supplementary materials


pv2630 scheme

Acta Cryst. (2013). E69, o807    [ doi:10.1107/S1600536813011124 ]

6-Chloro-2-(thiophen-2-yl)-1-[(thiophen-2-yl)methyl]-1H-benzimidazole

D. K. Geiger and M. R. Nellist

Abstract top

The title compound, C16H11ClN2S2, co-crystallizes with a small amount of the 5-chloro- isomer. The ratio of 6-chloro- to 5-chloro- isomers is 0.969 (2):0.031 (2). One thiophen-2-yl substitutent displays rotational disorder with 80.6 (4)% of the molecules exhibiting the major orientation. In the crystal, weak C-H...N and C-H...S hydrogen-bonding interactions result in chains of molecules parallel to [001].

Comment top

The bond distances and angles in the title compound (Fig. 1) agree very well with the corresponding bond distances and angles reported in closely related compounds (Geiger et al., 2012; Geiger & Destefano, 2012). Crystallization of the title compound occurs with 3.1 (2)% of the sites occupied by the 5-chloro isomer. The 2-thiophene substituent is rotationally disordered with the major component having a refined occupancy of 81.0 (4)%. The benzimidazole moiety is planar (r. m. s. deviation = 0.0079 Å) with the largest deviation being for C1, which is 0.014 (3) Å out of the plane. The 2-thiophene substitutents are canted 33.2 (2)% from the benzimidazole plane for the major disorder component and 27 (1)% for the minor component.

Molecules are joined by weak C16—H16···N2 H-bonding resulting in chains parallel to [0 0 1]. The H16···N2 distance is 2.62 Å and the C16—H16···N2 angle is 136°. Weak C12—H12B···N2 and C12—H12B···S1 H-bonding joins the chains of molecules parallel to [0 0 1] (Tab. 1 & Fig. 2).

Related literature top

For the structure of 2-(thiophen-2-yl)-1-(thiophen-2-ylmethyl)-1H-benzimidazole, see: Geiger et al. (2012). For the structure of the 5-bromo analogue, see: Geiger & Destefano (2012).

Experimental top

1,2-Diamine-4-chlorobenzene (6.3 mmol, 0.90 g) was dissolved in 30 ml ethanol under nitrogen. Two equivalents of 2-thiophenecarboxaldehyde (1.3 ml) was added dropwise. After three days, the solvent was removed under reduced pressure and the crude product was chromatographed (silica gel) using a mixture of 30% hexane in ethyl acetate. The first fraction produced hexagonal shaped crystals (1) and the second fraction produced needle-shaped crystals (2) on slow evaporation. Crystals from the first fraction were used for X-ray diffraction experiments. The overall yield was 59%.

Refinement top

All hydrogen atoms were observed in difference fourier maps. The H atoms were refined using a riding model with a C—H distance of 0.99 Å for the methylene carbon atoms and 0.95 Å for the phenyl and thiophene carbon atoms. All C—H hydrogen atom thermal parameters were set using the approximation Uiso = 1.2Ueq. The Cl and H atoms of the major and minor co-crystallization components were modeled as a disorder involving two parts, each containing a chlorine atom and a hydrogen atom. The major component refined to a site occupancy of 0.969 (2).

In addition, the 2-thiophene substituent is rotationally disordered. A model was developed in which the minor component of the thiophene ring was defined using the metrics of the major component as a guide. The disordered five-member rings were constrained to planarity using FLAT. Corresponding bond distances of the minor component and major component were set equal using SAME and corresponding thermal parameters were held the same using EADP. All atoms were refined anisotropically with hydrogen atoms in calculated positions using a riding model. With these constraints, the site occupancy of the major component refined to 0.806 (4).

