Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807037373/rt2008sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807037373/rt2008Isup2.hkl |
CCDC reference: 660197
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (C-C) = 0.003 Å
- R factor = 0.052
- wR factor = 0.135
- Data-to-parameter ratio = 14.6
checkCIF/PLATON results
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0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For related literature, see: Johnson (1976); Ma et al. (2006); Migawa et al. (1998); Porcari et al. (1998); Roth et al. (1997); Tamm (1957); Tamm & Seghal (1978).
The title compound was synthesized according to the reported procedure (Ma et al., 2006). o-Phenylenediamine (10 mmol) and p-Tolualdehyde (10 mmol) were mixed in DMF (30 ml) thoroughly, followed by the addition of KHSO4 (3.4 mmol), heating and stirring for one hour. When the reaction was finished, the solution was cooled to room temperature. The reaction mixture was added dropwise with vigorous stirring into a mixture of Na2CO3 (3.4 mmol) and H2O (250 ml). The precipitate was collected by filtration, and recrystalized from ethanol to form the brown block crystals of the title compound. Yield: 416.5 mg (20%).
The H atoms were placed in calculated positions (aromatic C—H 0.93 Å and methyl C—H 0.96 Å; U 1.2UeqC) and were included in the refinement in the riding model approximation. The nitrogen-bound H atom was located and refined with an N—H distance restraint of 0.85 Å.
2-Substituted benzimidazoles have attracted considerable interest as intermediates in the development of molecules of pharmaceutical interest. Benzimidazole derivatives exhibit significant activity against several viruses such as HIV, herpes (HSV-1), RNA, influenza, and human cytomegalovirus (HCMV) (Tamm, 1957; Tamm & Seghal, 1978; Roth et al., 1997; Migawa et al., 1998; Porcari et al., 1998). The objective of this study therefore was to synthesize and elucidate the crystal structure of a new benzimidazole compound.
A view of the molecule of (I) is shown in Fig. 1 and selected geometric parameters are given in Table 1. The dihedral angle between the benzimidazole and tolyl portions of the title compound, (I), is 27.5 °. The molecules are linked into a linear chain through N—H···N hydrogen bonds interactions (N2···H1 2.072 Å, N1—H1···N2 170.8 °), as shown in Fig. 2. There exist π–π stacking interactions in adjacent linear chains, adjacent tolyl rings are exactly parallel, the perpendicular spacing of the rings is 3.504 Å, and the ring centroid-to-centroid distance is 4.080 Å. These π–π stacking interactions form a two dimensional supramolecular array.
For related literature, see: Johnson (1976); Ma et al. (2006); Migawa et al. (1998); Porcari et al. (1998); Roth et al. (1997); Tamm (1957); Tamm & Seghal (1978).
Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97.
C14H12N2 | F(000) = 880 |
Mr = 208.26 | Dx = 1.262 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 2911 reflections |
a = 9.0763 (10) Å | θ = 2.8–24.9° |
b = 9.8053 (11) Å | µ = 0.08 mm−1 |
c = 24.628 (3) Å | T = 295 K |
V = 2191.8 (4) Å3 | Block, brown |
Z = 8 | 0.40 × 0.20 × 0.16 mm |
Bruker APEX area-detector diffractometer | 2133 independent reflections |
