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In the mol­ecule of the title compound, C10H10N2O2S, the benzimidazole ring system and the plane through the non-H atoms of the methyl mercaptoacetate group form a dihedral angle of 81.75 (1)°. The crystal structure is stabilized by N—H...N hydrogen bonds, giving infinite chains along the [001] direction.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807042572/cf2115sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807042572/cf2115Isup2.hkl
Contains datablock I

CCDC reference: 663712

Key indicators

  • Single-crystal X-ray study
  • T = 295 K
  • Mean [sigma](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

Comment top

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).

Related literature top

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).

Experimental top

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 (CN), 168.15 (CO).

Refinement top

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.

Structure description top

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).

Computing details top

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.

Figures top
[Figure 1] Fig. 1. The molecular structure of compound (I) and the atomic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 2] Fig. 2. Crystal packing of compound (I) viewed down the b axis, showing the hydrogen-bonded chains along the c axis. H atoms not involved in hydrogen bonds have been omitted for clarity. Dashed lines indicate N—H···N hydrogen bonds.
Methyl (1H-benzimidazol-2-ylsulfanyl)acetate top
Crystal data top
C10H10N2O2SF(000) = 464
Mr = 222.27Dx = 1.357 Mg m3
Monoclinic, CcMelting point: 393 K
Hall symbol: C -2ycMo Kα radiation, λ = 0.71073 Å
a = 9.337 (9) ÅCell parameters from 10772 reflections
b = 13.418 (15) Åθ = 3–28°
c = 9.667 (8) ŵ = 0.28 mm1
β = 116.04 (7)°T = 295 K
V = 1088 (2) Å3Lozenge, white
Z = 40.40 × 0.20 × 0.15 mm
Data collection top
Nonius KappaCCD
diffractometer
2248 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.037
φ scansθmax = 27.9°, θmin = 3.0°
Absorption correction: multi-scan
(SORTAV; Blessing, 1995)
h = 1212
Tmin = 0.88, Tmax = 0.96k = 1717
10772 measured reflectionsl = 1211
2434 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-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 = 0.92Δρmax = 0.15 e Å3
2434 reflectionsΔρmin = 0.13 e Å3
137 parametersAbsolute structure: Flack (1983), 1156 Friedel pairs
2 restraintsAbsolute structure parameter: 0.01 (7)
Primary atom site location: structure-invariant direct methods
Crystal data top
C10H10N2O2SV = 1088 (2) Å3
Mr = 222.27Z = 4
Monoclinic, CcMo Kα radiation
a = 9.337 (9) ŵ = 0.28 mm1
b = 13.418 (15) ÅT = 295 K
c = 9.667 (8) Å0.40 × 0.20 × 0.15 mm
β = 116.04 (7)°
Data collection top
Nonius KappaCCD
diffractometer
2434 independent reflections
Absorption correction: multi-scan
(SORTAV; Blessing, 1995)
2248 reflections with I > 2σ(I)
Tmin = 0.88, Tmax = 0.96Rint = 0.037
10772 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.037H-atom parameters constrained
wR(F2) = 0.062Δρmax = 0.15 e Å3
S = 0.92Δρmin = 0.13 e Å3
2434 reflectionsAbsolute structure: Flack (1983), 1156 Friedel pairs
137 parametersAbsolute structure parameter: 0.01 (7)
2 restraints
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.13266 (12)0.07154 (4)0.70877 (11)0.0629
N10.3917 (2)0.00112 (13)0.95018 (18)0.0512
N20.3656 (2)0.05903 (13)0.72407 (18)0.0539
O10.0254 (2)0.11704 (13)0.73910 (19)0.0868
O20.1561 (2)0.14742 (14)0.48884 (18)0.0771
C10.5178 (2)0.06469 (16)0.9834 (2)0.0481
C20.6407 (2)0.09640 (19)1.1223 (2)0.0642
C30.7432 (3)0.1657 (2)1.1134 (3)0.0746
C40.7264 (3)0.2027 (2)0.9725 (3)0.0758
C50.6069 (3)0.17041 (19)0.8362 (3)0.0684