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Perspective view of the title compound. Thermal parameters are drawn at the 50% probability level. Only major contributors to the disorder model are shown.
[Figure 2] Fig. 2. Packing diagram showing the chains along [0 0 1] formed by weak C—H···N H-bonding interactions. Only the major contributor to the disorder model is shown.
6-Chloro-2-(thiophen-2-yl)-1-[(thiophen-2-yl)methyl]-1H-benzimidazole top
Crystal data top
C16H11ClN2S2F(000) = 680
Mr = 330.84Dx = 1.471 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 15.465 (3) ÅCell parameters from 7129 reflections
b = 6.3578 (10) Åθ = 2.7–25.0°
c = 15.634 (3) ŵ = 0.53 mm1
β = 103.687 (5)°T = 200 K
V = 1493.5 (4) Å3Plate, colourless
Z = 40.80 × 0.60 × 0.20 mm
Data collection top
Bruker SMART X2S CCD
diffractometer
2665 independent reflections
Radiation source: XOS X-beam microfocus source2184 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromatorRint = 0.088
Detector resolution: 8.3330 pixels mm-1θmax = 25.4°, θmin = 2.7°
ω scansh = 1818
Absorption correction: multi-scan
(SADABS; Bruker, 2010)
k = 77
Tmin = 0.62, Tmax = 0.90l = 1818
23773 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.056Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.148H-atom parameters constrained
S = 1.11 w = 1/[σ2(Fo2) + (0.0645P)2 + 1.4022P]
where P = (Fo2 + 2Fc2)/3
2665 reflections(Δ/σ)max < 0.001
210 parametersΔρmax = 0.49 e Å3
38 restraintsΔρmin = 0.46 e Å3
Crystal data top
C16H11ClN2S2V = 1493.5 (4) Å3
Mr = 330.84Z = 4
Monoclinic, P21/cMo Kα radiation
a = 15.465 (3) ŵ = 0.53 mm1
b = 6.3578 (10) ÅT = 200 K
c = 15.634 (3) Å0.80 × 0.60 × 0.20 mm
β = 103.687 (5)°
Data collection top
Bruker SMART X2S CCD
diffractometer
2665 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2010)
2184 reflections with I > 2σ(I)
Tmin = 0.62, Tmax = 0.90Rint = 0.088
23773 measured reflectionsθmax = 25.4°
Refinement top
R[F2 > 2σ(F2)] = 0.056H-atom parameters constrained
wR(F2) = 0.148Δρmax = 0.49 e Å3
S = 1.11Δρmin = 0.46 e Å3
2665 reflectionsAbsolute structure: ?
210 parametersFlack parameter: ?
38 restraintsRogers parameter: ?
Special details top

Experimental. 1H NMR spectrum (CDCl3, 400 MHz, p.p.m.): 7.71 (1 H, d), 7.53 (1 H, d), 7.48 (1 H, d), 7.34 (1 H, s), 7.28 (2 H, m), 7.17 (1 H, t), 6.96 (1 H, t), 6.91 (1 H, d), 5.60 (2 H, s).

