organic compounds
Ethyl 1-sec-butyl-2-(4-chlorophenyl)-1H-benzimidazole-5-carboxylate
aSchool of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, bSchool of Chemical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and cX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
In the title compound, C20H21ClN2O2, the ethyl 1H-benzimidazole-5-carboxylate ring system, excluding the methylene and methyl H atoms, is almost planar, with a maximum deviation of 0.055 (1) Å, and makes a dihedral angle of 40.63 (4)° with the benzene ring. The sec-butyl group is disordered over two positions, with refined site occupancies of 0.855 (4) and 0.145 (4). In the crystal, molecules are linked into chains along [010] via intermolecular C—H⋯O hydrogen bonds and are further interconnected by C—H⋯Cl interactions into two-dimensional networks parallel to (001). The is further consolidated by C—H⋯π interactions.
Related literature
For the synthesis of the title compound, see: Arumugam et al. (2010a,b,c). For general background to and the therapeutic properties of benzimidazole derivatives, see: Bonfanti et al. (2008); Evans et al. (1997); Hori et al. (2002); Snow (2007). For a related structure, see: Eltayeb et al. (2009). For reference bond lengths, see: Allen et al. (1987). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell 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).
Supporting information
https://doi.org/10.1107/S1600536810033945/wn2406sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810033945/wn2406Isup2.hkl
The title compound was synthesized using previously reported procedures (Arumugam et al., 2010a,b,c). The crude product was recrystallized from ethyl acetate to yield the title compound as colourless crystals.
All H atoms were positioned geometrically and refined using a riding model, with C—H = 0.93–0.98 Å and Uiso(H) = xUeq(C), where x = 1.5 for methyl H and 1.2 for all other H atoms. A rotating-group model was applied for the methyl groups. The sec-butyl group attached to the benzimidazole ring system is disordered over two positions, with refined site-occupancies of 0.855 (4) and 0.145 (4).
Benzimidazole is an important pharmacophore in drug discovery and its derivatives have shown various therapeutic properties such as antiviral (Bonfanti et al., 2008) and anti-HIV-1 (Evans et al., 1997) activities. Benzimidazoles are used as biomimetics of guanine residues and selectively inhibit endothelial cell growth and suppress angiogenesis in vitro and in vivo (Hori et al., 2002). In particular, substituted benzimidazole derivatives are also inhibitors of tyrosine kinase and are useful for inhibiting cell proliferation for the treatment of cancer (Snow et al., 2007). In view of their importance, the
determination of the title compound was carried out and the results are presented here.The molecular structure of the title compound is shown in Fig. 1. The ethyl 1H-benzimidazole-5-carboxylate ring system (O1/O2/N1/N2/C7–C16), excluding methylene and methyl H atoms, is almost planar, with a maximum deviation of 0.055 (1) Å for atom O2, and makes a dihedral angle of 40.63 (4)° with the benzene (C1–C6) ring. The sec-butyl group is disordered over two positions with refined site-occupancies of 0.855 (4) and 0.145 (4). The bond lengths (Allen et al., 1987) and angles in the title compound are within normal ranges and comparable to those in a related
(Eltayeb et al., 2009).In the
(Fig. 2), the molecules are linked into one-dimensional chains along [010] via intermolecular C12—H12A···O2 hydrogen bonds and are further interconnected by C16–H16A···Cl1 interactions into two-dimensional networks parallel to (001). The is further consolidated by C—H···Cg1 (Table 1) interactions; Cg1 is the centroid of the N1/C7/N2/C13/C8 ring.For the synthesis of the title compound, see: Arumugam et al. (2010a,b,c). For general background to and the therapeutic properties of benzimidazole derivatives, see: Bonfanti et al. (2008); Evans et al. (1997); Hori et al. (2002); Snow (2007). For a related structure, see: Eltayeb et al. (2009). For reference bond lengths, see: Allen et al. (1987). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).
