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The molecule of the title compound, C23H24N2O2, has a mirror plane passing through the benzimidazole ring system. The mol­ecule adopts a bowed conformation and the two terminal benzene rings subtend a dihedral angle of 34.3 (1)°. Mol­ecules are linked by C—H...π hydrogen bonds, forming an (010) sheet of R44(28) rings.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807044601/bg2092sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807044601/bg2092Isup2.hkl
Contains datablock I

CCDC reference: 656666

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.038
  • wR factor = 0.118
  • Data-to-parameter ratio = 7.3

checkCIF/PLATON results

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Alert level C PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) ..... 7.30 PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ... 5 PLAT391_ALERT_3_C Deviating Methyl C12 H-C-H Bond Angle ...... 101.00 Deg. PLAT391_ALERT_3_C Deviating Methyl C13 H-C-H Bond Angle ...... 101.00 Deg.
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 25.00 From the CIF: _reflns_number_total 934 Count of symmetry unique reflns 950 Completeness (_total/calc) 98.32% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 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 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 5 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

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)

Related literature top

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).

Experimental top

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).

Refinement top

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.

Structure description top

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).

Computing details top

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).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the atom-numbering scheme and intramolecular hydrogen-bonds S(6) pattern. Displacement ellipsoids are drawn at the 30% probability level. Dashed lines indicate hydrogen bonds.[Symmetry codes: (*)-x,y,z]
[Figure 2] Fig. 2. Packing diagram of (I), showing the formation of a [010] sheet of R44(28) rings linked by a C—H···π hydrogen bond. For clarity, H atoms not involved in the motif shown have been omitted. Dashed lines indicate hydrogen bonds.[Symmetry codes: (*)-x,y,z; (&)-1/2 + x,1 - y,-1/2 + z; (&)-x,y,-1 + z; (#)1/2 - x,1 - y,-1/2 + z; (@)x,y,-1 + z].
1,3-Bis(2-hydroxybenzyl)-2,2-dimethyl-2,3-dihydro-1H-benzimidazole top
Crystal data top
C23H24N2O2F(000) = 384
Mr = 360.44Dx = 1.261 Mg m3
Orthorhombic, Pmn21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac -2Cell parameters from 2085 reflections
a = 19.137 (2) Åθ = 2.5–26.2°
b = 8.0716 (15) ŵ = 0.08 mm1
c = 6.1464 (13) ÅT = 298 K
V = 949.4 (3) Å3Block, yellow
Z = 20.21 × 0.17 × 0.16 mm
Data collection top
Siemens SMART 1000 CCD area-detector
diffractometer
934 independent reflections
Radiation source: fine-focus sealed tube810 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
φ and ω scansθmax = 25.0°, θmin = 2.1°
Absorption correction: multi-scan
SADABS (Sheldrick, 1996)
h = 2222
Tmin = 0.98, Tmax = 0.99k = 79
4535 measured reflectionsl = 77
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)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.118H-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 parametersΔρmax = 0.11 e Å3
1 restraintΔρmin = 0.19 e Å3
Crystal data top
C23H24N2O2V = 949.4 (3) Å3
Mr = 360.44Z = 2
Orthorhombic, Pmn21Mo Kα radiation
a = 19.137 (2) ŵ = 0.08 mm1
b = 8.0716 (15) ÅT = 298 K
c = 6.1464 (13) Å0.21 × 0.17 × 0.16 mm
Data collection top
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 = 0.99Rint = 0.032
4535 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0381 restraint
wR(F2) = 0.118H-atom parameters constrained
S = 1.19Δρmax = 0.11 e Å3
934 reflectionsΔρmin = 0.19 e Å3
128 parameters
Special details top

