organic compounds
2-(4-Methylsulfanylphenyl)-1H-benzimidazol-3-ium bromide
aDepartment of Chemistry, Bangalore University, Bangalore 560 001, India, and bSolid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
*Correspondence e-mail: noorsb@rediffmail.com
In the cation of the title compound, C14H13N2S+·Br−, the essentially planar benzimidazole system (r.m.s. deviation = 0.0082 Å) is substituted with a 4-methylsulfanylphenyl ring. The dihedral angle between the benzimidazole system and the 4-methylsulfanylphenyl ring is 2.133 (2)°. The is characterized by strong and highly directional intermolecular N—H⋯Br hydrogen bonds involving the bromide ion. Moreover, C—H⋯S interactions result in chains of molecules along the c axis. The supramolecular assembly is further stabilized by π–π stacking interactions between the benzimidazole system and 4-methylsulfanylphenyl rings [centroid–centroid distance = 3.477 (4) Å].
Related literature
For general background to benzimidazoles and their derivatives, see: Huang & Scarborough (1999); Preston (1974); Zarrinmayeh et al. (1998); Zhu et al. (2000). For related structures, see: Goker et al. (1995); Ozbey et al. (1998); Vasudevan et al. (1994). For hydrogen bonding, see: Bernstein et al. (1995); Nardelli (1983).
Experimental
Crystal data
|
Refinement
|
Data collection: SMART (Bruker, 1998); cell SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and CAMERON (Watkin et al., 1996); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
10.1107/S1600536811000146/pb2053sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811000146/pb2053Isup2.hkl
A ethanol solution (20 ml) of zinc bromide (2.25 mg, 1.0 mmol) was treated with 2-(p-thiomethylphenyl)benzimidazole (4.80 mg, 2.0 mmol) in ethanol (20 ml). The mixture was then treated with 48% HBr (2–3 ml) followed by liquid Br2 (2–3 ml). The mixture was refluxed for 6 hrs on a steam bath filtered and allowed to stand at room temperature for two days. Coloured crystals separated and these were washed with ethanol and dried. (yield 4.00 mg; 83%).
Data collection: SMART (Bruker, 1998); cell
SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and CAMERON (Watkin et al., 1996); software used to prepare material for publication: WinGX (Farrugia, 1999).C14H13N2S+·Br− | F(000) = 648 |
Mr = 321.23 | Dx = 1.546 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 3009 reflections |
a = 5.3289 (2) Å | θ = 1.7–27.0° |
b = 24.0195 (12) Å | µ = 3.11 mm−1 |
c = 10.9544 (5) Å | T = 296 K |
β = 100.113 (2)° | Block, yellow |
V = 1380.35 (11) Å3 | 0.20 × 0.18 × 0.16 mm |
Z = 4 |
Bruker SMART APEX CCD detector diffractometer | 3009 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 2273 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.039 |
ω scans | θmax = 27.0°, θmin = 1.7° |
Absorption correction: multi-scan Bruker Kappa APEX | h = −6→6 |
