Literature DB >> 23476157

1-[4-(Prop-2-en-1-yl-oxy)benz-yl]-2-[4-(prop-2-en-1-yl-oxy)phen-yl]-1H-benzimidazole.

Md Lutfor Rahman1, Huey Chong Kwong, Mashitah Mohd Yusoff, Gurumurthy Hegde, Mohamed Ibrahim Mohamed Tahir.   

Abstract

In the title compound, C26H24N2O2, the benzimidazole ring system is almost planar [maximum displacement = 0.025 (1) Å] and makes dihedral angles of 80.48 (5) and 41.57 (5)° with the benzene rings, which are inclined to one another by 65.33 (6)°. In the crystal, mol-ecules are linked via C-H⋯π and weak π-π inter-actions [centroid-centroid distance = 3.8070 (7) Å and inter-planar distance = 3.6160 (5) Å].

Entities:  

Year:  2012        PMID: 23476157      PMCID: PMC3588921          DOI: 10.1107/S160053681204559X

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


Related literature

For the activity of benzimidazole derivatives against viruses, see: Tamm & Sehgal (1978 ▶); Porcari et al. (1998 ▶); Migawa et al. (1998 ▶). For their other biological activity, see: Spasov et al. (1999 ▶); Nakano et al. (2000 ▶); Zhao et al. (2000 ▶); White et al. (2000 ▶); Xiangming et al. (2007 ▶). For related structures, see: Kia et al. (2009 ▶); Zhou et al. (2009 ▶). For synthetic details, see: Lutfor et al. (2008 ▶). For standard bond lengths, see Allen et al. (1987 ▶).

Experimental

Crystal data

C26H24N2O2 M = 396.49 Monoclinic, a = 12.5455 (1) Å b = 10.1989 (1) Å c = 15.9340 (2) Å β = 99.5027 (11)° V = 2010.78 (4) Å3 Z = 4 Cu Kα radiation μ = 0.66 mm−1 T = 100 K 0.35 × 0.23 × 0.08 mm

Data collection

Agilent Technologies Gemini diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011 ▶) T min = 0.80, T max = 0.95 38976 measured reflections 3908 independent reflections 3563 reflections with I > 2.0σ(I) R int = 0.029

