Literature DB >> 22346899

Ethyl 1-[3-(2-oxopyrrolidin-1-yl)prop-yl]-2-phenyl-1H-benzimidazole-5-carboxyl-ate.

Yeong Keng Yoon, Mohamed Ashraf Ali, Tan Soo Choon, Safra Izuani Jama Asik, Ibrahim Abdul Razak.   

Abstract

In the title compound, C(23)H(25)N(3)O(3), the benzimidazole ring system is essentially planar [maximum deviation = 0.0240 (18) Å]. The mean plane through this ring system forms a dihedral angle of 42.23 (7)° with the benzene ring. The pyrrolidine ring is in an envelope conformation with the flap atom disordered over two sites with occupancies of 0.813 (11) and 0.187 (11). In the crystal, weak C-H⋯O hydrogen bonds form R(2) (2)(10) ring motifs, which are connected by further C-H⋯O inter-actions, forming ribbons along the b axis. The crystal structure is further stabilized by weak π-π inter-actions involving the imidazole and benzene rings of the benzimidazole ring system [centroid-centroid distances = 3.6788 (11) and 3.6316 (10) Å] and weak C-H⋯π inter-actions.

Entities:  

Year:  2012        PMID: 22346899      PMCID: PMC3274946          DOI: 10.1107/S1600536811054833

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


Related literature

For the biological activity of benzimidazole derivatives, see: Ozden et al. (2008 ▶); Garuti et al. (2000 ▶); Rao et al. (2002 ▶); Thakurdesai et al. (2007 ▶). For ring conformations, see: Cremer & Pople (1975 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C23H25N3O3 M = 391.46 Triclinic, a = 9.9469 (3) Å b = 10.5845 (3) Å c = 11.3184 (3) Å α = 69.679 (1)° β = 67.374 (1)° γ = 70.135 (1)° V = 1001.77 (5) Å3 Z = 2 Mo Kα radiation μ = 0.09 mm−1 T = 100 K 0.39 × 0.36 × 0.25 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.967, T max = 0.979 17976 measured reflections 4530 independent reflections 3768 reflections with I > 2σ(I) R int = 0.038

