1,3-Bis(2-hydroxy­benz­yl)-2,2-dimethyl-2,3-dihydro-1H-benzimidazole

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.

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

No syntax errors found



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

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S1. Comment

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

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).

S2. Experimental

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).

S3. Refinement

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 U_iso(H)= 1.5U_eq(C) for methyl H atoms, O—H = 0.82Å and U_iso(H)= 1.2U_eq(C) for hydroxy H atoms, C—H = 0.97Å and U_iso(H)= 1.2U_eq(C) for methylene H atoms, and C—H = 0.93Å and U_iso(H) = 1.2U_eq(C) for all other H atom.

Computing details

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

	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]
	Fig. 2. Packing diagram of (I), showing the formation of a [010] sheet of R4^4(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

Crystal data

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) Å^3	Block, yellow
Z = 2	0.21 × 0.17 × 0.16 mm

Data collection

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

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.118	H-atom parameters constrained
S = 1.19	w = 1/[σ^2(Fo^2) + (0.0649P)^2 + 0.1011P] where P = (Fo^2 + 2Fc^2)/3
934 reflections	(Δ/σ)max < 0.001
128 parameters	Δρmax = 0.11 e Å^−3
1 restraint	Δρmin = −0.19 e Å^−3

Special details

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 (Ų)

	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*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

N1—C9	1.420 (4)	C6—H6	0.9300
N1—C1	1.472 (4)	C7—H7	0.9300
N1—C8	1.505 (4)	C8—N1^i	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—C9^i	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—C11^i	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—N1^i	99.3 (3)
N1—C1—C2	113.3 (3)	N1—C8—C13	111.5 (3)
N1—C1—H1A	108.9	N1^i—C8—C13	111.5 (3)
C2—C1—H1A	108.9	N1—C8—C12	110.8 (2)
N1—C1—H1B	108.9	N1^i—C8—C12	110.8 (2)
C2—C1—H1B	108.9	C13—C8—C12	112.3 (4)
H1A—C1—H1B	107.7	C10—C9—C9^i	121.6 (2)
C3—C2—C7	117.7 (3)	C10—C9—N1	130.0 (3)
C3—C2—C1	122.3 (3)	C9^i—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)	C11^i—C11—C10	121.5 (2)
C5—C4—C3	120.5 (4)	C11^i—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—N1^i	35.7 (4)
N1—C1—C2—C3	−37.1 (4)	C1—N1—C8—N1^i	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—C9^i	−157.9 (2)
C3—C4—C5—C6	−0.3 (5)	C8—N1—C9—C9^i	−23.4 (2)
C4—C5—C6—C7	−0.4 (6)	C9^i—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—C11^i	0.4 (4)

Symmetry code: (i) −x, y, z.

Hydrogen-bond geometry (Å, º)

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···Cg1^ii	0.93	2.71	3.51 (2)	144

Symmetry code: (ii) −x+1/2, −y+1, z−1/2.