Refinement

R[F 2 > 2σ(F 2)] = 0.038 wR(F 2) = 0.100 S = 0.99 3891 reflections 271 parameters H-atom parameters constrained Δρmax = 0.26 e Å−3 Δρmin = −0.25 e Å−3 Data collection: CrysAlis PRO (Agilent, 2011 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ▶); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ▶); molecular graphics: Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: CRYSTALS. Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681204559X/su2508sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681204559X/su2508Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S160053681204559X/su2508Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C26H24N2O2F(000) = 840
Mr = 396.49Dx = 1.310 Mg m3
Monoclinic, P21/nCu Kα radiation, λ = 1.54180 Å
Hall symbol: -P 2ynCell parameters from 17352 reflections
a = 12.5455 (1) Åθ = 4–71°
b = 10.1989 (1) ŵ = 0.66 mm1
c = 15.9340 (2) ÅT = 100 K
β = 99.5027 (11)°Block, pale brown
V = 2010.78 (4) Å30.35 × 0.23 × 0.08 mm
Z = 4
Agilent Technologies Gemini diffractometer3908 independent reflections
Radiation source: sealed x-ray tube3563 reflections with I > 2.0σ(I)
Graphite monochromatorRint = 0.029
ω scansθmax = 71.4°, θmin = 4.2°
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)h = −15→15
Tmin = 0.80, Tmax = 0.95k = −12→12
38976 measured reflectionsl = −19→19
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.100 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.06P)2 + 1.04P], where P = (max(Fo2,0) + 2Fc2)/3
S = 0.99(Δ/σ)max = 0.002
3891 reflectionsΔρmax = 0.26 e Å3
271 parametersΔρmin = −0.25 e Å3
0 restraints
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell esds are taken into account in the estimation of distances, angles and torsion angles
xyzUiso*/Ueq
O1−0.10938 (7)0.03132 (9)0.75160 (6)0.0210 (3)
O20−0.08975 (7)0.86587 (8)0.53875 (6)0.0204 (3)
N70.26914 (8)0.41707 (10)0.66850 (6)0.0168 (3)
N90.32584 (8)0.49128 (10)0.55014 (7)0.0187 (3)
C2−0.02893 (10)0.12293 (12)0.75473 (8)0.0183 (3)
C3−0.01085 (10)0.22357 (13)0.81468 (8)0.0207 (3)
C40.06903 (10)0.31589 (13)0.80889 (8)0.0205 (3)
C50.13284 (9)0.30980 (12)0.74543 (7)0.0174 (3)
C60.21706 (10)0.41599 (12)0.74388 (7)0.0180 (3)
C80.25200 (10)0.50155 (12)0.59986 (8)0.0169 (3)
C100.39729 (10)0.39581 (12)0.58841 (8)0.0180 (3)
C110.36292 (9)0.34893 (12)0.66226 (8)0.0174 (3)
C120.41964 (10)0.25513 (12)0.71540 (8)0.0207 (3)
C130.51416 (10)0.20871 (13)0.69185 (9)0.0233 (4)
C140.55011 (10)0.25460 (13)0.61838 (9)0.0227 (4)
C150.49311 (10)0.34782 (12)0.56574 (8)0.0208 (3)
C160.16006 (10)0.59333 (12)0.58484 (7)0.0170 (3)
C170.17631 (10)0.72115 (12)0.55660 (7)0.0181 (3)
C180.09167 (10)0.80926 (12)0.54134 (8)0.0185 (3)
C19−0.01170 (10)0.77117 (12)0.55381 (7)0.0172 (3)
C21−0.19187 (10)0.83706 (13)0.56480 (8)0.0218 (4)
C22−0.25815 (10)0.95958 (13)0.55465 (8)0.0211 (3)
C23−0.35254 (11)0.96766 (14)0.50457 (9)0.0262 (4)
C24−0.02971 (10)0.64406 (12)0.58006 (8)0.0181 (3)
C250.05619 (10)0.55642 (12)0.59561 (7)0.0180 (3)
C260.11566 (10)0.20690 (12)0.68709 (8)0.0190 (3)
C270.03538 (10)0.11448 (12)0.69133 (8)0.0196 (3)
C28−0.18801 (10)0.05439 (13)0.80606 (8)0.0212 (3)
C29−0.27537 (10)−0.04607 (13)0.78754 (8)0.0208 (3)
C30−0.31212 (10)−0.11109 (13)0.84837 (9)0.0229 (4)
H31−0.053500.229200.860000.0269*
H410.080400.386800.849600.0251*
H610.274300.404300.793400.0235*
H620.182600.502400.747400.0230*
H1210.396100.225900.767100.0255*
H1310.555800.143100.727600.0285*
H1410.617500.220600.605300.0280*