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Cl10.55843 (7)1.26049 (17)0.40613 (7)0.0561 (3)0.969 (2)
Cl010.5861 (12)0.817 (5)0.327 (2)0.0561 (3)0.031 (2)
S10.06013 (11)0.5424 (3)0.29173 (10)0.0530 (5)0.806 (4)
C80.1134 (4)0.7175 (17)0.3728 (6)0.0402 (8)0.806 (4)
C90.0602 (5)0.7532 (12)0.4316 (6)0.054 (2)0.806 (4)
H90.07870.83490.48360.065*0.806 (4)
C100.0230 (4)0.6567 (13)0.4065 (5)0.0593 (16)0.806 (4)
H100.06840.67490.43750.071*0.806 (4)
C110.0327 (4)0.5363 (12)0.3347 (5)0.0610 (18)0.806 (4)
H110.08470.45670.31030.073*0.806 (4)
S1010.0553 (7)0.8069 (15)0.4406 (7)0.0530 (5)0.194 (4)
C1080.1165 (15)0.718 (7)0.370 (3)0.0402 (8)0.194 (4)
C1090.0711 (18)0.573 (5)0.3138 (19)0.054 (2)0.194 (4)
H1090.09430.50690.26970.065*0.194 (4)
C1100.0137 (18)0.531 (6)0.327 (2)0.0593 (16)0.194 (4)
H1100.05360.43140.29360.071*0.194 (4)
C1110.0324 (15)0.647 (5)0.393 (2)0.0610 (18)0.194 (4)
H1110.08710.64150.41040.073*0.194 (4)
S20.22671 (7)1.02453 (14)0.60821 (6)0.0445 (3)
C130.2293 (2)1.2089 (5)0.52711 (19)0.0334 (7)
C140.2588 (2)1.3996 (5)0.5637 (2)0.0412 (8)
H140.26461.52150.53040.049*
C150.2795 (3)1.3940 (6)0.6571 (2)0.0473 (9)
H150.30141.51170.69320.057*
C160.2647 (2)1.2027 (6)0.6895 (2)0.0464 (9)
H160.27451.1720.75050.056*
N10.24103 (19)0.9760 (4)0.40255 (16)0.0352 (6)
N20.2615 (2)0.6596 (4)0.34595 (18)0.0414 (7)
C10.3275 (2)0.9754 (5)0.39196 (19)0.0357 (8)
C20.3389 (2)0.7765 (5)0.3565 (2)0.0397 (8)
C30.4206 (3)0.7300 (6)0.3371 (2)0.0485 (10)
H30.43040.5970.31330.058*
C40.4859 (3)0.8794 (6)0.3528 (2)0.0482 (9)
H40.54160.84950.33980.058*0.969 (2)
C50.4722 (2)1.0756 (6)0.3878 (2)0.0438 (9)
H5'0.51921.17550.39790.053*0.031 (2)
C60.3929 (2)1.1299 (6)0.4083 (2)0.0397 (8)
H60.38381.26350.43190.048*
C70.2048 (2)0.7813 (5)0.3739 (2)0.0381 (8)
C120.1983 (2)1.1614 (5)0.4306 (2)0.0368 (8)
H12A0.13321.1390.41620.044*
H12B0.21041.2850.39670.044*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0502 (6)0.0575 (7)0.0627 (7)0.0008 (5)0.0178 (5)0.0148 (5)
Cl010.0502 (6)0.0575 (7)0.0627 (7)0.0008 (5)0.0178 (5)0.0148 (5)
S10.0640 (9)0.0371 (9)0.0530 (9)0.0065 (6)0.0038 (7)0.0067 (6)
C80.055 (2)0.0272 (18)0.0366 (19)0.0077 (16)0.0083 (16)0.0024 (14)
C90.052 (3)0.031 (4)0.084 (5)0.002 (3)0.024 (3)0.008 (3)
C100.049 (3)0.058 (4)0.071 (4)0.002 (3)0.016 (3)0.002 (3)
C110.056 (4)0.044 (3)0.078 (4)0.007 (3)0.005 (3)0.005 (3)
S1010.0640 (9)0.0371 (9)0.0530 (9)0.0065 (6)0.0038 (7)0.0067 (6)
C1080.055 (2)0.0272 (18)0.0366 (19)0.0077 (16)0.0083 (16)0.0024 (14)
C1090.052 (3)0.031 (4)0.084 (5)0.002 (3)0.024 (3)0.008 (3)
C1100.049 (3)0.058 (4)0.071 (4)0.002 (3)0.016 (3)0.002 (3)
C1110.056 (4)0.044 (3)0.078 (4)0.007 (3)0.005 (3)0.005 (3)
S20.0658 (6)0.0309 (5)0.0383 (5)0.0023 (4)0.0152 (4)0.0043 (4)
