Literature DB >> 24454088

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

Bao-Cheng Liu1, Shou-Jin Zhu1, Fa-Qian Liu1.   

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.

Entities:  

Year:  2013        PMID: 24454088      PMCID: PMC3884312          DOI: 10.1107/S1600536813027578

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


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

C9H11N2NO3 M = 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) 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[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 Δρmax = 0.18 e Å−3 Δρmin = −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. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813027578/hg5349sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813027578/hg5349Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813027578/hg5349Isup3.cdx Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813027578/hg5349Isup4.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
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
Rigaku R-AXIS Spider diffractometer1617 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.028
Graphite monochromatorθmax = 26.0°, θmin = 2.5°
ω scansh = −8→8
Absorption correction: multi-scan (ABSCOR; Higashi 1995)k = −17→18
Tmin = 0.970, Tmax = 0.977l = −8→12
5401 measured reflections13 standard reflections every 0 reflections
1973 independent reflections intensity decay: none
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) = 0.136w = 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)
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.
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)
H3A0.26250.3319−0.09560.065*
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)
H9A0.06780.6289−0.28240.072*
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)*
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)
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—C5−0.2 (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—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—C41.2 (2)
C5—C6—C7—C8−179.48 (16)C4—C5—N2—C90.16 (18)
C3—C2—C7—C6−1.1 (3)C6—C5—N2—C9−179.36 (17)
C1—C2—C7—C6179.06 (18)C5—N2—C9—N1−0.22 (19)
C3—C2—C7—C8178.23 (17)N2—C9—N1—C40.19 (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)
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)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯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) ; (ii) .

  3 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Bisbenzimidazoles. Potent inhibitors of rhinoviruses.

Authors:  W R Roderick; C W Nordeen; A M Von Esch; R N Appell
Journal:  J Med Chem       Date:  1972-06       Impact factor: 7.446

3.  Bis(5,6-dicarboxy-benzimidazolium) sulfate monohydrate.

Authors:  Yue Cui; Qian Gao; Chao-Yan Zhang; Ya-Bo Xie
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-05-20
  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.