Literature DB >> 22347035

Ethyl 1-(2-hy-droxy-eth-yl)-2-(4-meth-oxy-phen-yl)-1H-benzimidazole-5-carboxyl-ate monohydrate.

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

Abstract

In the title mol-ecule, C(19)H(20)N(2)O(4)·H(2)O, the benzimidazole ring system is essentially planar [maximum deviation = 0.013 (11) Å] and is inclined to the 4-meth-oxy-phenyl ring by 30.98 (5)°. In the crystal, O-H⋯O and O-H⋯N hydrogen bonds involving the water mol-ecule link neighbouring mol-ecules, forming a two-dimensional network lying parallel to the bc plane. There are also C-H⋯π and π-π inter-actions present. The latter involve inversion-related benzimidazole rings with centroid-centroid distances of 3.5552 (8) and 3.7466 (8) Å.

Entities:  

Year:  2012        PMID: 22347035      PMCID: PMC3275179          DOI: 10.1107/S1600536812001262

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 ▶). For the biological activity of benzimidazole derivatives, see: Cosar & Julou (1959 ▶); Gudmundsson et al. (1999 ▶); De Clercq et al. (1993 ▶); Spasov et al. (1999 ▶). For standard bond lengths, see: Allen et al. (1987 ▶).

Experimental

Crystal data

C19H20N2O4·H2O M = 358.39 Monoclinic, a = 10.6364 (11) Å b = 9.5089 (10) Å c = 19.3765 (17) Å β = 112.899 (5)° V = 1805.3 (3) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 293 K 0.35 × 0.25 × 0.18 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.967, T max = 0.983 13982 measured reflections 3140 independent reflections 2856 reflections with I > 2σ(I) R int = 0.033

