organic compounds
1-{2-Benzyloxy-2-[4-(morpholin-4-yl)phenyl]ethyl}-1H-benzimidazole
aDepartment of Chemistry, Bülent Ecevit University, 67100 Zonguldak, Turkey, bDepartment of Chemistry, Southampton University, SO17 1BJ Southampton, England, and cDepartment of Physics, Hacettepe University, 06800 Beytepe, Ankara, Turkey
*Correspondence e-mail: merzifon@hacettepe.edu.tr
In the title compound, C26H27N3O2, the morpholine ring adopts a chair conformation. The benzene and phenyl rings are inclined to the benzimidazole mean plane by 7.28 (6) and 61.45 (4)°, respectively. In the crystal, pairs of weak C—H⋯O hydrogen bonds link the molecules into inversion dimers. These dimers are further connected via weak C—H⋯N hydrogen bonds. A weak C—H⋯π interaction is also observed.
Related literature
For general background to the biological activity of benzimidazole derivatives, see: Özel Güven et al. (2007a,b). For related structures, see: Caira et al. (2004); Freer et al. (1986); Özel Güven et al. (2008a,b,c); Peeters et al. (1979a,b, 1996). For hydrogen-bonding motifs, see: Bernstein et al. (1995). For ring puckering parameters, see: Cremer & Pople (1975).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: CrystalClear-SM Expert (Rigaku, 2011); cell CrystalClear-SM Expert; data reduction: CrystalClear-SM Expert; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012) and PLATON (Spek, 2009).
Supporting information
https://doi.org/10.1107/S1600536812051306/cv5371sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812051306/cv5371Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S1600536812051306/cv5371Isup3.cml
The title compound, (I), was synthesized by the reaction of 2-(1H-benzimidazol-1-yl)-1-(4-morpholinophenyl)ethanol with aryl halide using sodium hydrate. NaH (0.025 g, 0.618 mmol) was added to a solution of alcohol (0.2 g, 0.618 mmol) in DMF (4 ml) in small fractions. After stirring the mixture a few minutes, benzyl bromide (0.073 ml, 0.618 mmol) was added dropwise. Then, the reaction mixture was stirred additional 3 h at room temperature. The reaction was stopped by adding a small amount of methyl alcohol. After evaporation of the solvent, dichloromethane was added to the reaction mixture and extracted with water. The organic phase was separated and dried with anhydrous magnesium sulfate, then evaporated to dryness. The residue was purified by
using chloroform and crystallized from DMSO:H2O (1:1) to obtain colorless crystals suitable for X-ray analysis (yield; 0.089 g, 35%).H atoms were positioned geometrically with C—H = 0.98, 0.93 and 0.97 Å for methine, aromatic and methylene H, respectively, and constrained to ride on their parent atoms, with Uiso(H) = 1.2 Ueq(C). The highest residual electron density was found 1.10 Å from H1 and the deepest hole 0.59 Å from O1.
The azole compounds possessing an imidazole or triazole ring (such as econazole, miconazole, ketoconazole, fluconazole and itraconazole) have been known as antifungal agents and used in clinics. Similar structures possessing benzimidazole ring in place of imidazole ring of miconazole and econazole have been reported to show antibacterial activity higher than antifungal activity (Özel Güven et al., 2007a,b). The crystal structures of econazole (Freer et al., 1986), miconazole (Peeters et al., 1979a), ketoconazole (Peeters et al., 1979b), fluconazole (Caira et al., 2004) and itraconazole (Peeters et al., 1996) have been reported, previously. Crystal structures of similar ether compounds having benzimidazole ring have been reported (Özel Güven et al., 2008a,b,c). Herewith we report the
of the title compound (I), which is a new benzimidazole derivative.In (I) (Fig. 1), the bond lengths and angles are within normal ranges. The benzimidazole [A (N1/N2/C3–C9)] ring system is approximately planar with a maximum deviation of -0.010 (2) Å for atom C2 and its mean plane is oriented with respect to the benzene [B (C11–C16)] and phenyl [C (C17–C22)] rings at dihedral angles of A/B = 7.28 (6) and A/C = 61.45 (4) °. The dihedral angle between benzene and phenyl rings is B/C = 54.96 (5)°. Atom C10 is -0.008 (2) Å away from the plane of the benzene ring and atoms C1 and N3 are 0.056 (2) and 0.076 (2) Å away from the plane of the phenyl ring. The morpholine ring D (C23–C26/O2/N3) is not planar, but adopting a chair conformation with puckering parameters (Cremer & Pople, 1975) QT = 1.060 (5)Å, φ = 34.3 (2)° and θ = 57.3 (1)°.
