supplementary materials


cv5217 scheme

Acta Cryst. (2012). E68, o197-o198    [ doi:10.1107/S160053681105389X ]

Ethyl 1-(2-hydroxyethyl)-2-[2-(methylsulfanyl)ethyl]-1H-benzimidazole-5-carboxylate

N. Hamzah, N. Ngah, S. Abd Hamid and A. S. Abdul Rahim

Abstract top

In the crystal structure of the title compound, C15H20N2O3S, the hydroxy group is involved in the formation of O-H...N hydrogen bonds, which link two molecules into a centrosymmetric dimer. Weak C-H...O hydrogen bonds further link these dimers into chains propagating along the a axis. The crystal packing exhibits [pi]-[pi] interactions between the five- and six-membered rings of neighbouring molecules [centroid-centroid distance = 3.819 (2) Å] and short intermolecular S...S contacts of 3.495 (1) Å.

Comment top

Heteroaromatic compounds of benzimidazoles exhibit important values particularly in biological and pharmaceutical fields. The previledge sub-structures of benzimidazoles have been reported as potential inhibitors (Sasmal et al., 2011), probes for β-amyloid (Aβ) plaques in Alzheimer's disease (Cui et al., 2010), showed anti- cancer activities (Demirayak et al., 2011), anti hepatitis B (Li et al., 2006) and C virus (Hwu et al., 2008). Various methods have been employed to synthesize benzimidazole derivatives (Wright, 1951; Preston, 1974). However, two common methods widely used are either by reacting diamine with carboxylic acid or diamine with aldehyde using solid catalyst (Ruiz et al., 2010) or polymer bounds (Chou et al., 2011). In continuation of our work (Hamzah et al., 2010; Arumugam et al. 2011), we report herein the crystal structure of the title compound, (I).

The title molecule (Fig. 1), is similar with those reported earlier - ethyl 1-(2- hydroxyethyl)-2-phenyl-1H-benzimidazole-5-carboxylate (Hamzah et al., 2010) and ethyl 1-(2-hydroxyethyl)-2-propyl-1H-benzimidazole -5-carboxylate (Hamzah et al., 2011), in that only the 2-methylthioethyl substituent at the imidazole ring is different. The benzimidazole ring [N1/N2/C1—C7] is essentially planar and the C4 atom deviates by 0.012 (2)Å from that plane. The bond lengths and angles are in normal ranges (Allen et al., 1987) and are in agreement with those reported by Hamzah et al. (2010, 2011).

In the crystal structure, the hydroxy group is involved in formation intermolecular hydrogen bond O—H···N (Table 1), which link two molecules into centrosymmetric dimer (Fig. 2). Weak intermolecular C—H···O hydrogen bonds (Table 1) link further these dimers into chains propagated along a axis. The crystal packing exhibits ππ interactions between the benzimidazole fragments with Cg1···Cg2 distance of 3.819 (2)Å (Cg1 and Cg2 are centroids of N1/N2/C1/C6/C7 and C1-C6, respectively) and short intermolecular S···S contacts of 3.495 (1) Å.

Related literature top

For details of the synthesis and related structures, see: Wright (1951); Preston (1974); Hamzah et al. (2010); Arumugam et al. 2011); Ruiz et al. (2010); Chou et al. (2011). For the therapeutic properties of benzimidazole derivatives, see: Li et al. (2006); Hwu et al. (2008); Cui et al. (2010); Sasmal et al. (2011); Demirayak et al. (2011). For bond lengths in organic compounds, see: Allen et al. (1987). For the low-temperature device used in the data collection, see: Cosier & Glazer (1986).

Experimental top

A mixture of 3-amino-4-(2-hydroxylethanolamine)benzoic acid ethyl ester (0.1.0 g, 0.45 mmol), K10-montmorillonite (2.0 g), 3-(methylthio) propionaldehyde (0.098 g, 0.91 mmol) and 1 ml MeCN were irradiated in CEMTM microwave at 80°C, 150 W, 5 bar and hold for 5 minutes. Then, another aliquot of aldehyde was added and the reation mixture was irradiated again at the same condition as before. The reaction was monitored by TLC (Hex:EtOAc,1:4). Upon completion, K10-montmorillonite was removed by filtration, washed with DCM and later evaporated in vacuo to afford brown precipitate. The compound was purified with PLC (Hex:EtOAc, 1:4) before it was recrystallized with hot MeOH to afford colourless crystals.