Refinement

R[F 2 > 2σ(F 2)] = 0.032 wR(F 2) = 0.086 S = 1.02 3140 reflections 249 parameters 3 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.19 e Å−3 Δρmin = −0.20 e Å−3 Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812001262/su2368sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812001262/su2368Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812001262/su2368Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C19H20N2O4·H2OF(000) = 760
Mr = 358.39Dx = 1.319 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 9429 reflections
a = 10.6364 (11) Åθ = 2.9–25.0°
b = 9.5089 (10) ŵ = 0.10 mm1
c = 19.3765 (17) ÅT = 293 K
β = 112.899 (5)°Block, colourless
V = 1805.3 (3) Å30.35 × 0.25 × 0.18 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer3140 independent reflections
Radiation source: fine-focus sealed tube2856 reflections with I > 2σ(I)
graphiteRint = 0.033
Detector resolution: 83.66 pixels mm-1θmax = 25.0°, θmin = 2.9°
φ and ω scanh = −12→12
Absorption correction: multi-scan (SADABS; Bruker, 2009)k = −11→11
Tmin = 0.967, Tmax = 0.983l = −23→21
13982 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)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.02w = 1/[σ2(Fo2) + (0.0382P)2 + 0.7017P] where P = (Fo2 + 2Fc2)/3
3140 reflections(Δ/σ)max < 0.001
249 parametersΔρmax = 0.19 e Å3
3 restraintsΔρmin = −0.20 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*/Ueq
O10.03607 (9)0.11092 (10)−0.10495 (5)0.0273 (2)
O20.13828 (10)0.11955 (10)0.02067 (5)0.0318 (2)
O31.05219 (9)−0.64334 (10)0.19548 (5)0.0299 (2)
O40.56061 (11)−0.49083 (10)−0.20486 (5)0.0308 (2)
H4B0.5547 (19)−0.4247 (16)−0.2358 (9)0.055 (6)*
N10.54707 (10)−0.27695 (10)−0.04766 (5)0.0195 (2)
N20.53184 (10)−0.24427 (10)0.06353 (6)0.0207 (2)
C10.79606 (13)−0.37042 (14)0.14242 (7)0.0246 (3)
H1A0.7743−0.29300.16500.029*
C20.90530 (13)−0.45375 (15)0.18365 (7)0.0277 (3)
H2A0.9560−0.43280.23370.033*
C30.94031 (12)−0.56962 (14)0.15058 (7)0.0235 (3)
C40.86192 (13)−0.60221 (13)0.07631 (7)0.0243 (3)
H4A0.8838−0.67990.05400.029*
C50.75072 (13)−0.51868 (13)0.03529 (7)0.0231 (3)
H5A0.6979−0.5421−0.01420.028*
C60.71694 (12)−0.40026 (13)0.06695 (7)0.0206 (3)
C70.59923 (12)−0.30890 (12)0.02771 (7)0.0194 (3)
C80.43855 (12)−0.18642 (12)−0.06055 (7)0.0197 (3)
C90.34925 (13)−0.12055 (13)−0.12536 (7)0.0219 (3)
H9A0.3561−0.1332−0.17140.026*
C100.24989 (12)−0.03538 (13)−0.11789 (7)0.0224 (3)
H10A0.18750.0093−0.16000.027*
C110.24092 (12)−0.01465 (12)−0.04771 (7)0.0217 (3)
C120.33239 (12)−0.07870 (12)0.01676 (7)0.0212 (3)
H12A0.3277−0.06340.06310.025*
C130.43118 (12)−0.16652 (12)0.00957 (7)0.0196 (3)
C140.13541 (13)0.07845 (13)−0.03903 (7)0.0234 (3)
C15−0.06792 (14)0.20632 (16)−0.10130 (8)0.0328 (3)
H15A−0.02960.2992−0.08580.039*
H15B−0.10420.1723−0.06560.039*
C16−0.17773 (17)0.2119 (2)−0.17790 (10)0.0550 (5)
H16A−0.24630.2782−0.17850.082*
H16B−0.21820.1205−0.19140.082*
H16C−0.13950.2407−0.21310.082*
C171.10325 (14)−0.74776 (15)0.15978 (7)0.0292 (3)
H17A1.1895−0.78190.19460.044*
H17B1.1148−0.70700.11730.044*
H17C1.0396−0.82430.14350.044*
C180.59596 (12)−0.31970 (13)−0.10568 (7)0.0213 (3)
H18A0.6892−0.3533−0.08220.026*
H18B0.5952−0.2393−0.13660.026*
C190.50589 (13)−0.43538 (13)−0.15438 (7)0.0235 (3)
H19A0.4971−0.5104−0.12260.028*
H19B0.4155−0.3979−0.18260.028*
O50.54527 (11)−0.26408 (11)−0.28926 (5)0.0342 (2)
