Literature DB >> 22347079

Ethyl 2-(1,3-benzodioxol-5-yl)-1-[3-(2-oxopyrrolidin-1-yl)prop-yl]-1H-benz-imidazole-5-carboxyl-ate.

Yeong Keng Yoon, Mohamed Ashraf Ali, Ang Chee Wei, Safra Izuani Jama Asik, Ibrahim Abdul Razak.   

Abstract

In the title compound, C(24)H(25)N(3)O(5), the benzimidazole and benzodioxole ring systems are each approximately planar [maximum deviations = 0.043 (1) and 0.036 (1) Å, respectively]. Their mean planes form a dihedral angle of 42.85 (4)°. The pyrrolidine ring has an envelope conformation with one of the methyl-ene C atoms forming the flap. In the crystal, weak C-H⋯O hydrogen bonds link the mol-ecules into a three-dimensional network. The crystal packing is further stabillized by weak π-π inter-actions between the benzene rings within the benzimidazole ring system [centroid-centroid distance = 3.7955 (7) Å]. A weak C-H⋯π inter-action involving the benzodioxole ring is also present.

Entities:  

Year:  2012        PMID: 22347079      PMCID: PMC3275223          DOI: 10.1107/S1600536812001420

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


Related literature

For the pharmacological appplications of benzimidazole derivatives, see: Grassmann et al. (2002 ▶); Demirayak et al. (2002 ▶); Evans et al. (1997 ▶). For ring conformation analysis, see: Cremer & Pople (1975 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶). For related structures, see: Yoon et al. (2012a ▶,b ▶,c ▶)

Experimental

Crystal data

C24H25N3O5 M = 435.47 Monoclinic, a = 11.1692 (2) Å b = 11.5498 (2) Å c = 17.4607 (3) Å β = 109.210 (1)° V = 2127.05 (6) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 100 K 0.50 × 0.49 × 0.21 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.954, T max = 0.980 50292 measured reflections 7050 independent reflections 5762 reflections with I > 2σ(I) R int = 0.032