Refinement top

X-ray data were collected at 100 K (Cosier & Glazer, 1986). Hydroxyl atom H3 was located from difference Fourier map, and isotropically refined with restraint O3—H3 = 0.843 (10) Å. The remaining H atoms attached to C atoms were fixed geometrically and refined as riding, with C—H= 0.95–0.99Å and with Uiso(H)=1.2 or 1.5Ueq(C). A rotating group model was applied to the methyl groups.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing the atomic numbering and 50% probability displacement ellipsods.
[Figure 2] Fig. 2. A portion of the crystal packing viewed down the b axis and showing the hydrogen-bonded (dashed lines) dimers.
Ethyl 1-(2-hydroxyethyl)-2-[2-(methylsulfanyl)ethyl]- 1H-benzimidazole-5-carboxylate top
Crystal data top
C15H20N2O3SZ = 2
Mr = 308.39F(000) = 328
Triclinic, P1Dx = 1.357 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.3909 (1) ÅCell parameters from 2401 reflections
b = 8.8277 (2) Åθ = 1.9–25.0°
c = 11.5025 (2) ŵ = 0.23 mm1
α = 110.218 (1)°T = 100 K
β = 102.529 (1)°Plate, colourless
γ = 99.101 (1)°0.27 × 0.24 × 0.07 mm
V = 754.78 (2) Å3
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
2627 independent reflections
Radiation source: fine-focus sealed tube2243 reflections with I > 2σ(I)
graphiteRint = 0.026
Detector resolution: 83.66 pixels mm-1θmax = 25.0°, θmin = 1.9°
φ and ω scanh = 99
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
k = 910
Tmin = 0.941, Tmax = 0.985l = 1313
6027 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0307P)2 + 0.5234P]
where P = (Fo2 + 2Fc2)/3
2627 reflections(Δ/σ)max < 0.001
196 parametersΔρmax = 0.24 e Å3
1 restraintΔρmin = 0.26 e Å3
Crystal data top
C15H20N2O3Sγ = 99.101 (1)°
Mr = 308.39V = 754.78 (2) Å3
Triclinic, P1Z = 2
a = 8.3909 (1) ÅMo Kα radiation
b = 8.8277 (2) ŵ = 0.23 mm1
c = 11.5025 (2) ÅT = 100 K
α = 110.218 (1)°0.27 × 0.24 × 0.07 mm
β = 102.529 (1)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
2627 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
2243 reflections with I > 2σ(I)
Tmin = 0.941, Tmax = 0.985Rint = 0.026
6027 measured reflectionsθmax = 25.0°
Refinement top
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.086Δρmax = 0.24 e Å3
S = 1.04Δρmin = 0.26 e Å3
2627 reflectionsAbsolute structure: ?
196 parametersFlack parameter: ?
1 restraintRogers parameter: ?
Special details top