H1510.518800.378400.515600.0261*
H1710.249000.747700.549500.0226*
H1810.102600.896800.522200.0235*
H211−0.229500.765700.528900.0264*
H212−0.178800.809300.626700.0282*
H221−0.228501.036900.587400.0259*
H231−0.380100.894200.469900.0337*
H232−0.394701.046700.501200.0328*
H241−0.101800.615800.586400.0238*
H2510.043100.468100.613200.0223*
H2610.158100.202300.641600.0234*
H2710.022800.043200.650500.0239*
H281−0.220600.143900.794400.0266*
H282−0.153900.048700.867200.0255*
H291−0.30710−0.060000.727800.0250*
H301−0.36980−0.172300.835600.0284*
H302−0.27840−0.096700.906600.0289*
U11U22U33U12U13U23
O10.0197 (4)0.0206 (4)0.0237 (5)−0.0026 (3)0.0067 (4)−0.0017 (4)
O200.0186 (4)0.0183 (4)0.0248 (5)0.0026 (3)0.0054 (3)0.0036 (3)
N70.0171 (5)0.0166 (5)0.0167 (5)0.0001 (4)0.0027 (4)0.0015 (4)
N90.0188 (5)0.0188 (5)0.0189 (5)0.0005 (4)0.0040 (4)0.0009 (4)
C20.0165 (6)0.0176 (6)0.0202 (6)0.0009 (5)0.0010 (5)0.0044 (5)
C30.0208 (6)0.0250 (6)0.0170 (6)−0.0007 (5)0.0048 (5)0.0012 (5)
C40.0225 (6)0.0224 (6)0.0163 (6)−0.0005 (5)0.0020 (5)−0.0018 (5)
C50.0167 (6)0.0184 (6)0.0164 (6)0.0022 (5)0.0010 (4)0.0040 (5)
C60.0198 (6)0.0193 (6)0.0149 (6)−0.0002 (5)0.0029 (5)0.0009 (5)
C80.0193 (6)0.0153 (6)0.0155 (6)−0.0022 (5)0.0010 (5)−0.0004 (4)
C100.0190 (6)0.0155 (6)0.0190 (6)−0.0020 (5)0.0014 (5)−0.0011 (5)
C110.0166 (6)0.0158 (6)0.0193 (6)−0.0017 (5)0.0012 (5)−0.0020 (5)
C120.0217 (6)0.0179 (6)0.0211 (6)−0.0014 (5)−0.0002 (5)0.0018 (5)
C130.0216 (6)0.0182 (6)0.0276 (7)0.0019 (5)−0.0032 (5)0.0004 (5)
C140.0162 (6)0.0211 (6)0.0302 (7)0.0003 (5)0.0023 (5)−0.0062 (5)
C150.0200 (6)0.0194 (6)0.0234 (6)−0.0025 (5)0.0051 (5)−0.0034 (5)
C160.0201 (6)0.0178 (6)0.0126 (5)0.0009 (5)0.0012 (4)−0.0012 (4)
C170.0190 (6)0.0200 (6)0.0155 (6)−0.0011 (5)0.0035 (4)0.0000 (5)
C180.0229 (6)0.0157 (6)0.0170 (6)−0.0006 (5)0.0035 (5)0.0015 (5)
C190.0194 (6)0.0180 (6)0.0137 (5)0.0022 (5)0.0011 (4)−0.0012 (4)
C210.0176 (6)0.0221 (6)0.0262 (7)0.0002 (5)0.0049 (5)0.0028 (5)
C220.0222 (6)0.0210 (6)0.0209 (6)0.0004 (5)0.0063 (5)0.0009 (5)
C230.0242 (7)0.0251 (7)0.0285 (7)0.0027 (5)0.0019 (5)−0.0005 (5)
C240.0171 (6)0.0194 (6)0.0173 (6)−0.0013 (5)0.0015 (4)−0.0007 (5)
C250.0220 (6)0.0154 (6)0.0158 (6)−0.0014 (5)0.0008 (5)−0.0005 (4)
C260.0187 (6)0.0205 (6)0.0185 (6)0.0023 (5)0.0051 (5)0.0014 (5)
C270.0205 (6)0.0179 (6)0.0202 (6)0.0019 (5)0.0030 (5)−0.0019 (5)
C280.0200 (6)0.0223 (6)0.0223 (6)0.0003 (5)0.0068 (5)−0.0001 (5)
C290.0187 (6)0.0228 (6)0.0205 (6)0.0015 (5)0.0023 (5)−0.0016 (5)
C300.0207 (6)0.0230 (6)0.0251 (7)−0.0018 (5)0.0040 (5)−0.0030 (5)
O1—C21.3702 (15)C24—C251.3905 (18)
O1—C281.4367 (16)C26—C271.3892 (18)
O20—C191.3681 (15)C28—C291.4937 (18)
O20—C211.4407 (16)C29—C301.3188 (19)
N7—C61.4590 (15)C3—H310.9700
N7—C81.3810 (16)C4—H410.9700
N7—C111.3841 (15)C6—H610.9800
N9—C81.3187 (16)C6—H620.9900
N9—C101.3939 (16)C12—H1210.9700
C2—C31.3950 (18)C13—H1310.9700
C2—C271.3957 (18)C14—H1410.9700
C3—C41.3892 (18)C15—H1510.9600
C4—C51.3908 (17)C17—H1710.9800
C5—C61.5161 (17)C18—H1810.9600
C5—C261.3949 (17)C21—H2111.0000
C8—C161.4740 (18)C21—H2121.0100
C10—C111.4024 (18)C22—H2210.9800
C10—C151.3995 (18)C23—H2310.9600
C11—C121.3927 (17)C23—H2320.9600
C12—C131.3849 (18)C24—H2410.9700
C13—C141.4026 (19)C25—H2510.9700
C14—C151.3859 (18)C26—H2610.9700
C16—C171.4049 (17)C27—H2710.9700
C16—C251.3939 (18)C28—H2811.0000
C17—C181.3816 (18)C28—H2821.0000
C18—C191.3990 (18)C29—H2910.9800
C19—C241.3921 (17)C30—H3010.9500
