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ISSN: 2056-9890

2-(Pyridin-4-yl)-1H-benzimidazole

aDepartment of Chemistry, State University of New York-College at Geneseo, 1 College Circle, Geneseo, NY 14454, USA
*Correspondence e-mail: geiger@geneseo.edu

(Received 16 April 2013; accepted 7 May 2013; online 11 May 2013)

The title compound, C12H9N3, is an unhydrated analogue of the previously reported trihydrate. The mol­ecule is essentially planar, with a 3.62 (11)° angle between the pyridine and benzimidazole planes. In the crystal, N—H⋯N hydrogen bonds result in chains of mol­ecules parallel to [010], which are additionally linked by weak ππ stacking inter­actions [centroid–centroid distance = 3.7469 (17) Å], resulting in extended sheets of molecules parallel to (103).

Related literature

For the structure of the trihydrate of the title compound, see: Huang et al. (2004[Huang, X.-C., Zeng, M.-H. & Ng, S. W. (2004). Acta Cryst. E60, o939-o940.])

[Scheme 1]

Experimental

Crystal data
  • C12H9N3

  • Mr = 195.22

  • Monoclinic, P 21 /n

  • a = 6.0602 (14) Å

  • b = 11.610 (3) Å

  • c = 13.892 (4) Å

  • β = 101.838 (8)°

  • V = 956.6 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 200 K

  • 0.50 × 0.20 × 0.20 mm

Data collection
  • Bruker SMART X2S CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2010[Bruker (2010). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.53, Tmax = 0.98

  • 4809 measured reflections

  • 1699 independent reflections

  • 1125 reflections with I > 2σ(I)

  • Rint = 0.058

Refinement
  • R[F2 > 2σ(F2)] = 0.046

  • wR(F2) = 0.128

  • S = 0.96

  • 1699 reflections

  • 140 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.26 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯N3i 0.99 (2) 1.96 (2) 2.924 (2) 165 (2)
Symmetry code: (i) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2010[Bruker (2010). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2010[Bruker (2010). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; 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: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

Single crystals of the title compound were obtained by slow evaporation of an ethylacetate solution.

Figure 1 shows a perspective view of the title compound with the atom numbering scheme. The non-hydrogen atoms of the molecule are essentially planar with a r. m. s. deviation of 0.0308 Å. The maximum deviation is 0.0480 (18) Å for C12. The pyridine and benzimidazole planes exhibit a dihedral angle of 3.62 (11)°, which is similar to the value (2.8 (1)°) reported for the trihydrate analogue (Huang et al., 2004).

Hydrogen-bonding interactions involving the benzimidazole N—H and the pyridine result in chains of molecules parallel to [0 1 0]. Figure 2 shows a packing diagram with the hydrogen-bonded chains displayed. The trihydrate (Huang et al., 2004) hydrogen-bonding network is much more extensive, involving the three waters of hydration, the benzimidazole amine group and the pyridine. As seen in figure 2, pairs of molecules related by an inversion center exhibit π stacking. The spacing between the mean planes formed by the molecules is 3.43 Å. The shortest internuclear separation between related molecules is 3.460 (2) Å (N2···C7).

Related literature top

For the structure of the trihydrate of the title compound, see: Huang et al. (2004)

Experimental top

The title compound was prepared by stirring 0.373 g (3.45 mmole) o-phenylenediamine, 0.67 ml (7.1 mmole) 4-pyridinecarboxaldehyde, and 0.75 g NH4Cl in 25 ml CHCl3 for 5 days at room temperature. After removal of the solvent, the crude product mixture was extracted with water and ethylacetate and the solvent was removed from the organic phase. The resulting solid was passed through a short silica column using a 30:70 mixture of hexanes: ethyl acetate, yielding 0.442 g of solid that contained two components based on TLC analysis was obtained. The mixture was passed through a second silica column using 90:10 ethyl acetate: ethanol. The first component isolated was the title compound (0.380 g, 1.95 mmole, 56% yield). 1H NMR (400 MHz, DMSO-d6): δ, 7.27 (m, 2H), 7.64 (m, 2H), 8.09 (d, 2H), 8.75, (d, 2H). 13C NMR (DMSO-d6): δ, 120.89, 123.52, 137.77, 149.06, 150.67, 163.55.

Refinement top

All hydrogen atoms were observed in difference Fourier maps. The H atoms bonded to carbon were refined using a riding model with C—H = 0.95 Å and Uiso = 1.2Ueq(C). The coordinates and isotropic thermal parameters of the amine H atom were refined without constraints.

