Literature DB >> 21578873

Dimethyl 9-benzyl-3-cyano-9H-pyrrolo[1,2-a]benzimidazole-1,2-dicarboxyl-ate.

Wei-Jin Gu1, Yu-Liang Jiang, Bing-Xiang Wang.   

Abstract

The title compound, C(22)H(17)N(3)O(4), was prepared through 1,3-dipolar cyclo-addition: the dihedral angle between the benzimidazole and benzene rings is 80.93 (6)°. The crystal structure is stabilized by weak π-π inter-actions between the planar pyrrolobenzimidazole rings (r.m.s. deviation = 0.0293 Å) of neighbouring mol-ecules, 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.

Entities:  

Year:  2009        PMID: 21578873      PMCID: PMC2972134          DOI: 10.1107/S1600536809048867

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


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 ▶). For the applications of nitro­gen heteroaromatic ring systems, see: Ansari & Lal (2009 ▶); Shen et al. (2006 ▶, 2008 ▶); Zhang et al. (2009 ▶). For the synthesis, see: Wang et al. (2000 ▶).

Experimental

Crystal data

C22H17N3O4 M = 387.39 Monoclinic, 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 ▶) 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 ▶); cell refinement: SAINT (Bruker, 2000 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL. 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
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
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 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
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.
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)
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)
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)
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1.  Synthesis and evaluation of some new benzimidazole derivatives as potential antimicrobial agents.

Authors:  K F Ansari; C Lal
Journal:  Eur J Med Chem       Date:  2008-01-31       Impact factor: 6.514

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Design, synthesis and antibacterial activity of novel actinonin derivatives containing benzimidazole heterocycles.

Authors:  Datong Zhang; Zongheng Wang; Weiren Xu; Fanggang Sun; Lida Tang; Jianwu Wang
Journal:  Eur J Med Chem       Date:  2008-05-23       Impact factor: 6.514

4.  Cycloaddition reactions of thiazolium azomethine ylides: application to pyrrolo[2,1-b]thiazoles.

Authors:  Craig R Berry; Craig A Zificsak; Alan C Gibbs; Dennis J Hlasta
Journal:  Org Lett       Date:  2007-09-14       Impact factor: 6.005

  4 in total

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