Refinement

R[F 2 > 2σ(F 2)] = 0.050 wR(F 2) = 0.134 S = 1.04 7050 reflections 290 parameters H-atom parameters constrained Δρmax = 0.45 e Å−3 Δρmin = −0.38 e Å−3 Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); 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 and PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812001420/lh5402sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812001420/lh5402Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812001420/lh5402Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C24H25N3O5F(000) = 920
Mr = 435.47Dx = 1.360 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 9946 reflections
a = 11.1692 (2) Åθ = 2.5–31.5°
b = 11.5498 (2) ŵ = 0.10 mm1
c = 17.4607 (3) ÅT = 100 K
β = 109.210 (1)°Block, yellow
V = 2127.05 (6) Å30.50 × 0.49 × 0.21 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer7050 independent reflections
Radiation source: fine-focus sealed tube5762 reflections with I > 2σ(I)
graphiteRint = 0.032
φ and ω scansθmax = 31.5°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −13→16
Tmin = 0.954, Tmax = 0.980k = −16→16
50292 measured reflectionsl = −23→25
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.134H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0625P)2 + 0.8818P] where P = (Fo2 + 2Fc2)/3
7050 reflections(Δ/σ)max < 0.001
290 parametersΔρmax = 0.45 e Å3
0 restraintsΔρmin = −0.38 e Å3
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
O11.36916 (8)0.64900 (8)1.00135 (6)0.02630 (19)
O21.46990 (9)0.52246 (9)1.09862 (6)0.0351 (2)
O30.53054 (11)0.16025 (9)0.79853 (8)0.0412 (3)
O40.75646 (11)−0.15864 (9)1.14027 (6)0.0373 (2)
O50.83670 (11)−0.00736 (10)1.23064 (6)0.0413 (3)
N11.08459 (9)0.25301 (8)1.08845 (5)0.01863 (18)
N20.94409 (9)0.27310 (8)0.96239 (5)0.01759 (18)
N30.68842 (9)0.06821 (9)0.76740 (6)0.0242 (2)
C11.12627 (10)0.33875 (9)1.04755 (6)0.0178 (2)
C21.23809 (11)0.40311 (10)1.07214 (6)0.0198 (2)
H2A1.30050.39101.12370.024*
C31.25516 (11)0.48569 (9)1.01862 (7)0.0201 (2)
C41.16207 (11)0.50423 (10)0.94229 (7)0.0215 (2)
H4A1.17450.56400.90830.026*
C51.05304 (11)0.43769 (10)0.91560 (7)0.0209 (2)
H5A0.99150.44870.86360.025*
C61.03832 (10)0.35349 (9)0.96927 (6)0.01764 (19)
C70.97710 (10)0.21525 (9)1.03573 (6)0.01711 (19)
C80.90606 (10)0.11885 (9)1.05532 (6)0.01784 (19)
C90.85386 (11)0.02908 (10)1.00098 (7)0.0210 (2)
H9A0.85480.03440.94690.025*
C100.80006 (11)−0.06882 (10)1.02441 (7)0.0235 (2)
H10A0.7655−0.13020.98760.028*
C110.79959 (11)−0.07201 (10)1.10277 (7)0.0230 (2)
C120.84914 (11)0.01780 (11)1.15672 (7)0.0231 (2)
C130.90412 (11)0.11341 (10)1.13575 (7)0.0207 (2)
H13A0.93940.17341.17370.025*
C141.37606 (12)0.55209 (10)1.04449 (7)0.0231 (2)
C151.48387 (12)0.71957 (11)1.02515 (8)0.0285 (3)
H15A1.55510.67611.01690.034*
H15B1.50760.74131.08310.034*
