(1H-Benzimidazol-1-yl)methanol

Rivera, A.; Maldonado, M.; Ríos-Motta, J.; Fejfarová, K.; Dušek, M.

doi:10.1107/S1600536812004114

organic compounds

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ISSN: 2056-9890

Volume 68| Part 3| March 2012| Page o615

doi:10.1107/S1600536812004114

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(1H-Benzimidazol-1-yl)methanol

Augusto Rivera,^a ^* Mauricio Maldonado,^a Jaime Ríos-Motta,^a Karla Fejfarová ^b and Michal Dušek ^b

^aDepartamento de Química, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá, Colombia, and ^bInstitute of Physics ASCR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic
^*Correspondence e-mail: ariverau@unal.edu.co

(Received 16 January 2012; accepted 31 January 2012; online 4 February 2012)

In the title compound, C₈H₈N₂O, the N—CH₂ and CH₂—O bond lengths can be correlated to the manifestation of an anomeric effect in the N—CH₂—O moiety. In the crystal, intermolecular O—H⋯N hydrogen bonds link the molecules into zigzag chains, with graph-set motif C(6), parallel to [001]. These chains are further linked into sheets by weak nonclassical C—H⋯O hydrogen bonds.

Related literature

For a related structure, see: Shi et al. (2011 ). For bond-length data, see: Allen et al. (1987 ). For chemical background on the synthesis and uses of the title compound, see: Milata et al. (2001 ). For graph-set analysis, see: Bernstein et al. (1995 ).

Experimental

Crystal data

C₈H₈N₂O
M_r = 148.2
Monoclinic, P 2₁ /c
a = 13.3181 (10) Å
b = 4.2677 (3) Å
c = 12.4795 (10) Å
β = 95.143 (6)°
V = 706.45 (9) Å³
Z = 4
Cu Kα radiation
μ = 0.78 mm⁻¹
T = 120 K
0.41 × 0.30 × 0.23 mm

Data collection

Agilent Xcalibur diffractometer with an Atlas (Gemini Ultra Cu) detector
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ) T_min = 0.744, T_max = 1
4736 measured reflections
1248 independent reflections
1086 reflections with I > 3σ(I)
R_int = 0.032

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.105
S = 1.78
1248 reflections
103 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1o⋯N2ⁱ	0.894 (19)	1.85 (2)	2.7355 (16)	173.8 (17)
C1—H1⋯O1ⁱⁱ	0.96	2.41	3.2887 (17)	152
Symmetry codes: (i) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (ii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: CrysAlis PRO (Agilent, 2010); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR2002 (Burla et al., 2003 ); program(s) used to refine structure: JANA2006 (Petříček et al., 2006 ); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ); software used to prepare material for publication: JANA2006.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812004114/bx2398sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812004114/bx2398Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812004114/bx2398Isup3.cml

checkCIF report

Comment top

Benzimidazole derivatives are compounds that have received much attention because of their applications in several areas. Although the synthesis of title compound had been reported in the literature (Milata et al., 2001), we have developed an alternative route to prepare this compound starting from the synthetically available benzoaminal 6H,13H-5:12,7:14-dimethanedibenzo[d,i][1,3,6,8]tetraazecine (DMDBTA).

In the title compound, C₈H₈N₂O, (Fig.1) the benzimidazole ring is essentially planar, with a maximum deviation for N1 of 0.0089 (12)Å from the least-squares plane defined by the nine constituent atoms. The sum of bond angles around this nitrogen atom was 359.90 (11)°, which is consistent with the planarization of the heterocyclic ring. The distances within the benzimidazole ring of the title compound are very similar to those found in bis(1H-benzimidazol-1-yl)methane monohydrate (Shi et al., 2011). However, the observed N—CH₂ bond length [N1—C8, 1.4638 (17) Å] is longer in relation to the mentioned mean value observed in related structure [N—CH₂, 1.452 (4) Å] (Shi et al., 2011). Moreover, the CH₂—O bonds in the residue tend to be shorter than the normal values by 0.033 Å (Allen et al., 1987). This fact can be correlated to the manifestation of an anomeric effect in N—CH₂—O moiety, but it operates in the opposite direction.In the crystal structure, intermolecular O—H···N hydrogen bonds link the molecules into zigzag chains with graph-set motif C(6) parallel to [001], (Bernstein et al., 1995) (Fig. 2). These chains are further linked into sheet by weak non-classical C—H···O hydrogen bonds between H atom of the benzimidazole ring and the O atom of a neighbouring molecule.

