Literature DB >> 22199745

Ethyl 1-(butan-2-yl)-2-(2-meth-oxy-phen-yl)-1H-benzimidazole-5-carboxyl-ate.

Natarajan Arumugam, Nurziana Ngah, Hasnah Osman, Aisyah Saad Abdul Rahim.   

Abstract

In the title compound, C(21)H(24)N(2)O(3), the mean planes of the benzene ring and the benzimidazole ring system form a dihedral angle of 69.94 (7)°. The ethyl group atoms of the ethano-ate fragment are disordered over two sets of sites, with refined occupancies of 0.742 (6) and 0.258 (6). In the crystal, there are weak C-H⋯N hydrogen bonds which connect mol-ecules into chains along the b axis. A weak inter-molecular C-H⋯π inter-action is also observed.

Entities:  

Year:  2011        PMID: 22199745      PMCID: PMC3238892          DOI: 10.1107/S1600536811046095

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


Related literature

For the synthesis and a closely related structure, see: Arumugam et al. (2010 ▶). For background to microwave chemistry, see: Kappe & Dallinger (2006 ▶); Hamzah et al. (2011 ▶). For the synthesis of benzimidazole derivatives and their applications, see: Wang et al. (2011 ▶); VanVliet et al. (2005 ▶); Loupy (2002 ▶); Santagada et al. (2001 ▶); Nicolaou et al. (2000 ▶); Evans et al. (1988 ▶). For standard bond lengths, see: Allen et al. (1987 ▶).

Experimental

Crystal data

C21H24N2O3 M = 352.42 Monoclinic, a = 10.6746 (3) Å b = 12.3344 (4) Å c = 15.6158 (5) Å β = 106.901 (1)° V = 1967.25 (11) Å3 Z = 4 Mo Kα radiation μ = 0.08 mm−1 T = 296 K 0.52 × 0.44 × 0.32 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.959, T max = 0.975 17688 measured reflections 3475 independent reflections 2712 reflections with I > 2σ(I) R int = 0.025

