Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807042572/cf2115sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807042572/cf2115Isup2.hkl |
CCDC reference: 663712
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (C-C) = 0.004 Å
- R factor = 0.037
- wR factor = 0.062
- Data-to-parameter ratio = 17.8
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT148_ALERT_3_B su on the b - Axis is Too Large (x 1000) . 15 Ang. PLAT149_ALERT_3_B su on the beta Angle is Too Large (x 100) .. 7 Deg.
Alert level C PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.98 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C9
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 27.93 From the CIF: _reflns_number_total 2434 Count of symmetry unique reflns 1311 Completeness (_total/calc) 185.66% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 1123 Fraction of Friedel pairs measured 0.857 Are heavy atom types Z>Si present yes PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 2
0 ALERT level A = In general: serious problem 2 ALERT level B = Potentially serious problem 2 ALERT level C = Check and explain 2 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 4 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
2.25 ml of triethylamine (15.98 mmol, 1.2 eq) and 1.4 ml of methyl bromoacetate (14.65 mmol, 1.1 eq) were added to 2-mercaptobenzimidazole (13.32 mmol, 2 g) in 10 ml of anhydrous ethanol. The mixture was stirred for half an hour at ambient temperature, then was refluxed for 3 h. The solvent was removed and 20 ml of water was added to the residue. The organic residues were collected, then they were dried, filtered and concentrated with a rotary evaporator. The addition of hexane to the substrate led to a precipitate which was recrystallized from a mixture of dichloromethane/hexane 20/80 to obtain white crystals of the title compound with a yield of 75%; m.p. 393 K. 1H-NMR (DMSO-d6, 300 MHz), δ(p.p.m.): 3.66 (s, 3H, OCH3), 4.24 (s, 2H, CH2), 7.1O-7.51 (m, 4H, C6H4), 12.63 (1 s, 1H, NH). 13C-NMR (DMSO-d6, 300 MHz), δ(p.p.m.): 33.98 (CH2), 52.89 (OCH3), 113.35, 114.53, 124.59, 126.13, 126.68, 133.72 (C6H4), 149.51 (C═N), 168.15 (C═O).
H atoms were located in a difference Fourier map, but those attached to C10 were geometrically repositioned. They were all initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.90–0.98, N—H 0.85 Å and Uiso(H) in the range 1.1–1.5 times Ueq of the parent atom), after which their positions were refined with riding constraints.
The synthesis of new benzimidazole derivatives presents is of considerable interest in pharmacology because of their therapeutic benefits in many diseases. Several studies showed that benzimidazole derivatives possess versatile pharmacological properties, such as anthelmintic, fungicidal, antitumour, analgesic and antiviral activities. It was reported that benzimidazole ring systems are an important pharmacophore in the discovery and design of new drugs (Tebbe et al., 1997). Furthermore, a recent study showed that 2-[(4-diarylmethoxy)phenyl]-benzimidazoles are potent inhibitors of the hepatitis C virus NS5B polymerase (Tomio et al., 2006). The title compound (I) was synthesized and we have determined its crystal structure in conjunction with new investigations of 2-substituted benzimidazole derivative properties. The molecular structure of (I) and the atomic numbering scheme are shown in Fig. 1. The results are comparable to those obtained in recent studies related to 2-substitued benzimidazole derivatives (Langer et al., 2006; Eltayeb et al., 2007; Jian et al., 2007; Yıldırım et al., 2007). The benzimidazole ring system is essentially planar, with a maximum deviation of 0.051 (1) Å for atom C1. The dihedral angle between the benzimidazole ring system and the plane through S1/C8/C9/O1/O2/C10 is 81.75 (1)°. The crystal packing is stabilized by an intermolecular N—H···N hydrogen bond which leads to the formation of infinite molecular chains along the [001] direction (Fig. 2).
The crystal structures of some related 2-substituted benzimidazole derivatives have previously been reported (Langer et al., 2006; Eltayeb et al., 2007; Jian et al., 2007; Yıldırım et al., 2007). For related literature see: Tebbe et al. (1997); Tomio et al. (2006). For the refinement weighting scheme, see: Watkin (1994); Prince (1982).
Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO (Otwinowski & Minor, 1997) and SORTAV (Blessing, 1995); data reduction: DENZO and SORTAV; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: CRYSTALS.