Data collection: APEX2 (Bruker, 2009); cell
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).C20H21ClN2O2 | F(000) = 752 |
Mr = 356.84 | Dx = 1.325 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5929 reflections |
a = 10.4321 (9) Å | θ = 2.8–36.1° |
b = 12.6218 (12) Å | µ = 0.23 mm−1 |
c = 13.6896 (12) Å | T = 100 K |
β = 97.043 (3)° | Plate, colourless |
V = 1788.9 (3) Å3 | 0.45 × 0.34 × 0.10 mm |
Z = 4 |
Bruker SMART APEXII DUO CCD area-detector diffractometer | 8437 independent reflections |
Radiation source: fine-focus sealed tube | 6651 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.038 |
φ and ω scans | θmax = 36.2°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −17→17 |
Tmin = 0.904, Tmax = 0.977 | k = −14→20 |
21234 measured reflections | l = −22→22 |
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)] = 0.050 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.175 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0914P)2 + 0.4364P] where P = (Fo2 + 2Fc2)/3 |
8437 reflections | (Δ/σ)max < 0.001 |
248 parameters | Δρmax = 0.75 e Å−3 |
0 restraints | Δρmin = −0.39 e Å−3 |
C20H21ClN2O2 | V = 1788.9 (3) Å3 |
Mr = 356.84 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 10.4321 (9) Å | µ = 0.23 mm−1 |
b = 12.6218 (12) Å | T = 100 K |
c = 13.6896 (12) Å | 0.45 × 0.34 × 0.10 mm |
β = 97.043 (3)° |
Bruker SMART APEXII DUO CCD area-detector diffractometer | 8437 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 6651 reflections with I > 2σ(I) |
Tmin = 0.904, Tmax = 0.977 | Rint = 0.038 |
21234 measured reflections |
R[F2 > 2σ(F2)] = 0.050 | 0 restraints |
wR(F2) = 0.175 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.75 e Å−3 |
8437 reflections | Δρmin = −0.39 e Å−3 |
248 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems 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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
Cl1 | 1.44482 (3) | −0.12780 (3) | 0.05943 (3) | 0.02804 (10) | |
O1 | 0.66151 (9) | 0.53169 (7) | 0.09366 (8) | 0.02287 (19) | |
O2 | 0.49447 (10) | 0.47833 (8) | 0.17101 (8) | 0.0244 (2) | |
N1 | 0.97430 (9) | 0.22053 (7) | 0.11935 (8) | 0.01566 (17) | |
N2 | 0.88205 (10) | 0.08363 (8) | 0.19214 (8) | 0.01724 (18) | |
C1 | 1.08637 (12) | −0.04972 (9) | 0.10289 (9) | 0.0184 (2) | |
H1A | 1.0056 | −0.0819 | 0.0969 | 0.022* | |
C2 | 1.19323 (13) | −0.10669 (10) | 0.08102 (9) | 0.0198 (2) | |
H2A | 1.1846 | −0.1769 | 0.0607 | 0.024* | |
C3 | 1.31246 (12) | −0.05767 (10) | 0.08982 (9) | 0.0193 (2) | |
C4 | 1.32851 (12) | 0.04663 (10) | 0.12105 (10) | 0.0204 (2) | |
H4A | 1.4096 | 0.0782 | 0.1271 | 0.025* | |
C5 | 1.22138 (12) | 0.10309 (9) | 0.14312 (9) | 0.0186 (2) | |
H5A | 1.2310 | 0.1730 | 0.1643 | 0.022* | |
C6 | 1.09949 (11) | 0.05585 (9) | 0.13384 (8) | 0.01582 (18) | |
C7 | 0.98702 (11) | 0.12116 (9) | 0.14997 (8) | 0.01543 (18) | |