Radiation source: fine-focus sealed tube | 1850 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.025 |
φ and ω scans | θmax = 26.0°, θmin = 1.7° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −11→11 |
Tmin = 0.970, Tmax = 0.988 | k = −11→4 |
9605 measured reflections | l = −30→24 |
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)] = 0.052 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.10 | w = 1/[σ2(Fo2) + (0.0639P)2 + 0.6749P] where P = (Fo2 + 2Fc2)/3 |
2133 reflections | (Δ/σ)max < 0.001 |
146 parameters | Δρmax = 0.21 e Å−3 |
0 restraints | Δρmin = −0.18 e Å−3 |
C14H12N2 | V = 2191.8 (4) Å3 |
Mr = 208.26 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 9.0763 (10) Å | µ = 0.08 mm−1 |
b = 9.8053 (11) Å | T = 295 K |
c = 24.628 (3) Å | 0.40 × 0.20 × 0.16 mm |
Bruker APEX area-detector diffractometer | 2133 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 1850 reflections with I > 2σ(I) |
Tmin = 0.970, Tmax = 0.988 | Rint = 0.025 |
9605 measured reflections |
R[F2 > 2σ(F2)] = 0.052 | 0 restraints |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.10 | Δρmax = 0.21 e Å−3 |
2133 reflections | Δρmin = −0.18 e Å−3 |
146 parameters |
x | y | z | Uiso*/Ueq | ||
N1 | 0.21900 (15) | 0.85838 (14) | 0.35353 (6) | 0.0377 (4) | |
N2 | 0.16814 (14) | 1.08050 (14) | 0.35983 (6) | 0.0386 (4) | |
C1 | 0.26414 (18) | 0.98288 (16) | 0.37105 (6) | 0.0352 (4) | |
C2 | 0.05379 (17) | 1.01519 (17) | 0.33254 (7) | 0.0363 (4) | |
C3 | −0.0747 (2) | 1.06679 (19) | 0.30950 (8) | 0.0477 (5) | |
H3 | −0.0977 | 1.1590 | 0.3120 | 0.057* | |
C4 | −0.1665 (2) | 0.9773 (2) | 0.28295 (8) | 0.0523 (5) | |
H4 | −0.2523 | 1.0100 | 0.2670 | 0.063* | |
C5 | −0.1337 (2) | 0.8385 (2) | 0.27942 (8) | 0.0494 (5) | |
H5 | −0.1980 | 0.7810 | 0.2610 | 0.059* | |
C6 | −0.00918 (19) | 0.78515 (18) | 0.30242 (7) | 0.0445 (4) | |
H6 | 0.0118 | 0.6924 | 0.3006 | 0.053* | |
C7 | 0.08437 (17) | 0.87557 (17) | 0.32862 (7) | 0.0349 (4) | |
C8 | 0.40695 (17) | 1.00359 (17) | 0.39761 (7) | 0.0369 (4) | |
C9 | 0.5242 (2) | 0.9178 (2) | 0.38676 (8) | 0.0514 (5) | |
H9 | 0.5111 | 0.8441 | 0.3635 | 0.062* | |
C10 | 0.6605 (2) | 0.9398 (2) | 0.40998 (9) | 0.0557 (5) | |
H10 | 0.7378 | 0.8810 | 0.4019 | 0.067* | |
C11 | 0.68392 (19) | 1.0476 (2) | 0.44493 (8) | 0.0478 (5) | |
C12 | 0.5668 (2) | 1.1330 (2) | 0.45579 (8) | 0.0497 (5) | |
H12 | 0.5803 | 1.2065 | 0.4791 | 0.060* | |
C13 | 0.42976 (19) | 1.11181 (18) | 0.43277 (7) | 0.0429 (4) | |
H13 | 0.3524 | 1.1706 | 0.4409 | 0.052* | |
C14 | 0.8329 (2) | 1.0698 (3) | 0.47036 (11) | 0.0714 (7) | |
H14A | 0.8284 | 1.0475 | 0.5083 | 0.107* | |
H14B | 0.8612 | 1.1635 | 0.4662 | 0.107* | |
H14C | 0.9042 | 1.0124 | 0.4528 | 0.107* | |
H1 | 0.2595 | 0.7809 | 0.3577 | 0.086* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0392 (8) | 0.0252 (7) | 0.0488 (8) | 0.0010 (6) | −0.0021 (6) | −0.0011 (6) |
N2 | 0.0376 (7) | 0.0267 (7) | 0.0513 (8) | −0.0004 (5) | −0.0035 (6) | −0.0013 (6) |
C1 | 0.0384 (8) | 0.0263 (8) | 0.0410 (9) | −0.0015 (6) | 0.0025 (7) | −0.0005 (7) |
C2 | 0.0364 (8) | 0.0285 (9) | 0.0440 (9) | −0.0025 (6) | 0.0002 (7) | 0.0011 (7) |
C3 | 0.0463 (10) | 0.0342 (10) | 0.0625 (12) | 0.0031 (7) | −0.0092 (9) | 0.0020 (9) |
