5,6-Dimethyl-1H-benzimidazol-3-ium nitrate

Liu, B.-C.; Zhu, S.-J.; Liu, F.-Q.

doi:10.1107/S1600536813027578

organic compounds

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ISSN: 2056-9890

Volume 69| Part 11| November 2013| Page o1645

doi:10.1107/S1600536813027578

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5,6-Dimethyl-1H-benzimidazol-3-ium nitrate

Bao-Cheng Liu,^a Shou-Jin Zhu ^a and Fa-Qian Liu ^a ^*

^aKey Laboratory of Advanced Materials, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
^*Correspondence e-mail: qdplastics@163.com

(Received 22 September 2013; accepted 9 October 2013; online 16 October 2013)

The title salt, C₉H₁₁N₂⁺·NO₃⁻, features a planar cation (r.m.s. for 11 non-H atoms = 0.016 Å). In the crystal, N—H⋯O hydrogen bonds link nitrate and benzimidazole ions into a three-dimensional network.

CCDC reference: 965529

Related literature

For background to benzimidazole, see: Roderick et al. (1972 ). For related crystal structures, see: Lee & Scheidt (1986 ), Liu (2012 ), Cui et al. (2009 ).

Experimental

Crystal data

C₉H₁₁N₂⁺·NO₃⁻
M_r = 209.21
Monoclinic, P 2₁ /c
a = 6.938 (4) Å
b = 14.694 (8) Å
c = 10.379 (6) Å
β = 108.598 (9)°
V = 1002.8 (10) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 296 K
0.29 × 0.27 × 0.22 mm

Data collection

Rigaku R-AXIS Spider diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi 1995 ) T_min = 0.970, T_max = 0.977
5401 measured reflections
1973 independent reflections
1617 reflections with I > 2σ(I)
R_int = 0.028

Refinement

R[F² > 2σ(F²)] = 0.045
wR(F²) = 0.136
S = 1.05
1973 reflections
145 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯O1ⁱ	0.96 (3)	2.31 (3)	3.043 (3)	133.0 (15)
N2—H2⋯O3ⁱ	0.96 (3)	1.86 (3)	2.797 (3)	165 (2)
N1—H1⋯O1ⁱⁱ	0.90 (3)	2.60 (2)	3.191 (3)	123.8 (17)
N1—H1⋯O2ⁱⁱ	0.90 (3)	1.89 (2)	2.797 (3)	178 (2)
Symmetry codes: (i) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) x-1, y, z-1.

Data collection: RAPID-AUTO (Rigaku, 2004 ); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

CCDC reference: 965529

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536813027578/hg5349sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813027578/hg5349Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813027578/hg5349Isup3.cdx

Supporting information file. DOI: 10.1107/S1600536813027578/hg5349Isup4.cml

checkCIF report

Comment top

Benzimidazole and its derivatives have attracted increased interest, not only because of their biological activity, but their abilities to bind to different metal ions (Roderick et al., 1972). In this paper, we describe the synthesis and structure of the title compound C₉H₁₁N₃O₃. In the title compound the molecules are linked by N—H···O hydrogen bonds between nitrate and benzimidazole ions into a three-dimensional network structure. Some 5,6-dimethylbenzimidazole derivatives with similar structures have been reported, which include 5.6-Dimethylbenzimidazole (Lee & Scheidt, 1986), 5,6-dimethyl-lH-benzo[d]imidazol-3-ium 2-(4-chlorophenoxy)acetate (Liu, 2012),and Bis(5,6-dicarboxybenzimidazolium) sulfate monohydrate (Cui et al., 2009).

Related literature top

For background to benzimidazole, see: Roderick et al. (1972). For related crystal structures, see: Lee & Scheidt (1986), Liu (2012), Cui et al. (2009).

