Literature DB >> 24046705

5-Nitro-1,3-bis-(prop-2-yn-yl)-1H-1,3-benzimidazol-2(3H)-one.

Youssef Kandri Rodi1, Khalid Misbahi, Abdelkrim El-Ghayoury, Leokadiya Zorina, El Mokhtar Essassi, Lahcen El Ammari.   

Abstract

The title compound, C13H9N3O3, crystallizes with two identical but differently oriented mol-ecules in the asymmetric unit, the dihedral angle between the fused-ring systems of the two molecules being 64.39 (7)°. The two prop-2-ynyl chains are located on opposite sides of the mol-ecule and are nearly perpendicular to the fused ring plane, as indicated by the C-N-C-C torsion angles in the range 106.0 (3)-113.4 (3)°. In the crystal, the two mol-ecules are linked through C-H⋯O hydrogen bonds into dimers, which are subsequently linked by further C-H⋯O inter-actions, building a three-dimensional network.

Entities:  

Year:  2013        PMID: 24046705      PMCID: PMC3770420          DOI: 10.1107/S1600536813016814

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


Related literature

For the biological activity of benzimidazole derivatives, see: Horton et al. (2003 ▶); Kim et al. (1996 ▶); Roth et al. (1997 ▶). For examples of benzimidazol-2-one derivatives, see: Ouzidan et al. (2011a ▶,b ▶,c ▶).

Experimental

Crystal data

C13H9N3O3 M = 255.23 Orthorhombic, a = 20.0988 (16) Å b = 4.2645 (3) Å c = 28.669 (2) Å V = 2457.3 (3) Å3 Z = 8 Mo Kα radiation μ = 0.10 mm−1 T = 150 K 0.48 × 0.2 × 0.13 mm

Data collection

Agilent Xcalibur (Ruby, Gemini) diffractometer Absorption correction: multi-scan (ABSFAC; Agilent, 2012 ▶) T min = 0.520, T max = 1 16703 measured reflections 3233 independent reflections 2971 reflections with I > 2σ(I) R int = 0.032

