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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2010 Jun 26;66(Pt 7):o1832. doi: 10.1107/S1600536810024487

1,3,3-Trimethyl-1,2,3,4-tetra­hydro­pyrido[1,2-a]benzimidazol-1-ol

Sayed Hasan Mehdi a, Rokiah Hashim a, Raza Murad Ghalib a, Chin Sing Yeap b,, Hoong-Kun Fun b,*,§
PMCID: PMC3006987  PMID: 21588036

Abstract

In the title compound, C14H18N2O, the benzimidazole grouping is close to planar, with a maximum deviation of 0.042 Å; the six-membered non-aromatic ring adopts an envelope conformation. In the crystal structure, mol­ecules are linked into infinite sheets lying parallel to the bc plane by O—H⋯N and C—H⋯O hydrogen bonds.

Related literature

For applications of benzimidazole derivatives, see: Horton et al. (2003); Insuasty et al. (2008a ,b ). For the preparation of the title compound, see: Grech et al. (1994). For ring conformations, see Cremer & Pople (1975). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).graphic file with name e-66-o1832-scheme1.jpg

Experimental

Crystal data

  • C14H18N2O

  • M r = 230.30

  • Monoclinic, Inline graphic

  • a = 9.615 (5) Å

  • b = 8.194 (4) Å

  • c = 15.965 (8) Å

  • β = 99.601 (12)°

  • V = 1240.2 (11) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.08 mm−1

  • T = 100 K

  • 0.38 × 0.12 × 0.07 mm

Data collection

  • Bruker APEXII DUO CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009) T min = 0.971, T max = 0.995

  • 13460 measured reflections

  • 3597 independent reflections

  • 2612 reflections with I > 2σ(I)

  • R int = 0.052

Refinement

  • R[F 2 > 2σ(F 2)] = 0.046

  • wR(F 2) = 0.117

  • S = 1.02

  • 3597 reflections

  • 226 parameters

  • All H-atom parameters refined

  • Δρmax = 0.33 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).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810024487/hb5508sup1.cif

e-66-o1832-sup1.cif (19.2KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810024487/hb5508Isup2.hkl

e-66-o1832-Isup2.hkl (176.4KB, hkl)

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1O1⋯N1i 0.97 (2) 1.84 (2) 2.803 (2) 174 (2)
C5—H5A⋯O1ii 0.962 (15) 2.499 (15) 3.216 (2) 131.3 (11)

Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

Acknowledgments

SHM and RMG thank Universiti Sains Malaysia (USM) for the University Grant (1001/PTEKIND/8140152). HKF and CSY thank USM for the Research University Golden Goose Grant (1001/PFIZIK/811012). CSY also thanks USM for the award of a USM Fellowship.

supplementary crystallographic information

Comment

Benzimidazole derivatives are an important class of bioactive molecules and are well known due to their wide range of pharmacological activities as an anti-ulcers, anti-hypertensive, anti-viral, anti-fungal, anti-cancer, and anti-histaminic (Horton et al., 2003; Insuasty et al., 2008a, b) agents. Here we report the synthesis and the crystal structure of title compound.

In the title compound (Fig. 1), the benzimidazole group is essentially coplanar (N1/C1–C6/N2/C11) with the maximum deviation of 0.042 Å at atom C6. The N2/C7–C11 ring adopts an envelope conformation with Q=0.4933 (14) Å, θ=52.81 (15)° and φ=182.3 (2)° (Cremer & Pople, 1975).

In the crystal structure, the molecules are linked into infinite two-dimensional planes parallel to bc plane by the intermolecular O1—H1O1···N1 and C5—H5A···O1 hydrogen bonds (Fig. 2, Table 1).

Experimental

A mixture of o-phenylenediamine (0.108 g m) and dimedone (0.140 g m) in molar ratio 1:1 was refluxed in a mixture of acetic acid-ethanol (1:1 v/v) for 3 h (Grech et al., 1994). The reaction mixture was dried on rotavapor at low pressure and further fractionated successively with diethyl ether, chloroform and ethanol. The ethanol fraction was dried on rotavapor and the dry mass so obtained was crystallized in methanol:chloroform (1:1) mixture to give yellow needles of (I) (55%, m.p. 451 K).

