Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807044601/bg2092sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807044601/bg2092Isup2.hkl |
CCDC reference: 656666
The reaction mixture containing salicylaldehyde (21 ml, 20 mmol) and o-phenylene diamine (1.08 g, 10 mmol) was refluxed for about 4 h in ethanol (30 ml), then sodium borohydride (1.52 g, 40 mmol) was added and the reaction mixture was refluxed continuely for 4 h, then acetone (20 ml) and water (40 ml) were added in turn, and the reaction mixture was cooled and the product filtered off, washed with ethanol and dried. Yellow crystals of (I) suitable for X-ray structure analysis were obtained by recrystallizing the crude product from ethanol (m.p.465–467 K).
Due to the abscense of significant anomalous dispersion effects, Friedel pairs were merged, for what the number of independent reflections is rather low.
All H atoms were positioned geometrically and refined as riding on their parent atoms,with C—H = 0.96Å and Uiso(H)= 1.5Ueq(C) for methyl H atoms, O—H = 0.82Å and Uiso(H)= 1.2Ueq(C) for hydroxy H atoms, C—H = 0.97Å and Uiso(H)= 1.2Ueq(C) for methylene H atoms, and C—H = 0.93Å and Uiso(H) = 1.2Ueq(C) for all other H atom.
Benzimidazole derivatives display wide-ranging biological activities, such as inhibitors of hepatitis C virus NS5B polymerase (Ishida et al., 2006) and heparanase (Xu et al., 2006) and antimicrobial activities (Özden et al., 2005). The crystal structure of a benzimidazole derivative has been recently reported (Yang et al., 2007). Here we report the crystal structure of a new benzimidazole derivative, 1,3-Bis(2-hydroxybenzyl) -2,2-dimethyl-2,3-dihydrogen 1H-benzimidazole,(I).(Fig. 1)
The molecule presents a mirror symmetry plane through the central phenyl ring, and two intramolecular O—H···N hydrogen-bonds define two S(6) patterns (García-Báez et al.,2003). The molecule adopts a "hawk "conformation; the two benzyl rings located at both sides of the benzimidazole rings subtend a dihedral angle of 34.3 (1)°. (Table 1 and Fig.1). The geometric parameters for (I) are normal.
The molecules are linked by four C—H···π hydrogen bonds. The C4 atom in the molecules at (x,y,z) acts as hydrogen-bond donor to the Cg1i centroid of the ring C2—C7, i: 1/2 - x,1 - y,-1/2 + z], generating a [010] sheet of R44(28) rings by translation and reflection of the hydrogen-bond, the sheets lying in the domain 0.26 < y < 1.26. (Table 1 and Fig. 2)
For related literature, see: García-Báez et al. (2003); Ishida et al. (2006); Xu et al. (2006); Yang et al. (2007); Özden et al. (2005).
Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXTL (Sheldrick, 1997b).
C23H24N2O2 | F(000) = 384 |
Mr = 360.44 | Dx = 1.261 Mg m−3 |
Orthorhombic, Pmn21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac -2 | Cell parameters from 2085 reflections |
a = 19.137 (2) Å | θ = 2.5–26.2° |
b = 8.0716 (15) Å | µ = 0.08 mm−1 |
c = 6.1464 (13) Å | T = 298 K |
V = 949.4 (3) Å3 | Block, yellow |
Z = 2 | 0.21 × 0.17 × 0.16 mm |