C8 | 0.85402 (10) | 0.25092 (8) | 0.14249 (8) | 0.01417 (17) | |
C9 | 0.79079 (11) | 0.34784 (9) | 0.12560 (8) | 0.01504 (18) | |
H9A | 0.8286 | 0.4032 | 0.0947 | 0.018* | |
C10 | 0.66963 (11) | 0.35881 (8) | 0.15650 (8) | 0.01520 (18) | |
C11 | 0.61175 (11) | 0.27463 (9) | 0.20282 (9) | 0.0176 (2) | |
H11A | 0.5306 | 0.2846 | 0.2229 | 0.021* | |
C12 | 0.67240 (12) | 0.17741 (9) | 0.21918 (9) | 0.0187 (2) | |
H12A | 0.6338 | 0.1219 | 0.2493 | 0.022* | |
C13 | 0.79468 (11) | 0.16691 (9) | 0.18806 (8) | 0.01594 (19) | |
C14 | 0.59808 (11) | 0.46053 (9) | 0.14271 (9) | 0.01683 (19) | |
C15 | 0.60047 (14) | 0.63413 (10) | 0.07588 (11) | 0.0256 (3) | |
H15A | 0.6041 | 0.6740 | 0.1367 | 0.031* | |
H15B | 0.5107 | 0.6256 | 0.0489 | 0.031* | |
C16 | 0.67404 (16) | 0.69051 (12) | 0.00368 (13) | 0.0320 (3) | |
H16A | 0.6341 | 0.7577 | −0.0131 | 0.048* | |
H16B | 0.6735 | 0.6483 | −0.0547 | 0.048* | |
H16C | 0.7615 | 0.7016 | 0.0327 | 0.048* | |
C17A | 0.87973 (15) | −0.01159 (11) | 0.25461 (12) | 0.0170 (3) | 0.855 (4) |
H17A | 0.9624 | −0.0480 | 0.2532 | 0.020* | 0.855 (4) |
C18A | 0.87305 (16) | 0.02241 (14) | 0.36090 (11) | 0.0228 (3) | 0.855 (4) |
H18A | 0.7882 | 0.0516 | 0.3663 | 0.027* | 0.855 (4) |
H18B | 0.8847 | −0.0393 | 0.4034 | 0.027* | 0.855 (4) |
C19A | 0.97501 (17) | 0.10445 (16) | 0.39550 (12) | 0.0268 (4) | 0.855 (4) |
H19A | 0.9705 | 0.1207 | 0.4635 | 0.040* | 0.855 (4) |
H19B | 0.9599 | 0.1676 | 0.3568 | 0.040* | 0.855 (4) |
H19C | 1.0590 | 0.0768 | 0.3881 | 0.040* | 0.855 (4) |
C20A | 0.77336 (17) | −0.08965 (12) | 0.21576 (16) | 0.0277 (4) | 0.855 (4) |
H20A | 0.7817 | −0.1070 | 0.1486 | 0.042* | 0.855 (4) |
H20B | 0.6904 | −0.0579 | 0.2194 | 0.042* | 0.855 (4) |
H20C | 0.7812 | −0.1529 | 0.2549 | 0.042* | 0.855 (4) |
C17B | 0.9122 (10) | 0.0082 (8) | 0.2857 (7) | 0.0179 (16)* | 0.145 (4) |
H17B | 0.9924 | −0.0301 | 0.2791 | 0.021* | 0.145 (4) |
C18B | 0.8027 (10) | −0.0706 (8) | 0.2733 (8) | 0.027 (2)* | 0.145 (4) |
H18C | 0.7234 | −0.0335 | 0.2817 | 0.032* | 0.145 (4) |
H18D | 0.8175 | −0.1225 | 0.3257 | 0.032* | 0.145 (4) |
C19B | 0.7823 (14) | −0.1313 (11) | 0.1720 (11) | 0.039 (3)* | 0.145 (4) |
H19D | 0.7234 | −0.1891 | 0.1764 | 0.059* | 0.145 (4) |
H19E | 0.8636 | −0.1582 | 0.1569 | 0.059* | 0.145 (4) |
H19F | 0.7472 | −0.0836 | 0.1210 | 0.059* | 0.145 (4) |
C20B | 0.9247 (12) | 0.0562 (10) | 0.3823 (8) | 0.027 (2)* | 0.145 (4) |
H20D | 0.9400 | 0.0021 | 0.4316 | 0.040* | 0.145 (4) |
H20E | 0.8466 | 0.0934 | 0.3909 | 0.040* | 0.145 (4) |
H20F | 0.9959 | 0.1050 | 0.3886 | 0.040* | 0.145 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.02775 (17) | 0.02678 (16) | 0.03220 (17) | 0.01538 (12) | 0.01408 (13) | 0.00528 (12) |
O1 | 0.0225 (4) | 0.0148 (4) | 0.0334 (5) | 0.0082 (3) | 0.0119 (4) | 0.0077 (3) |