In the π interaction (Table 1) is also observed.
weak intermolecular C—H···O hydrogen bonds (Table 1) link the molecules into centrosymmetric R22(28) dimers (Bernstein et al., 1995). These dimers are further connected via weak intermolecular C—H···N hydrogen bonds (Table 1), linking the molecules into centrosymmetric R44(16) dimers, to form a 2-D network (Fig. 2). A weak C—H···For general background to the biological activity of benzimidazole derivatives, see: Özel Güven et al. (2007a,b). For related structures, see: Caira et al. (2004); Freer et al. (1986); Özel Güven et al. (2008a,b,c); Peeters et al. (1979a,b, 1996). For hydrogen-bonding motifs, see: Bernstein et al. (1995). For ring puckering parameters, see: Cremer & Pople (1975).
Data collection: CrystalClear-SM Expert (Rigaku, 2011); cell
CrystalClear-SM Expert (Rigaku, 2011); data reduction: CrystalClear-SM Expert (Rigaku, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012) and PLATON (Spek, 2009).C26H27N3O2 | Z = 2 |
Mr = 413.51 | F(000) = 440 |
Triclinic, P1 | Dx = 1.269 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 9.4719 (3) Å | Cell parameters from 11428 reflections |
b = 10.5057 (3) Å | θ = 3.0–27.6° |
c = 11.8110 (4) Å | µ = 0.08 mm−1 |
α = 96.824 (3)° | T = 100 K |
β = 108.953 (4)° | Prism, colourless |
γ = 98.312 (3)° | 0.32 × 0.25 × 0.22 mm |
V = 1082.51 (7) Å3 |
Rigaku Saturn724+ diffractometer | Rint = 0.043 |
Radiation source: fine-focus sealed tube | θmax = 27.5°, θmin = 3.1° |
Graphite monochromator | h = −12→12 |
profile data from ω–scans | k = −13→13 |
13756 measured reflections | l = −15→15 |
4972 independent reflections | 3 standard reflections every 2 min |
3736 reflections with I > 2σ(I) | intensity decay: 1% |
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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0577P)2 + 0.355P] where P = (Fo2 + 2Fc2)/3 |
4972 reflections | (Δ/σ)max < 0.001 |
280 parameters | Δρmax = 0.63 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
C26H27N3O2 | γ = 98.312 (3)° |
Mr = 413.51 | V = 1082.51 (7) Å3 |
Triclinic, P1 | Z = 2 |
a = 9.4719 (3) Å | Mo Kα radiation |
b = 10.5057 (3) Å | µ = 0.08 mm−1 |
c = 11.8110 (4) Å | T = 100 K |
α = 96.824 (3)° | 0.32 × 0.25 × 0.22 mm |
β = 108.953 (4)° |
Rigaku Saturn724+ diffractometer | Rint = 0.043 |
13756 measured reflections | 3 standard reflections every 2 min |
4972 independent reflections | intensity decay: 1% |
3736 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.63 e Å−3 |
4972 reflections | Δρmin = −0.24 e Å−3 |