Experimental top

A mixture of 5,6-Dimethylbenzimidazole (2.86 mg, 0.02 mmol) and Co(NO₃)₂.6H₂O (5.82 mg, 0.02 mmol) was added to H₂O (20 ml). The mixture was refluxed for half an hour then filtered. The resulting solution was allowed to stand at room temperature to give yellow block crystals suitable for structural determination after 3 weeks. Analysis, calculated for C₉H₁₁N₃O₃: C 51.67, H 5.30, N 20.09%; Found: C 51.61, H 5.25, N 20.19%.

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2004); cell refinement: RAPID-AUTO (Rigaku, 2004); data reduction: RAPID-AUTO (Rigaku, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 2. The crystal packing diagram viewed down the a axis.

5,6-Dimethyl-1H-benzimidazol-3-ium nitrate top

Crystal data top

C₉H₁₁N₂⁺·NO₃⁻	F(000) = 440
M_r = 209.21	D_x = 1.386 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 3271 reflections
a = 6.938 (4) Å	θ = 2.5–26.6°
b = 14.694 (8) Å	µ = 0.11 mm⁻¹
c = 10.379 (6) Å	T = 296 K
β = 108.598 (9)°	Block, yellow
V = 1002.8 (10) Å³	0.29 × 0.27 × 0.22 mm
Z = 4

Data collection top

Rigaku R-AXIS Spider diffractometer	1617 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.028
Graphite monochromator	θ_max = 26.0°, θ_min = 2.5°
ω scans	h = −8→8
Absorption correction: multi-scan (ABSCOR; Higashi 1995)	k = −17→18
T_min = 0.970, T_max = 0.977	l = −8→12
5401 measured reflections	13 standard reflections every 0 reflections
1973 independent reflections	intensity decay: none

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.045	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.136	w = 1/[σ²(F_o²) + (0.0764P)² + 0.1519P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
1973 reflections	Δρ_max = 0.18 e Å⁻³
145 parameters	Δρ_min = −0.16 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.102 (10)

Crystal data top

C₉H₁₁N₂⁺·NO₃⁻	V = 1002.8 (10) Å³
M_r = 209.21	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.938 (4) Å	µ = 0.11 mm⁻¹
b = 14.694 (8) Å	T = 296 K
c = 10.379 (6) Å	0.29 × 0.27 × 0.22 mm
β = 108.598 (9)°

Data collection top

Rigaku R-AXIS Spider diffractometer	1617 reflections with I > 2σ(I)
Absorption correction: multi-scan (ABSCOR; Higashi 1995)	R_int = 0.028
T_min = 0.970, T_max = 0.977	13 standard reflections every 0 reflections
5401 measured reflections	intensity decay: none
1973 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.045	0 restraints
wR(F²) = 0.136	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	Δρ_max = 0.18 e Å⁻³
1973 reflections	Δρ_min = −0.16 e Å⁻³
145 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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