C161.45570 (18)0.82402 (18)0.97368 (14)0.0613 (6)
H16A1.52900.87620.99020.092*
H16B1.38170.86360.97980.092*
H16C1.43770.80170.91680.092*
C170.83289 (10)0.25829 (10)0.88998 (6)0.0194 (2)
H17A0.79360.33480.87200.023*
H17B0.76970.20930.90340.023*
C180.86814 (11)0.20207 (12)0.82103 (7)0.0253 (2)
H18A0.92100.25620.80200.030*
H18B0.91860.13130.84130.030*
C190.74954 (12)0.17057 (12)0.75023 (7)0.0282 (3)
H19A0.68920.23620.73900.034*
H19B0.77330.15700.70110.034*
C200.72393 (14)−0.04871 (14)0.75131 (11)0.0436 (4)
H20A0.8155−0.06270.77910.052*
H20B0.7041−0.06170.69240.052*
C210.64389 (16)−0.12635 (13)0.78542 (12)0.0522 (5)
H21A0.6121−0.19400.74970.063*
H21B0.6939−0.15440.84020.063*
C220.53501 (15)−0.05070 (12)0.78894 (9)0.0363 (3)
H22A0.4576−0.06640.74230.044*
H22B0.5162−0.06420.83980.044*
C230.58101 (12)0.07147 (11)0.78574 (7)0.0249 (2)
C240.77364 (13)−0.11782 (12)1.22069 (8)0.0297 (3)
H24A0.8254−0.17361.26110.036*
H24B0.6904−0.10961.22880.036*
U11U22U33U12U13U23
O10.0228 (4)0.0255 (4)0.0303 (4)−0.0072 (3)0.0083 (3)0.0011 (3)
O20.0270 (5)0.0331 (5)0.0367 (5)−0.0086 (4)−0.0010 (4)0.0027 (4)
O30.0344 (6)0.0334 (5)0.0616 (7)0.0032 (4)0.0238 (5)−0.0088 (5)
O40.0471 (6)0.0343 (5)0.0314 (5)−0.0208 (5)0.0142 (4)−0.0004 (4)
O50.0557 (7)0.0490 (6)0.0199 (4)−0.0313 (5)0.0135 (4)−0.0020 (4)
N10.0190 (4)0.0193 (4)0.0163 (4)−0.0022 (3)0.0041 (3)−0.0008 (3)
N20.0172 (4)0.0206 (4)0.0138 (4)−0.0022 (3)0.0035 (3)−0.0012 (3)
N30.0183 (4)0.0263 (5)0.0240 (5)0.0014 (4)0.0014 (4)−0.0073 (4)
C10.0186 (5)0.0187 (4)0.0157 (4)−0.0011 (4)0.0051 (4)−0.0018 (3)
C20.0195 (5)0.0209 (5)0.0173 (5)−0.0017 (4)0.0037 (4)−0.0025 (4)
C30.0204 (5)0.0197 (5)0.0208 (5)−0.0036 (4)0.0078 (4)−0.0036 (4)
C40.0241 (5)0.0222 (5)0.0196 (5)−0.0022 (4)0.0092 (4)0.0010 (4)
C50.0211 (5)0.0241 (5)0.0168 (5)−0.0013 (4)0.0052 (4)0.0010 (4)
C60.0171 (5)0.0194 (4)0.0163 (4)−0.0017 (4)0.0053 (4)−0.0020 (4)
C70.0180 (5)0.0182 (4)0.0149 (4)−0.0002 (4)0.0051 (4)−0.0014 (3)
C80.0163 (4)0.0200 (5)0.0168 (4)−0.0012 (4)0.0048 (4)−0.0009 (4)
C90.0215 (5)0.0233 (5)0.0193 (5)−0.0024 (4)0.0081 (4)−0.0041 (4)
C100.0232 (5)0.0222 (5)0.0259 (5)−0.0046 (4)0.0092 (4)−0.0061 (4)
C110.0195 (5)0.0233 (5)0.0254 (5)−0.0043 (4)0.0062 (4)0.0012 (4)
C120.0224 (5)0.0288 (6)0.0168 (5)−0.0061 (4)0.0047 (4)0.0009 (4)
C130.0200 (5)0.0245 (5)0.0165 (4)−0.0050 (4)0.0045 (4)−0.0019 (4)
C140.0242 (5)0.0221 (5)0.0242 (5)−0.0045 (4)0.0094 (4)−0.0040 (4)
C150.0238 (6)0.0273 (6)0.0345 (6)−0.0083 (5)0.0097 (5)−0.0031 (5)
C160.0378 (9)0.0587 (11)0.0704 (12)−0.0228 (8)−0.0052 (8)0.0337 (10)
C170.0162 (5)0.0259 (5)0.0143 (4)−0.0013 (4)0.0027 (4)−0.0016 (4)
C180.0206 (5)0.0383 (6)0.0175 (5)−0.0066 (5)0.0069 (4)−0.0073 (4)
C190.0254 (6)0.0418 (7)0.0159 (5)−0.0068 (5)0.0047 (4)−0.0046 (5)
C200.0256 (6)0.0396 (8)0.0529 (9)0.0102 (6)−0.0042 (6)−0.0242 (7)