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*/Ueq
N10.05992 (13)0.7643 (3)0.2677 (4)0.0380 (7)
O10.11741 (12)0.5707 (3)0.0445 (4)0.0562 (7)
H10.08660.60490.03660.084*
C10.13090 (16)0.7587 (4)0.3599 (6)0.0475 (9)
H1A0.13430.66440.45720.057*
H1B0.13870.85810.44530.057*
C20.18718 (17)0.7456 (4)0.1898 (6)0.0415 (8)
C30.17888 (16)0.6515 (4)0.0007 (6)0.0403 (8)
C40.23433 (18)0.6332 (4)0.1444 (7)0.0501 (9)
H40.22830.57120.27060.060*
C50.2979 (2)0.7061 (5)0.1026 (7)0.0596 (11)
H50.33450.69260.20040.072*
C60.3079 (2)0.7990 (5)0.0828 (9)0.0641 (11)
H60.35100.84760.11130.077*
C70.25254 (17)0.8190 (5)0.2264 (7)0.0505 (10)
H70.25900.88300.35060.061*
C80.00000.7094 (6)0.4089 (7)0.0388 (11)
C90.03658 (16)0.9138 (4)0.1698 (5)0.0361 (7)
C100.07437 (17)1.0423 (4)0.0804 (6)0.0430 (8)
H100.12301.04250.08120.052*
C110.03590 (19)1.1734 (4)0.0123 (7)0.0553 (10)
H110.05961.26190.07480.066*
C120.00000.8038 (8)0.6262 (8)0.0549 (14)
H12A0.03860.76700.71350.082*
H12B0.00000.92050.59930.082*
C130.00000.5227 (6)0.4407 (9)0.0558 (14)
H13A0.03880.49170.53110.084*
H13B0.00000.46880.30200.084*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0354 (15)0.0457 (16)0.0328 (13)0.0022 (12)0.0027 (11)0.0001 (11)
O10.0520 (15)0.0622 (15)0.0545 (16)0.0005 (12)0.0054 (12)0.0179 (13)
C10.049 (2)0.055 (2)0.0384 (18)0.0024 (15)0.0090 (18)0.0074 (17)
C20.0366 (18)0.0411 (17)0.0469 (18)0.0058 (14)0.0076 (16)0.0004 (16)
C30.0365 (18)0.0395 (17)0.0449 (18)0.0085 (14)0.0066 (15)0.0019 (15)
C40.046 (2)0.054 (2)0.050 (2)0.0123 (16)0.0004 (17)0.0021 (18)
C50.056 (2)0.056 (2)0.067 (3)0.0104 (18)0.014 (2)0.020 (2)
C60.042 (2)0.057 (2)0.093 (3)0.0062 (17)0.002 (2)0.012 (2)
C70.0351 (19)0.055 (2)0.062 (3)0.0009 (15)0.0094 (18)0.0043 (17)
C80.036 (2)0.045 (2)0.035 (3)0.0000.0000.001 (2)
C90.0387 (15)0.0391 (15)0.0307 (15)0.0013 (14)0.0008 (15)0.0056 (13)
C100.0295 (16)0.0492 (19)0.0504 (19)0.0041 (14)0.0008 (16)0.0064 (16)
C110.069 (2)0.0404 (19)0.056 (2)0.0060 (16)0.005 (2)0.0039 (16)
C120.049 (3)0.082 (4)0.035 (3)0.0000.0000.008 (3)
C130.056 (3)0.055 (3)0.056 (3)0.0000.0000.008 (3)
Geometric parameters (Å, º) top
N1—C91.420 (4)C6—H60.9300
N1—C11.472 (4)C7—H70.9300
N1—C81.505 (4)C8—N1i1.505 (4)
O1—C31.373 (4)C8—C131.520 (7)
O1—H10.8200C8—C121.538 (7)
C1—C21.505 (5)C9—C101.379 (5)
C1—H1A0.9700C9—C9i1.400 (6)
C1—H1B0.9700C10—C111.409 (5)
C2—C31.397 (5)C10—H100.9300
C2—C71.402 (5)C11—C11i1.374 (7)
C3—C41.394 (5)C11—H110.9300
C4—C51.376 (5)C12—H12A0.9600
C4—H40.9300C12—H12B0.9564
C5—C61.377 (6)C13—H13A0.9599
C5—H50.9300C13—H13B0.9567
C6—C71.387 (6)
