Literature DB >> 22058794

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

Nurasyikin Hamzah, Nurziana Ngah, Shafida Abd Hamid, Aisyah Saad Abdul Rahim.   

Abstract

In the title compound, C(15)H(20)N(2)O(3), the benzimidazole ring is essentially planar, with a maximum deviation from the mean plane of 0.012 (1) Å. The crystal structure is stabilized by inter-molecular O-H⋯N hydrogen bonds, forming centrosymmetric dimers, which are connected in the [100] direction through weak C-H⋯O contacts.

Entities:  

Year:  2011        PMID: 22058794      PMCID: PMC3201285          DOI: 10.1107/S1600536811037421

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


Related literature

For the synthesis of the title compound, see: Arumugam et al. (2010 ▶); Kappe (2004 ▶). For general background and therapeutic properties of benzimidazole derivatives, see: Rao et al. (2002 ▶); Khalafi-Nezhad et al. (2005 ▶); Tonelli et al. (2010 ▶); Chen et al. (2007 ▶). For the low-temperature device used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C15H20N2O3 M = 276.33 Triclinic, a = 8.5081 (3) Å b = 8.5573 (3) Å c = 10.0117 (4) Å α = 94.671 (3)° β = 106.903 (2)° γ = 98.334 (3)° V = 684.16 (4) Å3 Z = 2 Mo Kα radiation μ = 0.09 mm−1 T = 100 K 0.60 × 0.20 × 0.07 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.946, T max = 0.994 10526 measured reflections 2401 independent reflections 2075 reflections with I > 2σ(I) R int = 0.026