O2 | 0.0204 (4) | 0.0219 (4) | 0.0331 (5) | 0.0080 (3) | 0.0115 (4) | 0.0027 (4) |
N1 | 0.0143 (4) | 0.0123 (3) | 0.0216 (4) | 0.0030 (3) | 0.0068 (3) | 0.0023 (3) |
N2 | 0.0176 (4) | 0.0122 (4) | 0.0236 (4) | 0.0040 (3) | 0.0091 (3) | 0.0050 (3) |
C1 | 0.0196 (5) | 0.0148 (4) | 0.0209 (5) | 0.0035 (4) | 0.0035 (4) | 0.0002 (4) |
C2 | 0.0244 (5) | 0.0156 (4) | 0.0200 (5) | 0.0062 (4) | 0.0052 (4) | −0.0001 (4) |
C3 | 0.0211 (5) | 0.0189 (5) | 0.0189 (5) | 0.0093 (4) | 0.0070 (4) | 0.0035 (4) |
C4 | 0.0175 (5) | 0.0192 (5) | 0.0256 (5) | 0.0044 (4) | 0.0068 (4) | 0.0022 (4) |
C5 | 0.0178 (5) | 0.0153 (4) | 0.0237 (5) | 0.0031 (4) | 0.0071 (4) | 0.0010 (4) |
C6 | 0.0171 (4) | 0.0135 (4) | 0.0177 (4) | 0.0043 (3) | 0.0054 (4) | 0.0023 (3) |
C7 | 0.0156 (4) | 0.0130 (4) | 0.0186 (4) | 0.0034 (3) | 0.0059 (3) | 0.0023 (3) |
C8 | 0.0140 (4) | 0.0114 (4) | 0.0179 (4) | 0.0019 (3) | 0.0054 (3) | 0.0021 (3) |
C9 | 0.0155 (4) | 0.0121 (4) | 0.0181 (4) | 0.0025 (3) | 0.0046 (3) | 0.0019 (3) |
C10 | 0.0155 (4) | 0.0131 (4) | 0.0175 (4) | 0.0033 (3) | 0.0042 (3) | 0.0005 (3) |
C11 | 0.0158 (4) | 0.0169 (4) | 0.0212 (5) | 0.0025 (4) | 0.0064 (4) | 0.0017 (4) |
C12 | 0.0169 (5) | 0.0161 (4) | 0.0246 (5) | 0.0019 (4) | 0.0089 (4) | 0.0045 (4) |
C13 | 0.0162 (4) | 0.0136 (4) | 0.0191 (4) | 0.0033 (3) | 0.0064 (4) | 0.0032 (3) |
C14 | 0.0170 (5) | 0.0149 (4) | 0.0189 (4) | 0.0040 (3) | 0.0034 (4) | 0.0007 (3) |
C15 | 0.0283 (6) | 0.0170 (5) | 0.0334 (6) | 0.0121 (4) | 0.0118 (5) | 0.0070 (4) |
C16 | 0.0335 (7) | 0.0215 (6) | 0.0440 (8) | 0.0110 (5) | 0.0171 (6) | 0.0111 (6) |
C17A | 0.0178 (6) | 0.0125 (5) | 0.0212 (6) | 0.0013 (4) | 0.0039 (5) | 0.0058 (5) |
C18A | 0.0219 (7) | 0.0279 (7) | 0.0197 (6) | 0.0051 (6) | 0.0064 (5) | 0.0090 (5) |
C19A | 0.0267 (8) | 0.0356 (9) | 0.0180 (6) | 0.0097 (7) | 0.0016 (5) | −0.0007 (6) |
C20A | 0.0229 (7) | 0.0157 (6) | 0.0456 (11) | −0.0037 (5) | 0.0083 (7) | 0.0041 (6) |
Cl1—C3 | 1.7332 (12) | C15—C16 | 1.503 (2) |
O1—C14 | 1.3433 (15) | C15—H15A | 0.9700 |
O1—C15 | 1.4486 (15) | C15—H15B | 0.9700 |
O2—C14 | 1.2131 (15) | C16—H16A | 0.9600 |
N1—C7 | 1.3240 (14) | C16—H16B | 0.9600 |
N1—C8 | 1.3854 (14) | C16—H16C | 0.9600 |
N2—C7 | 1.3828 (15) | C17A—C18A | 1.527 (2) |
N2—C13 | 1.3879 (14) | C17A—C20A | 1.530 (2) |
N2—C17A | 1.4769 (16) | C17A—H17A | 0.9800 |
N2—C17B | 1.595 (9) | C18A—C19A | 1.518 (3) |
C1—C2 | 1.3897 (17) | C18A—H18A | 0.9700 |
C1—C6 | 1.3998 (16) | C18A—H18B | 0.9700 |
C1—H1A | 0.9300 | C19A—H19A | 0.9600 |
C2—C3 | 1.3812 (19) | C19A—H19B | 0.9600 |
C2—H2A | 0.9300 | C19A—H19C | 0.9600 |
C3—C4 | 1.3879 (18) | C20A—H20A | 0.9600 |
C4—C5 | 1.3895 (17) | C20A—H20B | 0.9600 |
C4—H4A | 0.9300 | C20A—H20C | 0.9600 |
C5—C6 | 1.3960 (17) | C17B—C20B | 1.447 (15) |
C5—H5A | 0.9300 | C17B—C18B | 1.508 (15) |
C6—C7 | 1.4725 (15) | C17B—H17B | 0.9800 |
C8—C9 | 1.3956 (15) | C18B—C19B | 1.576 (18) |