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Perspective view of the title compound. Thermal parameters are drawn at the 50% probability level.
[Figure 2] Fig. 2. Packing diagram down [1 0 0] displaying the H-bonding network.
2-(Pyridin-4-yl)-1H-benzimidazole top
Crystal data top
C12H9N3F(000) = 408
Mr = 195.22Dx = 1.356 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 6.0602 (14) ÅCell parameters from 1098 reflections
b = 11.610 (3) Åθ = 2.3–24.2°
c = 13.892 (4) ŵ = 0.09 mm1
β = 101.838 (8)°T = 200 K
V = 956.6 (4) Å3Prism, clear yellow
Z = 40.50 × 0.20 × 0.20 mm
Data collection top
Bruker SMART X2S CCD
diffractometer
1699 independent reflections
Radiation source: XOS X-beam microfocus source1125 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromatorRint = 0.058
Detector resolution: 8.3330 pixels mm-1θmax = 25.4°, θmin = 3.0°
ω scansh = 77
Absorption correction: multi-scan
(SADABS; Bruker, 2010)
k = 138
Tmin = 0.53, Tmax = 0.98l = 1616
4809 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.128H atoms treated by a mixture of independent and constrained refinement
S = 0.96 w = 1/[σ2(Fo2) + (0.0664P)2]
where P = (Fo2 + 2Fc2)/3
1699 reflections(Δ/σ)max < 0.001
140 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = 0.25 e Å3
Crystal data top
C12H9N3V = 956.6 (4) Å3
Mr = 195.22Z = 4
Monoclinic, P21/nMo Kα radiation
a = 6.0602 (14) ŵ = 0.09 mm1
b = 11.610 (3) ÅT = 200 K
c = 13.892 (4) Å0.50 × 0.20 × 0.20 mm
β = 101.838 (8)°
Data collection top
Bruker SMART X2S CCD
diffractometer
1699 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2010)
1125 reflections with I > 2σ(I)
Tmin = 0.53, Tmax = 0.98Rint = 0.058
4809 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0460 restraints
wR(F2) = 0.128H atoms treated by a mixture of independent and constrained refinement
S = 0.96Δρmax = 0.26 e Å3
1699 reflectionsΔρmin = 0.25 e Å3
140 parameters
Special details top