280 parameters |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.28084 (13) | 0.57424 (10) | 0.27381 (10) | 0.0245 (3) | |
O2 | −0.08746 (15) | −0.09871 (11) | −0.38295 (11) | 0.0336 (3) | |
N1 | 0.18512 (16) | 0.52783 (12) | 0.47120 (12) | 0.0239 (3) | |
N2 | 0.28757 (19) | 0.70971 (13) | 0.61301 (13) | 0.0312 (3) | |
N3 | 0.03315 (15) | 0.10262 (12) | −0.17348 (11) | 0.0203 (3) | |
C1 | 0.24066 (19) | 0.44368 (15) | 0.28999 (14) | 0.0240 (3) | |
H1 | 0.3308 | 0.4185 | 0.3444 | 0.029* | |
C2 | 0.12280 (19) | 0.44506 (15) | 0.35127 (14) | 0.0243 (3) | |
H2A | 0.0368 | 0.4768 | 0.3008 | 0.029* | |
H2B | 0.0864 | 0.3566 | 0.3593 | 0.029* | |
C3 | 0.2357 (2) | 0.65983 (15) | 0.49714 (15) | 0.0296 (4) | |
H3 | 0.2334 | 0.7103 | 0.4372 | 0.036* | |
C4 | 0.20304 (18) | 0.48813 (15) | 0.58148 (13) | 0.0211 (3) | |
C5 | 0.16909 (19) | 0.36691 (15) | 0.61283 (14) | 0.0240 (3) | |
H5 | 0.1268 | 0.2914 | 0.5544 | 0.029* | |
C6 | 0.2014 (2) | 0.36446 (16) | 0.73509 (15) | 0.0288 (4) | |
H6 | 0.1793 | 0.2854 | 0.7596 | 0.035* | |
C7 | 0.2668 (2) | 0.47816 (17) | 0.82337 (15) | 0.0303 (4) | |
H7 | 0.2874 | 0.4726 | 0.9050 | 0.036* | |
C8 | 0.3011 (2) | 0.59754 (16) | 0.79188 (15) | 0.0298 (4) | |
H8 | 0.3452 | 0.6724 | 0.8509 | 0.036* | |
C9 | 0.26797 (19) | 0.60318 (15) | 0.66909 (15) | 0.0244 (3) | |
C10 | 0.4207 (2) | 0.59640 (17) | 0.25038 (18) | 0.0319 (4) | |
H10A | 0.4128 | 0.5376 | 0.1778 | 0.038* | |
H10B | 0.5034 | 0.5810 | 0.3182 | 0.038* | |
C11 | 0.45016 (18) | 0.73490 (16) | 0.23337 (15) | 0.0253 (3) | |
C12 | 0.5176 (2) | 0.83670 (17) | 0.33221 (16) | 0.0313 (4) | |
H12 | 0.5461 | 0.8184 | 0.4108 | 0.038* | |
C13 | 0.5426 (2) | 0.96468 (17) | 0.31489 (16) | 0.0317 (4) | |
H13 | 0.5868 | 1.0319 | 0.3817 | 0.038* | |
C14 | 0.5024 (2) | 0.99292 (17) | 0.19901 (16) | 0.0293 (4) | |
H14 | 0.5206 | 1.0789 | 0.1874 | 0.035* | |
C15 | 0.4350 (2) | 0.89280 (18) | 0.10032 (16) | 0.0320 (4) | |
H15 | 0.4065 | 0.9114 | 0.0219 | 0.038* | |
C16 | 0.4096 (2) | 0.76504 (17) | 0.11782 (16) | 0.0303 (4) | |
H16 | 0.3645 | 0.6982 | 0.0507 | 0.036* | |
C17 | 0.18236 (19) | 0.34981 (15) | 0.17011 (14) | 0.0224 (3) | |
C18 | 0.0535 (2) | 0.36116 (17) | 0.07608 (16) | 0.0307 (4) | |
H18 | −0.0005 | 0.4254 | 0.0888 | 0.037* | |
C19 | 0.0033 (2) | 0.27977 (17) | −0.03558 (15) | 0.0296 (4) | |
H19 | −0.0826 | 0.2910 | −0.0968 | 0.036* | |
C20 | 0.07978 (18) | 0.18079 (14) | −0.05807 (13) | 0.0199 (3) | |
C21 | 0.2087 (2) | 0.16989 (17) | 0.03657 (16) | 0.0326 (4) | |
H21 | 0.2625 | 0.1051 | 0.0250 | 0.039* | |