C8—C13 | 1.4112 (15) | C18B—H18C | 0.9700 |
C9—C10 | 1.3881 (16) | C18B—H18D | 0.9700 |
C9—H9A | 0.9300 | C19B—H19D | 0.9600 |
C10—C11 | 1.4104 (16) | C19B—H19E | 0.9600 |
C10—C14 | 1.4854 (15) | C19B—H19F | 0.9600 |
C11—C12 | 1.3863 (16) | C20B—H20D | 0.9600 |
C11—H11A | 0.9300 | C20B—H20E | 0.9600 |
C12—C13 | 1.3998 (16) | C20B—H20F | 0.9600 |
C12—H12A | 0.9300 | ||
C14—O1—C15 | 116.59 (10) | O1—C15—C16 | 106.49 (11) |
C7—N1—C8 | 104.38 (9) | O1—C15—H15A | 110.4 |
C7—N2—C13 | 105.87 (9) | C16—C15—H15A | 110.4 |
C7—N2—C17A | 126.20 (10) | O1—C15—H15B | 110.4 |
C13—N2—C17A | 125.61 (10) | C16—C15—H15B | 110.4 |
C7—N2—C17B | 116.8 (4) | H15A—C15—H15B | 108.6 |
C13—N2—C17B | 123.2 (3) | C15—C16—H16A | 109.5 |
C2—C1—C6 | 120.43 (12) | C15—C16—H16B | 109.5 |
C2—C1—H1A | 119.8 | H16A—C16—H16B | 109.5 |
C6—C1—H1A | 119.8 | C15—C16—H16C | 109.5 |
C3—C2—C1 | 119.14 (11) | H16A—C16—H16C | 109.5 |
C3—C2—H2A | 120.4 | H16B—C16—H16C | 109.5 |
C1—C2—H2A | 120.4 | N2—C17A—C18A | 109.21 (12) |
C2—C3—C4 | 121.67 (11) | N2—C17A—C20A | 112.67 (14) |
C2—C3—Cl1 | 119.06 (10) | C18A—C17A—C20A | 113.35 (13) |
C4—C3—Cl1 | 119.26 (10) | N2—C17A—H17A | 107.1 |
C3—C4—C5 | 118.92 (12) | C18A—C17A—H17A | 107.1 |
C3—C4—H4A | 120.5 | C20A—C17A—H17A | 107.1 |
C5—C4—H4A | 120.5 | C19A—C18A—C17A | 112.15 (12) |
C4—C5—C6 | 120.60 (11) | C19A—C18A—H18A | 109.2 |
C4—C5—H5A | 119.7 | C17A—C18A—H18A | 109.2 |
C6—C5—H5A | 119.7 | C19A—C18A—H18B | 109.2 |
C5—C6—C1 | 119.22 (10) | C17A—C18A—H18B | 109.2 |
C5—C6—C7 | 118.75 (10) | H18A—C18A—H18B | 107.9 |
C1—C6—C7 | 121.88 (11) | C20B—C17B—C18B | 111.2 (9) |
N1—C7—N2 | 113.76 (9) | C20B—C17B—N2 | 118.1 (8) |
N1—C7—C6 | 122.25 (10) | C18B—C17B—N2 | 103.4 (8) |
N2—C7—C6 | 123.86 (10) | C20B—C17B—H17B | 107.9 |
N1—C8—C9 | 128.88 (10) | C18B—C17B—H17B | 107.9 |
N1—C8—C13 | 110.60 (9) | N2—C17B—H17B | 107.9 |
C9—C8—C13 | 120.52 (10) | C17B—C18B—C19B | 116.0 (9) |
C10—C9—C8 | 117.80 (10) | C17B—C18B—H18C | 108.3 |
C10—C9—H9A | 121.1 | C19B—C18B—H18C | 108.3 |
C8—C9—H9A | 121.1 | C17B—C18B—H18D | 108.3 |
C9—C10—C11 | 121.19 (10) | C19B—C18B—H18D | 108.3 |
C9—C10—C14 | 120.64 (10) | H18C—C18B—H18D | 107.4 |
C11—C10—C14 | 118.17 (10) | C18B—C19B—H19D | 109.5 |
C12—C11—C10 | 121.83 (10) | C18B—C19B—H19E | 109.5 |
C12—C11—H11A | 119.1 | H19D—C19B—H19E | 109.5 |
C10—C11—H11A | 119.1 | C18B—C19B—H19F | 109.5 |
C11—C12—C13 | 116.72 (10) | H19D—C19B—H19F | 109.5 |
C11—C12—H12A | 121.6 | H19E—C19B—H19F | 109.5 |
C13—C12—H12A | 121.6 | C17B—C20B—H20D | 109.5 |
N2—C13—C12 | 132.68 (10) | C17B—C20B—H20E | 109.5 |
N2—C13—C8 | 105.39 (9) | H20D—C20B—H20E | 109.5 |
C12—C13—C8 | 121.93 (10) | C17B—C20B—H20F | 109.5 |
O2—C14—O1 | 123.27 (11) | H20D—C20B—H20F | 109.5 |
O2—C14—C10 | 124.96 (11) | H20E—C20B—H20F | 109.5 |
O1—C14—C10 | 111.77 (10) | ||
C6—C1—C2—C3 | −0.27 (18) | C17B—N2—C13—C12 | −41.3 (5) |