Experimental. The H atoms bonded to carbon were refined using a riding model with C—H = 0.95 Å and Uiso = 1.2Ueq(C). The coordinates and isotropic thermal parameters of the amine H atom were refined freely.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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
N10.4979 (3)0.67895 (13)0.38292 (14)0.0331 (5)
H10.618 (4)0.7118 (19)0.3528 (19)0.062 (7)*
N20.2493 (3)0.54899 (13)0.41681 (13)0.0303 (5)
N30.7075 (3)0.30522 (13)0.22238 (14)0.0357 (5)
C10.3669 (3)0.73593 (15)0.43732 (16)0.0294 (5)
C20.2130 (3)0.65460 (15)0.45835 (16)0.0286 (5)
C30.0506 (3)0.68515 (17)0.51158 (17)0.0338 (6)
H30.05480.63050.52590.041*
C40.0490 (3)0.79775 (16)0.54271 (18)0.0389 (6)
H40.05940.82110.57940.047*
C50.2039 (3)0.87851 (17)0.52133 (19)0.0412 (6)
H50.19680.95560.54340.049*
C60.3650 (4)0.84967 (16)0.46965 (18)0.0398 (6)
H60.4710.90460.45630.048*
C70.4191 (3)0.56767 (15)0.37324 (16)0.0284 (5)
C80.5194 (3)0.47905 (15)0.32041 (16)0.0295 (5)
C90.7077 (4)0.49937 (16)0.28180 (18)0.0368 (6)
H90.77690.57320.28780.044*
C100.7947 (4)0.41118 (17)0.23429 (18)0.0395 (6)
H100.92510.42680.20840.047*
C110.5260 (3)0.28667 (16)0.26116 (17)0.0352 (6)
H110.46090.21190.25450.042*
C120.4278 (3)0.36867 (15)0.30996 (17)0.0336 (6)
H120.29920.35030.33620.04*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0314 (10)0.0239 (9)0.0474 (13)0.0038 (7)0.0161 (9)0.0026 (8)
N20.0291 (10)0.0267 (9)0.0376 (12)0.0014 (7)0.0130 (9)0.0002 (7)
N30.0372 (11)0.0305 (9)0.0406 (13)0.0062 (8)0.0110 (9)0.0012 (8)
C10.0284 (11)0.0270 (10)0.0342 (14)0.0005 (8)0.0098 (10)0.0002 (9)
C20.0270 (11)0.0259 (10)0.0334 (13)0.0006 (8)0.0075 (10)0.0002 (9)
C30.0296 (12)0.0350 (11)0.0381 (15)0.0014 (9)0.0104 (11)0.0019 (9)
C40.0375 (13)0.0379 (12)0.0454 (16)0.0028 (10)0.0182 (12)0.0031 (10)
C50.0478 (14)0.0292 (11)0.0501 (16)0.0011 (9)0.0185 (12)0.0083 (10)
C60.0426 (14)0.0274 (11)0.0519 (17)0.0073 (9)0.0158 (12)0.0059 (10)
C70.0261 (11)0.0242 (10)0.0353 (14)0.0011 (8)0.0074 (10)0.0010 (9)
C80.0279 (12)0.0241 (9)0.0362 (14)0.0036 (8)0.0056 (10)0.0019 (9)
C90.0380 (13)0.0252 (10)0.0511 (17)0.0010 (9)0.0183 (12)0.0008 (9)
C100.0374 (13)0.0362 (11)0.0496 (16)0.0028 (9)0.0201 (12)0.0032 (10)
C110.0339 (13)0.0276 (10)0.0450 (16)0.0005 (9)0.0105 (11)0.0047 (9)
C120.0297 (12)0.0293 (11)0.0437 (15)0.0021 (9)0.0119 (11)0.0013 (9)
Geometric parameters (Å, º) top
N1—C11.373 (3)C4—H40.95
N1—C71.374 (2)C5—C61.367 (3)
N1—H10.99 (2)C5—H50.95
N2—C71.315 (3)C6—H60.95
N2—C21.392 (2)C7—C81.466 (3)
N3—C101.336 (2)C8—C91.377 (3)
N3—C111.338 (3)C8—C121.392 (3)
C1—C61.396 (3)C9—C101.380 (3)
C1—C21.399 (3)C9—H90.95
C2—C31.393 (3)C10—H100.95
C3—C41.378 (3)C11—C121.373 (3)
C3—H30.95C11—H110.95
C4—C51.401 (3)C12—H120.95
C1—N1—C7106.18 (16)C5—C6—H6121.5
C1—N1—H1127.4 (13)C1—C6—H6121.5
C7—N1—H1126.4 (14)N2—C7—N1113.51 (17)
C7—N2—C2104.53 (15)N2—C7—C8123.97 (16)
C10—N3—C11115.83 (18)N1—C7—C8122.52 (18)
N1—C1—C6132.60 (19)C9—C8—C12117.48 (19)
N1—C1—C2105.96 (16)C9—C8—C7122.43 (17)
C6—C1—C2121.44 (19)C12—C8—C7120.06 (19)
N2—C2—C3129.31 (18)C8—C9—C10119.18 (18)
N2—C2—C1109.83 (18)C8—C9—H9120.4
C3—C2—C1120.84 (18)C10—C9—H9120.4
C4—C3—C2117.37 (19)N3—C10—C9124.2 (2)
C4—C3—H3121.3N3—C10—H10117.9
C2—C3—H3121.3C9—C10—H10117.9
C3—C4—C5121.4 (2)N3—C11—C12124.24 (18)
C3—C4—H4119.3N3—C11—H11117.9
C5—C4—H4119.3C12—C11—H11117.9
C6—C5—C4121.96 (19)C11—C12—C8119.1 (2)
C6—C5—H5119.0C11—C12—H12120.5
C4—C5—H5119.0C8—C12—H12120.5
C5—C6—C1117.04 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N3i0.99 (2)1.96 (2)2.924 (2)165 (2)
Symmetry code: (i) x+3/2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC12H9N3
Mr195.22
Crystal system, space groupMonoclinic, P21/n
Temperature (K)200
a, b, c (Å)6.0602 (14), 11.610 (3), 13.892 (4)
β (°) 101.838 (8)
V3)956.6 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.50 × 0.20 × 0.20
Data collection
DiffractometerBruker SMART X2S CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2010)
Tmin, Tmax0.53, 0.98
No. of measured, independent and
observed [I > 2σ(I)] reflections
4809, 1699, 1125
Rint0.058
(sin θ/λ)max1)0.603
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.046, 0.128, 0.96
No. of reflections1699
No. of parameters140
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.26, 0.25

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and Mercury (Macrae et al., 2008), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N3i0.99 (2)1.96 (2)2.924 (2)165 (2)
Symmetry code: (i) x+3/2, y+1/2, z+1/2.
 

Acknowledgements

This work was supported by a Congressionally directed grant from the US Department of Education (grant No. P116Z100020) for the X-ray diffractometer.

References

First citationBruker (2010). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationHuang, X.-C., Zeng, M.-H. & Ng, S. W. (2004). Acta Cryst. E60, o939–o940.  Web of Science CSD CrossRef CAS IUCr Journals
First citationMacrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.  Web of Science CrossRef CAS IUCr Journals
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals

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ISSN: 2056-9890
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