	x	y	z	U_iso*/U_eq
C6	0.3017 (3)	0.52774 (14)	0.13819 (18)	0.0638 (5)
H6A	0.3096	0.5767	0.1965	0.077*
C3	0.2734 (3)	0.38091 (11)	−0.03709 (17)	0.0545 (4)
H3A	0.2625	0.3319	−0.0956	0.065*
N3	0.9477 (2)	0.33163 (9)	0.55623 (14)	0.0615 (4)
C4	0.2174 (2)	0.46728 (10)	−0.08774 (14)	0.0451 (4)
C1	0.4099 (4)	0.27501 (17)	0.1557 (2)	0.0936 (8)
H1A	0.3917	0.2333	0.0816	0.140*
H1B	0.3287	0.2558	0.2102	0.140*
H1C	0.5506	0.2761	0.2104	0.140*
C2	0.3452 (3)	0.36885 (13)	0.10052 (19)	0.0613 (5)
C8	0.4308 (4)	0.4293 (2)	0.3399 (2)	0.1049 (9)
H8A	0.4287	0.4865	0.3839	0.157*
H8B	0.5670	0.4058	0.3678	0.157*
H8C	0.3432	0.3870	0.3647	0.157*
C7	0.3576 (3)	0.44249 (15)	0.18821 (18)	0.0645 (5)
C5	0.2327 (2)	0.53977 (10)	−0.00159 (17)	0.0493 (4)
N2	0.1683 (2)	0.61491 (10)	−0.08221 (17)	0.0609 (4)
C9	0.1169 (3)	0.58998 (12)	−0.20846 (19)	0.0602 (5)
H9A	0.0678	0.6289	−0.2824	0.072*
N1	0.1439 (2)	0.50169 (10)	−0.21736 (13)	0.0519 (4)
O1	0.9388 (3)	0.31136 (10)	0.66814 (13)	0.0858 (5)
O2	1.0253 (3)	0.40438 (9)	0.53833 (14)	0.0857 (5)
O3	0.8828 (3)	0.27846 (9)	0.45932 (13)	0.0829 (5)
H1	0.108 (3)	0.4713 (15)	−0.297 (2)	0.082 (7)*
H2	0.156 (4)	0.6760 (18)	−0.053 (2)	0.097 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C6	0.0503 (9)	0.0868 (13)	0.0550 (10)	−0.0109 (9)	0.0176 (7)	−0.0263 (9)
C3	0.0557 (9)	0.0498 (9)	0.0583 (9)	−0.0039 (7)	0.0187 (7)	−0.0015 (7)
N3	0.0792 (10)	0.0433 (7)	0.0533 (8)	0.0036 (7)	0.0090 (7)	0.0041 (6)
C4	0.0417 (8)	0.0517 (8)	0.0436 (7)	−0.0050 (6)	0.0161 (6)	−0.0024 (6)
C1	0.0874 (16)	0.0854 (15)	0.0949 (16)	−0.0108 (12)	0.0109 (12)	0.0373 (12)
C2	0.0511 (9)	0.0712 (11)	0.0599 (10)	−0.0090 (8)	0.0155 (7)	0.0135 (8)
C8	0.0874 (16)	0.175 (3)	0.0469 (11)	−0.0045 (17)	0.0142 (10)	0.0111 (14)
C7	0.0479 (9)	0.0968 (14)	0.0472 (9)	−0.0077 (9)	0.0128 (7)	0.0073 (9)
C5	0.0413 (8)	0.0518 (9)	0.0559 (9)	−0.0042 (6)	0.0172 (6)	−0.0079 (7)
N2	0.0529 (8)	0.0488 (8)	0.0779 (10)	0.0012 (6)	0.0163 (7)	−0.0064 (7)
C9	0.0499 (9)	0.0584 (10)	0.0699 (11)	0.0022 (7)	0.0156 (8)	0.0138 (8)
N1	0.0517 (8)	0.0601 (9)	0.0442 (7)	−0.0023 (6)	0.0157 (6)	−0.0004 (6)
O1	0.1216 (13)	0.0780 (9)	0.0593 (8)	−0.0232 (8)	0.0309 (8)	−0.0002 (7)
O2	0.1434 (14)	0.0470 (7)	0.0653 (9)	−0.0202 (7)	0.0315 (9)	0.0006 (6)
O3	0.1287 (13)	0.0498 (7)	0.0549 (7)	−0.0080 (7)	0.0078 (7)	−0.0012 (6)

Geometric parameters (Å, º) top

C6—C7	1.364 (3)	C1—H1B	0.9600
C6—C5	1.386 (3)	C1—H1C	0.9600
C6—H6A	0.9300	C2—C7	1.399 (3)
C3—C2	1.366 (3)	C8—C7	1.505 (3)
C3—C4	1.381 (2)	C8—H8A	0.9600
C3—H3A	0.9300	C8—H8B	0.9600
N3—O1	1.2197 (19)	C8—H8C	0.9600
N3—O2	1.237 (2)	C5—N2	1.371 (2)
N3—O3	1.2393 (19)	N2—C9	1.296 (2)
C4—C5	1.373 (2)	N2—H2	0.96 (3)
C4—N1	1.374 (2)	C9—N1	1.318 (2)
C1—C2	1.505 (3)	C9—H9A	0.9300
C1—H1A	0.9600	N1—H1	0.90 (2)

