organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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.

Related literature

For background to benzimidazole, see: Roderick et al. (1972[Roderick, W. R., Nordeen, C. W., Von Esch, A. M. & Appell, R. N. J. (1972). J. Med. Chem. 15, 655-658.]). For related crystal structures, see: Lee & Scheidt (1986[Lee, Y. J. & Scheidt, W. R. (1986). Acta Cryst. C42, 1652-1654.]), Liu (2012[Liu, H.-L. (2012). Z. Kristallogr. New Cryst. Struct. 227, 339-340.]), Cui et al. (2009[Cui, Y., Gao, Q., Zhang, C.-Y. & Xie, Y.-B. (2009). Acta Cryst. E65, o1335.]).

[Scheme 1]

Experimental

Crystal data
  • C9H11N2+·NO3

  • Mr = 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.970, Tmax = 0.977

  • 5401 measured reflections

  • 1973 independent reflections

  • 1617 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.16 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku (2004). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


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%.

Refinement top

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 Uiso(H) = 1.5 times Ueq(C). All the other H atoms were positioned geometrically(C—H = 0.93 Å) and allowed to ride on their parent atoms with Uiso(H) = 1.2 times Ueq(C).

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
[Figure 1] Fig. 1. The structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
[Figure 2] Fig. 2. The crystal packing diagram viewed down the a axis.
5,6-Dimethyl-1H-benzimidazol-3-ium nitrate top
Crystal data top
C9H11N2+·NO3F(000) = 440
Mr = 209.21Dx = 1.386 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3271 reflections
a = 6.938 (4) Åθ = 2.5–26.6°
b = 14.694 (8) ŵ = 0.11 mm1
c = 10.379 (6) ÅT = 296 K
β = 108.598 (9)°Block, yellow
V = 1002.8 (10) Å30.29 × 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 tubeRint = 0.028
Graphite monochromatorθmax = 26.0°, θmin = 2.5°
ω scansh = 88
Absorption correction: multi-scan
(ABSCOR; Higashi 1995)
k = 1718
Tmin = 0.970, Tmax = 0.977l = 812
5401 measured reflections13 standard reflections every 0 reflections
1973 independent reflections intensity decay: none
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.045H 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 reflectionsΔρmax = 0.18 e Å3
145 parametersΔρmin = 0.16 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.102 (10)
Crystal data top
C9H11N2+·NO3V = 1002.8 (10) Å3
Mr = 209.21Z = 4
Monoclinic, P21/cMo Kα radiation
a = 6.938 (4) ŵ = 0.11 mm1
b = 14.694 (8) ÅT = 296 K
c = 10.379 (6) Å0.29 × 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)
Rint = 0.028
Tmin = 0.970, Tmax = 0.97713 standard reflections every 0 reflections
5401 measured reflections intensity decay: none
1973 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0450 restraints
wR(F2) = 0.136H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.18 e Å3
1973 reflectionsΔρmin = 0.16 e Å3
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
xyzUiso*/Ueq
C60.3017 (3)0.52774 (14)0.13819 (18)0.0638 (5)
H6A0.30960.57670.19650.077*
C30.2734 (3)0.38091 (11)0.03709 (17)0.0545 (4)
H3A0.26250.33190.09560.065*
N30.9477 (2)0.33163 (9)0.55623 (14)0.0615 (4)
C40.2174 (2)0.46728 (10)0.08774 (14)0.0451 (4)
C10.4099 (4)0.27501 (17)0.1557 (2)0.0936 (8)
H1A0.39170.23330.08160.140*
H1B0.32870.25580.21020.140*
H1C0.55060.27610.21040.140*
C20.3452 (3)0.36885 (13)0.10052 (19)0.0613 (5)
C80.4308 (4)0.4293 (2)0.3399 (2)0.1049 (9)
H8A0.42870.48650.38390.157*
H8B0.56700.40580.36780.157*
H8C0.34320.38700.36470.157*
C70.3576 (3)0.44249 (15)0.18821 (18)0.0645 (5)
C50.2327 (2)0.53977 (10)0.00159 (17)0.0493 (4)
N20.1683 (2)0.61491 (10)0.08221 (17)0.0609 (4)
C90.1169 (3)0.58998 (12)0.20846 (19)0.0602 (5)
H9A0.06780.62890.28240.072*
N10.1439 (2)0.50169 (10)0.21736 (13)0.0519 (4)
O10.9388 (3)0.31136 (10)0.66814 (13)0.0858 (5)
O21.0253 (3)0.40438 (9)0.53833 (14)0.0857 (5)
O30.8828 (3)0.27846 (9)0.45932 (13)0.0829 (5)
H10.108 (3)0.4713 (15)0.297 (2)0.082 (7)*