C60.5009 (2)0.10176 (16)0.8420 (2)0.0500
C70.3049 (2)0.00213 (15)0.7947 (2)0.0484
C80.0081 (3)0.01087 (17)0.5564 (2)0.0598
C90.0568 (3)0.09576 (15)0.6092 (2)0.0543
C100.2304 (4)0.2342 (2)0.5187 (4)0.0984
H1010.28890.26930.42570.1501*
H1020.30510.21010.55200.1500*
H1030.15620.27610.59310.1500*
H20.65090.07251.21840.0740*
H820.06930.03980.50530.0659*
H30.82430.19081.20600.0843*
H40.79150.25240.97230.0907*
H10.36830.02801.01510.0619*
H810.07360.02950.48480.0681*
H50.59480.19400.73900.0841*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0686 (3)0.0556 (3)0.0471 (3)0.0007 (3)0.0094 (2)0.0013 (3)
N10.0571 (9)0.0653 (10)0.0303 (7)0.0007 (8)0.0184 (7)0.0052 (7)
N20.0656 (10)0.0634 (10)0.0304 (7)0.0074 (8)0.0190 (7)0.0026 (7)
O10.1244 (15)0.0847 (12)0.0467 (9)0.0190 (12)0.0332 (9)0.0042 (8)
O20.0834 (11)0.0879 (12)0.0508 (9)0.0263 (9)0.0212 (8)0.0110 (8)
C10.0476 (10)0.0619 (12)0.0346 (8)0.0086 (9)0.0177 (7)0.0024 (8)
C20.0511 (11)0.0960 (17)0.0375 (10)0.0016 (11)0.0121 (9)0.0059 (10)
C30.0511 (12)0.0985 (18)0.0608 (14)0.0046 (13)0.0121 (10)0.0025 (13)
C40.0605 (13)0.0882 (16)0.0754 (15)0.0070 (12)0.0267 (11)0.0150 (14)
C50.0697 (14)0.0845 (16)0.0543 (12)0.0022 (12)0.0304 (11)0.0170 (11)
C60.0546 (10)0.0593 (11)0.0369 (9)0.0107 (9)0.0207 (8)0.0056 (8)
C70.0561 (10)0.0541 (11)0.0313 (8)0.0115 (9)0.0160 (8)0.0009 (8)
C80.0616 (12)0.0709 (13)0.0332 (9)0.0035 (11)0.0081 (9)0.0051 (9)
C90.0588 (11)0.0604 (12)0.0408 (10)0.0041 (9)0.0194 (8)0.0011 (8)
C100.112 (2)0.0871 (19)0.104 (2)0.0331 (17)0.054 (2)0.0222 (16)
Geometric parameters (Å, º) top
S1—C71.755 (3)C2—H20.947
S1—C81.800 (2)C3—C41.392 (4)
N1—C11.373 (3)C3—H30.945
N1—C71.359 (3)C4—C51.371 (4)
N1—H10.845C4—H40.902
N2—C61.400 (3)C5—C61.371 (3)
N2—C71.308 (3)C5—H50.949
O1—C91.192 (2)C8—C91.482 (3)
O2—C91.322 (3)C8—H820.985
O2—C101.448 (3)C8—H810.944
C1—C21.395 (3)C10—H1010.947
C1—C61.397 (3)C10—H1020.944
C2—C31.364 (3)C10—H1030.936
C7—S1—C899.78 (13)N2—C6—C1108.96 (19)
C1—N1—C7106.67 (17)N2—C6—C5130.61 (19)
C1—N1—H1126.0C1—C6—C5120.4 (2)
C7—N1—H1127.1S1—C7—N1119.73 (16)
C6—N2—C7104.87 (17)S1—C7—N2126.76 (15)
C9—O2—C10117.3 (2)N1—C7—N2113.49 (18)
N1—C1—C2132.32 (18)S1—C8—C9113.90 (16)
N1—C1—C6105.98 (17)S1—C8—H82110.1
C2—C1—C6121.6 (2)C9—C8—H82106.5
C1—C2—C3116.8 (2)S1—C8—H81105.7
C1—C2—H2121.8C9—C8—H81111.9
C3—C2—H2121.4H82—C8—H81108.6
C2—C3—C4121.6 (2)C8—C9—O2109.53 (17)
C2—C3—H3118.4C8—C9—O1126.75 (19)
C4—C3—H3119.9O2—C9—O1123.7 (2)
C3—C4—C5121.5 (2)O2—C10—H101109.8
C3—C4—H4118.6O2—C10—H102106.5
C5—C4—H4119.8H101—C10—H102106.8
C4—C5—C6118.1 (2)O2—C10—H103112.2
C4—C5—H5122.6H101—C10—H103110.7
C6—C5—H5119.3H102—C10—H103110.6
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N2i0.852.072.879 (2)159
Symmetry code: (i) x, y, z+1/2.

Experimental details

Crystal data
Chemical formulaC10H10N2O2S
Mr222.27
Crystal system, space groupMonoclinic, Cc
Temperature (K)295
a, b, c (Å)9.337 (9), 13.418 (15), 9.667 (8)
β (°) 116.04 (7)
V3)1088 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.28
Crystal size (mm)0.40 × 0.20 × 0.15
Data collection
DiffractometerNonius KappaCCD
Absorption correctionMulti-scan
(SORTAV; Blessing, 1995)
Tmin, Tmax0.88, 0.96
No. of measured, independent and
observed [I > 2σ(I)] reflections
10772, 2434, 2248
Rint0.037
(sin θ/λ)max1)0.659
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.062, 0.92
No. of reflections2434
No. of parameters137
No. of restraints2
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.15, 0.13
Absolute structureFlack (1983), 1156 Friedel pairs
Absolute structure parameter0.01 (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.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N2i0.852.072.879 (2)159
Symmetry code: (i) x, y, z+1/2.
 

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