C1—C2—C3—C4 | 0.76 (19) | C7—N2—C13—C8 | 0.12 (13) |
C1—C2—C3—Cl1 | −178.33 (9) | C17A—N2—C13—C8 | 163.64 (13) |
C2—C3—C4—C5 | −0.55 (19) | C17B—N2—C13—C8 | 138.5 (5) |
Cl1—C3—C4—C5 | 178.54 (10) | C11—C12—C13—N2 | 179.91 (13) |
C3—C4—C5—C6 | −0.15 (19) | C11—C12—C13—C8 | 0.17 (18) |
C4—C5—C6—C1 | 0.63 (18) | N1—C8—C13—N2 | −0.11 (13) |
C4—C5—C6—C7 | −174.93 (11) | C9—C8—C13—N2 | 179.26 (10) |
C2—C1—C6—C5 | −0.42 (17) | N1—C8—C13—C12 | 179.69 (11) |
C2—C1—C6—C7 | 175.00 (11) | C9—C8—C13—C12 | −0.94 (18) |
C8—N1—C7—N2 | 0.02 (14) | C15—O1—C14—O2 | 0.54 (19) |
C8—N1—C7—C6 | 176.15 (11) | C15—O1—C14—C10 | 179.96 (11) |
C13—N2—C7—N1 | −0.09 (14) | C9—C10—C14—O2 | −176.84 (12) |
C17A—N2—C7—N1 | −163.48 (13) | C11—C10—C14—O2 | 2.36 (19) |
C17B—N2—C7—N1 | −141.6 (4) | C9—C10—C14—O1 | 3.75 (16) |
C13—N2—C7—C6 | −176.15 (11) | C11—C10—C14—O1 | −177.05 (11) |
C17A—N2—C7—C6 | 20.5 (2) | C14—O1—C15—C16 | −168.74 (13) |
C17B—N2—C7—C6 | 42.4 (5) | C7—N2—C17A—C18A | 108.23 (14) |
C5—C6—C7—N1 | 38.83 (17) | C13—N2—C17A—C18A | −52.01 (18) |
C1—C6—C7—N1 | −136.61 (12) | C17B—N2—C17A—C18A | 38.7 (9) |
C5—C6—C7—N2 | −145.43 (12) | C7—N2—C17A—C20A | −124.87 (14) |
C1—C6—C7—N2 | 39.13 (17) | C13—N2—C17A—C20A | 74.90 (18) |
C7—N1—C8—C9 | −179.25 (12) | C17B—N2—C17A—C20A | 165.6 (10) |
C7—N1—C8—C13 | 0.06 (13) | N2—C17A—C18A—C19A | −50.27 (16) |
N1—C8—C9—C10 | −179.71 (11) | C20A—C17A—C18A—C19A | −176.79 (13) |
C13—C8—C9—C10 | 1.04 (17) | C7—N2—C17B—C20B | 92.8 (8) |
C8—C9—C10—C11 | −0.44 (17) | C13—N2—C17B—C20B | −41.5 (10) |
C8—C9—C10—C14 | 178.73 (10) | C17A—N2—C17B—C20B | −145.1 (15) |
C9—C10—C11—C12 | −0.32 (18) | C7—N2—C17B—C18B | −144.0 (5) |
C14—C10—C11—C12 | −179.51 (11) | C13—N2—C17B—C18B | 81.8 (7) |
C10—C11—C12—C13 | 0.44 (18) | C17A—N2—C17B—C18B | −21.9 (7) |
C7—N2—C13—C12 | −179.65 (13) | C20B—C17B—C18B—C19B | −178.0 (9) |
C17A—N2—C13—C12 | −16.1 (2) | N2—C17B—C18B—C19B | 54.3 (10) |
Cg1 is the centroid of the N1/C7/N2/C13/C8 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C12—H12A···O2i | 0.93 | 2.57 | 3.4994 (16) | 174 |
C16—H16A···Cl1ii | 0.96 | 2.73 | 3.4651 (17) | 134 |
C19A—H19B···Cg1 | 0.96 | 2.71 | 3.3457 (18) | 124 |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x−1, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C20H21ClN2O2 |
Mr | 356.84 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 10.4321 (9), 12.6218 (12), 13.6896 (12) |
β (°) | 97.043 (3) |
V (Å3) | 1788.9 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.23 |
Crystal size (mm) | 0.45 × 0.34 × 0.10 |
Data collection | |
Diffractometer | Bruker SMART APEXII DUO CCD area-detector |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.904, 0.977 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 21234, 8437, 6651 |
Rint | 0.038 |
(sin θ/λ)max (Å−1) | 0.830 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.050, 0.175, 1.09 |