Refinement

R[F 2 > 2σ(F 2)] = 0.045 wR(F 2) = 0.122 S = 1.05 3475 reflections 245 parameters 3 restraints H-atom parameters constrained Δρmax = 0.35 e Å−3 Δρmin = −0.18 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/S1600536811046095/lh5357sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811046095/lh5357Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811046095/lh5357Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C21H24N2O3F(000) = 752
Mr = 352.42Dx = 1.190 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 8039 reflections
a = 10.6746 (3) Åθ = 2.1–25.0°
b = 12.3344 (4) ŵ = 0.08 mm1
c = 15.6158 (5) ÅT = 296 K
β = 106.901 (1)°Block, colourless
V = 1967.25 (11) Å30.52 × 0.44 × 0.32 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer3475 independent reflections
Radiation source: fine-focus sealed tube2712 reflections with I > 2σ(I)
graphiteRint = 0.025
Detector resolution: 83.66 pixels mm-1θmax = 25.0°, θmin = 2.1°
φ and ω scanh = −11→12
Absorption correction: multi-scan (SADABS; Bruker, 2009)k = −11→14
Tmin = 0.959, Tmax = 0.975l = −18→17
17688 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.122H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.0526P)2 + 0.5324P] where P = (Fo2 + 2Fc2)/3
3475 reflections(Δ/σ)max < 0.001
245 parametersΔρmax = 0.35 e Å3
3 restraintsΔρmin = −0.18 e Å3
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.
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*/UeqOcc. (<1)
O10.22019 (14)0.60261 (11)0.83252 (9)0.0694 (4)
O20.16647 (18)1.12078 (12)1.21044 (10)0.0894 (5)
O30.10964 (19)1.17279 (12)1.06857 (10)0.0917 (5)
N10.29480 (16)0.88252 (11)0.90695 (9)0.0562 (4)
N20.36352 (14)0.74369 (11)1.00207 (8)0.0475 (3)
C10.34617 (16)0.78558 (13)0.91776 (10)0.0467 (4)
C20.32104 (16)0.82294 (12)1.04995 (10)0.0445 (4)
C30.31600 (18)0.82949 (14)1.13790 (11)0.0551 (5)
H30.34500.77291.17810.066*
C40.26638 (18)0.92316 (14)1.16254 (11)0.0542 (4)
H40.26380.93041.22130.065*
C50.21963 (17)1.00806 (13)1.10246 (11)0.0496 (4)
C60.22494 (19)1.00099 (13)1.01515 (11)0.0540 (5)
H60.19421.05720.97480.065*
C70.27727 (17)0.90788 (13)0.98941 (10)0.0473 (4)
C80.38804 (17)0.72852 (14)0.84697 (10)0.0498 (4)
C90.49117 (19)0.76994 (16)0.82051 (12)0.0606 (5)
H90.53450.83160.84840.073*
C100.5308 (2)0.72096 (19)0.75319 (13)0.0711 (6)
H100.60030.74930.73580.085*
C110.4666 (2)0.63017 (18)0.71234 (13)0.0694 (6)
H110.49390.59660.66750.083*
C120.3627 (2)0.58773 (16)0.73630 (11)0.0608 (5)
H120.31960.52640.70760.073*
C130.32254 (18)0.63726 (14)0.80372 (11)0.0517 (4)
C140.1359 (2)0.52171 (19)0.78162 (15)0.0819 (6)
H14A0.09810.54730.72160.123*
H14B0.06750.50630.80840.123*
H14C0.18520.45690.78050.123*
C150.42814 (19)0.63962 (14)1.03579 (12)0.0601 (5)
H150.44830.60420.98520.072*
C160.3357 (2)0.56259 (16)1.06687 (15)0.0782 (6)
H16A0.31080.59571.11510.117*
H16B0.38000.49551.08690.117*
H16C0.25890.54881.01790.117*
C170.5563 (2)0.65788 (19)1.10606 (15)0.0816 (6)
H17A0.53950.69001.15830.098*
H17B0.59840.58841.12380.098*
C180.6475 (2)0.7294 (2)1.07565 (18)0.1013 (8)
H18A0.65830.70171.02080.152*
H18B0.73080.73121.12060.152*
H18C0.61200.80141.06600.152*
C190.1636 (2)1.10442 (15)1.13428 (13)0.0599 (5)
C200.0550 (11)1.2722 (4)1.0931 (10)0.103 (2)0.742 (6)
H20A−0.02071.25601.11340.124*0.742 (6)
H20B0.11961.30911.14090.124*0.742 (6)