C22 | 0.2586 (2) | 0.25367 (17) | 0.14774 (15) | 0.0320 (4) | |
H22 | 0.3459 | 0.2444 | 0.2087 | 0.038* | |
C23 | −0.1301 (2) | 0.06684 (18) | −0.24194 (16) | 0.0332 (4) | |
H23A | −0.1756 | 0.1436 | −0.2386 | 0.040* | |
H23B | −0.1772 | 0.0031 | −0.2055 | 0.040* | |
C24 | −0.1588 (2) | 0.0102 (2) | −0.37283 (17) | 0.0406 (5) | |
H24A | −0.2675 | −0.0169 | −0.4157 | 0.049* | |
H24B | −0.1206 | 0.0772 | −0.4112 | 0.049* | |
C25 | 0.0716 (2) | −0.05690 (18) | −0.32175 (16) | 0.0332 (4) | |
H25A | 0.1098 | 0.0112 | −0.3590 | 0.040* | |
H25B | 0.1220 | −0.1297 | −0.3305 | 0.040* | |
C26 | 0.1096 (2) | −0.00560 (17) | −0.18839 (15) | 0.0296 (4) | |
H26A | 0.0774 | −0.0750 | −0.1495 | 0.036* | |
H26B | 0.2187 | 0.0238 | −0.1497 | 0.036* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0256 (6) | 0.0211 (6) | 0.0273 (6) | 0.0030 (5) | 0.0113 (5) | 0.0010 (5) |
O2 | 0.0349 (7) | 0.0277 (6) | 0.0291 (7) | 0.0044 (5) | 0.0054 (5) | −0.0115 (5) |
N1 | 0.0350 (8) | 0.0173 (6) | 0.0204 (7) | 0.0025 (5) | 0.0133 (6) | −0.0004 (5) |
N2 | 0.0486 (10) | 0.0190 (7) | 0.0279 (8) | 0.0018 (6) | 0.0198 (7) | −0.0012 (6) |
N3 | 0.0219 (7) | 0.0198 (6) | 0.0177 (6) | 0.0028 (5) | 0.0071 (5) | −0.0013 (5) |
C1 | 0.0287 (9) | 0.0198 (8) | 0.0213 (8) | 0.0024 (6) | 0.0085 (6) | −0.0009 (6) |
C2 | 0.0298 (9) | 0.0210 (8) | 0.0210 (8) | 0.0004 (6) | 0.0110 (7) | −0.0011 (6) |
C3 | 0.0475 (11) | 0.0171 (8) | 0.0273 (9) | 0.0044 (7) | 0.0188 (8) | 0.0010 (6) |
C4 | 0.0234 (8) | 0.0207 (7) | 0.0199 (7) | 0.0027 (6) | 0.0108 (6) | −0.0006 (6) |
C5 | 0.0273 (9) | 0.0186 (7) | 0.0249 (8) | −0.0005 (6) | 0.0116 (7) | −0.0013 (6) |
C6 | 0.0368 (10) | 0.0241 (8) | 0.0286 (9) | 0.0022 (7) | 0.0164 (7) | 0.0058 (7) |
C7 | 0.0373 (10) | 0.0336 (9) | 0.0202 (8) | 0.0032 (8) | 0.0127 (7) | 0.0023 (7) |
C8 | 0.0371 (10) | 0.0252 (8) | 0.0238 (8) | −0.0011 (7) | 0.0129 (7) | −0.0056 (7) |
C9 | 0.0285 (9) | 0.0186 (8) | 0.0263 (8) | 0.0003 (6) | 0.0136 (7) | −0.0019 (6) |
C10 | 0.0268 (9) | 0.0280 (9) | 0.0419 (10) | 0.0021 (7) | 0.0153 (8) | 0.0044 (7) |
C11 | 0.0181 (8) | 0.0262 (8) | 0.0312 (9) | 0.0023 (6) | 0.0099 (6) | 0.0019 (7) |
C12 | 0.0299 (9) | 0.0330 (9) | 0.0247 (9) | 0.0044 (7) | 0.0030 (7) | 0.0025 (7) |
C13 | 0.0273 (9) | 0.0262 (9) | 0.0334 (9) | 0.0015 (7) | 0.0044 (7) | −0.0040 (7) |
C14 | 0.0246 (9) | 0.0249 (8) | 0.0403 (10) | 0.0046 (7) | 0.0134 (7) | 0.0067 (7) |
C15 | 0.0344 (10) | 0.0351 (10) | 0.0295 (9) | 0.0070 (8) | 0.0145 (8) | 0.0070 (7) |
C16 | 0.0308 (10) | 0.0303 (9) | 0.0277 (9) | −0.0011 (7) | 0.0135 (7) | −0.0041 (7) |