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) top
xyzUiso*/Ueq
S11.33465 (6)0.81922 (6)0.91756 (5)0.02048 (15)
O10.36330 (17)0.07772 (17)0.28863 (14)0.0244 (3)
O20.46252 (16)0.29862 (16)0.19992 (13)0.0195 (3)
O31.32576 (17)0.48466 (17)0.39325 (14)0.0213 (3)
H31.2305 (18)0.505 (3)0.391 (2)0.035 (7)*
N10.94054 (19)0.36073 (19)0.58614 (15)0.0151 (3)
N21.14023 (19)0.26662 (19)0.50164 (15)0.0140 (3)
C10.8668 (2)0.2070 (2)0.48209 (18)0.0140 (4)
C20.6994 (2)0.1144 (2)0.43009 (18)0.0158 (4)
H20.61380.15490.46400.019*
C30.6610 (2)0.0396 (2)0.32689 (18)0.0153 (4)
C40.7890 (2)0.0998 (2)0.27731 (18)0.0166 (4)
H40.75970.20630.20810.020*
C50.9553 (2)0.0084 (2)0.32637 (18)0.0164 (4)
H51.04080.04850.29210.020*
C60.9912 (2)0.1465 (2)0.42935 (18)0.0141 (4)
C71.1022 (2)0.3904 (2)0.59415 (18)0.0145 (4)
C80.4814 (2)0.1364 (2)0.27111 (18)0.0169 (4)
C90.2882 (3)0.3974 (2)0.1397 (2)0.0231 (5)
H9A0.22710.35370.07980.028*
H9B0.23010.39270.20670.028*
C100.2919 (3)0.5719 (3)0.0675 (2)0.0391 (6)
H10A0.35340.57430.00380.059*
H10B0.17620.64120.02270.059*
H10C0.34860.61530.12820.059*
C111.3032 (2)0.2629 (2)0.47536 (19)0.0165 (4)
H11A1.31950.14900.45520.020*
H11B1.39490.34030.55380.020*
C121.3139 (2)0.3126 (2)0.36286 (19)0.0181 (4)
H12A1.41390.28520.33630.022*
H12B1.21250.24630.28840.022*
C131.2355 (2)0.5380 (2)0.69567 (18)0.0171 (4)
H13A1.29230.60130.65330.021*
H13B1.32140.49890.74360.021*
C141.1634 (2)0.6532 (2)0.79092 (18)0.0179 (4)
H14A1.09950.58930.82930.022*
H14B1.08500.70120.74520.022*
C151.2132 (3)0.9482 (3)0.9979 (2)0.0253 (5)
H15A1.14660.98620.93730.038*
H15B1.28961.04521.07250.038*
H15C1.13730.88361.02750.038*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0191 (3)0.0174 (3)0.0193 (3)0.0018 (2)0.0047 (2)0.0024 (2)
O10.0171 (8)0.0243 (8)0.0270 (8)0.0040 (6)0.0062 (6)0.0053 (7)
O20.0192 (7)0.0149 (7)0.0191 (7)0.0003 (6)0.0016 (6)0.0046 (6)
O30.0165 (8)0.0198 (7)0.0332 (9)0.0064 (6)0.0106 (7)0.0144 (7)
N10.0152 (8)0.0137 (8)0.0161 (8)0.0033 (6)0.0047 (7)0.0054 (7)
N20.0126 (8)0.0142 (8)0.0167 (8)0.0043 (6)0.0057 (7)0.0065 (7)
C10.0168 (10)0.0131 (9)0.0135 (10)0.0056 (8)0.0046 (8)0.0062 (8)
C20.0161 (10)0.0172 (10)0.0160 (10)0.0059 (8)0.0058 (8)0.0075 (8)
C30.0174 (10)0.0162 (10)0.0144 (10)0.0040 (8)0.0038 (8)0.0090 (8)
C40.0224 (11)0.0129 (9)0.0141 (10)0.0039 (8)0.0054 (8)0.0049 (8)
C50.0189 (10)0.0167 (10)0.0175 (10)0.0070 (8)0.0095 (8)0.0077 (8)
C60.0143 (10)0.0146 (9)0.0153 (10)0.0037 (8)0.0043 (8)0.0083 (8)
C70.0176 (10)0.0132 (9)0.0153 (10)0.0057 (8)0.0059 (8)0.0074 (8)
C80.0208 (11)0.0174 (10)0.0136 (10)0.0040 (8)0.0049 (8)0.0079 (8)
C90.0184 (11)0.0230 (11)0.0224 (11)0.0025 (8)0.0015 (9)0.0085 (9)
C100.0296 (13)0.0301 (13)0.0410 (15)0.0038 (10)0.0105 (12)0.0004 (11)
C110.0140 (10)0.0162 (10)0.0213 (11)0.0070 (8)0.0075 (8)0.0070 (8)
C120.0170 (10)0.0185 (10)0.0219 (11)0.0072 (8)0.0094 (9)0.0082 (9)
C130.0161 (10)0.0169 (10)0.0183 (11)0.0038 (8)0.0056 (8)0.0065 (8)
C140.0161 (10)0.0187 (10)0.0161 (10)0.0032 (8)0.0034 (8)0.0047 (8)
C150.0294 (12)0.0214 (11)0.0222 (11)0.0087 (9)0.0075 (10)0.0043 (9)
Geometric parameters (Å, °) top
S1—C151.799 (2)C5—H50.9500
S1—C141.812 (2)C7—C131.495 (3)
O1—C81.212 (2)C9—C101.485 (3)
O2—C81.345 (2)C9—H9A0.9900
O2—C91.456 (2)C9—H9B0.9900
O3—C121.417 (2)C10—H10A0.9800
O3—H30.843 (10)C10—H10B0.9800
N1—C71.317 (2)C10—H10C0.9800
N1—C11.395 (2)C11—C121.518 (3)