Tmin = 0.575, Tmax = 0.636 | k = −30→30 |
23823 measured reflections | l = −13→13 |
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)] = 0.029 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.069 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0338P)2 + 0.3109P] where P = (Fo2 + 2Fc2)/3 |
3009 reflections | (Δ/σ)max = 0.001 |
215 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
C14H13N2S+·Br− | V = 1380.35 (11) Å3 |
Mr = 321.23 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 5.3289 (2) Å | µ = 3.11 mm−1 |
b = 24.0195 (12) Å | T = 296 K |
c = 10.9544 (5) Å | 0.20 × 0.18 × 0.16 mm |
β = 100.113 (2)° |
Bruker SMART APEX CCD detector diffractometer | 3009 independent reflections |
Absorption correction: multi-scan Bruker Kappa APEX | 2273 reflections with I > 2σ(I) |
Tmin = 0.575, Tmax = 0.636 | Rint = 0.039 |
23823 measured reflections |
R[F2 > 2σ(F2)] = 0.029 | 0 restraints |
wR(F2) = 0.069 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.35 e Å−3 |
3009 reflections | Δρmin = −0.29 e Å−3 |
215 parameters |
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 | ||
Br1 | 0.27225 (4) | 0.295277 (10) | 0.33608 (2) | 0.04982 (10) | |
S1 | 0.57379 (16) | −0.00128 (3) | 0.21720 (8) | 0.0710 (2) | |
N1 | 0.6485 (4) | 0.28057 (8) | 0.13508 (19) | 0.0421 (5) | |
N2 | 0.9186 (4) | 0.25577 (8) | 0.01982 (17) | 0.0408 (4) | |
C1 | 0.9109 (4) | 0.31328 (10) | 0.0161 (2) | 0.0415 (5) | |
C2 | 1.0437 (5) | 0.35189 (11) | −0.0424 (2) | 0.0555 (6) | |
C3 | 0.9910 (6) | 0.40696 (12) | −0.0233 (3) | 0.0644 (7) | |
C4 | 0.8149 (6) | 0.42307 (12) | 0.0504 (3) | 0.0659 (8) | |
C5 | 0.6847 (5) | 0.38481 (11) | 0.1084 (3) | 0.0555 (6) | |
C6 | 0.7381 (4) | 0.32913 (10) | 0.0906 (2) | 0.0430 (5) | |
C7 | 0.7610 (4) | 0.23676 (9) | 0.09243 (19) | 0.0387 (5) | |
C8 | 0.7198 (4) | 0.17861 (9) | 0.1213 (2) | 0.0391 (5) | |
C9 | 0.5449 (5) | 0.16389 (11) | 0.1960 (2) | 0.0516 (6) | |
C10 | 0.5058 (5) | 0.10930 (11) | 0.2220 (2) | 0.0558 (6) | |
C11 | 0.6392 (5) | 0.06710 (10) | 0.1762 (2) | 0.0453 (5) | |
C12 | 0.8139 (6) | 0.08164 (11) | 0.1013 (3) | 0.0586 (7) | |
C13 | 0.8530 (5) | 0.13648 (11) | 0.0746 (3) | 0.0548 (7) | |
C14 | 0.7734 (8) | −0.04379 (14) | 0.1398 (4) | 0.0721 (9) | |
H1N | 0.562 (5) | 0.2802 (10) | 0.181 (2) | 0.042 (7)* | |
H9 | 0.464 (5) | 0.1907 (12) | 0.233 (2) | 0.062 (8)* | |
H2N | 0.991 (5) | 0.2357 (11) | −0.017 (2) | 0.049 (8)* | |
H12 | 0.909 (5) | 0.0539 (11) | 0.070 (2) | 0.065 (8)* | |
H14C | 0.736 (6) | −0.0776 (16) | 0.159 (3) | 0.086 (11)* | |
H14B | 0.947 (7) | −0.0359 (13) | 0.169 (3) | 0.090 (11)* | |
H5 | 0.567 (5) | 0.3946 (12) | 0.163 (2) | 0.075 (9)* | |
H4 | 0.781 (6) | 0.4619 (13) | 0.063 (3) | 0.085 (10)* | |
H2 | 1.159 (5) | 0.3398 (11) | −0.092 (2) | 0.058 (7)* | |
H13 | 0.975 (5) | 0.1462 (12) | 0.022 (3) | 0.079 (9)* | |