Related literature top

For a related structure, see: Shi et al. (2011). For bond-length data, see: Allen et al. (1987). For chemical background on the synthesis and uses of the title compound, see: Milata et al. (2001). For graph-set analysis, see: Bernstein et al. (1995).

Experimental top

A solution of 6H,13H-5:12,7:14-dimethanedibenzo[d,i][1,3,6,8] tetraazecine (DMDBTA) (0.25 mmol) and p-nitrophenol (0.5 mmol) in propan-2-ol (15 ml) was placed in a round-bottomed flask equipped with a water-cooled condenser. The reaction mixture was heated at 347 K for 3 h. giving a white precipitate which was filtered off, and the mother liquor was then concentrated by a rotary evaporator to give an oil accompanied by precipitates, which was removed by filtration. Single crystal of the precipitate (title compound), suitable for X-ray crystallography, was grown by slow evaporation from water:propan-2-ol solution at room temperature after several days. Melting point 407 K.

The NMR spectra were acquired at room temperature on a Bruker AMX 400 Avance spectrometer. ¹H NMR (δ, 400 MHz, CDCl₃): 5.60, 6.78, 7.23, 7.29, 7.66, 8.28. ¹³C NMR (δ, 100 MHz, CDCl₃): 67.8, 111.4, 119.8, 122.3, 122.9, 133.7, 144.1, 144.8.

Computing details top

Data collection: CrysAlis PRO (Agilent, 2010); cell refinement: CrysAlis PRO (Agilent, 2010); data reduction: CrysAlis PRO (Agilent, 2010); program(s) used to solve structure: SIR2002 (Burla et al., 2003); program(s) used to refine structure: JANA2006 (Petříček et al., 2006); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: JANA2006 (Petříček et al., 2006).

Figures top

	Fig. 1. A view of the title molecule. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Packing of the molecules of the title compound view along the b axis. Dashed lines indicate the intermolecular hydrogen bonds.

(1H-Benzimidazol-1-yl)methanol top

Crystal data top

C₈H₈N₂O	F(000) = 312
M_r = 148.2	D_x = 1.393 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.5418 Å
Hall symbol: -P 2ybc	Cell parameters from 2690 reflections
a = 13.3181 (10) Å	θ = 3.3–66.8°
b = 4.2677 (3) Å	µ = 0.78 mm⁻¹
c = 12.4795 (10) Å	T = 120 K
β = 95.143 (6)°	Block, colourless
V = 706.45 (9) Å³	0.41 × 0.30 × 0.23 mm
Z = 4

Data collection top

Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector	1248 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source	1086 reflections with I > 3σ(I)
Mirror monochromator	R_int = 0.032
Detector resolution: 10.3784 pixels mm^-1	θ_max = 67.1°, θ_min = 3.3°
rotation method data acquisition using ω scans	h = −15→15
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)	k = −5→5
T_min = 0.744, T_max = 1	l = −14→14
4736 measured reflections

Refinement top

Refinement on F²	29 constraints
R[F² > 2σ(F²)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.105	Weighting scheme based on measured s.u.'s w = 1/[σ²(I) + 0.0016I²]
S = 1.78	(Δ/σ)_max = 0.002
1248 reflections	Δρ_max = 0.18 e Å⁻³
103 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints

Crystal data top

C₈H₈N₂O	V = 706.45 (9) Å³
M_r = 148.2	Z = 4
Monoclinic, P2₁/c	Cu Kα radiation
a = 13.3181 (10) Å	µ = 0.78 mm⁻¹
b = 4.2677 (3) Å	T = 120 K
c = 12.4795 (10) Å	0.41 × 0.30 × 0.23 mm
β = 95.143 (6)°

Data collection top

Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector	1248 independent reflections
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)	1086 reflections with I > 3σ(I)
T_min = 0.744, T_max = 1	R_int = 0.032
4736 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.105	H atoms treated by a mixture of independent and constrained refinement
S = 1.78	Δρ_max = 0.18 e Å⁻³
1248 reflections	Δρ_min = −0.22 e Å⁻³
103 parameters

Special details top

Experimental. CrysAlisPro (Agilent , 2010) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Refinement. The refinement was carried out against all reflections. The conventional R-factor is always based on F. The goodness of fit as well as the weighted R-factor are based on F and F² for refinement carried out on F and F², respectively. The threshold expression is used only for calculating R-factors etc. and it is not relevant to the choice of reflections for refinement.