C4 | 0.0447 (10) | 0.0510 (12) | 0.0610 (12) | −0.0014 (8) | −0.0150 (9) | 0.0056 (10) |
C5 | 0.0501 (10) | 0.0454 (11) | 0.0528 (11) | −0.0134 (8) | −0.0090 (8) | −0.0005 (9) |
C6 | 0.0501 (10) | 0.0315 (9) | 0.0518 (10) | −0.0063 (7) | −0.0021 (8) | −0.0016 (8) |
C7 | 0.0365 (8) | 0.0282 (9) | 0.0399 (9) | −0.0025 (6) | 0.0026 (7) | 0.0019 (7) |
C8 | 0.0382 (8) | 0.0295 (9) | 0.0430 (9) | −0.0020 (7) | −0.0007 (7) | 0.0021 (7) |
C9 | 0.0449 (10) | 0.0441 (11) | 0.0651 (12) | 0.0054 (8) | −0.0048 (9) | −0.0164 (9) |
C10 | 0.0394 (10) | 0.0581 (13) | 0.0697 (13) | 0.0092 (8) | −0.0020 (9) | −0.0072 (11) |
C11 | 0.0430 (10) | 0.0499 (12) | 0.0506 (11) | −0.0057 (8) | −0.0054 (8) | 0.0060 (9) |
C12 | 0.0532 (11) | 0.0434 (11) | 0.0525 (11) | −0.0043 (8) | −0.0098 (9) | −0.0067 (9) |
C13 | 0.0439 (9) | 0.0347 (10) | 0.0502 (10) | 0.0030 (7) | −0.0031 (8) | −0.0036 (8) |
C14 | 0.0489 (12) | 0.0831 (18) | 0.0821 (16) | −0.0062 (11) | −0.0174 (11) | 0.0000 (14) |
N1—C1 | 1.358 (2) | C6—H6 | 0.9300 |
N1—C7 | 1.378 (2) | C8—C9 | 1.383 (2) |
N1—H1 | 0.8500 | C8—C13 | 1.385 (2) |
N2—C1 | 1.323 (2) | C9—C10 | 1.379 (3) |
N2—C2 | 1.392 (2) | C9—H9 | 0.9300 |
C1—C8 | 1.466 (2) | C10—C11 | 1.380 (3) |
C2—C3 | 1.392 (2) | C10—H10 | 0.9300 |
C2—C7 | 1.400 (2) | C11—C12 | 1.379 (3) |
C3—C4 | 1.375 (3) | C11—C14 | 1.506 (3) |
C3—H3 | 0.9300 | C12—C13 | 1.382 (2) |
C4—C5 | 1.396 (3) | C12—H12 | 0.9300 |
C4—H4 | 0.9300 | C13—H13 | 0.9300 |
C5—C6 | 1.368 (3) | C14—H14A | 0.9600 |
C5—H5 | 0.9300 | C14—H14B | 0.9600 |
C6—C7 | 1.387 (2) | C14—H14C | 0.9600 |
C1—N1—C7 | 107.41 (13) | C9—C8—C13 | 118.16 (16) |
C1—N1—H1 | 129.3 | C9—C8—C1 | 120.67 (15) |
C7—N1—H1 | 123.2 | C13—C8—C1 | 121.14 (15) |
C1—N2—C2 | 105.01 (13) | C10—C9—C8 | 120.97 (18) |
N2—C1—N1 | 112.65 (14) | C10—C9—H9 | 119.5 |
N2—C1—C8 | 125.11 (14) | C8—C9—H9 | 119.5 |
N1—C1—C8 | 122.21 (14) | C9—C10—C11 | 121.14 (18) |
C3—C2—N2 | 130.84 (16) | C9—C10—H10 | 119.4 |
C3—C2—C7 | 119.56 (15) | C11—C10—H10 | 119.4 |
N2—C2—C7 | 109.59 (14) | C12—C11—C10 | 117.83 (17) |
C4—C3—C2 | 118.00 (17) | C12—C11—C14 | 121.60 (19) |
C4—C3—H3 | 121.0 | C10—C11—C14 | 120.57 (19) |
C2—C3—H3 | 121.0 | C11—C12—C13 | 121.52 (18) |
C3—C4—C5 | 121.50 (17) | C11—C12—H12 | 119.2 |
C3—C4—H4 | 119.3 | C13—C12—H12 | 119.2 |
C5—C4—H4 | 119.3 | C12—C13—C8 | 120.39 (16) |
C6—C5—C4 | 121.55 (17) | C12—C13—H13 | 119.8 |
C6—C5—H5 | 119.2 | C8—C13—H13 | 119.8 |
C4—C5—H5 | 119.2 | C11—C14—H14A | 109.5 |
C5—C6—C7 | 116.98 (17) | C11—C14—H14B | 109.5 |
C5—C6—H6 | 121.5 | H14A—C14—H14B | 109.5 |
C7—C6—H6 | 121.5 | C11—C14—H14C | 109.5 |
N1—C7—C6 | 132.22 (15) | H14A—C14—H14C | 109.5 |
N1—C7—C2 | 105.35 (14) | H14B—C14—H14C | 109.5 |
C6—C7—C2 | 122.40 (15) | ||
C2—N2—C1—N1 | −0.80 (18) | C3—C2—C7—C6 | 0.0 (3) |
C2—N2—C1—C8 | 177.07 (15) | N2—C2—C7—C6 | −178.71 (15) |
C7—N1—C1—N2 | 0.53 (19) | N2—C1—C8—C9 | −150.60 (19) |
C7—N1—C1—C8 | −177.40 (14) | N1—C1—C8—C9 | 27.1 (2) |
C1—N2—C2—C3 | −177.71 (18) | N2—C1—C8—C13 | 27.3 (3) |
C1—N2—C2—C7 | 0.76 (18) | N1—C1—C8—C13 | −155.08 (17) |
N2—C2—C3—C4 | 177.59 (18) | C13—C8—C9—C10 | −0.5 (3) |
C7—C2—C3—C4 | −0.8 (3) | C1—C8—C9—C10 | 177.46 (18) |
C2—C3—C4—C5 | 0.6 (3) | C8—C9—C10—C11 | 0.3 (3) |