Refinement

R[F 2 > 2σ(F 2)] = 0.055 wR(F 2) = 0.148 S = 1.04 4530 reflections 273 parameters H-atom parameters constrained Δρmax = 0.48 e Å−3 Δρmin = −0.29 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/S1600536811054833/lh5398sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811054833/lh5398Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811054833/lh5398Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C23H25N3O3Z = 2
Mr = 391.46F(000) = 416
Triclinic, P1Dx = 1.298 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 9.9469 (3) ÅCell parameters from 8488 reflections
b = 10.5845 (3) Åθ = 2.5–30.0°
c = 11.3184 (3) ŵ = 0.09 mm1
α = 69.679 (1)°T = 100 K
β = 67.374 (1)°Block, yellow
γ = 70.135 (1)°0.39 × 0.36 × 0.25 mm
V = 1001.77 (5) Å3
Bruker SMART APEXII CCD area-detector diffractometer4530 independent reflections
Radiation source: fine-focus sealed tube3768 reflections with I > 2σ(I)
graphiteRint = 0.038
φ and ω scansθmax = 27.5°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −12→12
Tmin = 0.967, Tmax = 0.979k = −13→13
17976 measured reflectionsl = −14→14
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.055Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.148H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0797P)2 + 0.518P] where P = (Fo2 + 2Fc2)/3
4530 reflections(Δ/σ)max < 0.001
273 parametersΔρmax = 0.48 e Å3
0 restraintsΔρmin = −0.29 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*/UeqOcc. (<1)
O10.51811 (13)0.43185 (12)0.18372 (11)0.0238 (3)
O20.72338 (14)0.26966 (13)0.11427 (12)0.0278 (3)
O30.38369 (15)−0.62929 (14)0.65226 (14)0.0336 (3)
N10.16338 (15)0.14323 (14)0.56013 (13)0.0183 (3)
N20.25147 (15)−0.07610 (14)0.53712 (13)0.0173 (3)
N30.17813 (16)−0.48401 (14)0.59087 (14)0.0223 (3)
C10.29539 (17)0.13446 (17)0.45592 (15)0.0175 (3)
C20.37149 (18)0.23727 (17)0.37207 (15)0.0180 (3)
H2A0.33290.33050.37940.022*
C30.50599 (18)0.19825 (17)0.27734 (15)0.0190 (3)
C40.56275 (18)0.05964 (17)0.26704 (15)0.0197 (3)
H4A0.65610.03590.20280.024*
C50.48733 (18)−0.04269 (17)0.34713 (15)0.0192 (3)
H5A0.5251−0.13560.33880.023*
C60.35264 (18)−0.00195 (17)0.44091 (15)0.0173 (3)
C70.14155 (17)0.01636 (17)0.60518 (15)0.0178 (3)
C80.01066 (17)−0.01765 (16)0.71822 (15)0.0182 (3)
C9−0.07626 (18)−0.09810 (17)0.71996 (16)0.0201 (3)
H9A−0.0472−0.14010.64930.024*
C10−0.20564 (19)−0.11690 (18)0.82509 (16)0.0235 (4)
H10A−0.2640−0.17230.82620.028*
C11−0.24936 (19)−0.05501 (19)0.92789 (17)0.0254 (4)
H11A−0.3375−0.06810.99950.030*
C12−0.1640 (2)0.02624 (19)0.92607 (17)0.0251 (4)
H12A−0.19430.06960.99600.030*
C13−0.03462 (19)0.04401 (17)0.82207 (16)0.0212 (3)
H13A0.02380.09900.82170.025*
C140.59541 (18)0.30010 (17)0.18400 (15)0.0198 (3)
C150.5951 (2)0.53843 (19)0.08991 (17)0.0267 (4)
H15A0.62700.5271−0.00090.032*
H15B0.68520.53170.11150.032*
C160.4870 (2)0.6758 (2)0.09972 (18)0.0315 (4)
H16A0.52930.74940.02850.047*
H16B0.46860.69210.18530.047*