C10H10N2O2S | F(000) = 464 |
Mr = 222.27 | Dx = 1.357 Mg m−3 |
Monoclinic, Cc | Melting point: 393 K |
Hall symbol: C -2yc | Mo Kα radiation, λ = 0.71073 Å |
a = 9.337 (9) Å | Cell parameters from 10772 reflections |
b = 13.418 (15) Å | θ = 3–28° |
c = 9.667 (8) Å | µ = 0.28 mm−1 |
β = 116.04 (7)° | T = 295 K |
V = 1088 (2) Å3 | Lozenge, white |
Z = 4 | 0.40 × 0.20 × 0.15 mm |
Nonius KappaCCD diffractometer | 2248 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.037 |
φ scans | θmax = 27.9°, θmin = 3.0° |
Absorption correction: multi-scan (SORTAV; Blessing, 1995) | h = −12→12 |
Tmin = 0.88, Tmax = 0.96 | k = −17→17 |
10772 measured reflections | l = −12→11 |
2434 independent reflections |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.037 | w =
[1-(Fo-Fc)2/36σ2(F)]2/[349T0(x) + 411T1(x) + 249T2(x) + 63.5T3(x)]
where Ti are Chebychev polynomials and x = Fc/Fmax (Prince, 1982; Watkin, 1994) |
wR(F2) = 0.062 | (Δ/σ)max = 0.000164 |
S = 0.92 | Δρmax = 0.15 e Å−3 |
2434 reflections | Δρmin = −0.13 e Å−3 |
137 parameters | Absolute structure: Flack (1983), 1156 Friedel pairs |
2 restraints | Absolute structure parameter: −0.01 (7) |
Primary atom site location: structure-invariant direct methods |
C10H10N2O2S | V = 1088 (2) Å3 |
Mr = 222.27 | Z = 4 |
Monoclinic, Cc | Mo Kα radiation |
a = 9.337 (9) Å | µ = 0.28 mm−1 |
b = 13.418 (15) Å | T = 295 K |
c = 9.667 (8) Å | 0.40 × 0.20 × 0.15 mm |
β = 116.04 (7)° |
Nonius KappaCCD diffractometer | 2434 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1995) | 2248 reflections with I > 2σ(I) |
Tmin = 0.88, Tmax = 0.96 | Rint = 0.037 |
10772 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | H-atom parameters constrained |
wR(F2) = 0.062 | Δρmax = 0.15 e Å−3 |
S = 0.92 | Δρmin = −0.13 e Å−3 |
2434 reflections | Absolute structure: Flack (1983), 1156 Friedel pairs |
137 parameters | Absolute structure parameter: −0.01 (7) |
2 restraints |
x | y | z | Uiso*/Ueq | ||
S1 | 0.13266 (12) | −0.07154 (4) | 0.70877 (11) | 0.0629 | |
N1 | 0.3917 (2) | 0.00112 (13) | 0.95018 (18) | 0.0512 | |
N2 | 0.3656 (2) | 0.05903 (13) | 0.72407 (18) | 0.0539 | |
O1 | −0.0254 (2) | 0.11704 (13) | 0.73910 (19) | 0.0868 | |
O2 | −0.1561 (2) | 0.14742 (14) | 0.48884 (18) | 0.0771 | |
C1 | 0.5178 (2) | 0.06469 (16) | 0.9834 (2) | 0.0481 | |
C2 | 0.6407 (2) | 0.09640 (19) | 1.1223 (2) | 0.0642 | |
C3 | 0.7432 (3) | 0.1657 (2) | 1.1134 (3) | 0.0746 | |
C4 | 0.7264 (3) | 0.2027 (2) | 0.9725 (3) | 0.0758 | |
C5 | 0.6069 (3) | 0.17041 (19) | 0.8362 (3) | 0.0684 | |
C6 | 0.5009 (2) | 0.10176 (16) | 0.8420 (2) | 0.0500 | |
C7 | 0.3049 (2) | 0.00213 (15) | 0.7947 (2) | 0.0484 | |
C8 | 0.0081 (3) | 0.01087 (17) | 0.5564 (2) | 0.0598 | |
C9 | −0.0568 (3) | 0.09576 (15) | 0.6092 (2) | 0.0543 | |
C10 | −0.2304 (4) | 0.2342 (2) | 0.5187 (4) | 0.0984 | |
H101 | −0.2889 | 0.2693 | 0.4257 | 0.1501* | |
H102 | −0.3051 | 0.2101 | 0.5520 | 0.1500* | |
H103 | −0.1562 | 0.2761 | 0.5931 | 0.1500* | |