H10 | 0.389 (5) | 0.0996 (11) | 0.276 (2) | 0.064 (7)* | |
H3 | 1.080 (5) | 0.4350 (12) | −0.060 (2) | 0.070 (8)* | |
H14A | 0.736 (6) | −0.0374 (14) | 0.054 (3) | 0.097 (12)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.05371 (15) | 0.05390 (17) | 0.04775 (15) | 0.00057 (11) | 0.02515 (10) | 0.00017 (11) |
S1 | 0.0965 (6) | 0.0390 (4) | 0.0891 (5) | −0.0055 (3) | 0.0480 (4) | 0.0060 (3) |
N1 | 0.0446 (11) | 0.0397 (11) | 0.0476 (11) | −0.0021 (8) | 0.0233 (9) | −0.0012 (9) |
N2 | 0.0441 (10) | 0.0396 (11) | 0.0436 (11) | −0.0006 (9) | 0.0212 (9) | −0.0029 (9) |
C1 | 0.0442 (12) | 0.0399 (12) | 0.0414 (12) | −0.0043 (10) | 0.0105 (10) | −0.0003 (10) |
C2 | 0.0593 (16) | 0.0521 (16) | 0.0598 (15) | −0.0093 (12) | 0.0233 (13) | 0.0045 (13) |
C3 | 0.0741 (19) | 0.0474 (16) | 0.0755 (18) | −0.0129 (14) | 0.0231 (15) | 0.0080 (14) |
C4 | 0.077 (2) | 0.0386 (16) | 0.082 (2) | −0.0056 (13) | 0.0140 (16) | −0.0001 (14) |
C5 | 0.0626 (16) | 0.0411 (15) | 0.0655 (16) | 0.0024 (12) | 0.0185 (13) | −0.0077 (13) |
C6 | 0.0433 (12) | 0.0414 (13) | 0.0450 (12) | −0.0031 (10) | 0.0099 (9) | −0.0011 (10) |
C7 | 0.0380 (11) | 0.0407 (13) | 0.0392 (11) | −0.0013 (10) | 0.0121 (9) | 0.0001 (10) |
C8 | 0.0400 (12) | 0.0394 (13) | 0.0392 (11) | −0.0015 (10) | 0.0109 (9) | 0.0009 (10) |
C9 | 0.0621 (16) | 0.0380 (13) | 0.0626 (15) | 0.0046 (11) | 0.0331 (13) | 0.0005 (12) |
C10 | 0.0620 (16) | 0.0484 (15) | 0.0665 (16) | −0.0018 (12) | 0.0377 (13) | 0.0054 (13) |
C11 | 0.0512 (13) | 0.0386 (13) | 0.0483 (13) | −0.0036 (10) | 0.0147 (10) | 0.0016 (10) |
C12 | 0.0705 (18) | 0.0389 (15) | 0.0762 (18) | 0.0019 (12) | 0.0400 (15) | −0.0019 (13) |
C13 | 0.0615 (16) | 0.0436 (15) | 0.0689 (16) | 0.0011 (12) | 0.0377 (14) | −0.0004 (12) |
C14 | 0.091 (3) | 0.0407 (18) | 0.089 (3) | 0.0024 (16) | 0.028 (2) | −0.0003 (16) |
S1—C11 | 1.754 (2) | C5—C6 | 1.388 (3) |
S1—C14 | 1.791 (4) | C5—H5 | 0.97 (3) |
N1—C7 | 1.335 (3) | C7—C8 | 1.457 (3) |
N1—C6 | 1.381 (3) | C8—C13 | 1.384 (3) |
N1—H1N | 0.74 (3) | C8—C9 | 1.390 (3) |
N2—C7 | 1.334 (3) | C9—C10 | 1.365 (4) |
N2—C1 | 1.382 (3) | C9—H9 | 0.91 (3) |
N2—H2N | 0.77 (3) | C10—C11 | 1.382 (3) |
C1—C6 | 1.386 (3) | C10—H10 | 0.96 (3) |
C1—C2 | 1.390 (3) | C11—C12 | 1.389 (3) |
C2—C3 | 1.376 (4) | C12—C13 | 1.373 (4) |
C2—H2 | 0.93 (3) | C12—H12 | 0.94 (3) |
C3—C4 | 1.395 (4) | C13—H13 | 0.97 (3) |
C3—H3 | 0.95 (3) | C14—H14C | 0.87 (4) |
C4—C5 | 1.373 (4) | C14—H14B | 0.94 (3) |
C4—H4 | 0.96 (3) | C14—H14A | 0.94 (3) |
C11—S1—C14 | 104.57 (15) | N2—C7—C8 | 126.29 (19) |
C7—N1—C6 | 109.73 (19) | N1—C7—C8 | 125.82 (18) |
C7—N1—H1N | 127.0 (19) | C13—C8—C9 | 118.2 (2) |
C6—N1—H1N | 123.0 (19) | C13—C8—C7 | 120.93 (19) |
C7—N2—C1 | 109.94 (18) | C9—C8—C7 | 120.9 (2) |
C7—N2—H2N | 121.6 (19) | C10—C9—C8 | 120.6 (2) |
C1—N2—H2N | 128.3 (19) | C10—C9—H9 | 118.9 (17) |
N2—C1—C6 | 106.04 (19) | C8—C9—H9 | 120.3 (17) |