The program used for refinement, Jana2006, uses the weighting scheme based on the experimental expectations, see _refine_ls_weighting_details, that does not force S to be one. Therefore the values of S are usually larger than the ones from the SHELX program.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.93101 (7)	0.3994 (2)	0.86004 (8)	0.0311 (3)
N1	0.83140 (8)	0.4446 (3)	0.69371 (9)	0.0247 (3)
N2	0.81868 (9)	0.2744 (3)	0.52326 (9)	0.0291 (4)
C1	0.86934 (10)	0.4481 (3)	0.59626 (11)	0.0277 (4)
C2	0.74835 (9)	0.2487 (3)	0.68347 (10)	0.0243 (4)
C3	0.68095 (10)	0.1551 (3)	0.75625 (11)	0.0268 (4)
C4	0.60448 (10)	−0.0444 (3)	0.71773 (11)	0.0289 (4)
C5	0.59534 (10)	−0.1479 (3)	0.61064 (12)	0.0308 (4)
C6	0.66286 (10)	−0.0572 (3)	0.53902 (11)	0.0296 (4)
C7	0.74087 (9)	0.1443 (3)	0.57631 (10)	0.0255 (4)
C8	0.87514 (9)	0.6034 (3)	0.79091 (10)	0.0271 (4)
H1	0.927903	0.566907	0.582034	0.0333*
H3	0.687318	0.225735	0.829577	0.0322*
H4	0.556364	−0.114071	0.765431	0.0347*
H5	0.540778	−0.285048	0.586627	0.037*
H6	0.656443	−0.13025	0.465963	0.0356*
H8a	0.91753	0.77186	0.771157	0.0325*
H8b	0.822274	0.695733	0.827835	0.0325*
H1o	0.8905 (14)	0.341 (4)	0.9098 (15)	0.0373*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0258 (5)	0.0439 (6)	0.0239 (5)	0.0053 (4)	0.0035 (4)	0.0043 (4)
N1	0.0236 (6)	0.0287 (6)	0.0218 (6)	−0.0009 (4)	0.0024 (4)	−0.0001 (4)
N2	0.0285 (6)	0.0358 (7)	0.0235 (6)	−0.0006 (4)	0.0053 (4)	−0.0005 (5)
C1	0.0253 (7)	0.0338 (8)	0.0248 (7)	−0.0016 (5)	0.0056 (5)	0.0012 (5)
C2	0.0235 (6)	0.0249 (7)	0.0244 (7)	0.0038 (5)	0.0017 (5)	0.0013 (5)
C3	0.0272 (7)	0.0287 (7)	0.0250 (7)	0.0048 (5)	0.0052 (5)	0.0014 (5)
C4	0.0252 (7)	0.0297 (7)	0.0327 (8)	0.0028 (5)	0.0070 (6)	0.0055 (5)
C5	0.0261 (7)	0.0300 (7)	0.0355 (8)	−0.0017 (5)	−0.0014 (6)	0.0024 (6)
C6	0.0323 (7)	0.0305 (7)	0.0255 (7)	0.0005 (5)	−0.0008 (6)	−0.0002 (5)
C7	0.0254 (7)	0.0267 (7)	0.0243 (7)	0.0030 (5)	0.0029 (5)	0.0008 (5)
C8	0.0268 (7)	0.0309 (7)	0.0234 (7)	−0.0002 (5)	0.0015 (5)	−0.0010 (5)