C3—C4—C5—C6 | 0.3 (3) | C9—C10—C11—C12 | −0.2 (3) |
C4—C5—C6—C7 | −1.1 (3) | C9—C10—C11—C14 | 179.5 (2) |
C1—N1—C7—C6 | 177.98 (18) | C10—C11—C12—C13 | 0.2 (3) |
C1—N1—C7—C2 | −0.02 (18) | C14—C11—C12—C13 | −179.46 (19) |
C5—C6—C7—N1 | −176.77 (17) | C11—C12—C13—C8 | −0.4 (3) |
C5—C6—C7—C2 | 0.9 (3) | C9—C8—C13—C12 | 0.5 (3) |
C3—C2—C7—N1 | 178.21 (15) | C1—C8—C13—C12 | −177.42 (16) |
N2—C2—C7—N1 | −0.46 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N2i | 0.85 | 2.07 | 2.9151 (19) | 171 |
Symmetry code: (i) −x+1/2, y−1/2, z. |
Experimental details
Crystal data | |
Chemical formula | C14H12N2 |
Mr | 208.26 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 295 |
a, b, c (Å) | 9.0763 (10), 9.8053 (11), 24.628 (3) |
V (Å3) | 2191.8 (4) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.40 × 0.20 × 0.16 |
Data collection | |
Diffractometer | Bruker APEX area-detector |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.970, 0.988 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9605, 2133, 1850 |
Rint | 0.025 |
(sin θ/λ)max (Å−1) | 0.617 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.052, 0.135, 1.10 |
No. of reflections | 2133 |
No. of parameters | 146 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.21, −0.18 |
Computer programs: SMART (Bruker, 2002), SAINT (Bruker, 2002), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1976), SHELXL97.
N1—C1 | 1.358 (2) | C1—C8 | 1.466 (2) |
N1—C7 | 1.378 (2) | C2—C3 | 1.392 (2) |
N2—C1 | 1.323 (2) | C2—C7 | 1.400 (2) |
N2—C2 | 1.392 (2) | C11—C14 | 1.506 (3) |
C1—N1—C7 | 107.41 (13) | C3—C2—C7 | 119.56 (15) |
C1—N2—C2 | 105.01 (13) | N2—C2—C7 | 109.59 (14) |
N2—C1—N1 | 112.65 (14) | N1—C7—C6 | 132.22 (15) |
N2—C1—C8 | 125.11 (14) | N1—C7—C2 | 105.35 (14) |
N1—C1—C8 | 122.21 (14) | C9—C8—C13 | 118.16 (16) |
C3—C2—N2 | 130.84 (16) | C12—C11—C10 | 117.83 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N2i | 0.85 | 2.07 | 2.9151 (19) | 170.8 |
Symmetry code: (i) −x+1/2, y−1/2, z. |
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2-Substituted benzimidazoles have attracted considerable interest as intermediates in the development of molecules of pharmaceutical interest. Benzimidazole derivatives exhibit significant activity against several viruses such as HIV, herpes (HSV-1), RNA, influenza, and human cytomegalovirus (HCMV) (Tamm, 1957; Tamm & Seghal, 1978; Roth et al., 1997; Migawa et al., 1998; Porcari et al., 1998). The objective of this study therefore was to synthesize and elucidate the crystal structure of a new benzimidazole compound.
A view of the molecule of (I) is shown in Fig. 1 and selected geometric parameters are given in Table 1. The dihedral angle between the benzimidazole and tolyl portions of the title compound, (I), is 27.5 °. The molecules are linked into a linear chain through N—H···N hydrogen bonds interactions (N2···H1 2.072 Å, N1—H1···N2 170.8 °), as shown in Fig. 2. There exist π–π stacking interactions in adjacent linear chains, adjacent tolyl rings are exactly parallel, the perpendicular spacing of the rings is 3.504 Å, and the ring centroid-to-centroid distance is 4.080 Å. These π–π stacking interactions form a two dimensional supramolecular array.