H16C0.39230.67580.09180.047*
C170.26948 (18)−0.22474 (16)0.55756 (15)0.0179 (3)
H17A0.2068−0.26200.64750.021*
H17B0.3754−0.27370.55090.021*
C180.22422 (18)−0.25223 (16)0.45568 (15)0.0189 (3)
H18A0.1154−0.21210.46930.023*
H18B0.2782−0.20500.36590.023*
C190.25864 (19)−0.40646 (17)0.46449 (16)0.0212 (3)
H19A0.2324−0.41750.39330.025*
H19B0.3677−0.44610.44950.025*
C200.0140 (2)−0.45478 (19)0.64291 (19)0.0285 (4)
H20A−0.0309−0.43590.57240.034*0.813 (11)
H20B−0.0264−0.37410.68210.034*0.813 (11)
H20C−0.0269−0.47250.58770.034*0.187 (11)
H20D−0.0269−0.35960.64700.034*0.187 (11)
C21−0.0168 (3)−0.5853 (3)0.7469 (3)0.0277 (8)0.813 (11)
H21A−0.0297−0.65060.70940.033*0.813 (11)
H21B−0.1075−0.56430.82120.033*0.813 (11)
C21X−0.0012 (16)−0.5530 (18)0.7962 (18)0.049 (5)0.187 (11)
H21C−0.0217−0.49570.85690.059*0.187 (11)
H21D−0.0842−0.59960.82750.059*0.187 (11)
C220.1275 (2)−0.6456 (2)0.7924 (2)0.0345 (5)
H22A0.1139−0.61360.86960.041*0.813 (11)
H22B0.1533−0.74830.81580.041*0.813 (11)
H22C0.1333−0.73850.79370.041*0.187 (11)
H22D0.1447−0.64890.87140.041*0.187 (11)
C230.2473 (2)−0.58904 (18)0.67283 (18)0.0257 (4)
U11U22U33U12U13U23
O10.0232 (6)0.0232 (6)0.0213 (6)−0.0115 (5)−0.0019 (5)−0.0008 (5)
O20.0200 (6)0.0320 (7)0.0274 (6)−0.0106 (5)−0.0004 (5)−0.0060 (5)
O30.0287 (7)0.0256 (7)0.0471 (8)−0.0023 (6)−0.0203 (6)−0.0037 (6)
N10.0162 (7)0.0205 (7)0.0176 (6)−0.0064 (5)−0.0046 (5)−0.0026 (5)
N20.0160 (7)0.0189 (7)0.0168 (6)−0.0057 (5)−0.0051 (5)−0.0028 (5)
N30.0185 (7)0.0178 (7)0.0285 (7)−0.0053 (5)−0.0064 (6)−0.0033 (6)
C10.0144 (7)0.0225 (8)0.0164 (7)−0.0051 (6)−0.0060 (6)−0.0038 (6)
C20.0176 (8)0.0186 (8)0.0190 (7)−0.0046 (6)−0.0072 (6)−0.0041 (6)
C30.0174 (8)0.0245 (8)0.0166 (7)−0.0082 (6)−0.0064 (6)−0.0022 (6)
C40.0150 (8)0.0261 (9)0.0166 (7)−0.0051 (6)−0.0034 (6)−0.0049 (6)
C50.0195 (8)0.0196 (8)0.0187 (7)−0.0031 (6)−0.0068 (6)−0.0054 (6)
C60.0164 (7)0.0202 (8)0.0167 (7)−0.0069 (6)−0.0071 (6)−0.0014 (6)
C70.0158 (8)0.0219 (8)0.0173 (7)−0.0043 (6)−0.0069 (6)−0.0048 (6)
C80.0163 (8)0.0178 (8)0.0176 (7)−0.0036 (6)−0.0058 (6)−0.0006 (6)
C90.0192 (8)0.0219 (8)0.0188 (7)−0.0061 (6)−0.0057 (6)−0.0037 (6)
C100.0211 (8)0.0261 (9)0.0241 (8)−0.0110 (7)−0.0069 (7)−0.0017 (7)
C110.0198 (8)0.0309 (9)0.0204 (8)−0.0097 (7)−0.0006 (6)−0.0031 (7)
C120.0266 (9)0.0277 (9)0.0193 (8)−0.0085 (7)−0.0025 (7)−0.0068 (7)
C130.0218 (8)0.0222 (8)0.0201 (8)−0.0090 (7)−0.0055 (6)−0.0032 (6)
C140.0192 (8)0.0255 (8)0.0172 (7)−0.0084 (7)−0.0059 (6)−0.0046 (6)
C150.0285 (9)0.0292 (9)0.0224 (8)−0.0171 (8)−0.0031 (7)−0.0014 (7)
C160.0375 (11)0.0290 (10)0.0270 (9)−0.0158 (8)−0.0071 (8)−0.0012 (7)
C170.0182 (8)0.0158 (8)0.0193 (7)−0.0046 (6)−0.0065 (6)−0.0024 (6)
C180.0190 (8)0.0191 (8)0.0190 (7)−0.0051 (6)−0.0069 (6)−0.0034 (6)
C190.0191 (8)0.0222 (8)0.0226 (8)−0.0050 (7)−0.0051 (6)−0.0071 (6)
C200.0213 (9)0.0289 (10)0.0341 (10)−0.0085 (7)−0.0057 (7)−0.0072 (8)