H2 | 0.6509 | 0.0725 | 1.2184 | 0.0740* | |
H82 | 0.0693 | 0.0398 | 0.5053 | 0.0659* | |
H3 | 0.8243 | 0.1908 | 1.2060 | 0.0843* | |
H4 | 0.7915 | 0.2524 | 0.9723 | 0.0907* | |
H1 | 0.3683 | −0.0280 | 1.0151 | 0.0619* | |
H81 | −0.0736 | −0.0295 | 0.4848 | 0.0681* | |
H5 | 0.5948 | 0.1940 | 0.7390 | 0.0841* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0686 (3) | 0.0556 (3) | 0.0471 (3) | −0.0007 (3) | 0.0094 (2) | −0.0013 (3) |
N1 | 0.0571 (9) | 0.0653 (10) | 0.0303 (7) | 0.0007 (8) | 0.0184 (7) | 0.0052 (7) |
N2 | 0.0656 (10) | 0.0634 (10) | 0.0304 (7) | 0.0074 (8) | 0.0190 (7) | 0.0026 (7) |
O1 | 0.1244 (15) | 0.0847 (12) | 0.0467 (9) | 0.0190 (12) | 0.0332 (9) | −0.0042 (8) |
O2 | 0.0834 (11) | 0.0879 (12) | 0.0508 (9) | 0.0263 (9) | 0.0212 (8) | 0.0110 (8) |
C1 | 0.0476 (10) | 0.0619 (12) | 0.0346 (8) | 0.0086 (9) | 0.0177 (7) | 0.0024 (8) |
C2 | 0.0511 (11) | 0.0960 (17) | 0.0375 (10) | −0.0016 (11) | 0.0121 (9) | 0.0059 (10) |
C3 | 0.0511 (12) | 0.0985 (18) | 0.0608 (14) | −0.0046 (13) | 0.0121 (10) | −0.0025 (13) |
C4 | 0.0605 (13) | 0.0882 (16) | 0.0754 (15) | −0.0070 (12) | 0.0267 (11) | 0.0150 (14) |
C5 | 0.0697 (14) | 0.0845 (16) | 0.0543 (12) | 0.0022 (12) | 0.0304 (11) | 0.0170 (11) |
C6 | 0.0546 (10) | 0.0593 (11) | 0.0369 (9) | 0.0107 (9) | 0.0207 (8) | 0.0056 (8) |
C7 | 0.0561 (10) | 0.0541 (11) | 0.0313 (8) | 0.0115 (9) | 0.0160 (8) | 0.0009 (8) |
C8 | 0.0616 (12) | 0.0709 (13) | 0.0332 (9) | 0.0035 (11) | 0.0081 (9) | −0.0051 (9) |
C9 | 0.0588 (11) | 0.0604 (12) | 0.0408 (10) | −0.0041 (9) | 0.0194 (8) | 0.0011 (8) |
C10 | 0.112 (2) | 0.0871 (19) | 0.104 (2) | 0.0331 (17) | 0.054 (2) | 0.0222 (16) |
S1—C7 | 1.755 (3) | C2—H2 | 0.947 |
S1—C8 | 1.800 (2) | C3—C4 | 1.392 (4) |
N1—C1 | 1.373 (3) | C3—H3 | 0.945 |
N1—C7 | 1.359 (3) | C4—C5 | 1.371 (4) |
N1—H1 | 0.845 | C4—H4 | 0.902 |
N2—C6 | 1.400 (3) | C5—C6 | 1.371 (3) |
N2—C7 | 1.308 (3) | C5—H5 | 0.949 |
O1—C9 | 1.192 (2) | C8—C9 | 1.482 (3) |
O2—C9 | 1.322 (3) | C8—H82 | 0.985 |
O2—C10 | 1.448 (3) | C8—H81 | 0.944 |
C1—C2 | 1.395 (3) | C10—H101 | 0.947 |
C1—C6 | 1.397 (3) | C10—H102 | 0.944 |
C2—C3 | 1.364 (3) | C10—H103 | 0.936 |
C7—S1—C8 | 99.78 (13) | N2—C6—C1 | 108.96 (19) |
C1—N1—C7 | 106.67 (17) | N2—C6—C5 | 130.61 (19) |
C1—N1—H1 | 126.0 | C1—C6—C5 | 120.4 (2) |
C7—N1—H1 | 127.1 | S1—C7—N1 | 119.73 (16) |
C6—N2—C7 | 104.87 (17) | S1—C7—N2 | 126.76 (15) |
C9—O2—C10 | 117.3 (2) | N1—C7—N2 | 113.49 (18) |
N1—C1—C2 | 132.32 (18) | S1—C8—C9 | 113.90 (16) |
N1—C1—C6 | 105.98 (17) | S1—C8—H82 | 110.1 |
C2—C1—C6 | 121.6 (2) | C9—C8—H82 | 106.5 |
C1—C2—C3 | 116.8 (2) | S1—C8—H81 | 105.7 |
C1—C2—H2 | 121.8 | C9—C8—H81 | 111.9 |
C3—C2—H2 | 121.4 | H82—C8—H81 | 108.6 |
C2—C3—C4 | 121.6 (2) | C8—C9—O2 | 109.53 (17) |
C2—C3—H3 | 118.4 | C8—C9—O1 | 126.75 (19) |
C4—C3—H3 | 119.9 | O2—C9—O1 | 123.7 (2) |
C3—C4—C5 | 121.5 (2) | O2—C10—H101 | 109.8 |
C3—C4—H4 | 118.6 | O2—C10—H102 | 106.5 |
C5—C4—H4 | 119.8 | H101—C10—H102 | 106.8 |