C9—N1—C1118.7 (3)C6—C7—C2122.0 (4)
C9—N1—C8104.8 (3)C6—C7—H7119.0
C1—N1—C8118.2 (3)C2—C7—H7119.0
C3—O1—H1109.5N1—C8—N1i99.3 (3)
N1—C1—C2113.3 (3)N1—C8—C13111.5 (3)
N1—C1—H1A108.9N1i—C8—C13111.5 (3)
C2—C1—H1A108.9N1—C8—C12110.8 (2)
N1—C1—H1B108.9N1i—C8—C12110.8 (2)
C2—C1—H1B108.9C13—C8—C12112.3 (4)
H1A—C1—H1B107.7C10—C9—C9i121.6 (2)
C3—C2—C7117.7 (3)C10—C9—N1130.0 (3)
C3—C2—C1122.3 (3)C9i—C9—N1108.33 (16)
C7—C2—C1119.8 (3)C9—C10—C11116.9 (3)
O1—C3—C4118.2 (3)C9—C10—H10121.6
O1—C3—C2121.6 (3)C11—C10—H10121.6
C4—C3—C2120.2 (3)C11i—C11—C10121.5 (2)
C5—C4—C3120.5 (4)C11i—C11—H11119.3
C5—C4—H4119.7C10—C11—H11119.3
C3—C4—H4119.7C8—C12—H12A109.4
C4—C5—C6120.6 (4)C8—C12—H12B109.7
C4—C5—H5119.7H12A—C12—H12B113.7
C6—C5—H5119.7C8—C13—H13A109.4
C5—C6—C7118.9 (3)C8—C13—H13B109.6
C5—C6—H6120.5H13A—C13—H13B113.4
C7—C6—H6120.5
C9—N1—C1—C275.7 (3)C1—C2—C7—C6174.7 (3)
C8—N1—C1—C2155.8 (3)C9—N1—C8—N1i35.7 (4)
N1—C1—C2—C337.1 (4)C1—N1—C8—N1i170.4 (2)
N1—C1—C2—C7147.9 (3)C9—N1—C8—C13153.2 (3)
C7—C2—C3—O1177.8 (3)C1—N1—C8—C1372.0 (4)
C1—C2—C3—O12.6 (5)C9—N1—C8—C1280.9 (3)
C7—C2—C3—C40.1 (5)C1—N1—C8—C1253.8 (4)
C1—C2—C3—C4175.3 (3)C1—N1—C9—C1023.7 (5)
O1—C3—C4—C5177.4 (3)C8—N1—C9—C10158.1 (4)
C2—C3—C4—C50.6 (5)C1—N1—C9—C9i157.9 (2)
C3—C4—C5—C60.3 (5)C8—N1—C9—C9i23.4 (2)
C4—C5—C6—C70.4 (6)C9i—C9—C10—C110.4 (4)
C5—C6—C7—C20.9 (6)N1—C9—C10—C11177.9 (3)
C3—C2—C7—C60.6 (5)C9—C10—C11—C11i0.4 (4)
Symmetry code: (i) x, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N10.821.982.708 (4)147
C4—H4···Cg1ii0.932.713.51 (2)144
Symmetry code: (ii) x+1/2, y+1, z1/2.

Experimental details

Crystal data
Chemical formulaC23H24N2O2
Mr360.44
Crystal system, space groupOrthorhombic, Pmn21
Temperature (K)298
a, b, c (Å)19.137 (2), 8.0716 (15), 6.1464 (13)
V3)949.4 (3)
Z2
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.21 × 0.17 × 0.16
Data collection
DiffractometerSiemens SMART 1000 CCD area-detector
Absorption correctionMulti-scan
SADABS (Sheldrick, 1996)
Tmin, Tmax0.98, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections
4535, 934, 810
Rint0.032
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.118, 1.19
No. of reflections934
No. of parameters128
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.11, 0.19

Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SHELXS97 (Sheldrick, 1997a), SHELXL97 (Sheldrick, 1997a), SHELXTL (Sheldrick, 1997b).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N10.821.982.708 (4)147.0
C4—H4···Cg1i0.932.713.51 (2)143.5
Symmetry code: (i) x+1/2, y+1, z1/2.
 

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