C210.0253 (12)0.0266 (13)0.0305 (14)−0.0117 (9)−0.0087 (10)−0.0007 (10)
C21X0.043 (8)0.059 (9)0.039 (8)−0.036 (7)−0.001 (6)0.005 (7)
C220.0406 (12)0.0322 (10)0.0328 (10)−0.0193 (9)−0.0144 (9)0.0034 (8)
C230.0303 (10)0.0175 (8)0.0326 (9)−0.0069 (7)−0.0136 (8)−0.0044 (7)
O1—C141.344 (2)C13—H13A0.9500
O1—C151.455 (2)C15—C161.497 (3)
O2—C141.213 (2)C15—H15A0.9900
O3—C231.229 (2)C15—H15B0.9900
N1—C71.322 (2)C16—H16A0.9800
N1—C11.388 (2)C16—H16B0.9800
N2—C71.377 (2)C16—H16C0.9800
N2—C61.384 (2)C17—C181.529 (2)
N2—C171.466 (2)C17—H17A0.9900
N3—C231.351 (2)C17—H17B0.9900
N3—C191.453 (2)C18—C191.525 (2)
N3—C201.466 (2)C18—H18A0.9900
C1—C21.396 (2)C18—H18B0.9900
C1—C61.405 (2)C19—H19A0.9900
C2—C31.392 (2)C19—H19B0.9900
C2—H2A0.9500C20—C211.507 (3)
C3—C41.411 (2)C20—C21X1.663 (16)
C3—C141.486 (2)C20—H20A0.9900
C4—C51.380 (2)C20—H20B0.9900
C4—H4A0.9500C20—H20C0.9600
C5—C61.392 (2)C20—H20D0.9600
C5—H5A0.9500C21—C221.566 (4)
C7—C81.476 (2)C21—H21A0.9900
C8—C131.391 (2)C21—H21B0.9900
C8—C91.396 (2)C21X—C221.318 (15)
C9—C101.394 (2)C21X—H21C0.9900
C9—H9A0.9500C21X—H21D0.9900
C10—C111.385 (2)C22—C231.514 (3)
C10—H10A0.9500C22—H22A0.9900
C11—C121.390 (3)C22—H22B0.9900
C11—H11A0.9500C22—H22C0.9601
C12—C131.386 (2)C22—H22D0.9599
C12—H12A0.9500
C14—O1—C15115.89 (13)C18—C17—H17B109.3
C7—N1—C1104.67 (13)H17A—C17—H17B108.0
C7—N2—C6106.22 (13)C19—C18—C17112.60 (13)
C7—N2—C17130.10 (13)C19—C18—H18A109.1
C6—N2—C17123.66 (13)C17—C18—H18A109.1
C23—N3—C19123.22 (15)C19—C18—H18B109.1
C23—N3—C20113.37 (15)C17—C18—H18B109.1
C19—N3—C20123.40 (14)H18A—C18—H18B107.8
N1—C1—C2129.67 (15)N3—C19—C18113.27 (13)
N1—C1—C6110.17 (14)N3—C19—H19A108.9
C2—C1—C6120.16 (14)C18—C19—H19A108.9
C3—C2—C1117.58 (15)N3—C19—H19B108.9
C3—C2—H2A121.2C18—C19—H19B108.9
C1—C2—H2A121.2H19A—C19—H19B107.7
C2—C3—C4120.96 (14)N3—C20—C21104.03 (16)
C2—C3—C14121.55 (15)N3—C20—C21X98.5 (5)
C4—C3—C14117.49 (14)N3—C20—H20A110.9
C5—C4—C3122.24 (15)C21—C20—H20A110.9
C5—C4—H4A118.9C21X—C20—H20A137.8
C3—C4—H4A118.9N3—C20—H20B110.9
C4—C5—C6116.13 (15)C21—C20—H20B110.9
C4—C5—H5A121.9C21X—C20—H20B86.5
C6—C5—H5A121.9H20A—C20—H20B109.0
N2—C6—C5131.52 (15)N3—C20—H20C110.6
N2—C6—C1105.56 (13)C21—C20—H20C91.1
C5—C6—C1122.89 (14)C21X—C20—H20C119.9
N1—C7—N2113.37 (14)H20B—C20—H20C125.6
N1—C7—C8121.39 (14)N3—C20—H20D110.5
N2—C7—C8125.23 (14)C21—C20—H20D129.9
C13—C8—C9119.02 (15)C21X—C20—H20D108.2
C13—C8—C7117.69 (14)H20A—C20—H20D89.5
C9—C8—C7123.04 (14)H20C—C20—H20D108.7
C10—C9—C8120.16 (15)C20—C21—C22102.78 (19)
C10—C9—H9A119.9C20—C21—H21A111.2
C8—C9—H9A119.9C22—C21—H21A111.2
C11—C10—C9120.22 (16)C20—C21—H21B111.2
C11—C10—H10A119.9C22—C21—H21B111.2
C9—C10—H10A119.9H21A—C21—H21B109.1
C10—C11—C12119.86 (15)C22—C21X—C20106.7 (10)
C10—C11—H11A120.1C22—C21X—H21C110.4
C12—C11—H11A120.1C20—C21X—H21C110.4
C13—C12—C11119.93 (16)C22—C21X—H21D110.4
C13—C12—H12A120.0C20—C21X—H21D110.4
C11—C12—H12A120.0H21C—C21X—H21D108.6
C12—C13—C8120.81 (15)C21X—C22—C23108.3 (5)