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.126 S = 1.05 3233 reflections 343 parameters 1 restraint H-atom parameters constrained Δρmax = 0.48 e Å−3 Δρmin = −0.29 e Å−3 Data collection: CrysAlis PRO (Agilent, 2012 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 2006 ▶); software used to prepare material for publication: WinGX (Farrugia, 2012 ▶) and publCIF (Westrip, 2010 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813016814/kj2228sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813016814/kj2228Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813016814/kj2228Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H9N3O3F(000) = 1056
Mr = 255.23Dx = 1.38 Mg m3
Orthorhombic, Pca21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2acCell parameters from 8380 reflections
a = 20.0988 (16) Åθ = 1.8–29.7°
b = 4.2645 (3) ŵ = 0.10 mm1
c = 28.669 (2) ÅT = 150 K
V = 2457.3 (3) Å3Prism, colourless
Z = 80.48 × 0.2 × 0.13 mm
Agilent Xcalibur (Ruby, Gemini) diffractometer3233 independent reflections
Graphite monochromator2971 reflections with I > 2σ(I)
Detector resolution: 10.4752 pixels mm-1Rint = 0.032
ω–scanθmax = 29.7°, θmin = 2.0°
Absorption correction: multi-scan (ABSFAC; Agilent, 2012)h = −27→25
Tmin = 0.520, Tmax = 1k = −5→5
16703 measured reflectionsl = −38→36
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.126H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.0875P)2 + 0.4146P] where P = (Fo2 + 2Fc2)/3
3233 reflections(Δ/σ)max = 0.002
343 parametersΔρmax = 0.48 e Å3
1 restraintΔρmin = −0.29 e Å3
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
O10.07911 (10)−0.4511 (5)0.39515 (8)0.0308 (5)
O20.29627 (10)0.6066 (6)0.25710 (8)0.0407 (5)
O30.24251 (12)0.5944 (5)0.19215 (8)0.0398 (5)
N10.15605 (10)−0.1129 (5)0.36150 (7)0.0211 (4)
N20.07187 (10)−0.2738 (5)0.31877 (7)0.0205 (4)
N30.24996 (12)0.5152 (5)0.23272 (10)0.0248 (5)
C10.09991 (12)−0.2962 (6)0.36290 (9)0.0225 (5)
C20.16290 (13)0.0211 (5)0.31805 (10)0.0185 (5)
C30.10972 (10)−0.0835 (5)0.29072 (8)0.0185 (4)
C40.21066 (11)0.2190 (5)0.30002 (8)0.0198 (4)
H40.24710.29220.31810.024*
C50.10186 (14)0.0045 (5)0.24439 (10)0.0208 (5)
H50.0655−0.06830.22620.025*
C60.20185 (11)0.3042 (5)0.25370 (8)0.0206 (4)
C70.14964 (12)0.2035 (6)0.22587 (9)0.0226 (5)
H70.14660.27040.19430.027*
C80.19954 (13)−0.0708 (6)0.40183 (9)0.0257 (5)
H8A0.1781−0.16250.42970.031*
H8B0.20600.15610.40760.031*
C90.26444 (13)−0.2195 (7)0.39468 (10)0.0317 (6)
C100.31652 (16)−0.3400 (10)0.38963 (14)0.0501 (9)
H100.3586−0.43740.38550.060*
C110.01090 (12)−0.4388 (6)0.30644 (10)0.0233 (5)
H11A0.0174−0.54560.27610.028*
H11B0.0020−0.60180.33020.028*
C12−0.04656 (12)−0.2329 (6)0.30314 (10)0.0279 (5)
C13−0.09362 (15)−0.0705 (8)0.29930 (15)0.0446 (8)
H13−0.13160.06050.29620.054*
O40.32562 (11)0.4775 (5)−0.01141 (8)0.0318 (5)
O50.54368 (10)−0.5661 (5)0.12857 (8)0.0394 (5)
O60.49109 (12)−0.5397 (6)0.19373 (8)0.0431 (6)