C17 | 0.0260 (8) | 0.0205 (7) | 0.0200 (8) | −0.0010 (6) | 0.0109 (6) | −0.0007 (6) |
C18 | 0.0289 (9) | 0.0310 (9) | 0.0301 (9) | 0.0102 (7) | 0.0097 (7) | −0.0063 (7) |
C19 | 0.0247 (9) | 0.0345 (9) | 0.0258 (9) | 0.0096 (7) | 0.0054 (7) | −0.0044 (7) |
C20 | 0.0229 (8) | 0.0178 (7) | 0.0186 (7) | 0.0002 (6) | 0.0093 (6) | 0.0004 (6) |
C21 | 0.0371 (10) | 0.0304 (9) | 0.0267 (9) | 0.0168 (8) | 0.0050 (7) | −0.0036 (7) |
C22 | 0.0345 (10) | 0.0326 (9) | 0.0221 (8) | 0.0122 (8) | 0.0010 (7) | −0.0023 (7) |
C23 | 0.0263 (9) | 0.0376 (10) | 0.0288 (9) | 0.0067 (8) | 0.0055 (7) | −0.0090 (7) |
C24 | 0.0395 (11) | 0.0433 (11) | 0.0270 (9) | 0.0153 (9) | −0.0011 (8) | −0.0123 (8) |
C25 | 0.0326 (10) | 0.0333 (9) | 0.0296 (9) | 0.0076 (8) | 0.0102 (7) | −0.0097 (7) |
C26 | 0.0302 (9) | 0.0279 (9) | 0.0265 (9) | 0.0099 (7) | 0.0061 (7) | −0.0057 (7) |
O1—C1 | 1.4218 (19) | C11—C12 | 1.391 (2) |
O1—C10 | 1.432 (2) | C12—H12 | 0.9300 |
O2—C24 | 1.423 (2) | C13—C12 | 1.382 (2) |
O2—C25 | 1.418 (2) | C13—H13 | 0.9300 |
N1—C2 | 1.4584 (19) | C14—C13 | 1.377 (3) |
N1—C3 | 1.363 (2) | C14—C15 | 1.380 (2) |
N1—C4 | 1.380 (2) | C14—H14 | 0.9300 |
N2—C3 | 1.307 (2) | C15—H15 | 0.9300 |
N2—C9 | 1.386 (2) | C16—C11 | 1.381 (2) |
N3—C20 | 1.4020 (18) | C16—C15 | 1.381 (2) |
N3—C23 | 1.461 (2) | C16—H16 | 0.9300 |
N3—C26 | 1.4562 (19) | C17—C18 | 1.389 (2) |
C1—C2 | 1.516 (2) | C17—C22 | 1.372 (2) |
C1—C17 | 1.512 (2) | C18—H18 | 0.9300 |
C1—H1 | 0.9800 | C19—C18 | 1.380 (2) |
C2—H2A | 0.9700 | C19—H19 | 0.9300 |
C2—H2B | 0.9700 | C20—C19 | 1.398 (2) |
C3—H3 | 0.9300 | C20—C21 | 1.392 (2) |
C5—C4 | 1.390 (2) | C21—H21 | 0.9300 |
C5—C6 | 1.380 (2) | C22—C21 | 1.387 (2) |
C5—H5 | 0.9300 | C22—H22 | 0.9300 |
C6—H6 | 0.9300 | C23—C24 | 1.510 (2) |
C7—C6 | 1.403 (2) | C23—H23A | 0.9700 |
C7—H7 | 0.9300 | C23—H23B | 0.9700 |
C8—C7 | 1.374 (2) | C24—H24A | 0.9700 |
C8—C9 | 1.391 (2) | C24—H24B | 0.9700 |
C8—H8 | 0.9300 | C25—H25A | 0.9700 |
C9—C4 | 1.409 (2) | C25—H25B | 0.9700 |
C10—H10A | 0.9700 | C26—C25 | 1.508 (2) |
C10—H10B | 0.9700 | C26—H26A | 0.9700 |
C11—C10 | 1.491 (2) | C26—H26B | 0.9700 |
C1—O1—C10 | 112.15 (12) | C12—C13—H13 | 119.9 |
C25—O2—C24 | 108.49 (13) | C14—C13—C12 | 120.23 (16) |
C3—N1—C2 | 127.13 (14) | C14—C13—H13 | 119.9 |
C3—N1—C4 | 106.11 (13) | C13—C14—C15 | 119.58 (16) |
C4—N1—C2 | 126.76 (13) | C13—C14—H14 | 120.2 |
C3—N2—C9 | 104.06 (13) | C15—C14—H14 | 120.2 |
C20—N3—C23 | 117.52 (12) | C14—C15—C16 | 120.10 (16) |
C20—N3—C26 | 118.08 (13) | C14—C15—H15 | 119.9 |