H20.156 (4)0.6760 (18)0.053 (2)0.097 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C60.0503 (9)0.0868 (13)0.0550 (10)0.0109 (9)0.0176 (7)0.0263 (9)
C30.0557 (9)0.0498 (9)0.0583 (9)0.0039 (7)0.0187 (7)0.0015 (7)
N30.0792 (10)0.0433 (7)0.0533 (8)0.0036 (7)0.0090 (7)0.0041 (6)
C40.0417 (8)0.0517 (8)0.0436 (7)0.0050 (6)0.0161 (6)0.0024 (6)
C10.0874 (16)0.0854 (15)0.0949 (16)0.0108 (12)0.0109 (12)0.0373 (12)
C20.0511 (9)0.0712 (11)0.0599 (10)0.0090 (8)0.0155 (7)0.0135 (8)
C80.0874 (16)0.175 (3)0.0469 (11)0.0045 (17)0.0142 (10)0.0111 (14)
C70.0479 (9)0.0968 (14)0.0472 (9)0.0077 (9)0.0128 (7)0.0073 (9)
C50.0413 (8)0.0518 (9)0.0559 (9)0.0042 (6)0.0172 (6)0.0079 (7)
N20.0529 (8)0.0488 (8)0.0779 (10)0.0012 (6)0.0163 (7)0.0064 (7)
C90.0499 (9)0.0584 (10)0.0699 (11)0.0022 (7)0.0156 (8)0.0138 (8)
N10.0517 (8)0.0601 (9)0.0442 (7)0.0023 (6)0.0157 (6)0.0004 (6)
O10.1216 (13)0.0780 (9)0.0593 (8)0.0232 (8)0.0309 (8)0.0002 (7)
O20.1434 (14)0.0470 (7)0.0653 (9)0.0202 (7)0.0315 (9)0.0006 (6)
O30.1287 (13)0.0498 (7)0.0549 (7)0.0080 (7)0.0078 (7)0.0012 (6)
Geometric parameters (Å, º) top
C6—C71.364 (3)C1—H1B0.9600
C6—C51.386 (3)C1—H1C0.9600
C6—H6A0.9300C2—C71.399 (3)
C3—C21.366 (3)C8—C71.505 (3)
C3—C41.381 (2)C8—H8A0.9600
C3—H3A0.9300C8—H8B0.9600
N3—O11.2197 (19)C8—H8C0.9600
N3—O21.237 (2)C5—N21.371 (2)
N3—O31.2393 (19)N2—C91.296 (2)
C4—C51.373 (2)N2—H20.96 (3)
C4—N11.374 (2)C9—N11.318 (2)
C1—C21.505 (3)C9—H9A0.9300
C1—H1A0.9600N1—H10.90 (2)
C7—C6—C5118.47 (16)C7—C8—H8A109.5
C7—C6—H6A120.8C7—C8—H8B109.5
C5—C6—H6A120.8H8A—C8—H8B109.5
C2—C3—C4118.80 (16)C7—C8—H8C109.5
C2—C3—H3A120.6H8A—C8—H8C109.5
C4—C3—H3A120.6H8B—C8—H8C109.5
O1—N3—O2120.70 (15)C6—C7—C2120.78 (17)
O1—N3—O3120.23 (15)C6—C7—C8118.5 (2)
O2—N3—O3119.06 (15)C2—C7—C8120.7 (2)
C5—C4—N1106.25 (15)N2—C5—C4106.54 (15)
C5—C4—C3120.73 (15)N2—C5—C6132.67 (16)
N1—C4—C3133.01 (14)C4—C5—C6120.79 (16)
C2—C1—H1A109.5C9—N2—C5108.69 (15)
C2—C1—H1B109.5C9—N2—H2124.2 (14)
H1A—C1—H1B109.5C5—N2—H2127.1 (14)
C2—C1—H1C109.5N2—C9—N1110.46 (16)
H1A—C1—H1C109.5N2—C9—H9A124.8
H1B—C1—H1C109.5N1—C9—H9A124.8
C3—C2—C7120.41 (18)C9—N1—C4108.06 (14)
C3—C2—C1118.79 (19)C9—N1—H1123.2 (14)
C7—C2—C1120.80 (18)C4—N1—H1128.6 (14)
C2—C3—C4—C50.2 (2)C3—C4—C5—N2179.37 (14)
C2—C3—C4—N1179.02 (15)N1—C4—C5—C6179.55 (13)
C4—C3—C2—C71.3 (2)C3—C4—C5—C61.0 (2)
C4—C3—C2—C1178.89 (16)C7—C6—C5—N2179.34 (16)
C5—C6—C7—C20.1 (3)C7—C6—C5—C41.2 (2)
C5—C6—C7—C8179.48 (16)C4—C5—N2—C90.16 (18)
C3—C2—C7—C61.1 (3)C6—C5—N2—C9179.36 (17)
C1—C2—C7—C6179.06 (18)C5—N2—C9—N10.22 (19)
C3—C2—C7—C8178.23 (17)N2—C9—N1—C40.19 (18)
C1—C2—C7—C81.6 (3)C5—C4—N1—C90.09 (16)
N1—C4—C5—N20.04 (16)C3—C4—N1—C9179.40 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O1i0.96 (3)2.31 (3)3.043 (3)133.0 (15)
N2—H2···O3i0.96 (3)1.86 (3)2.797 (3)165 (2)
N1—H1···O1ii0.90 (3)2.60 (2)3.191 (3)123.8 (17)
N1—H1···O2ii0.90 (3)1.89 (2)2.797 (3)178 (2)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x1, y, z1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O1i0.96 (3)2.31 (3)3.043 (3)133.0 (15)
N2—H2···O3i0.96 (3)1.86 (3)2.797 (3)165 (2)
N1—H1···O1ii0.90 (3)2.60 (2)3.191 (3)123.8 (17)
N1—H1···O2ii0.90 (3)1.89 (2)2.797 (3)178 (2)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x1, y, z1.
 

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

First citationCui, Y., Gao, Q., Zhang, C.-Y. & Xie, Y.-B. (2009). Acta Cryst. E65, o1335.  Web of Science CSD CrossRef IUCr Journals
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.
First citationLee, Y. J. & Scheidt, W. R. (1986). Acta Cryst. C42, 1652–1654.  CSD CrossRef CAS Web of Science IUCr Journals
First citationLiu, H.-L. (2012). Z. Kristallogr. New Cryst. Struct. 227, 339–340.  Web of Science CSD CrossRef CAS
First citationRigaku (2004). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.
First citationRoderick, W. R., Nordeen, C. W., Von Esch, A. M. & Appell, R. N. J. (1972). J. Med. Chem. 15, 655–658.  CrossRef CAS PubMed Web of Science
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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