C210.0176 (5)1.3391 (3)1.0141 (4)0.1145 (15)0.742 (6)
H21A−0.02251.40451.02690.172*0.742 (6)
H21B−0.04361.30050.96670.172*0.742 (6)
H21C0.09381.35710.99630.172*0.742 (6)
C21A0.0967 (16)1.3540 (11)1.0711 (11)0.1145 (15)0.258 (6)
H21D0.05691.41751.08730.172*0.258 (6)
H21E0.09361.35811.00910.172*0.258 (6)
H21F0.18631.34951.10730.172*0.258 (6)
C20A0.027 (4)1.2591 (10)1.086 (3)0.103 (2)0.258 (6)
H20C−0.06051.25611.04390.124*0.258 (6)
H20D0.02101.25621.14630.124*0.258 (6)
U11U22U33U12U13U23
O10.0819 (9)0.0691 (9)0.0610 (8)−0.0156 (7)0.0268 (7)−0.0184 (6)
O20.1453 (15)0.0707 (10)0.0661 (9)0.0110 (9)0.0526 (10)−0.0165 (7)
O30.1471 (15)0.0615 (9)0.0743 (10)0.0397 (9)0.0445 (10)−0.0029 (8)
N10.0877 (11)0.0440 (8)0.0398 (8)0.0137 (7)0.0233 (7)0.0026 (6)
N20.0624 (9)0.0405 (7)0.0401 (7)0.0093 (6)0.0158 (6)0.0030 (6)
C10.0582 (10)0.0426 (9)0.0392 (9)0.0031 (8)0.0140 (7)−0.0008 (7)
C20.0558 (10)0.0399 (9)0.0390 (9)0.0005 (7)0.0158 (7)0.0000 (7)
C30.0745 (12)0.0514 (10)0.0420 (9)0.0053 (9)0.0212 (8)0.0077 (8)
C40.0724 (12)0.0558 (11)0.0394 (9)−0.0028 (9)0.0243 (8)−0.0021 (8)
C50.0639 (11)0.0422 (9)0.0473 (10)−0.0050 (8)0.0233 (8)−0.0073 (7)
C60.0795 (12)0.0391 (9)0.0451 (10)0.0076 (8)0.0207 (9)0.0020 (7)
C70.0662 (11)0.0398 (9)0.0377 (9)0.0034 (8)0.0179 (8)−0.0004 (7)
C80.0630 (11)0.0465 (10)0.0396 (9)0.0106 (8)0.0146 (8)−0.0004 (7)
C90.0673 (12)0.0607 (12)0.0557 (11)0.0019 (9)0.0206 (9)−0.0064 (9)
C100.0667 (12)0.0876 (15)0.0654 (12)0.0048 (11)0.0291 (10)−0.0104 (11)
C110.0724 (13)0.0841 (15)0.0542 (11)0.0195 (11)0.0224 (10)−0.0142 (10)
C120.0739 (13)0.0579 (11)0.0455 (10)0.0130 (10)0.0093 (9)−0.0108 (8)
C130.0608 (11)0.0507 (10)0.0417 (9)0.0078 (8)0.0118 (8)−0.0020 (8)
C140.0747 (14)0.0818 (15)0.0828 (15)−0.0122 (12)0.0129 (11)−0.0203 (12)
C150.0793 (13)0.0460 (10)0.0529 (11)0.0168 (9)0.0158 (9)0.0044 (8)
C160.1111 (18)0.0497 (11)0.0806 (14)0.0041 (11)0.0386 (13)0.0131 (10)
C170.0878 (15)0.0715 (14)0.0733 (14)0.0173 (11)0.0039 (11)0.0000 (11)
C180.0757 (16)0.101 (2)0.111 (2)−0.0132 (13)0.0018 (13)−0.0121 (15)
C190.0810 (13)0.0475 (10)0.0584 (12)−0.0050 (9)0.0315 (10)−0.0091 (9)
C200.153 (6)0.058 (2)0.108 (4)0.034 (3)0.053 (5)−0.011 (2)
C210.117 (4)0.081 (2)0.142 (4)0.041 (3)0.031 (3)0.006 (3)
C21A0.117 (4)0.081 (2)0.142 (4)0.041 (3)0.031 (3)0.006 (3)
C20A0.153 (6)0.058 (2)0.108 (4)0.034 (3)0.053 (5)−0.011 (2)
O1—C131.365 (2)C12—C131.388 (2)
O1—C141.422 (2)C12—H120.9300
O2—C191.198 (2)C14—H14A0.9600
O3—C191.324 (2)C14—H14B0.9600
O3—C20A1.456 (5)C14—H14C0.9600
O3—C201.456 (4)C15—C171.501 (3)
N1—C11.306 (2)C15—C161.546 (3)
N1—C71.390 (2)C15—H150.9800
N2—C11.376 (2)C16—H16A0.9600
N2—C21.385 (2)C16—H16B0.9600
N2—C151.480 (2)C16—H16C0.9600
C1—C81.485 (2)C17—C181.489 (3)
C2—C31.392 (2)C17—H17A0.9700
C2—C71.397 (2)C17—H17B0.9700
C3—C41.372 (2)C18—H18A0.9600
C3—H30.9300C18—H18B0.9600
C4—C51.398 (2)C18—H18C0.9600
C4—H40.9300C20—C211.441 (12)
C5—C61.384 (2)C20—H20A0.9700
C5—C191.480 (2)C20—H20B0.9700
C6—C71.387 (2)C21—H21A0.9600
C6—H60.9300C21—H21B0.9600
C8—C91.381 (3)C21—H21C0.9600
C8—C131.392 (2)C21A—C20A1.440 (13)
C9—C101.381 (3)C21A—H21D0.9600
C9—H90.9300C21A—H21E0.9600
C10—C111.370 (3)C21A—H21F0.9600
C10—H100.9300C20A—H20C0.9700
C11—C121.373 (3)C20A—H20D0.9700
C11—H110.9300
C13—O1—C14118.20 (15)N2—C15—C17111.19 (16)
C19—O3—C20A118.4 (17)N2—C15—C16111.76 (15)