C26—N3—C23 | 111.50 (13) | C16—C15—H15 | 119.9 |
O1—C1—C2 | 106.14 (12) | C11—C16—H16 | 119.5 |
O1—C1—C17 | 111.26 (12) | C15—C16—C11 | 121.07 (16) |
O1—C1—H1 | 108.9 | C15—C16—H16 | 119.5 |
C2—C1—H1 | 108.9 | C18—C17—C1 | 121.39 (14) |
C17—C1—C2 | 112.51 (13) | C22—C17—C1 | 121.31 (15) |
C17—C1—H1 | 108.9 | C22—C17—C18 | 117.24 (14) |
N1—C2—C1 | 111.66 (13) | C17—C18—H18 | 119.1 |
N1—C2—H2A | 109.3 | C19—C18—C17 | 121.85 (15) |
N1—C2—H2B | 109.3 | C19—C18—H18 | 119.1 |
C1—C2—H2A | 109.3 | C18—C19—C20 | 120.98 (16) |
C1—C2—H2B | 109.3 | C18—C19—H19 | 119.5 |
H2A—C2—H2B | 107.9 | C20—C19—H19 | 119.5 |
N1—C3—H3 | 122.7 | C19—C20—N3 | 120.82 (14) |
N2—C3—N1 | 114.56 (15) | C21—C20—N3 | 122.19 (14) |
N2—C3—H3 | 122.7 | C21—C20—C19 | 116.86 (14) |
N1—C4—C5 | 132.71 (14) | C20—C21—H21 | 119.3 |
N1—C4—C9 | 104.98 (13) | C22—C21—C20 | 121.35 (15) |
C5—C4—C9 | 122.31 (14) | C22—C21—H21 | 119.3 |
C4—C5—H5 | 121.7 | C17—C22—C21 | 121.70 (16) |
C6—C5—C4 | 116.56 (14) | C17—C22—H22 | 119.1 |
C6—C5—H5 | 121.7 | C21—C22—H22 | 119.1 |
C5—C6—C7 | 121.73 (16) | N3—C23—C24 | 110.50 (14) |
C5—C6—H6 | 119.1 | N3—C23—H23A | 109.5 |
C7—C6—H6 | 119.1 | N3—C23—H23B | 109.5 |
C6—C7—H7 | 119.3 | C24—C23—H23A | 109.5 |
C8—C7—C6 | 121.44 (15) | C24—C23—H23B | 109.5 |
C8—C7—H7 | 119.3 | H23A—C23—H23B | 108.1 |
C7—C8—C9 | 118.07 (15) | O2—C24—C23 | 112.00 (15) |
C7—C8—H8 | 121.0 | O2—C24—H24A | 109.2 |
C9—C8—H8 | 121.0 | O2—C24—H24B | 109.2 |
N2—C9—C4 | 110.28 (14) | C23—C24—H24A | 109.2 |
N2—C9—C8 | 129.83 (15) | C23—C24—H24B | 109.2 |
C8—C9—C4 | 119.89 (15) | H24A—C24—H24B | 107.9 |
O1—C10—C11 | 107.45 (13) | O2—C25—C26 | 111.75 (14) |
O1—C10—H10A | 110.2 | O2—C25—H25A | 109.3 |
O1—C10—H10B | 110.2 | O2—C25—H25B | 109.3 |
C11—C10—H10A | 110.2 | C26—C25—H25A | 109.3 |
C11—C10—H10B | 110.2 | C26—C25—H25B | 109.3 |
H10A—C10—H10B | 108.5 | H25A—C25—H25B | 107.9 |
C12—C11—C10 | 121.43 (16) | N3—C26—C25 | 110.05 (14) |
C16—C11—C10 | 120.25 (15) | N3—C26—H26A | 109.6 |
C16—C11—C12 | 118.32 (16) | N3—C26—H26B | 109.6 |
C11—C12—H12 | 119.7 | C25—C26—H26A | 109.6 |
C13—C12—C11 | 120.70 (16) | C25—C26—H26B | 109.7 |
C13—C12—H12 | 119.7 | H26A—C26—H26B | 108.2 |
C10—O1—C1—C2 | 162.84 (13) | C4—C5—C6—C7 | −0.7 (3) |
C10—O1—C1—C17 | −74.46 (17) | C8—C7—C6—C5 | 0.3 (3) |
C1—O1—C10—C11 | 179.24 (13) | C9—C8—C7—C6 | 0.5 (3) |
C25—O2—C24—C23 | −59.9 (2) | C7—C8—C9—N2 | 178.51 (17) |
C24—O2—C25—C26 | 60.96 (19) | C7—C8—C9—C4 | −0.8 (3) |
C3—N1—C2—C1 | 64.8 (2) | N2—C9—C4—N1 | 0.47 (18) |
C4—N1—C2—C1 | −116.02 (17) | N2—C9—C4—C5 | −179.06 (15) |