Geometric parameters (Å, º) top

O1—C8	1.3932 (16)	C3—C4	1.3804 (18)
O1—H1o	0.894 (19)	C3—H3	0.96
N1—C1	1.3581 (18)	C4—C5	1.402 (2)
N1—C2	1.3834 (16)	C4—H4	0.96
N1—C8	1.4638 (17)	C5—C6	1.379 (2)
N2—C1	1.3133 (17)	C5—H5	0.96
N2—C7	1.3941 (18)	C6—C7	1.3961 (18)
C1—H1	0.96	C6—H6	0.96
C2—C3	1.3916 (19)	C8—H8a	0.96
C2—C7	1.4045 (18)	C8—H8b	0.96

C8—O1—H1o	106.4 (11)	C5—C4—H4	119.1913
C1—N1—C2	106.41 (11)	C4—C5—C6	121.57 (12)
C1—N1—C8	125.77 (11)	C4—C5—H5	119.2139
C2—N1—C8	127.72 (11)	C6—C5—H5	119.2142
C1—N2—C7	104.65 (11)	C5—C6—C7	117.76 (13)
N1—C1—N2	113.94 (12)	C5—C6—H6	121.1194
N1—C1—H1	123.0293	C7—C6—H6	121.1187
N2—C1—H1	123.0296	N2—C7—C2	109.49 (11)
N1—C2—C3	132.10 (12)	N2—C7—C6	130.52 (12)
N1—C2—C7	105.52 (11)	C2—C7—C6	119.99 (12)
C3—C2—C7	122.38 (11)	O1—C8—N1	112.01 (11)
C2—C3—C4	116.66 (12)	O1—C8—H8a	109.4718
C2—C3—H3	121.6681	O1—C8—H8b	109.4708
C4—C3—H3	121.6689	N1—C8—H8a	109.4717
C3—C4—C5	121.62 (13)	N1—C8—H8b	109.4709
C3—C4—H4	119.1906	H8a—C8—H8b	106.8062

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1o···N2ⁱ	0.894 (19)	1.85 (2)	2.7355 (16)	173.8 (17)
C1—H1···O1ⁱⁱ	0.96	2.41	3.2887 (17)	152

Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x+2, y+1/2, −z+3/2.

Experimental details

Crystal data
Chemical formula	C₈H₈N₂O
M_r	148.2
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	120
a, b, c (Å)	13.3181 (10), 4.2677 (3), 12.4795 (10)
β (°)	95.143 (6)
V (Å³)	706.45 (9)
Z	4
Radiation type	Cu Kα
µ (mm⁻¹)	0.78
Crystal size (mm)	0.41 × 0.30 × 0.23

Data collection
Diffractometer	Agilent Xcalibur diffractometer with an Atlas (Gemini ultra Cu) detector
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2010)
T_min, T_max	0.744, 1
No. of measured, independent and observed [I > 3σ(I)] reflections	4736, 1248, 1086
R_int	0.032
(sin θ/λ)_max (Å⁻¹)	0.597

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.105, 1.78
No. of reflections	1248
No. of parameters	103
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.22

Computer programs: CrysAlis PRO (Agilent, 2010), SIR2002 (Burla et al., 2003), JANA2006 (Petříček et al., 2006), DIAMOND (Brandenburg & Putz, 2005).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1o···N2ⁱ	0.894 (19)	1.85 (2)	2.7355 (16)	173.8 (17)
C1—H1···O1ⁱⁱ	0.96	2.41	3.2887 (17)	151.49

Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x+2, y+1/2, −z+3/2.

Acknowledgements

We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de la Universidad Nacional de Colombia, for financial support of this work, as well as the institutional research plan No. AVOZ10100521 of the Institute of Physics and the Praemium Academiae project of the Academy of Sciences of the Czech Republic.

References

Agilent (2010). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England. Google Scholar
Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. CrossRef Web of Science Google Scholar
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact, Bonn, Germany. Google Scholar
Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103. CrossRef IUCr Journals Google Scholar
Milata, V., Kada, R., Zalibera, Ľ. & Belicová, A. (2001). Boll. Chim. Farm. 140, 215–220. PubMed CAS Google Scholar
Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006. Institute of Physics, Prague, Czech Republic. Google Scholar
Shi, T., Jin, S., Zhu, J., Liu, Y. J. & Shi, C. C. (2011). Acta Cryst. E67, o2943. Web of Science CSD CrossRef IUCr Journals Google Scholar