Siemens SMART 1000 CCD area-detector diffractometer | 934 independent reflections |
Radiation source: fine-focus sealed tube | 810 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.032 |
φ and ω scans | θmax = 25.0°, θmin = 2.1° |
Absorption correction: multi-scan SADABS (Sheldrick, 1996) | h = −22→22 |
Tmin = 0.98, Tmax = 0.99 | k = −7→9 |
4535 measured reflections | l = −7→7 |
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)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.19 | w = 1/[σ2(Fo2) + (0.0649P)2 + 0.1011P] where P = (Fo2 + 2Fc2)/3 |
934 reflections | (Δ/σ)max < 0.001 |
128 parameters | Δρmax = 0.11 e Å−3 |
1 restraint | Δρmin = −0.19 e Å−3 |
C23H24N2O2 | V = 949.4 (3) Å3 |
Mr = 360.44 | Z = 2 |
Orthorhombic, Pmn21 | Mo Kα radiation |
a = 19.137 (2) Å | µ = 0.08 mm−1 |
b = 8.0716 (15) Å | T = 298 K |
c = 6.1464 (13) Å | 0.21 × 0.17 × 0.16 mm |
Siemens SMART 1000 CCD area-detector diffractometer | 934 independent reflections |
Absorption correction: multi-scan SADABS (Sheldrick, 1996) | 810 reflections with I > 2σ(I) |
Tmin = 0.98, Tmax = 0.99 | Rint = 0.032 |
4535 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 1 restraint |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.19 | Δρmax = 0.11 e Å−3 |
934 reflections | Δρmin = −0.19 e Å−3 |
128 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 | ||
N1 | 0.05992 (13) | 0.7643 (3) | 0.2677 (4) | 0.0380 (7) | |
O1 | 0.11741 (12) | 0.5707 (3) | −0.0445 (4) | 0.0562 (7) | |
H1 | 0.0866 | 0.6049 | 0.0366 | 0.084* | |
C1 | 0.13090 (16) | 0.7587 (4) | 0.3599 (6) | 0.0475 (9) | |
H1A | 0.1343 | 0.6644 | 0.4572 | 0.057* | |
H1B | 0.1387 | 0.8581 | 0.4453 | 0.057* | |
C2 | 0.18718 (17) | 0.7456 (4) | 0.1898 (6) | 0.0415 (8) | |
C3 | 0.17888 (16) | 0.6515 (4) | 0.0007 (6) | 0.0403 (8) | |
C4 | 0.23433 (18) | 0.6332 (4) | −0.1444 (7) | 0.0501 (9) | |
H4 | 0.2283 | 0.5712 | −0.2706 | 0.060* | |
C5 | 0.2979 (2) | 0.7061 (5) | −0.1026 (7) | 0.0596 (11) | |
H5 | 0.3345 | 0.6926 | −0.2004 | 0.072* | |
C6 | 0.3079 (2) | 0.7990 (5) | 0.0828 (9) | 0.0641 (11) | |
H6 | 0.3510 | 0.8476 | 0.1113 | 0.077* | |
C7 | 0.25254 (17) | 0.8190 (5) | 0.2264 (7) | 0.0505 (10) | |
H7 | 0.2590 | 0.8830 | 0.3506 | 0.061* | |
C8 | 0.0000 | 0.7094 (6) | 0.4089 (7) | 0.0388 (11) | |
C9 | 0.03658 (16) | 0.9138 (4) | 0.1698 (5) | 0.0361 (7) | |
C10 | 0.07437 (17) | 1.0423 (4) | 0.0804 (6) | 0.0430 (8) | |
H10 | 0.1230 | 1.0425 | 0.0812 | 0.052* | |
C11 | 0.03590 (19) | 1.1734 (4) | −0.0123 (7) | 0.0553 (10) | |
H11 | 0.0596 | 1.2619 | −0.0748 | 0.066* | |
C12 | 0.0000 | 0.8038 (8) | 0.6262 (8) | 0.0549 (14) | |
H12A | −0.0386 | 0.7670 | 0.7135 | 0.082* | |
H12B | 0.0000 | 0.9205 | 0.5993 | 0.082* | |
C13 | 0.0000 | 0.5227 (6) | 0.4407 (9) | 0.0558 (14) | |
H13A | −0.0388 | 0.4917 | 0.5311 | 0.084* | |
H13B | 0.0000 | 0.4688 | 0.3020 | 0.084* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0354 (15) | 0.0457 (16) | 0.0328 (13) | 0.0022 (12) | −0.0027 (11) | 0.0001 (11) |