No. of reflections | 8437 |
No. of parameters | 248 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.75, −0.39 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
Cg1 is the centroid of the N1/C7/N2/C13/C8 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C12—H12A···O2i | 0.93 | 2.57 | 3.4994 (16) | 174 |
C16—H16A···Cl1ii | 0.96 | 2.73 | 3.4651 (17) | 134 |
C19A—H19B···Cg1 | 0.96 | 2.71 | 3.3457 (18) | 124 |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x−1, y+1, z. |
Acknowledgements
NA, ASAR and HO acknowledge Universiti Sains Malaysia (USM) for funding the synthetic chemistry work under Research University Grant No. 1001/PFARMASI/815026 and MOSTI Grant 304/PFARMASI/650512/I121. HKF and CKQ thank USM for the Research University Grant No. 1001/PFIZIK/811160 for funding the crystallography work done in this article. NA also thanks USM for the award of a postdoctoral fellowship. CKQ also thanks USM for the award of a research fellowship.
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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.
Benzimidazole is an important pharmacophore in drug discovery and its derivatives have shown various therapeutic properties such as antiviral (Bonfanti et al., 2008) and anti-HIV-1 (Evans et al., 1997) activities. Benzimidazoles are used as biomimetics of guanine residues and selectively inhibit endothelial cell growth and suppress angiogenesis in vitro and in vivo (Hori et al., 2002). In particular, substituted benzimidazole derivatives are also inhibitors of tyrosine kinase and are useful for inhibiting cell proliferation for the treatment of cancer (Snow et al., 2007). In view of their importance, the crystal structure determination of the title compound was carried out and the results are presented here.
The molecular structure of the title compound is shown in Fig. 1. The ethyl 1H-benzimidazole-5-carboxylate ring system (O1/O2/N1/N2/C7–C16), excluding methylene and methyl H atoms, is almost planar, with a maximum deviation of 0.055 (1) Å for atom O2, and makes a dihedral angle of 40.63 (4)° with the benzene (C1–C6) ring. The sec-butyl group is disordered over two positions with refined site-occupancies of 0.855 (4) and 0.145 (4). The bond lengths (Allen et al., 1987) and angles in the title compound are within normal ranges and comparable to those in a related crystal structure (Eltayeb et al., 2009).
In the crystal structure (Fig. 2), the molecules are linked into one-dimensional chains along [010] via intermolecular C12—H12A···O2 hydrogen bonds and are further interconnected by C16–H16A···Cl1 interactions into two-dimensional networks parallel to (001). The crystal structure is further consolidated by C—H···Cg1 (Table 1) interactions; Cg1 is the centroid of the N1/C7/N2/C13/C8 ring.