N2—C1—C2 | 131.7 (2) | C9—C10—C11 | 121.5 (2) |
C6—C1—C2 | 122.2 (2) | C9—C10—H10 | 120.0 (16) |
C3—C2—C1 | 115.9 (3) | C11—C10—H10 | 118.4 (16) |
C3—C2—H2 | 124.1 (16) | C10—C11—C12 | 118.1 (2) |
C1—C2—H2 | 120.0 (16) | C10—C11—S1 | 117.15 (18) |
C2—C3—C4 | 122.1 (3) | C12—C11—S1 | 124.79 (19) |
C2—C3—H3 | 119.2 (17) | C13—C12—C11 | 120.6 (2) |
C4—C3—H3 | 118.7 (17) | C13—C12—H12 | 119.2 (17) |
C5—C4—C3 | 121.9 (3) | C11—C12—H12 | 120.2 (17) |
C5—C4—H4 | 117.2 (19) | C12—C13—C8 | 121.1 (2) |
C3—C4—H4 | 121.0 (19) | C12—C13—H13 | 120.1 (17) |
C4—C5—C6 | 116.5 (3) | C8—C13—H13 | 118.9 (18) |
C4—C5—H5 | 123.9 (18) | S1—C14—H14C | 104 (2) |
C6—C5—H5 | 119.5 (18) | S1—C14—H14B | 111 (2) |
N1—C6—C1 | 106.4 (2) | H14C—C14—H14B | 111 (3) |
N1—C6—C5 | 132.2 (2) | S1—C14—H14A | 110 (2) |
C1—C6—C5 | 121.4 (2) | H14C—C14—H14A | 112 (3) |
N2—C7—N1 | 107.9 (2) | H14B—C14—H14A | 109 (3) |
C7—N2—C1—C6 | −0.2 (3) | C6—N1—C7—C8 | 178.60 (19) |
C7—N2—C1—C2 | 177.8 (3) | N2—C7—C8—C13 | 1.4 (3) |
N2—C1—C2—C3 | −178.5 (2) | N1—C7—C8—C13 | −178.0 (2) |
C6—C1—C2—C3 | −0.8 (4) | N2—C7—C8—C9 | −178.3 (2) |
C1—C2—C3—C4 | 0.0 (4) | N1—C7—C8—C9 | 2.2 (3) |
C2—C3—C4—C5 | 0.3 (5) | C13—C8—C9—C10 | −0.2 (4) |
C3—C4—C5—C6 | 0.3 (4) | C7—C8—C9—C10 | 179.5 (2) |
C7—N1—C6—C1 | 0.8 (3) | C8—C9—C10—C11 | 0.6 (4) |
C7—N1—C6—C5 | −179.2 (3) | C9—C10—C11—C12 | −0.7 (4) |
N2—C1—C6—N1 | −0.4 (2) | C9—C10—C11—S1 | 179.5 (2) |
C2—C1—C6—N1 | −178.6 (2) | C14—S1—C11—C10 | 178.8 (2) |
N2—C1—C6—C5 | 179.6 (2) | C14—S1—C11—C12 | −1.0 (3) |
C2—C1—C6—C5 | 1.4 (4) | C10—C11—C12—C13 | 0.4 (4) |
C4—C5—C6—N1 | 178.9 (3) | S1—C11—C12—C13 | −179.8 (2) |
C4—C5—C6—C1 | −1.1 (4) | C11—C12—C13—C8 | −0.1 (5) |
C1—N2—C7—N1 | 0.7 (3) | C9—C8—C13—C12 | −0.1 (4) |
C1—N2—C7—C8 | −178.83 (19) | C7—C8—C13—C12 | −179.8 (2) |
C6—N1—C7—N2 | −0.9 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···Br1 | 0.74 (2) | 2.51 (2) | 3.247 (2) | 171 (2) |
N2—H2N···Br1i | 0.77 (3) | 2.50 (2) | 3.231 (2) | 159 |
C5—H5···S1ii | 0.97 (3) | 2.98 (3) | 3.736 (3) | 135 |
Symmetry codes: (i) x+1, −y+1/2, z−1/2; (ii) −x+1, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C14H13N2S+·Br− |
Mr | 321.23 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 296 |
a, b, c (Å) | 5.3289 (2), 24.0195 (12), 10.9544 (5) |
β (°) | 100.113 (2) |
V (Å3) | 1380.35 (11) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 3.11 |
Crystal size (mm) | 0.20 × 0.18 × 0.16 |
Data collection | |
Diffractometer | Bruker SMART APEX CCD detector diffractometer |
Absorption correction | Multi-scan Bruker Kappa APEX |
Tmin, Tmax | 0.575, 0.636 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23823, 3009, 2273 |
Rint | 0.039 |
(sin θ/λ)max (Å−1) | 0.639 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.029, 0.069, 1.03 |
No. of reflections | 3009 |
No. of parameters | 215 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.35, −0.29 |