O1 | 0.0520 (15) | 0.0622 (15) | 0.0545 (16) | 0.0005 (12) | −0.0054 (12) | −0.0179 (13) |
C1 | 0.049 (2) | 0.055 (2) | 0.0384 (18) | 0.0024 (15) | −0.0090 (18) | −0.0074 (17) |
C2 | 0.0366 (18) | 0.0411 (17) | 0.0469 (18) | 0.0058 (14) | −0.0076 (16) | 0.0004 (16) |
C3 | 0.0365 (18) | 0.0395 (17) | 0.0449 (18) | 0.0085 (14) | −0.0066 (15) | 0.0019 (15) |
C4 | 0.046 (2) | 0.054 (2) | 0.050 (2) | 0.0123 (16) | 0.0004 (17) | 0.0021 (18) |
C5 | 0.056 (2) | 0.056 (2) | 0.067 (3) | 0.0104 (18) | 0.014 (2) | 0.020 (2) |
C6 | 0.042 (2) | 0.057 (2) | 0.093 (3) | −0.0062 (17) | −0.002 (2) | 0.012 (2) |
C7 | 0.0351 (19) | 0.055 (2) | 0.062 (3) | 0.0009 (15) | −0.0094 (18) | −0.0043 (17) |
C8 | 0.036 (2) | 0.045 (2) | 0.035 (3) | 0.000 | 0.000 | −0.001 (2) |
C9 | 0.0387 (15) | 0.0391 (15) | 0.0307 (15) | −0.0013 (14) | −0.0008 (15) | −0.0056 (13) |
C10 | 0.0295 (16) | 0.0492 (19) | 0.0504 (19) | −0.0041 (14) | 0.0008 (16) | −0.0064 (16) |
C11 | 0.069 (2) | 0.0404 (19) | 0.056 (2) | −0.0060 (16) | 0.005 (2) | 0.0039 (16) |
C12 | 0.049 (3) | 0.082 (4) | 0.035 (3) | 0.000 | 0.000 | −0.008 (3) |
C13 | 0.056 (3) | 0.055 (3) | 0.056 (3) | 0.000 | 0.000 | 0.008 (3) |
N1—C9 | 1.420 (4) | C6—H6 | 0.9300 |
N1—C1 | 1.472 (4) | C7—H7 | 0.9300 |
N1—C8 | 1.505 (4) | C8—N1i | 1.505 (4) |
O1—C3 | 1.373 (4) | C8—C13 | 1.520 (7) |
O1—H1 | 0.8200 | C8—C12 | 1.538 (7) |
C1—C2 | 1.505 (5) | C9—C10 | 1.379 (5) |
C1—H1A | 0.9700 | C9—C9i | 1.400 (6) |
C1—H1B | 0.9700 | C10—C11 | 1.409 (5) |
C2—C3 | 1.397 (5) | C10—H10 | 0.9300 |
C2—C7 | 1.402 (5) | C11—C11i | 1.374 (7) |
C3—C4 | 1.394 (5) | C11—H11 | 0.9300 |
C4—C5 | 1.376 (5) | C12—H12A | 0.9600 |
C4—H4 | 0.9300 | C12—H12B | 0.9564 |
C5—C6 | 1.377 (6) | C13—H13A | 0.9599 |
C5—H5 | 0.9300 | C13—H13B | 0.9567 |
C6—C7 | 1.387 (6) | ||
C9—N1—C1 | 118.7 (3) | C6—C7—C2 | 122.0 (4) |
C9—N1—C8 | 104.8 (3) | C6—C7—H7 | 119.0 |
C1—N1—C8 | 118.2 (3) | C2—C7—H7 | 119.0 |
C3—O1—H1 | 109.5 | N1—C8—N1i | 99.3 (3) |
N1—C1—C2 | 113.3 (3) | N1—C8—C13 | 111.5 (3) |
N1—C1—H1A | 108.9 | N1i—C8—C13 | 111.5 (3) |
C2—C1—H1A | 108.9 | N1—C8—C12 | 110.8 (2) |
N1—C1—H1B | 108.9 | N1i—C8—C12 | 110.8 (2) |
C2—C1—H1B | 108.9 | C13—C8—C12 | 112.3 (4) |
H1A—C1—H1B | 107.7 | C10—C9—C9i | 121.6 (2) |
C3—C2—C7 | 117.7 (3) | C10—C9—N1 | 130.0 (3) |
C3—C2—C1 | 122.3 (3) | C9i—C9—N1 | 108.33 (16) |
C7—C2—C1 | 119.8 (3) | C9—C10—C11 | 116.9 (3) |
O1—C3—C4 | 118.2 (3) | C9—C10—H10 | 121.6 |
O1—C3—C2 | 121.6 (3) | C11—C10—H10 | 121.6 |
C4—C3—C2 | 120.2 (3) | C11i—C11—C10 | 121.5 (2) |
C5—C4—C3 | 120.5 (4) | C11i—C11—H11 | 119.3 |
C5—C4—H4 | 119.7 | C10—C11—H11 | 119.3 |
C3—C4—H4 | 119.7 | C8—C12—H12A | 109.4 |
C4—C5—C6 | 120.6 (4) | C8—C12—H12B | 109.7 |
C4—C5—H5 | 119.7 | H12A—C12—H12B | 113.7 |
C6—C5—H5 | 119.7 | C8—C13—H13A | 109.4 |
C5—C6—C7 | 118.9 (3) | C8—C13—H13B | 109.6 |
C5—C6—H6 | 120.5 | H13A—C13—H13B | 113.4 |
C7—C6—H6 | 120.5 | ||
C9—N1—C1—C2 | −75.7 (3) | C1—C2—C7—C6 | 174.7 (3) |
C8—N1—C1—C2 | 155.8 (3) | C9—N1—C8—N1i | 35.7 (4) |
N1—C1—C2—C3 | −37.1 (4) | C1—N1—C8—N1i | 170.4 (2) |
N1—C1—C2—C7 | 147.9 (3) | C9—N1—C8—C13 | 153.2 (3) |