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.087 S = 1.08 2401 reflections 187 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.20 e Å−3 Δρmin = −0.25 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/S1600536811037421/bh2376sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811037421/bh2376Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811037421/bh2376Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C15H20N2O3Z = 2
Mr = 276.33F(000) = 296
Triclinic, P1Dx = 1.341 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.5081 (3) ÅCell parameters from 5332 reflections
b = 8.5573 (3) Åθ = 2.1–25.0°
c = 10.0117 (4) ŵ = 0.09 mm1
α = 94.671 (3)°T = 100 K
β = 106.903 (2)°Plate, colourless
γ = 98.334 (3)°0.60 × 0.20 × 0.07 mm
V = 684.16 (4) Å3
Bruker SMART APEXII CCD area-detector diffractometer2401 independent reflections
Radiation source: fine-focus sealed tube2075 reflections with I > 2σ(I)
graphiteRint = 0.026
Detector resolution: 83.66 pixels mm-1θmax = 25.0°, θmin = 2.1°
φ and ω scansh = −10→10
Absorption correction: multi-scan (SADABS; Bruker, 2009)k = −10→10
Tmin = 0.946, Tmax = 0.994l = −11→11
10526 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)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.087H atoms treated by a mixture of independent and constrained refinement
S = 1.08w = 1/[σ2(Fo2) + (0.0378P)2 + 0.2619P] where P = (Fo2 + 2Fc2)/3
2401 reflections(Δ/σ)max < 0.001
187 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = −0.25 e Å3
0 constraints
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.
xyzUiso*/Ueq
O10.27470 (12)0.59246 (12)0.65294 (11)0.0183 (3)
O20.45117 (13)0.43517 (13)0.75699 (12)0.0241 (3)
O3−0.40580 (13)−0.06135 (12)0.88681 (11)0.0184 (3)
H3A−0.315 (3)−0.088 (2)0.879 (2)0.045 (6)*
N1−0.14250 (14)0.23821 (13)0.99931 (12)0.0132 (3)
N20.12077 (14)0.19893 (14)1.09005 (12)0.0138 (3)
C10.11012 (17)0.28238 (16)0.97476 (15)0.0134 (3)
C20.23274 (18)0.33848 (16)0.91519 (15)0.0145 (3)
H2A0.34410.32130.95240.017*
C30.18718 (18)0.42060 (16)0.79936 (15)0.0146 (3)
C40.02190 (18)0.44787 (17)0.74524 (15)0.0152 (3)
H4A−0.00530.50610.66730.018*
C5−0.10116 (18)0.39202 (16)0.80289 (15)0.0149 (3)
H5A−0.21230.41000.76630.018*
C6−0.05419 (17)0.30799 (16)0.91746 (14)0.0130 (3)
C7−0.03154 (17)0.17548 (16)1.10106 (15)0.0134 (3)
C80.31874 (18)0.48006 (17)0.73628 (15)0.0160 (3)
C90.39782 (19)0.65961 (18)0.58856 (17)0.0207 (4)
H9A0.39870.58400.50860.025*
H9B0.51060.68130.65820.025*
C100.3502 (2)0.81088 (19)0.53830 (17)0.0239 (4)
H10A0.42650.85570.48880.036*
H10B0.35710.88730.61910.036*
H10C0.23570.78890.47410.036*
C11−0.32301 (17)0.22441 (17)0.97243 (15)0.0147 (3)
H11A−0.35640.32740.94920.018*
H11B−0.35080.20071.05890.018*
C12−0.42069 (18)0.09446 (17)0.85251 (15)0.0162 (3)
H12A−0.54000.10440.82520.019*
H12B−0.38090.11030.77010.019*
C13−0.08488 (18)0.09237 (17)1.21037 (15)0.0158 (3)
H13A−0.1637−0.00711.16380.019*
H13B−0.14560.16101.25400.019*
C140.05897 (19)0.05117 (18)1.32650 (16)0.0184 (3)
H14A0.0130−0.02771.37860.022*
H14B0.13280.00091.28270.022*
C150.1621 (2)0.19530 (19)1.43011 (16)0.0238 (4)
H15A0.25170.16151.50190.036*
H15B0.09040.24451.47540.036*
H15C0.21070.27271.37970.036*
U11U22U33U12U13U23
O10.0174 (5)0.0194 (5)0.0219 (6)0.0049 (4)0.0097 (5)0.0088 (5)
O20.0174 (6)0.0319 (6)0.0297 (6)0.0102 (5)0.0117 (5)0.0145 (5)
O30.0151 (6)0.0148 (5)0.0271 (6)0.0033 (4)0.0089 (5)0.0033 (5)
N10.0115 (6)0.0135 (6)0.0149 (6)0.0026 (5)0.0045 (5)0.0019 (5)
N20.0145 (6)0.0139 (6)0.0138 (6)0.0036 (5)0.0051 (5)0.0023 (5)
C10.0146 (7)0.0111 (7)0.0142 (7)0.0036 (6)0.0039 (6)0.0002 (6)
C20.0116 (7)0.0139 (7)0.0170 (7)0.0035 (6)0.0029 (6)−0.0004 (6)
C30.0154 (7)0.0111 (7)0.0169 (8)0.0016 (6)0.0054 (6)−0.0002 (6)
C40.0182 (8)0.0123 (7)0.0141 (7)0.0034 (6)0.0031 (6)0.0014 (6)