C210.0411 (8)0.0223 (6)0.0667 (11)0.0032 (6)−0.0181 (8)−0.0037 (7)
C220.0425 (8)0.0291 (6)0.0320 (7)−0.0088 (6)0.0053 (6)0.0026 (5)
C230.0251 (6)0.0255 (5)0.0227 (5)0.0001 (4)0.0062 (4)−0.0014 (4)
C240.0274 (6)0.0341 (6)0.0250 (6)−0.0085 (5)0.0054 (5)0.0079 (5)
O1—C141.3373 (15)C10—C111.3704 (17)
O1—C151.4588 (15)C10—H10A0.9500
O2—C141.2071 (15)C11—C121.3880 (17)
O3—C231.2256 (16)C12—C131.3706 (16)
O4—C111.3672 (14)C13—H13A0.9500
O4—C241.4330 (17)C15—C161.475 (2)
O5—C121.3738 (14)C15—H15A0.9900
O5—C241.4399 (16)C15—H15B0.9900
N1—C71.3235 (14)C16—H16A0.9800
N1—C11.3878 (14)C16—H16B0.9800
N2—C61.3788 (14)C16—H16C0.9800
N2—C71.3825 (14)C17—C181.5290 (16)
N2—C171.4618 (14)C17—H17A0.9900
N3—C231.3402 (16)C17—H17B0.9900
N3—C191.4450 (17)C18—C191.5289 (17)
N3—C201.4606 (17)C18—H18A0.9900
C1—C21.3943 (15)C18—H18B0.9900
C1—C61.4067 (15)C19—H19A0.9900
C2—C31.3916 (16)C19—H19B0.9900
C2—H2A0.9500C20—C211.519 (3)
C3—C41.4112 (16)C20—H20A0.9900
C3—C141.4880 (16)C20—H20B0.9900
C4—C51.3847 (16)C21—C221.515 (2)
C4—H4A0.9500C21—H21A0.9900
C5—C61.3971 (15)C21—H21B0.9900
C5—H5A0.9500C22—C231.5090 (18)
C7—C81.4714 (15)C22—H22A0.9900
C8—C91.3968 (15)C22—H22B0.9900
C8—C131.4130 (15)C24—H24A0.9900
C9—C101.4031 (16)C24—H24B0.9900
C9—H9A0.9500
C14—O1—C15115.14 (10)O1—C15—H15B110.3
C11—O4—C24105.89 (10)C16—C15—H15B110.3
C12—O5—C24105.71 (10)H15A—C15—H15B108.6
C7—N1—C1104.97 (9)C15—C16—H16A109.5
C6—N2—C7106.35 (9)C15—C16—H16B109.5
C6—N2—C17124.13 (9)H16A—C16—H16B109.5
C7—N2—C17129.52 (9)C15—C16—H16C109.5
C23—N3—C19123.21 (11)H16A—C16—H16C109.5
C23—N3—C20113.14 (12)H16B—C16—H16C109.5
C19—N3—C20122.67 (12)N2—C17—C18111.41 (9)
N1—C1—C2129.80 (10)N2—C17—H17A109.3
N1—C1—C6109.95 (9)C18—C17—H17A109.3
C2—C1—C6120.20 (10)N2—C17—H17B109.3
C3—C2—C1117.74 (10)C18—C17—H17B109.3
C3—C2—H2A121.1H17A—C17—H17B108.0
C1—C2—H2A121.1C19—C18—C17111.01 (10)
C2—C3—C4121.13 (10)C19—C18—H18A109.4
C2—C3—C14117.42 (10)C17—C18—H18A109.4
C4—C3—C14121.44 (10)C19—C18—H18B109.4
C5—C4—C3121.78 (10)C17—C18—H18B109.4
C5—C4—H4A119.1H18A—C18—H18B108.0
C3—C4—H4A119.1N3—C19—C18111.70 (10)
C4—C5—C6116.43 (10)N3—C19—H19A109.3
C4—C5—H5A121.8C18—C19—H19A109.3
C6—C5—H5A121.8N3—C19—H19B109.3
N2—C6—C5131.70 (10)C18—C19—H19B109.3
N2—C6—C1105.79 (9)H19A—C19—H19B107.9
C5—C6—C1122.50 (10)N3—C20—C21103.78 (13)
N1—C7—N2112.92 (9)N3—C20—H20A111.0
N1—C7—C8121.52 (9)C21—C20—H20A111.0
N2—C7—C8125.53 (9)N3—C20—H20B111.0
C9—C8—C13120.17 (10)C21—C20—H20B111.0
C9—C8—C7122.70 (10)H20A—C20—H20B109.0
C13—C8—C7116.78 (9)C22—C21—C20105.03 (12)
C8—C9—C10121.55 (10)C22—C21—H21A110.7
C8—C9—H9A119.2C20—C21—H21A110.7
C10—C9—H9A119.2C22—C21—H21B110.7
C11—C10—C9117.10 (10)C20—C21—H21B110.7
C11—C10—H10A121.5H21A—C21—H21B108.8
C9—C10—H10A121.5C23—C22—C21104.48 (13)
O4—C11—C10127.99 (11)C23—C22—H22A110.9
O4—C11—C12110.28 (10)C21—C22—H22A110.9