Refinement

All hydrogen atoms were located from the difference Fourier map and was refined freely.

Figures

Fig. 1.

Fig. 1.

The molecular structure of (I) with 50% probability ellipsoids for non-H atoms.

Fig. 2.

Fig. 2.

The crystal packing of (I), viewed down the b axis, showing the molecules linked into sheets lying parallel to bc. Intermolecular hydrogen bonds are shown as dashed lines.

Crystal data

C14H18N2O F(000) = 496
Mr = 230.30 Dx = 1.233 Mg m3
Monoclinic, P21/c Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc Cell parameters from 2162 reflections
a = 9.615 (5) Å θ = 3.1–29.6°
b = 8.194 (4) Å µ = 0.08 mm1
c = 15.965 (8) Å T = 100 K
β = 99.601 (12)° Needle, yellow
V = 1240.2 (11) Å3 0.38 × 0.12 × 0.07 mm
Z = 4

Data collection

Bruker APEXII DUO CCD diffractometer 3597 independent reflections
Radiation source: fine-focus sealed tube 2612 reflections with I > 2σ(I)
graphite Rint = 0.052
φ and ω scans θmax = 30.0°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2009) h = −13→13
Tmin = 0.971, Tmax = 0.995 k = −11→10
13460 measured reflections l = −22→18

Refinement

Refinement on F2 Primary atom site location: structure-invariant direct methods
Least-squares matrix: full Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.117 All H-atom parameters refined
S = 1.02 w = 1/[σ2(Fo2) + (0.0528P)2 + 0.2357P] where P = (Fo2 + 2Fc2)/3
3597 reflections (Δ/σ)max < 0.001
226 parameters Δρmax = 0.33 e Å3
0 restraints Δρmin = −0.25 e Å3