C50.0123 (7)0.0142 (7)0.0165 (7)0.0037 (6)0.0019 (6)0.0001 (6)
C60.0141 (7)0.0110 (7)0.0133 (7)0.0012 (6)0.0046 (6)−0.0018 (6)
C70.0159 (7)0.0107 (7)0.0137 (7)0.0033 (6)0.0048 (6)−0.0008 (6)
C80.0176 (8)0.0160 (7)0.0136 (7)0.0026 (6)0.0037 (6)0.0009 (6)
C90.0197 (8)0.0239 (8)0.0236 (8)0.0036 (7)0.0132 (7)0.0080 (7)
C100.0257 (9)0.0245 (9)0.0221 (8)0.0019 (7)0.0091 (7)0.0047 (7)
C110.0112 (7)0.0164 (7)0.0181 (8)0.0047 (6)0.0054 (6)0.0034 (6)
C120.0127 (7)0.0172 (8)0.0185 (8)0.0029 (6)0.0040 (6)0.0030 (6)
C130.0169 (8)0.0148 (7)0.0175 (8)0.0027 (6)0.0077 (6)0.0025 (6)
C140.0215 (8)0.0202 (8)0.0176 (8)0.0074 (6)0.0093 (7)0.0065 (6)
C150.0210 (8)0.0295 (9)0.0200 (8)0.0041 (7)0.0046 (7)0.0048 (7)
O1—C81.3471 (17)C9—C101.494 (2)
O1—C91.4565 (18)C9—H9A0.9900
O2—C81.2094 (18)C9—H9B0.9900
O3—C121.4177 (17)C10—H10A0.9800
O3—H3A0.86 (2)C10—H10B0.9800
N1—C71.3762 (18)C10—H10C0.9800
N1—C61.3785 (19)C11—C121.518 (2)
N1—C111.4653 (18)C11—H11A0.9900
N2—C71.3202 (18)C11—H11B0.9900
N2—C11.3937 (18)C12—H12A0.9900
C1—C21.392 (2)C12—H12B0.9900
C1—C61.405 (2)C13—C141.529 (2)
C2—C31.393 (2)C13—H13A0.9900
C2—H2A0.9500C13—H13B0.9900
C3—C41.414 (2)C14—C151.522 (2)
C3—C81.486 (2)C14—H14A0.9900
C4—C51.382 (2)C14—H14B0.9900
C4—H4A0.9500C15—H15A0.9800
C5—C61.394 (2)C15—H15B0.9800
C5—H5A0.9500C15—H15C0.9800
C7—C131.494 (2)
C8—O1—C9115.89 (11)C9—C10—H10A109.5
C12—O3—H3A111.6 (14)C9—C10—H10B109.5
C7—N1—C6106.93 (11)H10A—C10—H10B109.5
C7—N1—C11127.84 (12)C9—C10—H10C109.5
C6—N1—C11125.05 (12)H10A—C10—H10C109.5
C7—N2—C1105.09 (11)H10B—C10—H10C109.5
C2—C1—N2130.08 (13)N1—C11—C12111.97 (11)
C2—C1—C6120.14 (13)N1—C11—H11A109.2
N2—C1—C6109.77 (12)C12—C11—H11A109.2
C1—C2—C3117.98 (13)N1—C11—H11B109.2
C1—C2—H2A121.0C12—C11—H11B109.2
C3—C2—H2A121.0H11A—C11—H11B107.9
C2—C3—C4120.92 (13)O3—C12—C11113.35 (12)
C2—C3—C8117.67 (13)O3—C12—H12A108.9
C4—C3—C8121.40 (13)C11—C12—H12A108.9
C5—C4—C3121.66 (13)O3—C12—H12B108.9
C5—C4—H4A119.2C11—C12—H12B108.9
C3—C4—H4A119.2H12A—C12—H12B107.7
C4—C5—C6116.73 (13)C7—C13—C14114.12 (12)
C4—C5—H5A121.6C7—C13—H13A108.7
C6—C5—H5A121.6C14—C13—H13A108.7
N1—C6—C5131.94 (13)C7—C13—H13B108.7
N1—C6—C1105.49 (12)C14—C13—H13B108.7
C5—C6—C1122.55 (13)H13A—C13—H13B107.6
N2—C7—N1112.72 (12)C15—C14—C13113.25 (12)
N2—C7—C13125.88 (13)C15—C14—H14A108.9
N1—C7—C13121.40 (12)C13—C14—H14A108.9
O2—C8—O1123.07 (13)C15—C14—H14B108.9
O2—C8—C3124.77 (13)C13—C14—H14B108.9
O1—C8—C3112.16 (12)H14A—C14—H14B107.7
O1—C9—C10107.38 (12)C14—C15—H15A109.5
O1—C9—H9A110.2C14—C15—H15B109.5
C10—C9—H9A110.2H15A—C15—H15B109.5
O1—C9—H9B110.2C14—C15—H15C109.5
C10—C9—H9B110.2H15A—C15—H15C109.5
H9A—C9—H9B108.5H15B—C15—H15C109.5
C7—N2—C1—C2179.98 (14)C1—N2—C7—N10.20 (15)
C7—N2—C1—C60.06 (15)C1—N2—C7—C13−179.22 (13)
N2—C1—C2—C3−179.43 (14)C6—N1—C7—N2−0.39 (15)
C6—C1—C2—C30.5 (2)C11—N1—C7—N2174.91 (12)
C1—C2—C3—C40.8 (2)C6—N1—C7—C13179.07 (12)
C1—C2—C3—C8−179.97 (12)C11—N1—C7—C13−5.6 (2)
C2—C3—C4—C5−1.2 (2)C9—O1—C8—O2−0.5 (2)
C8—C3—C4—C5179.59 (13)C9—O1—C8—C3178.95 (12)
C3—C4—C5—C60.3 (2)C2—C3—C8—O216.6 (2)
C7—N1—C6—C5−178.15 (14)C4—C3—C8—O2−164.22 (14)
C11—N1—C6—C56.4 (2)C2—C3—C8—O1−162.86 (12)
C7—N1—C6—C10.39 (14)C4—C3—C8—O116.34 (19)
C11—N1—C6—C1−175.07 (12)C8—O1—C9—C10−163.28 (12)
C4—C5—C6—N1179.43 (13)C7—N1—C11—C12−98.59 (16)
C4—C5—C6—C11.1 (2)C6—N1—C11—C1275.92 (16)
C2—C1—C6—N1179.78 (12)N1—C11—C12—O370.35 (16)
N2—C1—C6—N1−0.28 (15)N2—C7—C13—C147.5 (2)
C2—C1—C6—C5−1.5 (2)N1—C7—C13—C14−171.87 (12)
N2—C1—C6—C5178.43 (12)C7—C13—C14—C1573.93 (16)
D—H···AD—HH···AD···AD—H···A
O3—H3A···N2i0.86 (3)1.98 (2)2.8047 (17)159.6 (17)
C11—H11A···O2ii0.992.483.2901 (19)139
C11—H11B···O3iii0.992.463.2457 (19)136
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O3—H3A⋯N2i0.86 (3)1.98 (2)2.8047 (17)159.6 (17)
C11—H11A⋯O2ii0.992.483.2901 (19)139