N40.40313 (10)0.1452 (5)0.02253 (7)0.0219 (4)
N50.31780 (10)0.3013 (5)0.06502 (7)0.0216 (4)
N60.49818 (12)−0.4715 (5)0.15248 (10)0.0248 (5)
C140.34636 (12)0.3236 (6)0.02130 (9)0.0225 (5)
C150.41073 (12)0.0130 (5)0.06653 (10)0.0176 (5)
C160.35634 (11)0.1154 (5)0.09333 (8)0.0189 (4)
C170.45827 (11)−0.1800 (5)0.08478 (8)0.0200 (4)
H170.4950−0.25270.06690.024*
C180.34914 (13)0.0292 (6)0.13955 (10)0.0215 (5)
H180.31240.10110.15740.026*
C190.44923 (11)−0.2632 (5)0.13144 (9)0.0210 (4)
C200.39648 (11)−0.1631 (6)0.15897 (9)0.0229 (5)
H200.3932−0.22640.19070.028*
C210.44756 (13)0.1050 (6)−0.01722 (9)0.0264 (5)
H21A0.4536−0.1217−0.02340.032*
H21B0.42700.2003−0.04520.032*
C220.51236 (13)0.2486 (7)−0.00918 (10)0.0317 (6)
C230.56438 (16)0.3678 (10)−0.00310 (14)0.0495 (8)
H230.60640.46420.00180.059*
C240.25700 (13)0.4618 (6)0.07741 (10)0.0236 (5)
H24A0.24590.61550.05270.028*
H24B0.26400.57910.10680.028*
C250.20067 (12)0.2450 (6)0.08344 (10)0.0280 (5)
C260.15561 (15)0.0767 (8)0.09000 (14)0.0414 (8)
H260.1190−0.05980.09530.050*
U11U22U33U12U13U23
O10.0307 (10)0.0354 (9)0.0264 (12)−0.0062 (8)0.0009 (8)0.0102 (8)
O20.0310 (10)0.0498 (12)0.0413 (13)−0.0166 (10)0.0000 (9)0.0027 (10)
O30.0417 (12)0.0488 (12)0.0289 (11)−0.0105 (10)0.0098 (9)0.0089 (10)
N10.0216 (9)0.0238 (9)0.0178 (9)−0.0001 (8)−0.0016 (7)0.0026 (8)
N20.0171 (9)0.0223 (9)0.0221 (10)−0.0024 (7)−0.0015 (7)0.0013 (7)
N30.0225 (10)0.0241 (9)0.0279 (14)−0.0008 (8)0.0069 (9)0.0002 (8)
C10.0220 (11)0.0234 (11)0.0222 (12)0.0015 (9)0.0005 (8)0.0014 (9)
C20.0174 (11)0.0189 (9)0.0193 (13)0.0033 (8)−0.0014 (9)0.0001 (8)
C30.0159 (9)0.0190 (10)0.0206 (11)0.0024 (8)0.0020 (8)−0.0008 (8)
C40.0177 (10)0.0207 (10)0.0209 (11)0.0016 (8)0.0003 (8)−0.0024 (8)
C50.0224 (13)0.0222 (10)0.0179 (13)−0.0014 (8)−0.0021 (9)−0.0024 (8)
C60.0195 (10)0.0219 (10)0.0204 (11)0.0016 (8)0.0029 (8)−0.0024 (8)
C70.0251 (11)0.0255 (10)0.0171 (10)0.0006 (9)0.0002 (9)−0.0010 (9)
C80.0281 (12)0.0331 (12)0.0158 (11)−0.0028 (10)−0.0055 (9)0.0021 (9)
C90.0282 (13)0.0429 (14)0.0239 (12)−0.0060 (11)−0.0087 (10)0.0057 (11)
C100.0288 (15)0.070 (2)0.051 (2)0.0051 (16)−0.0101 (14)0.0029 (17)
C110.0184 (12)0.0208 (10)0.0309 (14)−0.0019 (8)−0.0017 (10)−0.0008 (9)
C120.0195 (11)0.0273 (11)0.0368 (14)−0.0047 (9)−0.0009 (10)−0.0001 (10)
C130.0211 (13)0.0402 (15)0.072 (2)0.0006 (12)−0.0075 (14)−0.0002 (16)
O40.0327 (10)0.0383 (10)0.0245 (11)0.0086 (8)−0.0002 (8)0.0102 (8)
O50.0267 (10)0.0508 (12)0.0408 (12)0.0158 (9)0.0005 (9)0.0101 (10)
O60.0449 (13)0.0591 (14)0.0253 (11)0.0161 (10)−0.0056 (9)0.0117 (10)
N40.0198 (9)0.0282 (10)0.0177 (9)0.0022 (8)0.0013 (7)0.0044 (8)
N50.0195 (9)0.0221 (9)0.0232 (10)0.0009 (7)−0.0007 (7)0.0043 (8)
N60.0234 (10)0.0270 (10)0.0240 (13)0.0006 (8)−0.0081 (9)0.0032 (8)
C140.0201 (11)0.0233 (11)0.0239 (12)−0.0003 (9)−0.0012 (8)0.0027 (9)
C150.0173 (10)0.0200 (10)0.0154 (12)−0.0033 (8)−0.0017 (9)−0.0001 (8)