C7—C6—C5	118.47 (16)	C7—C8—H8A	109.5
C7—C6—H6A	120.8	C7—C8—H8B	109.5
C5—C6—H6A	120.8	H8A—C8—H8B	109.5
C2—C3—C4	118.80 (16)	C7—C8—H8C	109.5
C2—C3—H3A	120.6	H8A—C8—H8C	109.5
C4—C3—H3A	120.6	H8B—C8—H8C	109.5
O1—N3—O2	120.70 (15)	C6—C7—C2	120.78 (17)
O1—N3—O3	120.23 (15)	C6—C7—C8	118.5 (2)
O2—N3—O3	119.06 (15)	C2—C7—C8	120.7 (2)
C5—C4—N1	106.25 (15)	N2—C5—C4	106.54 (15)
C5—C4—C3	120.73 (15)	N2—C5—C6	132.67 (16)
N1—C4—C3	133.01 (14)	C4—C5—C6	120.79 (16)
C2—C1—H1A	109.5	C9—N2—C5	108.69 (15)
C2—C1—H1B	109.5	C9—N2—H2	124.2 (14)
H1A—C1—H1B	109.5	C5—N2—H2	127.1 (14)
C2—C1—H1C	109.5	N2—C9—N1	110.46 (16)
H1A—C1—H1C	109.5	N2—C9—H9A	124.8
H1B—C1—H1C	109.5	N1—C9—H9A	124.8
C3—C2—C7	120.41 (18)	C9—N1—C4	108.06 (14)
C3—C2—C1	118.79 (19)	C9—N1—H1	123.2 (14)
C7—C2—C1	120.80 (18)	C4—N1—H1	128.6 (14)

C2—C3—C4—C5	−0.2 (2)	C3—C4—C5—N2	179.37 (14)
C2—C3—C4—N1	179.02 (15)	N1—C4—C5—C6	179.55 (13)
C4—C3—C2—C7	1.3 (2)	C3—C4—C5—C6	−1.0 (2)
C4—C3—C2—C1	−178.89 (16)	C7—C6—C5—N2	−179.34 (16)
C5—C6—C7—C2	−0.1 (3)	C7—C6—C5—C4	1.2 (2)
C5—C6—C7—C8	−179.48 (16)	C4—C5—N2—C9	0.16 (18)
C3—C2—C7—C6	−1.1 (3)	C6—C5—N2—C9	−179.36 (17)
C1—C2—C7—C6	179.06 (18)	C5—N2—C9—N1	−0.22 (19)
C3—C2—C7—C8	178.23 (17)	N2—C9—N1—C4	0.19 (18)
C1—C2—C7—C8	−1.6 (3)	C5—C4—N1—C9	−0.09 (16)
N1—C4—C5—N2	−0.04 (16)	C3—C4—N1—C9	−179.40 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O1ⁱ	0.96 (3)	2.31 (3)	3.043 (3)	133.0 (15)
N2—H2···O3ⁱ	0.96 (3)	1.86 (3)	2.797 (3)	165 (2)
N1—H1···O1ⁱⁱ	0.90 (3)	2.60 (2)	3.191 (3)	123.8 (17)
N1—H1···O2ⁱⁱ	0.90 (3)	1.89 (2)	2.797 (3)	178 (2)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O1ⁱ	0.96 (3)	2.31 (3)	3.043 (3)	133.0 (15)
N2—H2···O3ⁱ	0.96 (3)	1.86 (3)	2.797 (3)	165 (2)
N1—H1···O1ⁱⁱ	0.90 (3)	2.60 (2)	3.191 (3)	123.8 (17)
N1—H1···O2ⁱⁱ	0.90 (3)	1.89 (2)	2.797 (3)	178 (2)

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

Acknowledgements

This work was supported by the NSF of Shandong Province (No. 2009ZRA02071) and the Scientific Development Plan of Universities in Shandong Province (No. J09LB53)

References

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