C130.0431 (18)0.0285 (18)0.0311 (16)0.0049 (14)0.0140 (14)0.0016 (13)
C140.055 (2)0.035 (2)0.0352 (18)0.0048 (16)0.0134 (16)0.0021 (15)
C150.066 (2)0.038 (2)0.0389 (19)0.0094 (18)0.0140 (17)0.0089 (16)
C160.056 (2)0.052 (2)0.0334 (18)0.0029 (18)0.0134 (16)0.0007 (16)
N10.0522 (17)0.0255 (15)0.0290 (14)0.0074 (12)0.0120 (12)0.0007 (11)
N20.0614 (19)0.0277 (15)0.0383 (15)0.0089 (14)0.0182 (14)0.0002 (12)
C10.051 (2)0.0329 (19)0.0247 (16)0.0087 (15)0.0121 (14)0.0065 (13)
C20.060 (2)0.0323 (19)0.0287 (17)0.0121 (16)0.0151 (16)0.0060 (14)
C30.069 (3)0.040 (2)0.042 (2)0.0144 (19)0.0252 (19)0.0075 (16)
C40.055 (2)0.051 (2)0.044 (2)0.0177 (19)0.0223 (17)0.0109 (17)
C50.051 (2)0.046 (2)0.0360 (18)0.0053 (17)0.0137 (16)0.0125 (16)
C60.056 (2)0.0347 (19)0.0305 (17)0.0082 (17)0.0137 (15)0.0050 (14)
C70.057 (2)0.0284 (19)0.0284 (16)0.0057 (16)0.0098 (15)0.0040 (13)
C120.0502 (19)0.0261 (17)0.0349 (17)0.0099 (15)0.0118 (15)0.0019 (14)
Geometric parameters (Å, º) top
Cl1—C51.750 (4)C13—C121.502 (4)
Cl01—C41.740 (5)C14—C151.419 (5)
S1—C111.724 (6)C14—H140.95
S1—C81.740 (7)C15—C161.357 (5)
C8—C91.389 (9)C15—H150.95
C8—C71.468 (6)C16—H160.95
C9—C101.396 (9)N1—C11.386 (4)
C9—H90.95N1—C71.388 (4)
C10—C111.337 (7)N1—C121.468 (4)
C10—H100.95N2—C71.319 (4)
C11—H110.95N2—C21.385 (5)
S101—C1081.707 (18)C1—C61.389 (5)
S101—C1111.717 (17)C1—C21.408 (5)
C108—C1091.351 (17)C2—C31.399 (5)
C108—C71.411 (15)C3—C41.366 (5)
C109—C1101.401 (17)C3—H30.95
C109—H1090.95C4—C51.398 (5)
C110—C1111.352 (16)C4—H40.95
C110—H1100.95C5—C61.383 (5)
C111—H1110.95C5—H5'0.95
S2—C161.700 (4)C6—H60.95
S2—C131.734 (3)C12—H12A0.99
C13—C141.372 (5)C12—H12B0.99
C11—S1—C891.4 (3)S2—C16—H16123.9
C9—C8—C7131.8 (6)C1—N1—C7106.6 (3)
C9—C8—S1109.5 (4)C1—N1—C12123.5 (3)
C7—C8—S1118.3 (4)C7—N1—C12129.6 (3)
C8—C9—C10113.1 (7)C7—N2—C2105.6 (3)
C8—C9—H9123.4N1—C1—C6131.1 (3)
C10—C9—H9123.4N1—C1—C2105.2 (3)
C11—C10—C9113.6 (6)C6—C1—C2123.7 (3)
C11—C10—H10123.2N2—C2—C3131.3 (3)
C9—C10—H10123.2N2—C2—C1110.1 (3)
C10—C11—S1112.0 (5)C3—C2—C1118.6 (3)
C10—C11—H11124.0C4—C3—C2118.8 (3)
S1—C11—H11124.0C4—C3—H3120.6
C108—S101—C11191.5 (11)C2—C3—H3120.6
C109—C108—C7124.7 (18)C3—C4—C5121.2 (3)
C109—C108—S101111.3 (12)C3—C4—Cl01117.4 (12)
C7—C108—S101123.9 (16)C5—C4—Cl01121.4 (12)
C108—C109—C110113.3 (16)C3—C4—H4119.4
C108—C109—H109123.4C5—C4—H4119.4
C110—C109—H109123.4C6—C5—C4122.5 (3)
C111—C110—C109112.5 (19)C6—C5—Cl1118.5 (3)
C111—C110—H110123.7C4—C5—Cl1118.9 (3)
C109—C110—H110123.7C6—C5—H5'118.7
C110—C111—S101111.4 (17)C4—C5—H5'118.7
C110—C111—H111124.3C5—C6—C1115.3 (3)
S101—C111—H111124.3C5—C6—H6122.3
C16—S2—C1391.85 (17)C1—C6—H6122.3
C14—C13—C12126.3 (3)N2—C7—N1112.4 (3)
C14—C13—S2110.8 (2)N2—C7—C108122.2 (13)
C12—C13—S2122.8 (2)N1—C7—C108125.3 (14)
C13—C14—C15112.3 (3)N2—C7—C8123.3 (4)