C19—O3—C20116.7 (6)C17—C15—C16113.08 (17)
C1—N1—C7104.53 (13)N2—C15—H15106.8
C1—N2—C2106.11 (12)C17—C15—H15106.8
C1—N2—C15125.83 (13)C16—C15—H15106.8
C2—N2—C15127.75 (13)C15—C16—H16A109.5
N1—C1—N2113.72 (13)C15—C16—H16B109.5
N1—C1—C8122.94 (14)H16A—C16—H16B109.5
N2—C1—C8123.27 (14)C15—C16—H16C109.5
N2—C2—C3133.33 (15)H16A—C16—H16C109.5
N2—C2—C7105.16 (13)H16B—C16—H16C109.5
C3—C2—C7121.52 (15)C18—C17—C15113.38 (19)
C4—C3—C2117.02 (15)C18—C17—H17A108.9
C4—C3—H3121.5C15—C17—H17A108.9
C2—C3—H3121.5C18—C17—H17B108.9
C3—C4—C5122.30 (15)C15—C17—H17B108.9
C3—C4—H4118.8H17A—C17—H17B107.7
C5—C4—H4118.8C17—C18—H18A109.5
C6—C5—C4120.35 (15)C17—C18—H18B109.5
C6—C5—C19121.18 (16)H18A—C18—H18B109.5
C4—C5—C19118.47 (15)C17—C18—H18C109.5
C5—C6—C7118.24 (15)H18A—C18—H18C109.5
C5—C6—H6120.9H18B—C18—H18C109.5
C7—C6—H6120.9O2—C19—O3122.81 (18)
C6—C7—N1128.98 (15)O2—C19—C5124.93 (19)
C6—C7—C2120.55 (14)O3—C19—C5112.26 (15)
N1—C7—C2110.46 (14)C21—C20—O3106.8 (8)
C9—C8—C13119.04 (15)C21—C20—H20A110.4
C9—C8—C1119.08 (16)O3—C20—H20A110.4
C13—C8—C1121.81 (16)C21—C20—H20B110.4
C10—C9—C8120.85 (19)O3—C20—H20B110.4
C10—C9—H9119.6H20A—C20—H20B108.6
C8—C9—H9119.6C20—C21—H21A109.5
C11—C10—C9119.33 (19)C20—C21—H21B109.5
C11—C10—H10120.3H21A—C21—H21B109.5
C9—C10—H10120.3C20—C21—H21C109.5
C10—C11—C12121.27 (17)H21A—C21—H21C109.5
C10—C11—H11119.4H21B—C21—H21C109.5
C12—C11—H11119.4C20A—C21A—H21D109.5
C11—C12—C13119.38 (18)C20A—C21A—H21E109.5
C11—C12—H12120.3H21D—C21A—H21E109.5
C13—C12—H12120.3C20A—C21A—H21F109.5
O1—C13—C12124.40 (17)H21D—C21A—H21F109.5
O1—C13—C8115.49 (14)H21E—C21A—H21F109.5
C12—C13—C8120.11 (17)C21A—C20A—O3101.4 (11)
O1—C14—H14A109.5C21A—C20A—H20C111.5
O1—C14—H14B109.5O3—C20A—H20C111.5
H14A—C14—H14B109.5C21A—C20A—H20D111.5
O1—C14—H14C109.5O3—C20A—H20D111.5
H14A—C14—H14C109.5H20C—C20A—H20D109.3
H14B—C14—H14C109.5
C7—N1—C1—N20.4 (2)C1—C8—C9—C10−178.21 (17)
C7—N1—C1—C8−176.62 (16)C8—C9—C10—C110.0 (3)
C2—N2—C1—N1−1.2 (2)C9—C10—C11—C120.8 (3)
C15—N2—C1—N1−175.22 (16)C10—C11—C12—C13−0.5 (3)
C2—N2—C1—C8175.86 (16)C14—O1—C13—C12−10.5 (3)
C15—N2—C1—C81.8 (3)C14—O1—C13—C8169.60 (17)
C1—N2—C2—C3−178.75 (18)C11—C12—C13—O1179.54 (17)
C15—N2—C2—C3−4.9 (3)C11—C12—C13—C8−0.6 (3)
C1—N2—C2—C71.37 (18)C9—C8—C13—O1−178.76 (16)
C15—N2—C2—C7175.26 (16)C1—C8—C13—O1−1.7 (2)
N2—C2—C3—C4180.00 (18)C9—C8—C13—C121.3 (3)
C7—C2—C3—C4−0.1 (3)C1—C8—C13—C12178.40 (16)
C2—C3—C4—C51.5 (3)C1—N2—C15—C17111.1 (2)
C3—C4—C5—C6−1.5 (3)C2—N2—C15—C17−61.7 (2)
C3—C4—C5—C19177.90 (17)C1—N2—C15—C16−121.50 (19)
C4—C5—C6—C70.2 (3)C2—N2—C15—C1665.7 (2)
C19—C5—C6—C7−179.26 (17)N2—C15—C17—C18−55.0 (2)
C5—C6—C7—N1−178.97 (17)C16—C15—C17—C18178.28 (19)
C5—C6—C7—C21.2 (3)C20A—O3—C19—O2−13.3 (18)
C1—N1—C7—C6−179.38 (19)C20—O3—C19—O21.3 (5)
C1—N1—C7—C20.5 (2)C20A—O3—C19—C5167.2 (17)
N2—C2—C7—C6178.70 (16)C20—O3—C19—C5−178.2 (5)
C3—C2—C7—C6−1.2 (3)C6—C5—C19—O2−172.8 (2)
N2—C2—C7—N1−1.19 (19)C4—C5—C19—O27.8 (3)
C3—C2—C7—N1178.91 (16)C6—C5—C19—O36.7 (3)
N1—C1—C8—C965.8 (2)C4—C5—C19—O3−172.74 (17)
N2—C1—C8—C9−110.9 (2)C19—O3—C20—C21172.8 (5)
N1—C1—C8—C13−111.2 (2)C20A—O3—C20—C21−86 (10)
N2—C1—C8—C1372.0 (2)C19—O3—C20A—C21A119 (2)
C13—C8—C9—C10−1.1 (3)C20—O3—C20A—C21A33 (6)
Cg is the centroid of the N1/N2/C1/C2/C7 ring.
D—H···AD—HH···AD···AD—H···A
C12—H12···N1i0.932.563.471 (2)165
C20A—H20C···Cgii0.972.903.71 (4)141
Table 1