H5B0.510 (2)−0.1856 (14)−0.2842 (12)0.062 (6)*
H5C0.542 (2)−0.267 (2)−0.3338 (7)0.061 (6)*
U11U22U33U12U13U23
O10.0236 (5)0.0305 (5)0.0275 (5)0.0048 (4)0.0096 (4)0.0009 (4)
O20.0326 (5)0.0363 (5)0.0274 (5)0.0044 (4)0.0126 (4)−0.0064 (4)
O30.0288 (5)0.0376 (5)0.0214 (5)0.0106 (4)0.0077 (4)−0.0008 (4)
O40.0533 (6)0.0220 (5)0.0257 (5)0.0010 (4)0.0248 (5)−0.0003 (4)
N10.0216 (5)0.0199 (5)0.0179 (5)−0.0012 (4)0.0086 (4)−0.0012 (4)
N20.0217 (5)0.0214 (5)0.0193 (5)−0.0026 (4)0.0085 (4)−0.0012 (4)
C10.0262 (6)0.0284 (7)0.0211 (6)0.0019 (5)0.0113 (5)−0.0031 (5)
C20.0274 (7)0.0361 (7)0.0182 (6)0.0024 (6)0.0074 (5)−0.0032 (5)
C30.0216 (6)0.0276 (6)0.0220 (6)0.0015 (5)0.0092 (5)0.0030 (5)
C40.0282 (7)0.0207 (6)0.0246 (6)−0.0003 (5)0.0111 (5)−0.0021 (5)
C50.0255 (6)0.0226 (6)0.0191 (6)−0.0044 (5)0.0065 (5)−0.0017 (5)
C60.0212 (6)0.0215 (6)0.0207 (6)−0.0039 (5)0.0099 (5)0.0011 (5)
C70.0213 (6)0.0186 (6)0.0187 (6)−0.0057 (5)0.0083 (5)−0.0018 (5)
C80.0210 (6)0.0175 (6)0.0212 (6)−0.0044 (5)0.0089 (5)−0.0026 (5)
C90.0262 (6)0.0221 (6)0.0182 (6)−0.0035 (5)0.0095 (5)−0.0023 (5)
C100.0229 (6)0.0211 (6)0.0205 (6)−0.0024 (5)0.0055 (5)0.0001 (5)
C110.0211 (6)0.0188 (6)0.0246 (6)−0.0041 (5)0.0084 (5)−0.0030 (5)
C120.0236 (6)0.0213 (6)0.0207 (6)−0.0062 (5)0.0109 (5)−0.0043 (5)
C130.0203 (6)0.0187 (6)0.0194 (6)−0.0050 (5)0.0071 (5)−0.0015 (5)
C140.0232 (6)0.0214 (6)0.0252 (7)−0.0043 (5)0.0091 (5)−0.0016 (5)
C150.0277 (7)0.0369 (8)0.0368 (8)0.0092 (6)0.0159 (6)0.0039 (6)
C160.0359 (9)0.0788 (13)0.0442 (10)0.0216 (9)0.0090 (8)0.0018 (9)
C170.0282 (7)0.0342 (7)0.0264 (7)0.0070 (6)0.0120 (6)−0.0001 (6)
C180.0252 (6)0.0225 (6)0.0195 (6)0.0001 (5)0.0123 (5)0.0004 (5)
C190.0302 (7)0.0231 (6)0.0189 (6)−0.0008 (5)0.0115 (5)−0.0008 (5)
O50.0533 (6)0.0309 (5)0.0247 (5)0.0084 (5)0.0219 (5)0.0080 (4)
O1—C141.3391 (16)C9—C101.3831 (18)
O1—C151.4533 (15)C9—H9A0.9300
O2—C141.2100 (16)C10—C111.4135 (18)
O3—C31.3633 (15)C10—H10A0.9300
O3—C171.4324 (16)C11—C121.3900 (18)
O4—C191.4200 (15)C11—C141.4895 (17)
O4—H4B0.854 (9)C12—C131.3909 (17)
N1—C71.3794 (15)C12—H12A0.9300
N1—C81.3825 (16)C15—C161.490 (2)
N1—C181.4677 (15)C15—H15A0.9700
N2—C71.3268 (16)C15—H15B0.9700
N2—C131.3838 (16)C16—H16A0.9600
C1—C21.3761 (19)C16—H16B0.9600
C1—C61.4033 (18)C16—H16C0.9600
C1—H1A0.9300C17—H17A0.9600
C2—C31.3961 (18)C17—H17B0.9600
C2—H2A0.9300C17—H17C0.9600
C3—C41.3887 (18)C18—C191.5215 (17)
C4—C51.3893 (18)C18—H18A0.9700
C4—H4A0.9300C18—H18B0.9700
C5—C61.3946 (17)C19—H19A0.9700
C5—H5A0.9300C19—H19B0.9700
C6—C71.4695 (17)O5—H5B0.855 (9)
C8—C91.3940 (17)O5—H5C0.852 (9)
C8—C131.4040 (17)
C14—O1—C15115.49 (10)C11—C12—C13117.71 (11)
C3—O3—C17116.68 (10)C11—C12—H12A121.1
C19—O4—H4B105.8 (13)C13—C12—H12A121.1
C7—N1—C8106.98 (10)N2—C13—C12129.62 (11)
C7—N1—C18129.31 (10)N2—C13—C8109.94 (10)
C8—N1—C18123.63 (10)C12—C13—C8120.44 (11)
C7—N2—C13105.60 (10)O2—C14—O1123.68 (12)
C2—C1—C6121.14 (12)O2—C14—C11124.06 (12)
C2—C1—H1A119.4O1—C14—C11112.26 (10)
C6—C1—H1A119.4O1—C15—C16106.87 (12)
C1—C2—C3120.24 (12)O1—C15—H15A110.3
C1—C2—H2A119.9C16—C15—H15A110.3
C3—C2—H2A119.9O1—C15—H15B110.3
O3—C3—C4124.72 (11)C16—C15—H15B110.3
O3—C3—C2115.81 (11)H15A—C15—H15B108.6
C4—C3—C2119.47 (11)C15—C16—H16A109.5
C3—C4—C5119.97 (12)C15—C16—H16B109.5
C3—C4—H4A120.0H16A—C16—H16B109.5
C5—C4—H4A120.0C15—C16—H16C109.5
C4—C5—C6121.18 (11)H16A—C16—H16C109.5
C4—C5—H5A119.4H16B—C16—H16C109.5