N2—C71.372 (2)C11—H11A0.9900
N2—C61.379 (2)C11—H11B0.9900
N2—C111.466 (2)C12—H12A0.9900
C1—C21.391 (3)C12—H12B0.9900
C1—C61.403 (2)C13—C141.521 (3)
C2—C31.393 (3)C13—H13A0.9900
C2—H20.9500C13—H13B0.9900
C3—C41.414 (3)C14—H14A0.9900
C3—C81.485 (3)C14—H14B0.9900
C4—C51.379 (3)C15—H15A0.9800
C4—H40.9500C15—H15B0.9800
C5—C61.400 (3)C15—H15C0.9800
C15—S1—C1499.19 (10)C9—C10—H10A109.5
C8—O2—C9114.83 (15)C9—C10—H10B109.5
C12—O3—H3110.8 (17)H10A—C10—H10B109.5
C7—N1—C1104.86 (15)C9—C10—H10C109.5
C7—N2—C6106.81 (14)H10A—C10—H10C109.5
C7—N2—C11128.13 (16)H10B—C10—H10C109.5
C6—N2—C11124.94 (15)N2—C11—C12111.81 (15)
C2—C1—N1130.07 (17)N2—C11—H11A109.3
C2—C1—C6120.17 (17)C12—C11—H11A109.3
N1—C1—C6109.76 (16)N2—C11—H11B109.3
C1—C2—C3118.05 (17)C12—C11—H11B109.3
C1—C2—H2121.0H11A—C11—H11B107.9
C3—C2—H2121.0O3—C12—C11113.02 (16)
C2—C3—C4120.76 (17)O3—C12—H12A109.0
C2—C3—C8117.54 (17)C11—C12—H12A109.0
C4—C3—C8121.69 (17)O3—C12—H12B109.0
C5—C4—C3121.96 (18)C11—C12—H12B109.0
C5—C4—H4119.0H12A—C12—H12B107.8
C3—C4—H4119.0C7—C13—C14112.12 (15)
C4—C5—C6116.42 (17)C7—C13—H13A109.2
C4—C5—H5121.8C14—C13—H13A109.2
C6—C5—H5121.8C7—C13—H13B109.2
N2—C6—C5131.88 (17)C14—C13—H13B109.2
N2—C6—C1105.50 (16)H13A—C13—H13B107.9
C5—C6—C1122.61 (17)C13—C14—S1109.23 (13)
N1—C7—N2113.06 (17)C13—C14—H14A109.8
N1—C7—C13124.93 (16)S1—C14—H14A109.8
N2—C7—C13121.95 (16)C13—C14—H14B109.8
O1—C8—O2122.83 (18)S1—C14—H14B109.8
O1—C8—C3124.28 (18)H14A—C14—H14B108.3
O2—C8—C3112.88 (16)S1—C15—H15A109.5
O2—C9—C10107.31 (17)S1—C15—H15B109.5
O2—C9—H9A110.3H15A—C15—H15B109.5
C10—C9—H9A110.3S1—C15—H15C109.5
O2—C9—H9B110.3H15A—C15—H15C109.5
C10—C9—H9B110.3H15B—C15—H15C109.5
H9A—C9—H9B108.5
C7—N1—C1—C2179.65 (19)C1—N1—C7—C13177.00 (17)
C7—N1—C1—C60.33 (19)C6—N2—C7—N10.9 (2)
N1—C1—C2—C3178.17 (17)C11—N2—C7—N1175.16 (16)
C6—C1—C2—C31.1 (3)C6—N2—C7—C13176.55 (16)
C1—C2—C3—C40.4 (3)C11—N2—C7—C137.4 (3)
C1—C2—C3—C8179.23 (16)C9—O2—C8—O13.0 (3)
C2—C3—C4—C51.4 (3)C9—O2—C8—C3178.05 (15)
C8—C3—C4—C5178.19 (17)C2—C3—C8—O116.9 (3)
C3—C4—C5—C60.8 (3)C4—C3—C8—O1162.71 (18)
C7—N2—C6—C5177.37 (19)C2—C3—C8—O2162.02 (16)
C11—N2—C6—C56.4 (3)C4—C3—C8—O218.4 (2)
C7—N2—C6—C11.00 (19)C8—O2—C9—C10179.17 (17)
C11—N2—C6—C1175.20 (16)C7—N2—C11—C1298.5 (2)
C4—C5—C6—N2178.81 (18)C6—N2—C11—C1276.8 (2)
C4—C5—C6—C10.7 (3)N2—C11—C12—O370.8 (2)
C2—C1—C6—N2179.76 (16)N1—C7—C13—C140.0 (3)
N1—C1—C6—N20.84 (19)N2—C7—C13—C14177.14 (16)
C2—C1—C6—C51.7 (3)C7—C13—C14—S1175.48 (13)
N1—C1—C6—C5177.72 (16)C15—S1—C14—C13171.67 (14)
C1—N1—C7—N20.3 (2)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O3—H3···N1i0.84 (2)2.01 (2)2.808 (2)159 (2)
C11—H11A···O1ii0.992.393.224 (2)142
C11—H11B···O3iii0.992.423.222 (2)138
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) x+1, y, z; (iii) −x+3, −y+1, −z+1.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
O3—H3···N1i0.84 (2)2.01 (2)2.808 (2)159 (2)
C11—H11A···O1ii0.992.393.224 (2)142
C11—H11B···O3iii0.992.423.222 (2)138
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) x+1, y, z; (iii) −x+3, −y+1, −z+1.
Acknowledgements top

NH, SAH and ASAR gratefully acknowledge the International Islamic University Malaysia (IIUM) for the FRGS Grant (No. FRGS0510–119), the USM Research Grant (No. 304/PFARMASI/650544/I121) and MOSTI (grant no. 09–05-lfn-med-004) for funding the synthetic chemistry work.

references
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