Hydrogen-bond geometry (Å, °)

Cg is the centroid of the N1/N2/C1/C2/C7 ring.

D—H⋯AD—HH⋯ADAD—H⋯A
C12—H12⋯N1i0.932.563.471 (2)165
C20A—H20CCgii0.972.903.71 (4)141

Symmetry codes: (i) ; (ii) .

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Journal:  ACS Comb Sci       Date:  2011-08-16       Impact factor: 3.784

4.  Methods for drug discovery: development of potent, selective, orally effective cholecystokinin antagonists.

Authors:  B E Evans; K E Rittle; M G Bock; R M DiPardo; R M Freidinger; W L Whitter; G F Lundell; D F Veber; P S Anderson; R S Chang
Journal:  J Med Chem       Date:  1988-12       Impact factor: 7.446

5.  Ethyl 1-sec-butyl-2-(4-methoxy-phen-yl)-1H-benzimidazole-5-carboxyl-ate.

Authors:  Natarajan Arumugam; Aisyah Saad Abdul Rahim; Hasnah Osman; Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-03-17

6.  Ethyl 1-(2-hy-droxy-eth-yl)-2-propyl-1H-benzimidazole-5-carboxyl-ate.

Authors:  Nurasyikin Hamzah; Nurziana Ngah; Shafida Abd Hamid; Aisyah Saad Abdul Rahim
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-09-30

7.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  7 in total

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