Computer programs: SMART (Bruker, 1998), SAINT-Plus (Bruker, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and CAMERON (Watkin et al., 1996), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···Br1 | 0.74 (2) | 2.51 (2) | 3.247 (2) | 171 (2) |
N2—H2N···Br1i | 0.77 (3) | 2.50 (2) | 3.231 (2) | 159 |
C5—H5···S1ii | 0.97 (3) | 2.98 (3) | 3.736 (3) | 135 |
Symmetry codes: (i) x+1, −y+1/2, z−1/2; (ii) −x+1, y+1/2, −z+1/2. |
Acknowledgements
NSB is thankful to the University Grants Commission (UGC), India, for financial assistance and the Department of Science and Technology (DST), India, for the data collection facility under the IRHPA–DST program. MNM thanks the M. S. Ramaiah Institute of Technology, Bangalore, for their support and encouragement.
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Benzimidazoles and their derivatives exhibit a number of important pharmacological properties, such as antihistaminic, anti-ulcerative, antiallergic, and antipyretic. In addition, benzimidazole derivatives are effective against the human cytomegalo virus (HCMV) (Zhu et al., 2000) and are also efficient selective neuropeptide Y Y1 receptor antagonists (Zarrinmayeh et al., 1998). Most of the described methods for the synthesisof benzimidazoles make use of volatile organic solvents and involve solid-phase synthesis via o-nitroanilines (Preston et al., 1974; Huang et al., 1999) or the condensation of o-phenylenediamines with carboxylic acid derivatives, aldehydes and aryl halides. In the title compound, there is one benzimidazole thiomethyl phenyl cation and one Br- anion in the asymmetric unit. The expected proton transfer from HBr to benzimidazole thiomethyl phenyl occurs at atom N1 of the benzimidazole ring. Consequently,atom N1 shows quaternary character and bears a positive charge. In the molecule, the benzimidazole and thiomethyl phenyl rings are planar inclined at an dihedral angle 2.133 (2)° between them. The molecular structure is primarily stabilized by strong intramolecular N—H···Br hydrogen bond. The bond lengths and angles for the benzimidazole moiety of the molecule are in good agreement, within experimental errors, with those observed in other benzimidazole derivatives (Goker et al., 1995; Ozbey et al., 1998; Vasudevan et al.,1994).Further, the crystal structure is stabilized by intermolecular interactions into three dimensional framework structure by the combination of C—H···S and N—H···Br. The C—H···S and N—H···Br interactions together generates tetramers linking the molecules into chain like pattern along crystallographic c-axis. Additionally,the supramolecular assembly is further stabilized by π-π-stacking interactions between the benzimidazole and thiomethyl phenyl rings. The C3—C10 (x, 0.5 - y, 1/2 + z) disposed at a distance of 3.477 (4) Å.