Special details

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 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
O1 0.65445 (9) 0.44319 (11) 0.12156 (6) 0.0178 (2)
N1 0.40305 (10) 0.05504 (14) 0.22183 (7) 0.0176 (2)
N2 0.54560 (10) 0.19700 (13) 0.15038 (6) 0.0148 (2)
C1 0.32424 (12) 0.11377 (16) 0.14618 (8) 0.0160 (3)
C2 0.17999 (13) 0.09810 (17) 0.11474 (9) 0.0199 (3)
C3 0.12707 (13) 0.17745 (18) 0.03945 (9) 0.0215 (3)
C4 0.21420 (13) 0.27314 (18) −0.00320 (8) 0.0199 (3)
C5 0.35783 (13) 0.28830 (17) 0.02639 (8) 0.0179 (3)
C6 0.41136 (12) 0.20479 (15) 0.10110 (8) 0.0152 (2)
C7 0.67647 (12) 0.27365 (16) 0.13019 (8) 0.0153 (3)
C8 0.79944 (12) 0.23815 (16) 0.20337 (8) 0.0164 (3)
C9 0.79390 (12) 0.07980 (16) 0.25468 (8) 0.0165 (3)
C10 0.65512 (13) 0.08393 (18) 0.29055 (8) 0.0186 (3)
C11 0.53240 (12) 0.10891 (16) 0.22157 (8) 0.0157 (3)
C12 0.70543 (14) 0.21133 (19) 0.04460 (9) 0.0208 (3)
C13 0.80018 (14) −0.07437 (18) 0.20160 (9) 0.0218 (3)
C14 0.91813 (13) 0.08019 (19) 0.32872 (9) 0.0224 (3)
H1A 0.0269 (15) 0.1672 (18) 0.0155 (9) 0.020 (4)*
H2A 0.1203 (16) 0.033 (2) 0.1467 (10) 0.026 (4)*
H4A 0.1727 (15) 0.3345 (18) −0.0553 (9) 0.016 (4)*
H5A 0.4140 (15) 0.3569 (19) −0.0037 (9) 0.017 (4)*
H8A 0.8923 (16) 0.241 (2) 0.1794 (10) 0.025 (4)*
H8B 0.8028 (15) 0.334 (2) 0.2438 (10) 0.025 (4)*
H10A 0.6384 (15) −0.0185 (19) 0.3209 (9) 0.018 (4)*
H10B 0.6583 (16) 0.177 (2) 0.3319 (10) 0.024 (4)*
H12A 0.7260 (17) 0.095 (2) 0.0457 (11) 0.030 (4)*
H12B 0.7853 (17) 0.279 (2) 0.0300 (11) 0.032 (4)*
H12C 0.6228 (18) 0.233 (2) −0.0008 (11) 0.034 (5)*
H13A 0.7168 (16) −0.0878 (19) 0.1571 (10) 0.024 (4)*
H13B 0.8059 (15) −0.171 (2) 0.2371 (10) 0.024 (4)*
H13C 0.8856 (17) −0.074 (2) 0.1725 (11) 0.032 (4)*
H14A 0.9187 (16) 0.180 (2) 0.3648 (10) 0.028 (4)*
H14B 0.9107 (17) −0.017 (2) 0.3658 (11) 0.034 (5)*
H14C 1.0108 (18) 0.082 (2) 0.3068 (11) 0.036 (5)*
H1O1 0.640 (2) 0.487 (3) 0.1756 (13) 0.050 (6)*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0215 (4) 0.0149 (5) 0.0175 (5) 0.0005 (3) 0.0047 (3) 0.0024 (4)
N1 0.0167 (5) 0.0195 (6) 0.0166 (5) −0.0010 (4) 0.0028 (4) 0.0018 (4)
N2 0.0138 (4) 0.0170 (5) 0.0130 (5) −0.0010 (4) 0.0009 (4) 0.0014 (4)
C1 0.0169 (5) 0.0153 (6) 0.0158 (6) 0.0004 (4) 0.0024 (4) −0.0007 (5)
C2 0.0155 (5) 0.0206 (7) 0.0232 (7) −0.0010 (5) 0.0020 (5) −0.0017 (6)
C3 0.0171 (6) 0.0229 (7) 0.0229 (7) 0.0009 (5) −0.0014 (5) −0.0041 (6)
C4 0.0208 (6) 0.0210 (7) 0.0164 (6) 0.0036 (5) −0.0018 (5) −0.0009 (5)
C5 0.0202 (6) 0.0173 (7) 0.0157 (6) 0.0013 (5) 0.0014 (5) 0.0001 (5)
C6 0.0148 (5) 0.0160 (6) 0.0144 (6) 0.0001 (4) 0.0010 (4) −0.0019 (5)
C7 0.0154 (5) 0.0150 (6) 0.0157 (6) −0.0013 (4) 0.0036 (4) 0.0021 (5)
C8 0.0157 (5) 0.0162 (6) 0.0167 (6) −0.0007 (4) 0.0007 (4) 0.0004 (5)
C9 0.0145 (5) 0.0169 (6) 0.0170 (6) 0.0002 (4) 0.0000 (4) 0.0018 (5)
C10 0.0176 (5) 0.0229 (7) 0.0147 (6) −0.0007 (5) 0.0012 (4) 0.0041 (6)
C11 0.0168 (5) 0.0153 (6) 0.0150 (6) 0.0006 (4) 0.0030 (4) 0.0017 (5)
C12 0.0223 (6) 0.0249 (8) 0.0164 (6) 0.0014 (5) 0.0067 (5) −0.0008 (6)
C13 0.0230 (6) 0.0177 (7) 0.0241 (7) 0.0018 (5) 0.0017 (5) 0.0002 (6)
C14 0.0185 (6) 0.0244 (8) 0.0220 (7) 0.0007 (5) −0.0030 (5) 0.0038 (6)