C2—N1—C3—N2 | −179.33 (16) | C8—C9—C4—N1 | 179.93 (15) |
C4—N1—C3—N2 | 1.4 (2) | C8—C9—C4—C5 | 0.4 (2) |
C2—N1—C4—C5 | −0.9 (3) | C12—C11—C10—O1 | 82.65 (19) |
C2—N1—C4—C9 | 179.66 (15) | C16—C11—C10—O1 | −96.93 (18) |
C3—N1—C4—C5 | 178.42 (18) | C10—C11—C12—C13 | −179.33 (16) |
C3—N1—C4—C9 | −1.04 (17) | C16—C11—C12—C13 | 0.3 (3) |
C9—N2—C3—N1 | −1.0 (2) | C14—C13—C12—C11 | −0.7 (3) |
C3—N2—C9—C4 | 0.32 (19) | C15—C14—C13—C12 | 0.9 (3) |
C3—N2—C9—C8 | −179.07 (18) | C13—C14—C15—C16 | −0.7 (3) |
C23—N3—C20—C19 | −36.8 (2) | C15—C16—C11—C10 | 179.54 (16) |
C23—N3—C20—C21 | 147.48 (17) | C15—C16—C11—C12 | 0.0 (3) |
C26—N3—C20—C19 | −175.07 (15) | C11—C16—C15—C14 | 0.3 (3) |
C26—N3—C20—C21 | 9.2 (2) | C1—C17—C18—C19 | 176.97 (16) |
C20—N3—C23—C24 | 167.07 (14) | C22—C17—C18—C19 | −0.1 (3) |
C26—N3—C23—C24 | −52.07 (19) | C1—C17—C22—C21 | −177.82 (17) |
C20—N3—C26—C25 | −166.46 (14) | C18—C17—C22—C21 | −0.8 (3) |
C23—N3—C26—C25 | 52.92 (19) | C20—C19—C18—C17 | 0.9 (3) |
O1—C1—C2—N1 | −62.84 (16) | N3—C20—C19—C18 | −176.71 (16) |
C17—C1—C2—N1 | 175.25 (13) | C21—C20—C19—C18 | −0.8 (3) |
O1—C1—C17—C18 | −60.9 (2) | N3—C20—C21—C22 | 175.82 (16) |
O1—C1—C17—C22 | 116.07 (17) | C19—C20—C21—C22 | −0.1 (3) |
C2—C1—C17—C18 | 58.1 (2) | C17—C22—C21—C20 | 0.8 (3) |
C2—C1—C17—C22 | −124.97 (17) | N3—C23—C24—O2 | 56.1 (2) |
C6—C5—C4—N1 | −179.01 (17) | N3—C26—C25—O2 | −58.1 (2) |
C6—C5—C4—C9 | 0.4 (2) |
Cg is the centroid of the C4–C9 benzene ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C5—H5···O2i | 0.93 | 2.58 | 3.478 (2) | 163 |
C6—H6···N3ii | 0.93 | 2.56 | 3.439 (2) | 159 |
C2—H2A···Cgiii | 0.97 | 2.66 | 3.451 (2) | 139 |
Symmetry codes: (i) −x, −y, −z; (ii) x, y, z+1; (iii) −x, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C26H27N3O2 |
Mr | 413.51 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 100 |
a, b, c (Å) | 9.4719 (3), 10.5057 (3), 11.8110 (4) |
α, β, γ (°) | 96.824 (3), 108.953 (4), 98.312 (3) |
V (Å3) | 1082.51 (7) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.32 × 0.25 × 0.22 |
Data collection | |
Diffractometer | Rigaku Saturn724+ |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13756, 4972, 3736 |
Rint | 0.043 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.135, 1.06 |
No. of reflections | 4972 |
No. of parameters | 280 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.63, −0.24 |
Computer programs: CrystalClear-SM Expert (Rigaku, 2011), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 2012), WinGX (Farrugia, 2012) and PLATON (Spek, 2009).