C21—C221.4949 (19)C30—H3020.9700
C22—C231.3167 (19)
C2—O1—C28116.19 (10)C5—C4—H41119.00
C19—O20—C21116.76 (9)N7—C6—H61107.00
C6—N7—C8128.63 (10)N7—C6—H62107.00
C6—N7—C11123.84 (10)C5—C6—H61109.00
C8—N7—C11106.23 (10)C5—C6—H62109.00
C8—N9—C10104.92 (10)H61—C6—H62109.00
O1—C2—C3124.21 (11)C11—C12—H121122.00
O1—C2—C27116.22 (11)C13—C12—H121121.00
C3—C2—C27119.54 (11)C12—C13—H131119.00
C2—C3—C4119.39 (12)C14—C13—H131120.00
C3—C4—C5121.74 (12)C13—C14—H141118.00
C4—C5—C6117.79 (11)C15—C14—H141120.00
C4—C5—C26118.29 (11)C10—C15—H151121.00
C6—C5—C26123.92 (10)C14—C15—H151121.00
N7—C6—C5115.27 (10)C16—C17—H171119.00
N7—C8—N9113.16 (11)C18—C17—H171120.00
N7—C8—C16122.69 (11)C17—C18—H181121.00
N9—C8—C16124.15 (11)C19—C18—H181119.00
N9—C10—C11109.92 (11)O20—C21—H211110.00
N9—C10—C15130.48 (11)O20—C21—H212109.00
C11—C10—C15119.57 (11)C22—C21—H211110.00
N7—C11—C10105.77 (10)C22—C21—H212110.00
N7—C11—C12131.02 (11)H211—C21—H212110.00
C10—C11—C12123.18 (11)C21—C22—H221117.00
C11—C12—C13116.39 (12)C23—C22—H221120.00
C12—C13—C14121.32 (12)C22—C23—H231120.00
C13—C14—C15121.95 (12)C22—C23—H232121.00
C10—C15—C14117.59 (12)H231—C23—H232119.00
C8—C16—C17119.36 (11)C19—C24—H241121.00
C8—C16—C25122.07 (11)C25—C24—H241120.00
C17—C16—C25118.56 (11)C16—C25—H251120.00
C16—C17—C18120.79 (12)C24—C25—H251119.00
C17—C18—C19119.86 (11)C5—C26—H261119.00
O20—C19—C18115.62 (11)C27—C26—H261120.00
O20—C19—C24124.28 (11)C2—C27—H271119.00
C18—C19—C24120.10 (11)C26—C27—H271121.00
O20—C21—C22107.67 (10)O1—C28—H281110.00
C21—C22—C23123.12 (12)O1—C28—H282111.00
C19—C24—C25119.52 (12)C29—C28—H281109.00
C16—C25—C24121.15 (11)C29—C28—H282110.00
C5—C26—C27120.77 (11)H281—C28—H282109.00
C2—C27—C26120.24 (11)C28—C29—H291117.00
O1—C28—C29108.84 (10)C30—C29—H291120.00
C28—C29—C30122.26 (12)C29—C30—H301121.00
C2—C3—H31120.00C29—C30—H302119.00
C4—C3—H31120.00H301—C30—H302120.00
C3—C4—H41119.00
C28—O1—C2—C39.44 (17)C4—C5—C26—C271.28 (18)
C28—O1—C2—C27−168.51 (11)N9—C8—C16—C17−40.64 (17)
C2—O1—C28—C29173.88 (10)N7—C8—C16—C25−42.45 (17)
C21—O20—C19—C18−169.69 (10)N7—C8—C16—C17139.28 (12)
C21—O20—C19—C2410.16 (16)N9—C8—C16—C25137.63 (13)
C19—O20—C21—C22171.61 (10)N9—C10—C15—C14177.71 (13)
C6—N7—C11—C10−168.56 (11)C11—C10—C15—C140.06 (19)
C8—N7—C11—C10−0.61 (13)C15—C10—C11—C12−0.17 (19)
C6—N7—C11—C129.7 (2)N9—C10—C11—N70.11 (14)
C8—N7—C11—C12177.59 (13)N9—C10—C11—C12−178.27 (11)
C8—N7—C6—C5104.28 (14)C15—C10—C11—N7178.21 (11)
C11—N7—C6—C5−90.59 (14)N7—C11—C12—C13−177.85 (13)
C6—N7—C8—N9168.14 (11)C10—C11—C12—C130.08 (19)
C11—N7—C8—N90.97 (14)C11—C12—C13—C140.11 (19)
C6—N7—C8—C16−11.79 (19)C12—C13—C14—C15−0.2 (2)
C11—N7—C8—C16−178.95 (11)C13—C14—C15—C100.1 (2)
C10—N9—C8—N7−0.88 (14)C8—C16—C17—C18179.53 (11)
C10—N9—C8—C16179.04 (11)C25—C16—C17—C181.20 (17)
C8—N9—C10—C110.46 (14)C8—C16—C25—C24−179.18 (11)
C8—N9—C10—C15−177.37 (13)C17—C16—C25—C24−0.90 (17)
O1—C2—C3—C4−176.16 (12)C16—C17—C18—C19−0.19 (18)
O1—C2—C27—C26176.99 (11)C17—C18—C19—O20178.71 (11)
C27—C2—C3—C41.74 (19)C17—C18—C19—C24−1.16 (18)
C3—C2—C27—C26−1.07 (19)O20—C19—C24—C25−178.39 (11)
C2—C3—C4—C5−0.92 (19)C18—C19—C24—C251.46 (18)
C3—C4—C5—C6179.34 (11)O20—C21—C22—C23120.11 (14)
C3—C4—C5—C26−0.59 (19)C19—C24—C25—C16−0.42 (18)
C4—C5—C6—N7−170.42 (11)C5—C26—C27—C2−0.46 (19)
C6—C5—C26—C27−178.65 (11)O1—C28—C29—C30133.16 (13)
C26—C5—C6—N79.50 (17)
D—H···AD—HH···AD···AD—H···A
C12—H121···Cg4i0.972.623.5064 (13)153
C23—H231···Cg3ii0.962.733.6859 (15)175
C30—H301···Cg2iii0.952.723.6202 (14)159
Table 1

Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C2–C5/C26/C27 ring; Cg3 is the centroid of the C10–C15 ring and Cg4 is the centroid of the C16–C19/C24/25 ring.

D—H⋯A D—HH⋯A DA D—H⋯A
C12—H121⋯Cg4i 0.972.623.5064 (13)153
C23—H231⋯Cg3ii 0.962.733.6859 (15)175
C30—H301⋯Cg2iii 0.952.723.6202 (14)159

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

  8 in total

1.  Design, synthesis, and antiviral activity of alpha-nucleosides: D- and L-isomers of lyxofuranosyl- and (5-deoxylyxofuranosyl)benzimidazoles.

Authors:  M T Migawa; J L Girardet; J A Walker; G W Koszalka; S D Chamberlain; J C Drach; L B Townsend
Journal:  J Med Chem       Date:  1998-04-09       Impact factor: 7.446

Review 2.  Halobenzimidazole ribosides and RNA synthesis of cells and viruses.

Authors:  I Tamm; P B Sehgal
Journal:  Adv Virus Res       Date:  1978       Impact factor: 9.937

3.  Design, synthesis, and antiviral evaluations of 1-(substituted benzyl)-2-substituted-5,6-dichlorobenzimidazoles as nonnucleoside analogues of 2,5,6-trichloro-1-(beta-D-ribofuranosyl)benzimidazole.

Authors:  A R Porcari; R V Devivar; L S Kucera; J C Drach; L B Townsend
Journal:  J Med Chem       Date:  1998-04-09       Impact factor: 7.446

4.  Design, synthesis, and in vitro biological activity of benzimidazole based factor Xa inhibitors.

Authors:  Z Zhao; D O Arnaiz; B Griedel; S Sakata; J L Dallas; M Whitlow; L Trinh; J Post; A Liang; M M Morrissey; K J Shaw
Journal:  Bioorg Med Chem Lett       Date:  2000-05-01       Impact factor: 2.823

5.  Synthesis and biological activities of novel antiallergic agents with 5-lipoxygenase inhibiting action.

Authors:  H Nakano; T Inoue; N Kawasaki; H Miyataka; H Matsumoto; T Taguchi; N Inagaki; H Nagai; T Satoh
Journal:  Bioorg Med Chem       Date:  2000-02       Impact factor: 3.641

6.  Resistance-modifying agents. 9. Synthesis and biological properties of benzimidazole inhibitors of the DNA repair enzyme poly(ADP-ribose) polymerase.

Authors:  A W White; R Almassy; A H Calvert; N J Curtin; R J Griffin; Z Hostomsky; K Maegley; D R Newell; S Srinivasan; B T Golding
Journal:  J Med Chem       Date:  2000-11-02       Impact factor: 7.446

7.  4-[1-(4-Cyano-benz-yl)-1H-benzimidazol-2-yl]benzonitrile.

Authors:  Reza Kia; Hoong-Kun Fun; Hadi Kargar
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-03-06

8.  1-(4-tert-Butyl-benz-yl)-2-(4-tert-butyl-phen-yl)-1H-benzimidazole.

Authors:  Jian-Cheng Zhou; Zheng-Yun Zhang; Nai-Xu Li; Chuan-Ming Zhang
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-11-07
  8 in total

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