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

Abstract

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.

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,

• a = 6.938 (4) Å

• b = 14.694 (8) Å

• c = 10.379 (6) Å

• β = 108.598 (9)°

• V = 1002.8 (10) ų

• 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[F ² > 2σ(F ²)] = 0.045

• wR(F ²) = 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

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.

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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) ; (ii) .

supplementary crystallographic information

1. Comment

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).

2. Experimental

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%.

3. Refinement

H atoms on N1 and N2 atoms were positioned geometrically and allowed to ride on their parent atoms with N—H = 0.90 or 0.96 Å. H atoms of the methyl groups were positioned geometrically (C—H = 0.96 Å) and allowed to ride on their parent atoms with U_iso(H) = 1.5 times U_eq(C). All the other H atoms were positioned geometrically(C—H = 0.93 Å) and allowed to ride on their parent atoms with U_iso(H) = 1.2 times U_eq(C).

Figures

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.

Crystal data

C9H11N2+·NO3−	F(000) = 440
Mr = 209.21	Dx = 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

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

Refinement

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(Fo2) + (0.0764P)2 + 0.1519P] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max < 0.001
1973 reflections	Δρmax = 0.18 e Å−3
145 parameters	Δρmin = −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)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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)

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)

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.