C12—C13—H13A119.6C23—C22—C21103.66 (16)
C8—C13—H13A119.6C21X—C22—H22A80.3
O2—C14—O1123.01 (15)C23—C22—H22A111.0
O2—C14—C3124.58 (16)C21—C22—H22A111.0
O1—C14—C3112.41 (14)C21X—C22—H22B132.2
O1—C15—C16107.21 (14)C23—C22—H22B111.0
O1—C15—H15A110.3C21—C22—H22B111.0
C16—C15—H15A110.3H22A—C22—H22B109.0
O1—C15—H15B110.3C21X—C22—H22C118.6
C16—C15—H15B110.3C23—C22—H22C109.4
H15A—C15—H15B108.5C21—C22—H22C92.5
C15—C16—H16A109.5H22A—C22—H22C125.7
C15—C16—H16B109.5C21X—C22—H22D102.6
H16A—C16—H16B109.5C23—C22—H22D109.4
C15—C16—H16C109.5C21—C22—H22D131.5
H16A—C16—H16C109.5H22B—C22—H22D89.0
H16B—C16—H16C109.5H22C—C22—H22D108.1
N2—C17—C18111.47 (13)O3—C23—N3125.09 (17)
N2—C17—H17A109.3O3—C23—C22126.97 (17)
C18—C17—H17A109.3N3—C23—C22107.94 (15)
N2—C17—H17B109.3
C7—N1—C1—C2179.81 (16)C9—C8—C13—C120.0 (2)
C7—N1—C1—C6−0.59 (17)C7—C8—C13—C12174.46 (15)
N1—C1—C2—C3177.87 (15)C15—O1—C14—O22.4 (2)
C6—C1—C2—C3−1.7 (2)C15—O1—C14—C3−176.97 (13)
C1—C2—C3—C40.0 (2)C2—C3—C14—O2167.58 (15)
C1—C2—C3—C14−179.74 (14)C4—C3—C14—O2−12.1 (2)
C2—C3—C4—C51.5 (2)C2—C3—C14—O1−13.1 (2)
C14—C3—C4—C5−178.76 (14)C4—C3—C14—O1167.23 (13)
C3—C4—C5—C6−1.1 (2)C14—O1—C15—C16176.49 (14)
C7—N2—C6—C5177.41 (16)C7—N2—C17—C18103.28 (18)
C17—N2—C6—C5−1.0 (3)C6—N2—C17—C18−78.68 (18)
C7—N2—C6—C1−0.75 (16)N2—C17—C18—C19173.40 (12)
C17—N2—C6—C1−179.19 (13)C23—N3—C19—C18−119.11 (17)
C4—C5—C6—N2−178.55 (15)C20—N3—C19—C1860.0 (2)
C4—C5—C6—C1−0.7 (2)C17—C18—C19—N361.78 (18)
N1—C1—C6—N20.85 (17)C23—N3—C20—C21−19.5 (2)
C2—C1—C6—N2−179.51 (13)C19—N3—C20—C21161.3 (2)
N1—C1—C6—C5−177.51 (14)C23—N3—C20—C21X10.4 (9)
C2—C1—C6—C52.1 (2)C19—N3—C20—C21X−168.8 (9)
C1—N1—C7—N20.10 (17)N3—C20—C21—C2227.4 (3)
C1—N1—C7—C8179.80 (13)C21X—C20—C21—C22−55.1 (10)
C6—N2—C7—N10.42 (18)N3—C20—C21X—C22−20.9 (15)
C17—N2—C7—N1178.73 (14)C21—C20—C21X—C2282.6 (17)
C6—N2—C7—C8−179.26 (14)C20—C21X—C22—C2323.0 (16)
C17—N2—C7—C8−1.0 (3)C20—C21X—C22—C21−63.6 (13)
N1—C7—C8—C13−38.6 (2)C20—C21—C22—C21X76.2 (10)
N2—C7—C8—C13141.03 (16)C20—C21—C22—C23−26.5 (3)
N1—C7—C8—C9135.58 (16)C19—N3—C23—O31.5 (3)
N2—C7—C8—C9−44.8 (2)C20—N3—C23—O3−177.71 (17)
C13—C8—C9—C10−0.6 (2)C19—N3—C23—C22−178.94 (15)
C7—C8—C9—C10−174.69 (15)C20—N3—C23—C221.9 (2)
C8—C9—C10—C110.5 (3)C21X—C22—C23—O3162.4 (12)
C9—C10—C11—C120.1 (3)C21—C22—C23—O3−164.6 (2)
C10—C11—C12—C13−0.6 (3)C21X—C22—C23—N3−17.2 (12)
C11—C12—C13—C80.6 (3)C21—C22—C23—N315.8 (2)
Cg is the centroid of the C1–C6 ring.
D—H···AD—HH···AD···AD—H···A
C5—H5A···O3i0.952.323.266 (2)172
C16—H16B···O3ii0.982.563.341 (3)137
C19—H19B···O3i0.992.573.391 (3)141
C10—H10A···Cgiii0.952.903.516 (2)124
Table 1

Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C1–C6 ring.

D—H⋯AD—HH⋯ADAD—H⋯A
C5—H5A⋯O3i0.952.323.266 (2)172
C16—H16B⋯O3ii0.982.563.341 (3)137
C19—H19B⋯O3i0.992.573.391 (3)141
C10—H10ACgiii0.952.903.516 (2)124

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

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