C160.0171 (10)0.0173 (9)0.0223 (11)−0.0005 (8)−0.0001 (8)0.0005 (8)
C170.0160 (9)0.0220 (10)0.0220 (11)−0.0010 (8)0.0006 (8)−0.0004 (8)
C180.0194 (12)0.0233 (10)0.0219 (14)−0.0015 (8)0.0036 (10)0.0006 (9)
C190.0180 (10)0.0195 (9)0.0255 (11)−0.0032 (8)−0.0051 (8)0.0034 (8)
C200.0255 (11)0.0248 (11)0.0185 (11)−0.0035 (9)−0.0010 (9)0.0019 (9)
C210.0285 (12)0.0306 (12)0.0200 (12)0.0027 (10)0.0058 (9)0.0019 (10)
C220.0272 (13)0.0399 (14)0.0279 (13)0.0063 (11)0.0087 (10)0.0067 (11)
C230.0265 (15)0.068 (2)0.054 (2)−0.0045 (15)0.0038 (13)0.0026 (17)
C240.0189 (11)0.0226 (10)0.0292 (14)0.0044 (9)0.0016 (10)0.0016 (9)
C250.0204 (11)0.0264 (11)0.0372 (14)0.0067 (10)0.0006 (10)−0.0042 (10)
C260.0232 (13)0.0369 (15)0.064 (2)−0.0037 (12)0.0085 (14)−0.0073 (15)
O1—C11.211 (3)O4—C141.218 (3)
O2—N31.228 (4)O5—N61.212 (4)
O3—N31.220 (4)O6—N61.226 (4)
N1—C11.373 (3)N4—C141.372 (3)
N1—C21.377 (3)N4—C151.390 (3)
N1—C81.461 (3)N4—C211.458 (3)
N2—C31.373 (3)N5—C161.374 (3)
N2—C11.388 (3)N5—C141.382 (3)
N2—C111.457 (3)N5—C241.445 (3)
N3—C61.451 (3)N6—C191.456 (3)
C2—C41.379 (3)C15—C171.365 (3)
C2—C31.398 (3)C15—C161.406 (4)
C3—C51.389 (4)C16—C181.383 (4)
C4—C61.388 (3)C17—C191.396 (3)
C4—H40.9500C17—H170.9500
C5—C71.387 (4)C18—C201.374 (4)
C5—H50.9500C18—H180.9500
C6—C71.386 (3)C19—C201.389 (3)
C7—H70.9500C20—H200.9500
C8—C91.465 (4)C21—C221.458 (4)
C8—H8A0.9900C21—H21A0.9900
C8—H8B0.9900C21—H21B0.9900
C9—C101.175 (4)C22—C231.176 (5)
C10—H100.9500C23—H230.9500
C11—C121.454 (4)C24—C251.472 (4)
C11—H11A0.9900C24—H24A0.9900
C11—H11B0.9900C24—H24B0.9900
C12—C131.177 (4)C25—C261.170 (4)
C13—H130.9500C26—H260.9500
C1—N1—C2110.2 (2)C14—N4—C15109.9 (2)
C1—N1—C8122.6 (2)C14—N4—C21123.7 (2)
C2—N1—C8127.2 (2)C15—N4—C21126.5 (2)
C3—N2—C1110.46 (19)C16—N5—C14109.97 (19)
C3—N2—C11127.6 (2)C16—N5—C24127.2 (2)
C1—N2—C11122.0 (2)C14—N5—C24122.8 (2)
O3—N3—O2123.2 (2)O5—N6—O6123.7 (2)
O3—N3—C6119.0 (2)O5—N6—C19118.6 (3)
O2—N3—C6117.8 (3)O6—N6—C19117.7 (3)
O1—C1—N1128.1 (2)O4—C14—N4127.1 (2)
O1—C1—N2126.4 (2)O4—C14—N5126.4 (2)
N1—C1—N2105.5 (2)N4—C14—N5106.5 (2)
N1—C2—C4131.5 (2)C17—C15—N4132.0 (2)
N1—C2—C3107.3 (2)C17—C15—C16121.5 (3)
C4—C2—C3121.2 (2)N4—C15—C16106.5 (2)
N2—C3—C5131.1 (2)N5—C16—C18131.4 (2)
N2—C3—C2106.5 (2)N5—C16—C15107.1 (2)
C5—C3—C2122.5 (2)C18—C16—C15121.5 (2)
C2—C4—C6115.5 (2)C15—C17—C19115.4 (2)
C2—C4—H4122.3C15—C17—H17122.3
C6—C4—H4122.3C19—C17—H17122.3
C7—C5—C3116.9 (2)C20—C18—C16118.3 (2)
C7—C5—H5121.6C20—C18—H18120.8
C3—C5—H5121.6C16—C18—H18120.8
C7—C6—C4124.5 (2)C20—C19—C17124.5 (2)
C7—C6—N3117.2 (2)C20—C19—N6117.9 (2)
C4—C6—N3118.3 (2)C17—C19—N6117.6 (2)
C6—C7—C5119.6 (2)C18—C20—C19118.8 (2)
C6—C7—H7120.2C18—C20—H20120.6
C5—C7—H7120.2C19—C20—H20120.6
N1—C8—C9111.6 (2)C22—C21—N4112.0 (2)
N1—C8—H8A109.3C22—C21—H21A109.2
C9—C8—H8A109.3N4—C21—H21A109.2
N1—C8—H8B109.3C22—C21—H21B109.2
C9—C8—H8B109.3N4—C21—H21B109.2
H8A—C8—H8B108.0H21A—C21—H21B107.9