Geometric parameters (Å, °)

O1—C7 1.4085 (17) C8—C9 1.5400 (19)
O1—H1O1 0.96 (2) C8—H8A 1.029 (15)
N1—C11 1.3203 (16) C8—H8B 1.012 (16)
N1—C1 1.3997 (17) C9—C13 1.528 (2)
N2—C11 1.3700 (17) C9—C14 1.5340 (18)
N2—C6 1.3965 (16) C9—C10 1.5378 (18)
N2—C7 1.4890 (16) C10—C11 1.4878 (18)
C1—C2 1.4000 (18) C10—H10A 0.995 (16)
C1—C6 1.4060 (18) C10—H10B 1.004 (16)
C2—C3 1.387 (2) C12—H12A 0.976 (18)
C2—H2A 0.988 (16) C12—H12B 1.006 (17)
C3—C4 1.404 (2) C12—H12C 0.998 (17)
C3—H1A 0.979 (14) C13—H13A 0.984 (16)
C4—C5 1.3886 (18) C13—H13B 0.967 (17)
C4—H4A 0.997 (15) C13—H13C 1.009 (17)
C5—C6 1.3968 (18) C14—H14A 1.000 (17)
C5—H5A 0.961 (15) C14—H14B 1.001 (18)
C7—C12 1.5271 (19) C14—H14C 1.010 (17)
C7—C8 1.5450 (18)
C7—O1—H1O1 108.6 (12) H8A—C8—H8B 106.5 (12)
C11—N1—C1 104.90 (11) C13—C9—C14 109.35 (11)
C11—N2—C6 106.65 (10) C13—C9—C10 109.98 (11)
C11—N2—C7 126.90 (10) C14—C9—C10 109.00 (11)
C6—N2—C7 126.43 (10) C13—C9—C8 113.17 (11)
N1—C1—C2 129.74 (12) C14—C9—C8 108.46 (11)
N1—C1—C6 109.93 (11) C10—C9—C8 106.78 (10)
C2—C1—C6 120.29 (12) C11—C10—C9 110.96 (11)
C3—C2—C1 117.79 (12) C11—C10—H10A 107.7 (8)
C3—C2—H2A 122.8 (9) C9—C10—H10A 112.6 (8)
C1—C2—H2A 119.4 (9) C11—C10—H10B 108.4 (9)
C2—C3—C4 121.33 (12) C9—C10—H10B 109.2 (9)
C2—C3—H1A 119.5 (9) H10A—C10—H10B 108.0 (12)
C4—C3—H1A 119.1 (9) N1—C11—N2 113.35 (11)
C5—C4—C3 121.67 (13) N1—C11—C10 125.66 (12)
C5—C4—H4A 118.4 (8) N2—C11—C10 120.98 (11)
C3—C4—H4A 119.9 (8) C7—C12—H12A 112.3 (10)
C4—C5—C6 116.79 (12) C7—C12—H12B 106.4 (10)
C4—C5—H5A 119.5 (9) H12A—C12—H12B 112.6 (14)
C6—C5—H5A 123.7 (9) C7—C12—H12C 110.3 (10)
N2—C6—C5 132.67 (11) H12A—C12—H12C 108.8 (14)
N2—C6—C1 105.13 (11) H12B—C12—H12C 106.2 (14)
C5—C6—C1 122.06 (11) C9—C13—H13A 112.9 (9)
O1—C7—N2 108.58 (10) C9—C13—H13B 110.6 (9)
O1—C7—C12 106.80 (10) H13A—C13—H13B 106.9 (13)
N2—C7—C12 109.84 (10) C9—C13—H13C 111.5 (10)
O1—C7—C8 110.08 (10) H13A—C13—H13C 107.1 (13)
N2—C7—C8 108.95 (10) H13B—C13—H13C 107.4 (13)
C12—C7—C8 112.51 (11) C9—C14—H14A 111.9 (9)
C9—C8—C7 118.09 (10) C9—C14—H14B 109.3 (10)
C9—C8—H8A 108.9 (9) H14A—C14—H14B 107.6 (13)
C7—C8—H8A 108.5 (9) C9—C14—H14C 110.6 (10)
C9—C8—H8B 108.3 (9) H14A—C14—H14C 105.5 (13)
C7—C8—H8B 106.0 (9) H14B—C14—H14C 111.8 (14)
C11—N1—C1—C2 −177.80 (14) C6—N2—C7—C12 −58.00 (16)
C11—N1—C1—C6 −0.14 (15) C11—N2—C7—C8 0.12 (17)
N1—C1—C2—C3 176.20 (13) C6—N2—C7—C8 178.34 (11)
C6—C1—C2—C3 −1.2 (2) O1—C7—C8—C9 148.09 (11)
C1—C2—C3—C4 −1.3 (2) N2—C7—C8—C9 29.14 (15)
C2—C3—C4—C5 2.2 (2) C12—C7—C8—C9 −92.92 (14)
C3—C4—C5—C6 −0.5 (2) C7—C8—C9—C13 64.20 (14)
C11—N2—C6—C5 173.80 (14) C7—C8—C9—C14 −174.28 (11)
C7—N2—C6—C5 −4.7 (2) C7—C8—C9—C10 −56.95 (15)
C11—N2—C6—C1 −1.75 (14) C13—C9—C10—C11 −68.67 (15)
C7—N2—C6—C1 179.73 (11) C14—C9—C10—C11 171.46 (11)
C4—C5—C6—N2 −176.96 (13) C8—C9—C10—C11 54.49 (14)
C4—C5—C6—C1 −2.03 (19) C1—N1—C11—N2 −1.04 (15)
N1—C1—C6—N2 1.20 (14) C1—N1—C11—C10 177.57 (12)
C2—C1—C6—N2 179.11 (11) C6—N2—C11—N1 1.82 (15)
N1—C1—C6—C5 −174.94 (11) C7—N2—C11—N1 −179.67 (11)
C2—C1—C6—C5 3.0 (2) C6—N2—C11—C10 −176.86 (12)
C11—N2—C7—O1 −119.77 (13) C7—N2—C11—C10 1.64 (19)
C6—N2—C7—O1 58.45 (16) C9—C10—C11—N1 150.69 (13)
C11—N2—C7—C12 123.78 (14) C9—C10—C11—N2 −30.80 (17)