Symmetry codes: (i) ; (ii) .

  8 in total

1.  Antiviral activity of benzimidazole derivatives. II. Antiviral activity of 2-phenylbenzimidazole derivatives.

Authors:  Michele Tonelli; Matteo Simone; Bruno Tasso; Federica Novelli; Vito Boido; Fabio Sparatore; Giuseppe Paglietti; Sabrina Pricl; Gabriele Giliberti; Sylvain Blois; Cristina Ibba; Giuseppina Sanna; Roberta Loddo; Paolo La Colla
Journal:  Bioorg Med Chem       Date:  2010-03-04       Impact factor: 3.641

Review 2.  Controlled microwave heating in modern organic synthesis.

Authors:  C Oliver Kappe
Journal:  Angew Chem Int Ed Engl       Date:  2004-11-26       Impact factor: 15.336

3.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

4.  Design, synthesis, antibacterial and QSAR studies of benzimidazole and imidazole chloroaryloxyalkyl derivatives.

Authors:  A Khalafi-Nezhad; M N Soltani Rad; H Mohabatkar; Z Asrari; B Hemmateenejad
Journal:  Bioorg Med Chem       Date:  2005-03-15       Impact factor: 3.641

5.  Synthesis and anti-hIV activity of 1-(2,6-difluorophenyl)-1H,3H-thiazolo[3,4-a]benzimidazole structurally-related 1,2-substituted benzimidazoles.

Authors:  Angela Rao; Alba Chimirri; Erik De Clercq; Anna Maria Monforte; Pietro Monforte; Christophe Pannecouque; Maria Zappalà
Journal:  Farmaco       Date:  2002-10

6.  Ethyl 1-sec-butyl-2-phenyl-1H-benzimidazole-5-carboxyl-ate.

Authors:  Natarajan Arumugam; Aisyah Saad Abdul Rahim; Shafida Abd Hamid; Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-03-13

7.  Synthesis and antifungal activities of 5-(3,4,5-trimethoxyphenyl)-2-sulfonyl-1,3,4-thiadiazole and 5-(3,4,5-trimethoxyphenyl)-2-sulfonyl-1,3,4-oxadiazole derivatives.

Authors:  Cai-Jun Chen; Bao-An Song; Song Yang; Guang-Fang Xu; Pinaki S Bhadury; Lin-Hong Jin; De-Yu Hu; Qian-Zhu Li; Fang Liu; Wei Xue; Ping Lu; Zhuo Chen
Journal:  Bioorg Med Chem       Date:  2007-04-10       Impact factor: 3.641

8.  Structure validation in chemical crystallography.

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

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

Authors:  Natarajan Arumugam; Nurziana Ngah; Hasnah Osman; Aisyah Saad Abdul Rahim
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-11-09
  1 in total

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