0.0365 (13)0.0428 (13)−0.0071 (9)0.0074 (9)−0.0026 (10)
C130.0175 (9)0.0341 (12)0.0361 (12)−0.0056 (9)0.0054 (8)0.0021 (9)
C140.0381 (13)0.0348 (13)0.0444 (13)−0.0044 (10)−0.0116 (10)−0.0010 (11)
C150.0522 (15)0.0540 (17)0.0316 (13)−0.0098 (13)−0.0143 (11)0.0006 (11)
C160.0535 (16)0.0536 (17)0.0406 (14)−0.0132 (13)−0.0033 (12)−0.0178 (12)
C170.0485 (15)0.0460 (15)0.0457 (15)−0.0021 (12)0.0038 (12)−0.0133 (12)
C180.0398 (13)0.0361 (14)0.0466 (14)0.0050 (11)−0.0073 (11)−0.0077 (11)
C190.0377 (13)0.0303 (13)0.0321 (12)0.0005 (10)−0.0074 (10)−0.0015 (9)
C200.076 (2)0.0544 (18)0.0425 (15)0.0009 (15)0.0044 (14)0.0349 (13)
C210.0348 (12)0.0373 (14)0.0403 (13)0.0018 (10)−0.0031 (10)0.0009 (11)
C220.0480 (15)0.0571 (18)0.0535 (16)0.0282 (13)0.0064 (13)−0.0133 (13)
N10.0211 (8)0.0270 (9)0.0249 (9)−0.0030 (7)0.0014 (7)−0.0028 (7)
N20.0221 (8)0.0295 (10)0.0319 (9)−0.0045 (7)0.0000 (7)−0.0004 (7)
N30.0303 (10)0.0528 (14)0.0404 (11)−0.0052 (10)0.0049 (8)0.0129 (10)
O10.0418 (9)0.0435 (10)0.0356 (9)0.0077 (8)0.0030 (7)0.0184 (7)
O20.0395 (10)0.0547 (11)0.0399 (9)−0.0098 (8)−0.0049 (7)0.0225 (8)
O30.0467 (10)0.0461 (11)0.0422 (9)0.0157 (8)−0.0041 (8)−0.0152 (8)
O40.0576 (12)0.0899 (16)0.0452 (11)0.0140 (11)−0.0211 (10)−0.0184 (11)

Geometric parameters (Å, °)

C1—C21.384 (3)C12—H12B0.9700
C1—C61.394 (3)C13—C141.357 (3)
C1—N11.401 (3)C13—C181.398 (3)
C2—C31.379 (3)C14—C151.392 (3)
C2—H20.9300C14—H140.9300
C3—C41.410 (4)C15—C161.395 (4)
C3—H30.9300C15—H150.9300
C4—C51.392 (3)C16—C171.352 (4)
C4—H40.9300C16—H160.9300
C5—C61.366 (3)C17—C181.405 (3)
C5—H50.9300C17—H170.9300
C6—N21.414 (3)C18—H180.9300
C7—N11.365 (3)C19—O21.201 (3)
C7—N21.371 (3)C19—O11.321 (3)
C7—C81.402 (3)C20—O11.454 (3)
C8—C91.429 (3)C20—H20A0.9600
C8—C191.477 (3)C20—H20B0.9600
C9—C101.378 (3)C20—H20C0.9600
C9—C211.491 (3)C21—O41.159 (3)
C10—N11.378 (3)C21—O31.318 (3)
C10—C111.401 (3)C22—O31.459 (3)
C11—N31.157 (3)C22—H22A0.9600
C12—N21.485 (3)C22—H22B0.9600
C12—C131.520 (3)C22—H22C0.9600
C12—H12A0.9700
C2—C1—C6123.7 (2)C13—C14—H14119.7
C2—C1—N1131.3 (2)C15—C14—H14119.7
C6—C1—N1104.97 (17)C14—C15—C16119.9 (2)
C3—C2—C1115.5 (2)C14—C15—H15120.0
C3—C2—H2122.2C16—C15—H15120.0
C1—C2—H2122.2C17—C16—C15120.7 (2)
C2—C3—C4121.2 (2)C17—C16—H16119.7
C2—C3—H3119.4C15—C16—H16119.7
C4—C3—H3119.4C16—C17—C18118.9 (3)
C5—C4—C3122.1 (2)C16—C17—H17120.5
C5—C4—H4118.9C18—C17—H17120.5
C3—C4—H4118.9C13—C18—C17121.0 (2)
C6—C5—C4116.5 (2)C13—C18—H18119.5
C6—C5—H5121.7C17—C18—H18119.5
C4—C5—H5121.7O2—C19—O1122.2 (2)
C5—C6—C1120.9 (2)O2—C19—C8127.4 (2)
C5—C6—N2129.9 (2)O1—C19—C8110.4 (2)
C1—C6—N2109.22 (17)O1—C20—H20A109.5
N1—C7—N2108.65 (18)O1—C20—H20B109.5
N1—C7—C8108.36 (18)H20A—C20—H20B109.5
N2—C7—C8142.99 (19)O1—C20—H20C109.5
C7—C8—C9104.67 (19)H20A—C20—H20C109.5
C7—C8—C19126.24 (19)H20B—C20—H20C109.5
C9—C8—C19128.1 (2)O4—C21—O3124.0 (2)
C10—C9—C8110.22 (19)O4—C21—C9123.7 (2)
C10—C9—C21120.5 (2)O3—C21—C9112.17 (19)
C8—C9—C21129.1 (2)O3—C22—H22A109.5
N1—C10—C9105.65 (18)O3—C22—H22B109.5
N1—C10—C11124.6 (2)H22A—C22—H22B109.5
C9—C10—C11129.77 (19)O3—C22—H22C109.5
N3—C11—C10177.5 (2)H22A—C22—H22C109.5
N2—C12—C13109.47 (17)H22B—C22—H22C109.5
N2—C12—H12A109.8C7—N1—C10111.09 (17)
C13—C12—H12A109.8C7—N1—C1110.29 (17)
N2—C12—H12B109.8C10—N1—C1138.55 (18)
C13—C12—H12B109.8C7—N2—C6106.77 (16)
H12A—C12—H12B108.2C7—N2—C12126.79 (18)
C14—C13—C18119.0 (2)C6—N2—C12124.71 (17)
C14—C13—C12120.0 (2)C19—O1—C20115.5 (2)
C18—C13—C12121.1 (2)C21—O3—C22115.44 (19)
C13—C14—C15120.6 (2)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZQ2016).

References

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