C13—C14—H14123.9N1—C7—C8124.3 (4)
C15—C14—H14123.9N1—C12—C13113.7 (3)
C16—C15—C14112.9 (3)N1—C12—H12A108.8
C16—C15—H15123.6C13—C12—H12A108.8
C14—C15—H15123.6N1—C12—H12B108.8
C15—C16—S2112.2 (3)C13—C12—H12B108.8
C15—C16—H16123.9H12A—C12—H12B107.7
C11—S1—C8—C93.5 (8)C2—C3—C4—Cl01179.3 (12)
C11—S1—C8—C7177.2 (8)C3—C4—C5—C60.0 (5)
C7—C8—C9—C10177.9 (10)Cl01—C4—C5—C6179.4 (13)
S1—C8—C9—C105.3 (11)C3—C4—C5—Cl1179.8 (3)
C8—C9—C10—C114.8 (9)Cl01—C4—C5—Cl10.4 (13)
C9—C10—C11—S12.0 (6)C4—C5—C6—C10.2 (5)
C8—S1—C11—C100.9 (6)Cl1—C5—C6—C1180.0 (2)
C111—S101—C108—C1090 (3)N1—C1—C6—C5178.5 (3)
C111—S101—C108—C7177 (4)C2—C1—C6—C50.4 (5)
C7—C108—C109—C110177 (4)C2—N2—C7—N10.2 (4)
S101—C108—C109—C1100 (4)C2—N2—C7—C108177 (2)
C108—C109—C110—C1111 (4)C2—N2—C7—C8179.1 (6)
C109—C110—C111—S1011.2 (17)C1—N1—C7—N20.2 (3)
C108—S101—C111—C1100.9 (16)C12—N1—C7—N2173.8 (3)
C16—S2—C13—C140.0 (3)C1—N1—C7—C108177 (2)
C16—S2—C13—C12177.1 (3)C12—N1—C7—C1083 (2)
C12—C13—C14—C15177.4 (3)C1—N1—C7—C8179.1 (6)
S2—C13—C14—C150.4 (4)C12—N1—C7—C85.1 (7)
C13—C14—C15—C160.7 (5)C109—C108—C7—N224 (5)
C14—C15—C16—S20.7 (4)S101—C108—C7—N2152 (2)
C13—S2—C16—C150.4 (3)C109—C108—C7—N1153 (3)
C7—N1—C1—C6178.5 (3)S101—C108—C7—N131 (5)
C12—N1—C1—C64.1 (5)C109—C108—C7—C8150..90
C7—N1—C1—C20.2 (3)S101—C108—C7—C820..80
C12—N1—C1—C2174.3 (3)C9—C8—C7—N2142.3 (10)
C7—N2—C2—C3179.0 (3)S1—C8—C7—N229.7 (11)
C7—N2—C2—C10.1 (4)C9—C8—C7—N139.0 (15)
N1—C1—C2—N20.1 (3)S1—C8—C7—N1149.0 (5)
C6—C1—C2—N2178.6 (3)C9—C8—C7—C108170..80
N1—C1—C2—C3179.0 (3)S1—C8—C7—C10820..80
C6—C1—C2—C30.5 (5)C1—N1—C12—C1375.6 (4)
N2—C2—C3—C4178.5 (3)C7—N1—C12—C13111.3 (4)
C1—C2—C3—C40.3 (5)C14—C13—C12—N1129.4 (3)
C2—C3—C4—C50.0 (5)S2—C13—C12—N154.0 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C16—H16···N2i0.952.623.369 (4)136
C12—H12B···N2ii0.992.693.654 (4)165
C12—H12B···S1ii0.992.993.599 (4)120
Symmetry codes: (i) x, y+3/2, z+1/2; (ii) x, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C16—H16···N2i0.952.623.369 (4)136.3
C12—H12B···N2ii0.992.693.654 (4)165.3
C12—H12B···S1ii0.992.993.599 (4)120.4
Symmetry codes: (i) x, y+3/2, z+1/2; (ii) x, y+1, z.
Acknowledgements top

This work was supported by a Congressionally directed grant from the US Department of Education (grant No. P116Z100020) for the X-ray diffractometer and a grant from the Geneseo Foundation. MRN thanks Dr Bruce Ristow for a summer research fellowship administered by the Geneseo Foundation.

references
References top

Bruker (2010). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.

Geiger, D. K. & Destefano, M. R. (2012). Acta Cryst. E68, o3123.

Geiger, D. K., Geiger, H. C., Williams, L. & Noll, B. C. (2012). Acta Cryst. E68, o420.

Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.