C4—C5—C6 | 118.1 (2) | O2—C10—H103 | 112.2 |
C4—C5—H5 | 122.6 | H101—C10—H103 | 110.7 |
C6—C5—H5 | 119.3 | H102—C10—H103 | 110.6 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N2i | 0.85 | 2.07 | 2.879 (2) | 159 |
Symmetry code: (i) x, −y, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C10H10N2O2S |
Mr | 222.27 |
Crystal system, space group | Monoclinic, Cc |
Temperature (K) | 295 |
a, b, c (Å) | 9.337 (9), 13.418 (15), 9.667 (8) |
β (°) | 116.04 (7) |
V (Å3) | 1088 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.28 |
Crystal size (mm) | 0.40 × 0.20 × 0.15 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | Multi-scan (SORTAV; Blessing, 1995) |
Tmin, Tmax | 0.88, 0.96 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10772, 2434, 2248 |
Rint | 0.037 |
(sin θ/λ)max (Å−1) | 0.659 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.062, 0.92 |
No. of reflections | 2434 |
No. of parameters | 137 |
No. of restraints | 2 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.15, −0.13 |
Absolute structure | Flack (1983), 1156 Friedel pairs |
Absolute structure parameter | −0.01 (7) |
Computer programs: COLLECT (Nonius, 2001), DENZO (Otwinowski & Minor, 1997) and SORTAV (Blessing, 1995), DENZO and SORTAV, SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2003), CRYSTALS.
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N2i | 0.85 | 2.07 | 2.879 (2) | 159 |
Symmetry code: (i) x, −y, z+1/2. |
The synthesis of new benzimidazole derivatives presents is of considerable interest in pharmacology because of their therapeutic benefits in many diseases. Several studies showed that benzimidazole derivatives possess versatile pharmacological properties, such as anthelmintic, fungicidal, antitumour, analgesic and antiviral activities. It was reported that benzimidazole ring systems are an important pharmacophore in the discovery and design of new drugs (Tebbe et al., 1997). Furthermore, a recent study showed that 2-[(4-diarylmethoxy)phenyl]-benzimidazoles are potent inhibitors of the hepatitis C virus NS5B polymerase (Tomio et al., 2006). The title compound (I) was synthesized and we have determined its crystal structure in conjunction with new investigations of 2-substituted benzimidazole derivative properties. The molecular structure of (I) and the atomic numbering scheme are shown in Fig. 1. The results are comparable to those obtained in recent studies related to 2-substitued benzimidazole derivatives (Langer et al., 2006; Eltayeb et al., 2007; Jian et al., 2007; Yıldırım et al., 2007). The benzimidazole ring system is essentially planar, with a maximum deviation of 0.051 (1) Å for atom C1. The dihedral angle between the benzimidazole ring system and the plane through S1/C8/C9/O1/O2/C10 is 81.75 (1)°. The crystal packing is stabilized by an intermolecular N—H···N hydrogen bond which leads to the formation of infinite molecular chains along the [001] direction (Fig. 2).