C7—C2—C3—O1 | 177.8 (3) | C1—N1—C8—C13 | −72.0 (4) |
C1—C2—C3—O1 | 2.6 (5) | C9—N1—C8—C12 | −80.9 (3) |
C7—C2—C3—C4 | −0.1 (5) | C1—N1—C8—C12 | 53.8 (4) |
C1—C2—C3—C4 | −175.3 (3) | C1—N1—C9—C10 | 23.7 (5) |
O1—C3—C4—C5 | −177.4 (3) | C8—N1—C9—C10 | 158.1 (4) |
C2—C3—C4—C5 | 0.6 (5) | C1—N1—C9—C9i | −157.9 (2) |
C3—C4—C5—C6 | −0.3 (5) | C8—N1—C9—C9i | −23.4 (2) |
C4—C5—C6—C7 | −0.4 (6) | C9i—C9—C10—C11 | −0.4 (4) |
C5—C6—C7—C2 | 0.9 (6) | N1—C9—C10—C11 | 177.9 (3) |
C3—C2—C7—C6 | −0.6 (5) | C9—C10—C11—C11i | 0.4 (4) |
Symmetry code: (i) −x, y, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···N1 | 0.82 | 1.98 | 2.708 (4) | 147 |
C4—H4···Cg1ii | 0.93 | 2.71 | 3.51 (2) | 144 |
Symmetry code: (ii) −x+1/2, −y+1, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C23H24N2O2 |
Mr | 360.44 |
Crystal system, space group | Orthorhombic, Pmn21 |
Temperature (K) | 298 |
a, b, c (Å) | 19.137 (2), 8.0716 (15), 6.1464 (13) |
V (Å3) | 949.4 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.21 × 0.17 × 0.16 |
Data collection | |
Diffractometer | Siemens SMART 1000 CCD area-detector |
Absorption correction | Multi-scan SADABS (Sheldrick, 1996) |
Tmin, Tmax | 0.98, 0.99 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4535, 934, 810 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.118, 1.19 |
No. of reflections | 934 |
No. of parameters | 128 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.11, −0.19 |
Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SHELXS97 (Sheldrick, 1997a), SHELXL97 (Sheldrick, 1997a), SHELXTL (Sheldrick, 1997b).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···N1 | 0.82 | 1.98 | 2.708 (4) | 147.0 |
C4—H4···Cg1i | 0.93 | 2.71 | 3.51 (2) | 143.5 |
Symmetry code: (i) −x+1/2, −y+1, z−1/2. |
Benzimidazole derivatives display wide-ranging biological activities, such as inhibitors of hepatitis C virus NS5B polymerase (Ishida et al., 2006) and heparanase (Xu et al., 2006) and antimicrobial activities (Özden et al., 2005). The crystal structure of a benzimidazole derivative has been recently reported (Yang et al., 2007). Here we report the crystal structure of a new benzimidazole derivative, 1,3-Bis(2-hydroxybenzyl) -2,2-dimethyl-2,3-dihydrogen 1H-benzimidazole,(I).(Fig. 1)
The molecule presents a mirror symmetry plane through the central phenyl ring, and two intramolecular O—H···N hydrogen-bonds define two S(6) patterns (García-Báez et al.,2003). The molecule adopts a "hawk "conformation; the two benzyl rings located at both sides of the benzimidazole rings subtend a dihedral angle of 34.3 (1)°. (Table 1 and Fig.1). The geometric parameters for (I) are normal.
The molecules are linked by four C—H···π hydrogen bonds. The C4 atom in the molecules at (x,y,z) acts as hydrogen-bond donor to the Cg1i centroid of the ring C2—C7, i: 1/2 - x,1 - y,-1/2 + z], generating a [010] sheet of R44(28) rings by translation and reflection of the hydrogen-bond, the sheets lying in the domain 0.26 < y < 1.26. (Table 1 and Fig. 2)