Cg is the centroid of the C4–C9 benzene ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C5—H5···O2i | 0.93 | 2.58 | 3.478 (2) | 163 |
C6—H6···N3ii | 0.93 | 2.56 | 3.439 (2) | 159 |
C2—H2A···Cgiii | 0.97 | 2.66 | 3.451 (2) | 139 |
Symmetry codes: (i) −x, −y, −z; (ii) x, y, z+1; (iii) −x, −y+1, −z+1. |
Acknowledgements
The authors are grateful to Zonguldak Karaelmas University Research Fund (project No. 2010-13-02-06).
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
The azole compounds possessing an imidazole or triazole ring (such as econazole, miconazole, ketoconazole, fluconazole and itraconazole) have been known as antifungal agents and used in clinics. Similar structures possessing benzimidazole ring in place of imidazole ring of miconazole and econazole have been reported to show antibacterial activity higher than antifungal activity (Özel Güven et al., 2007a,b). The crystal structures of econazole (Freer et al., 1986), miconazole (Peeters et al., 1979a), ketoconazole (Peeters et al., 1979b), fluconazole (Caira et al., 2004) and itraconazole (Peeters et al., 1996) have been reported, previously. Crystal structures of similar ether compounds having benzimidazole ring have been reported (Özel Güven et al., 2008a,b,c). Herewith we report the crystal structure of the title compound (I), which is a new benzimidazole derivative.
In (I) (Fig. 1), the bond lengths and angles are within normal ranges. The benzimidazole [A (N1/N2/C3–C9)] ring system is approximately planar with a maximum deviation of -0.010 (2) Å for atom C2 and its mean plane is oriented with respect to the benzene [B (C11–C16)] and phenyl [C (C17–C22)] rings at dihedral angles of A/B = 7.28 (6) and A/C = 61.45 (4) °. The dihedral angle between benzene and phenyl rings is B/C = 54.96 (5)°. Atom C10 is -0.008 (2) Å away from the plane of the benzene ring and atoms C1 and N3 are 0.056 (2) and 0.076 (2) Å away from the plane of the phenyl ring. The morpholine ring D (C23–C26/O2/N3) is not planar, but adopting a chair conformation with puckering parameters (Cremer & Pople, 1975) QT = 1.060 (5)Å, φ = 34.3 (2)° and θ = 57.3 (1)°.
In the crystal structure, weak intermolecular C—H···O hydrogen bonds (Table 1) link the molecules into centrosymmetric R22(28) dimers (Bernstein et al., 1995). These dimers are further connected via weak intermolecular C—H···N hydrogen bonds (Table 1), linking the molecules into centrosymmetric R44(16) dimers, to form a 2-D network (Fig. 2). A weak C—H···π interaction (Table 1) is also observed.