C10—C9—C8179.0 (3)C23—C22—C21179.1 (4)
C9—C10—H10180.0C22—C23—H23180.0
C12—C11—N2113.1 (2)N5—C24—C25112.4 (2)
C12—C11—H11A109.0N5—C24—H24A109.1
N2—C11—H11A109.0C25—C24—H24A109.1
C12—C11—H11B109.0N5—C24—H24B109.1
N2—C11—H11B109.0C25—C24—H24B109.1
H11A—C11—H11B107.8H24A—C24—H24B107.8
C13—C12—C11178.1 (3)C26—C25—C24177.4 (3)
C12—C13—H13180.0C25—C26—H26180.0
C2—N1—C1—O1179.0 (3)C15—N4—C14—O4178.2 (3)
C8—N1—C1—O1−2.1 (4)C21—N4—C14—O4−2.0 (4)
C2—N1—C1—N20.2 (3)C15—N4—C14—N5−0.4 (3)
C8—N1—C1—N2179.2 (2)C21—N4—C14—N5179.4 (2)
C3—N2—C1—O1−178.4 (2)C16—N5—C14—O4−177.9 (3)
C11—N2—C1—O11.1 (4)C24—N5—C14—O40.7 (4)
C3—N2—C1—N10.3 (3)C16—N5—C14—N40.7 (3)
C11—N2—C1—N1179.8 (2)C24—N5—C14—N4179.3 (2)
C1—N1—C2—C4−179.7 (2)C14—N4—C15—C17179.8 (2)
C8—N1—C2—C41.4 (4)C21—N4—C15—C170.0 (4)
C1—N1—C2—C3−0.7 (3)C14—N4—C15—C16−0.1 (3)
C8—N1—C2—C3−179.6 (2)C21—N4—C15—C16−179.9 (2)
C1—N2—C3—C5179.3 (2)C14—N5—C16—C18178.8 (2)
C11—N2—C3—C5−0.2 (4)C24—N5—C16—C180.2 (4)
C1—N2—C3—C2−0.8 (3)C14—N5—C16—C15−0.8 (3)
C11—N2—C3—C2179.8 (2)C24—N5—C16—C15−179.3 (2)
N1—C2—C3—N20.9 (3)C17—C15—C16—N5−179.4 (2)
C4—C2—C3—N2−180.0 (2)N4—C15—C16—N50.5 (3)
N1—C2—C3—C5−179.2 (2)C17—C15—C16—C181.0 (3)
C4—C2—C3—C50.0 (3)N4—C15—C16—C18−179.1 (2)
N1—C2—C4—C6179.0 (2)N4—C15—C17—C19179.4 (2)
C3—C2—C4—C60.1 (3)C16—C15—C17—C19−0.7 (3)
N2—C3—C5—C7180.0 (2)N5—C16—C18—C20180.0 (2)
C2—C3—C5—C70.0 (3)C15—C16—C18—C20−0.5 (3)
C2—C4—C6—C7−0.1 (3)C15—C17—C19—C200.0 (3)
C2—C4—C6—N3179.3 (2)C15—C17—C19—N6179.4 (2)
O3—N3—C6—C70.1 (3)O5—N6—C19—C20178.4 (2)
O2—N3—C6—C7179.8 (2)O6—N6—C19—C20−2.0 (3)
O3—N3—C6—C4−179.3 (2)O5—N6—C19—C17−1.0 (3)
O2—N3—C6—C40.3 (3)O6—N6—C19—C17178.5 (2)
C4—C6—C7—C50.2 (4)C16—C18—C20—C19−0.2 (3)
N3—C6—C7—C5−179.3 (2)C17—C19—C20—C180.5 (4)
C3—C5—C7—C6−0.1 (4)N6—C19—C20—C18−178.9 (2)
C1—N1—C8—C9111.8 (3)C14—N4—C21—C22113.4 (3)
C2—N1—C8—C9−69.5 (3)C15—N4—C21—C22−66.8 (3)
N1—C8—C9—C10−144 (20)N4—C21—C22—C23−104 (25)
C3—N2—C11—C12−74.5 (3)C16—N5—C24—C25−71.9 (3)
C1—N2—C11—C12106.0 (3)C14—N5—C24—C25109.8 (3)
N2—C11—C12—C13136 (10)N5—C24—C25—C26121 (7)
D—H···AD—HH···AD···AD—H···A
C5—H5···O6i0.952.433.316 (3)155
C8—H8A···O4ii0.992.283.186 (3)151
C11—H11A···O6i0.992.453.257 (4)139
C13—H13···O2iii0.952.323.205 (4)155
C21—H21B···O1iv0.992.273.191 (3)154
C24—H24B···O30.992.493.350 (4)146
C26—H26···O5i0.952.403.320 (4)164
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
C5—H5⋯O6i 0.952.433.316 (3)155
C8—H8A⋯O4ii 0.992.283.186 (3)151
C11—H11A⋯O6i 0.992.453.257 (4)139
C13—H13⋯O2iii 0.952.323.205 (4)155
C21—H21B⋯O1iv 0.992.273.191 (3)154
C24—H24B⋯O30.992.493.350 (4)146
C26—H26⋯O5i 0.952.403.320 (4)164

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

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1.  Crystal structure, Hirshfeld surface analysis and inter-action energy and DFT studies of 1-methyl-3-(prop-2-yn-1-yl)-2,3-di-hydro-1H-1,3-benzo-diazol-2-one.

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