Hydrogen-bond geometry (Å, °)

D—H···A D—H H···A D···A D—H···A
O1—H1O1···N1i 0.97 (2) 1.84 (2) 2.803 (2) 174 (2)
C5—H5A···O1ii 0.962 (15) 2.499 (15) 3.216 (2) 131.3 (11)

Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x+1, −y+1, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5508).

References

  1. Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  2. Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  3. Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc.97, 1354–1358.
  4. Grech, O., Sakellariou, R. & Speziale, V. (1994). J. Heterocycl. Chem.31, 509–511.
  5. Horton, D. A., Bourne, G. T. & Smythe, M. L. (2003). Chem. Rev.103, 893–930. [DOI] [PubMed]
  6. Insuasty, B., Orozco, F., Lizarazo, C., Quiroga, J., Abonía, R., Hursthouse, M., Nogueras, M. & Cobo, J. (2008a). Bioorg. Med. Chem.16, 8492–8500. [DOI] [PubMed]
  7. Insuasty, B., Orozco, F., Quiroga, J., Abonía, R., Nogueras, M. & Cobo, J. (2008b). Eur. J. Med. Chem.43, 1955–1962. [DOI] [PubMed]
  8. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
  9. Spek, A. L. (2009). Acta Cryst. D65, 148–155. [DOI] [PMC free article] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810024487/hb5508sup1.cif

e-66-o1832-sup1.cif (19.2KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810024487/hb5508Isup2.hkl

e-66-o1832-Isup2.hkl (176.4KB, hkl)

Additional supplementary materials: crystallographic information; 3D view; checkCIF report


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