C10—C11—C12121.72 (11)C23—C22—H22B110.9
C13—C12—O5127.89 (11)C21—C22—H22B110.9
C13—C12—C11122.30 (11)H22A—C22—H22B108.9
O5—C12—C11109.79 (10)O3—C23—N3124.65 (12)
C12—C13—C8117.14 (10)O3—C23—C22126.37 (13)
C12—C13—H13A121.4N3—C23—C22108.97 (11)
C8—C13—H13A121.4O4—C24—O5108.19 (10)
O2—C14—O1123.55 (11)O4—C24—H24A110.1
O2—C14—C3123.99 (11)O5—C24—H24A110.1
O1—C14—C3112.46 (10)O4—C24—H24B110.1
O1—C15—C16106.98 (12)O5—C24—H24B110.1
O1—C15—H15A110.3H24A—C24—H24B108.4
C16—C15—H15A110.3
C7—N1—C1—C2−175.77 (11)C24—O5—C12—C13−179.43 (13)
C7—N1—C1—C61.68 (12)C24—O5—C12—C11−1.18 (15)
N1—C1—C2—C3−179.21 (11)O4—C11—C12—C13177.00 (12)
C6—C1—C2—C33.56 (16)C10—C11—C12—C13−1.6 (2)
C1—C2—C3—C40.43 (16)O4—C11—C12—O5−1.37 (15)
C1—C2—C3—C14−178.59 (10)C10—C11—C12—O5180.00 (12)
C2—C3—C4—C5−3.24 (18)O5—C12—C13—C8179.51 (13)
C14—C3—C4—C5175.73 (11)C11—C12—C13—C81.46 (18)
C3—C4—C5—C61.83 (17)C9—C8—C13—C12−0.24 (17)
C7—N2—C6—C5−177.75 (12)C7—C8—C13—C12−173.63 (10)
C17—N2—C6—C51.48 (18)C15—O1—C14—O2−1.08 (18)
C7—N2—C6—C10.87 (12)C15—O1—C14—C3178.54 (10)
C17—N2—C6—C1−179.90 (10)C2—C3—C14—O217.46 (18)
C4—C5—C6—N2−179.30 (11)C4—C3—C14—O2−161.55 (12)
C4—C5—C6—C12.27 (17)C2—C3—C14—O1−162.16 (10)
N1—C1—C6—N2−1.60 (12)C4—C3—C14—O118.83 (16)
C2—C1—C6—N2176.14 (10)C14—O1—C15—C16−177.39 (14)
N1—C1—C6—C5177.18 (10)C6—N2—C17—C1872.07 (14)
C2—C1—C6—C5−5.09 (17)C7—N2—C17—C18−108.89 (13)
C1—N1—C7—N2−1.14 (12)N2—C17—C18—C19171.60 (10)
C1—N1—C7—C8176.98 (10)C23—N3—C19—C18105.15 (13)
C6—N2—C7—N10.17 (12)C20—N3—C19—C18−86.92 (14)
C17—N2—C7—N1−179.00 (10)C17—C18—C19—N3−75.98 (14)
C6—N2—C7—C8−177.86 (10)C23—N3—C20—C21−15.83 (15)
C17—N2—C7—C82.97 (18)C19—N3—C20—C21175.15 (11)
N1—C7—C8—C9−135.87 (12)N3—C20—C21—C2221.08 (15)
N2—C7—C8—C942.00 (16)C20—C21—C22—C23−19.27 (16)
N1—C7—C8—C1337.34 (15)C19—N3—C23—O3−8.2 (2)
N2—C7—C8—C13−144.79 (11)C20—N3—C23—O3−177.18 (14)
C13—C8—C9—C10−0.85 (17)C19—N3—C23—C22172.53 (11)
C7—C8—C9—C10172.14 (11)C20—N3—C23—C223.57 (15)
C8—C9—C10—C110.72 (18)C21—C22—C23—O3−168.92 (15)
C24—O4—C11—C10−178.17 (13)C21—C22—C23—N310.31 (15)
C24—O4—C11—C123.30 (14)C11—O4—C24—O5−3.98 (15)
C9—C10—C11—O4−177.89 (12)C12—O5—C24—O43.19 (15)
C9—C10—C11—C120.49 (18)
Cg is the centroid of the C8–C13 ring.
D—H···AD—HH···AD···AD—H···A
C5—H5A···O5i0.952.493.4324 (15)172
C15—H15B···O3ii0.992.523.4288 (18)153
C21—H21A···O3iii0.992.283.184 (2)151
C24—H24B···O3iv0.992.433.338 (2)153
C16—H16B···Cgii0.982.803.702 (2)154
Table 1

Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C8–C13 ring.

D—H⋯AD—HH⋯ADAD—H⋯A
C5—H5A⋯O5i0.952.493.4324 (15)172
C15—H15B⋯O3ii0.992.523.4288 (18)153
C21—H21A⋯O3iii0.992.283.184 (2)151
C24—H24B⋯O3iv0.992.433.338 (2)153
C16—H16BCgii0.982.803.702 (2)154

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

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