C6—C5—H5A119.4O3—C17—H17A109.5
C5—C6—C1117.97 (11)O3—C17—H17B109.5
C5—C6—C7124.27 (11)H17A—C17—H17B109.5
C1—C6—C7117.67 (11)O3—C17—H17C109.5
N2—C7—N1112.04 (10)H17A—C17—H17C109.5
N2—C7—C6121.88 (11)H17B—C17—H17C109.5
N1—C7—C6126.07 (11)N1—C18—C19110.49 (10)
N1—C8—C9132.13 (11)N1—C18—H18A109.6
N1—C8—C13105.44 (10)C19—C18—H18A109.6
C9—C8—C13122.43 (11)N1—C18—H18B109.6
C10—C9—C8116.70 (11)C19—C18—H18B109.6
C10—C9—H9A121.7H18A—C18—H18B108.1
C8—C9—H9A121.7O4—C19—C18111.58 (10)
C9—C10—C11121.52 (12)O4—C19—H19A109.3
C9—C10—H10A119.2C18—C19—H19A109.3
C11—C10—H10A119.2O4—C19—H19B109.3
C12—C11—C10121.19 (11)C18—C19—H19B109.3
C12—C11—C14116.97 (11)H19A—C19—H19B108.0
C10—C11—C14121.83 (11)H5B—O5—H5C107.1 (19)
C6—C1—C2—C30.6 (2)N1—C8—C9—C10179.73 (12)
C17—O3—C3—C49.95 (18)C13—C8—C9—C10−1.15 (17)
C17—O3—C3—C2−170.04 (11)C8—C9—C10—C110.95 (17)
C1—C2—C3—O3178.34 (12)C9—C10—C11—C120.34 (18)
C1—C2—C3—C4−1.65 (19)C9—C10—C11—C14179.15 (11)
O3—C3—C4—C5−179.16 (11)C10—C11—C12—C13−1.45 (17)
C2—C3—C4—C50.83 (19)C14—C11—C12—C13179.70 (10)
C3—C4—C5—C61.05 (18)C7—N2—C13—C12−179.60 (12)
C4—C5—C6—C1−2.05 (18)C7—N2—C13—C80.40 (13)
C4—C5—C6—C7−178.52 (11)C11—C12—C13—N2−178.75 (11)
C2—C1—C6—C51.22 (18)C11—C12—C13—C81.25 (16)
C2—C1—C6—C7177.92 (11)N1—C8—C13—N2−0.62 (13)
C13—N2—C7—N1−0.02 (13)C9—C8—C13—N2−179.95 (10)
C13—N2—C7—C6178.74 (10)N1—C8—C13—C12179.38 (10)
C8—N1—C7—N2−0.37 (13)C9—C8—C13—C120.05 (17)
C18—N1—C7—N2176.36 (11)C15—O1—C14—O22.88 (18)
C8—N1—C7—C6−179.06 (11)C15—O1—C14—C11−177.56 (10)
C18—N1—C7—C6−2.33 (19)C12—C11—C14—O212.75 (18)
C5—C6—C7—N2147.34 (12)C10—C11—C14—O2−166.10 (12)
C1—C6—C7—N2−29.13 (16)C12—C11—C14—O1−166.81 (10)
C5—C6—C7—N1−34.09 (18)C10—C11—C14—O114.34 (16)
C1—C6—C7—N1149.44 (12)C14—O1—C15—C16−171.89 (13)
C7—N1—C8—C9179.82 (12)C7—N1—C18—C19103.77 (13)
C18—N1—C8—C92.86 (19)C8—N1—C18—C19−79.98 (13)
C7—N1—C8—C130.59 (12)N1—C18—C19—O4−172.67 (10)
C18—N1—C8—C13−176.38 (10)
Cg2 is the centroid of the C1–C6 ring.
D—H···AD—HH···AD···AD—H···A
O5—H5B···O4i0.86 (2)1.98 (2)2.8165 (15)165 (2)
O5—H5C···N2ii0.85 (1)1.95 (1)2.8011 (15)175 (2)
C15—H15A···Cg2iii0.972.953.7247 (17)138
Table 1

Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C1–C6 ring.

D—H⋯AD—HH⋯ADAD—H⋯A
O5—H5B⋯O4i0.86 (2)1.98 (2)2.8165 (15)165 (2)
O5—H5C⋯N2ii0.85 (1)1.95 (1)2.8011 (15)175 (2)
C15—H15ACg2iii0.972.953.7247 (17)138

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

  5 in total

1.  [The activity of 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole (R. P. 8823) against experimental Trichomonas vaginalis infections].

Authors:  C COSAR; L JULOU
Journal:  Ann Inst Pasteur (Paris)       Date:  1959-02

2.  A short history of SHELX.

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

3.  Synthesis and antiviral activity of certain 5'-modified analogs of 2,5,6-trichloro-1-(beta-D-ribofuranosyl)benzimidazole.

Authors:  K S Gudmundsson; J C Drach; L L Wotring; L B Townsend
Journal:  J Med Chem       Date:  1997-02-28       Impact factor: 7.446

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

Authors:  Natarajan Arumugam; Aisyah Saad Abdul Rahim; Habibah A Wahab; Jia Hao Goh; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-06-05

5.  Structure validation in chemical crystallography.

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

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