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

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ISSN: 2056-9890

2-(4,5-Di­hydro-1H-imidazol-2-yl)­pyridine

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Chemistry, School of Science, Payame Noor University (PNU), Ardakan, Yazd, Iran
*Correspondence e-mail: hkfun@usm.my

(Received 10 March 2009; accepted 12 March 2009; online 19 March 2009)

In the mol­ecule of the title compound, C8H9N3, a new imidazoline derivative, the six- and five-membered rings are slightly twisted away from each other, forming a dihedral angle of 7.96 (15)°. In the crystal structure, neighbouring mol­ecules are linked together by inter­molecular N—H⋯N hydrogen bonds into extended one-dimensional chains along the a axis. The pyridine N atom is in close proximity to a carbon-bound H atom of the imidazoline ring, with an H⋯N distance of 2.70 Å, which is slightly shorter than the sum of the van der Waals radii of these atoms (2.75 Å). The crystal structure is further stabilized by inter­molecular C—H⋯π and ππ inter­actions (centroid-to-centroid distance 3.853 Å).

Related literature

For related structures and synthesis, see: Stibrany et al. (2004[Stibrany, R. T., Schugar, H. J. & Potenza, J. A. (2004). Acta Cryst. E60, o527-o529.]); Kia et al. (2008[Kia, R., Fun, H.-K. & Kargar, H. (2008). Acta Cryst. E64, o2406.], 2009a[Kia, R., Fun, H.-K. & Kargar, H. (2009a). Acta Cryst. E65, o338-o339.],b[Kia, R., Fun, H.-K. & Kargar, H. (2009b). Acta Cryst. E65, o724.]). For biological and pharmaceutical applications, see, for example: Blancafort (1978[Blancafort, P. (1978). Drugs Fut. 3, 592-592.]); Chan (1993[Chan, S. (1993). Clin. Sci. 85, 671-677.]); Vizi (1986[Vizi, E. S. (1986). Med. Res. Rev. 6, 431-449.]); Li et al. (1996[Li, H. Y., Drummond, S., De Lucca, I. & Boswell, G. A. (1996). Tetrahedron, 52, 11153-11162.]); Ueno et al. (1995[Ueno, M., Imaizumi, K., Sugita, T., Takata, I. & Takeshita, M. (1995). Int. J. Immunopharmacol. 17, 597-603.]); Corey & Grogan (1999[Corey, E. J. & Grogan, M. J. (1999). Org. Lett. 1, 157-160.]). For the stability of the temperature controller used for data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]). For standard bond-length data, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]).

[Scheme 1]

Experimental

Crystal data
  • C8H9N3

  • Mr = 147.18

  • Orthorhombic, P b c a

  • a = 10.0057 (8) Å

  • b = 7.9828 (7) Å

  • c = 17.6199 (14) Å

  • V = 1407.4 (2) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 100 K

  • 0.48 × 0.46 × 0.09 mm

Data collection
  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2005[Bruker (2005). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.959, Tmax = 0.992

  • 10642 measured reflections

  • 1238 independent reflections

  • 869 reflections with I > 2σ(I)

  • Rint = 0.094

Refinement
  • R[F2 > 2σ(F2)] = 0.051

  • wR(F2) = 0.146

  • S = 1.08

  • 1238 reflections

  • 104 parameters

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

  • Δρmax = 0.26 e Å−3

  • Δρmin = −0.31 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the N3/C4–C8 (pyridine) ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N1⋯N2i 0.85 (3) 2.27 (3) 3.084 (3) 160 (3)
C2—H3⋯Cg1ii 0.99 2.87 3.611 (3) 133
C6—H6⋯Cg1iii 0.95 2.84 3.561 (3) 134
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z]; (ii) -x+1, -y, -z; (iii) [-x-{\script{1\over 2}}, y-{\script{3\over 2}}, z].

Data collection: APEX2 (Bruker, 2005[Bruker (2005). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2005[Bruker (2005). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Imidazoline derivatives are of great importance because they exhibit significant biological and pharmacological activities, such as antihypertensive (Blancafort, 1978), antihyperglycemic (Chan, 1993), antidepressant (Vizi, 1986), antihypercholesterolemic (Li et al., 1996) and anti-inflammatory (Ueno et al., 1995) properties. These compounds are also used as catalysts and synthetic intermediates in some organic reactions (Corey & Grogan, 1999). With regard to these important applications of imidazolines, we report here the crystal structure of the title compound.

In the title compound (Fig. 1), bond lengths (Allen et al., 1987) and angles are within the normal ranges and are comparable with those in related structures (Stibrany et al., 2004; Kia et al., 2008, 2009a,b). The molecule is almost planar, with a maximum deviation from the mean plane of the molecule for atom N1: 0.106 (2) Å. The six- and five-membered rings are twisted from each other, forming a dihedral angle of 7.96 (15)°. Atom H1 of the imidazoline ring is in close proximity to atom N3 of the pyridine ring, with a distance of 2.70 Å [N3···H1], which is shorter than the sum of the van der Waals radii of these atoms (2.75 Å). In the crystal structure, neighbouring molecules are linked together by intermolecular N—H···N hydrogen bonds into one-dimensional extended chains along the a axis (Table 1, Fig. 2). The crystal structure is further stabilized by intermolecular C—H···π [Cg1 is the centroid of the N3/C4–C8 pyridine ring] and ππ interactions [Cg1···Cg2 = 3.853 Å and Cg2 is the centroid of the N1/C1/C2/N2/C3 ring].

Related literature top

For related structures and synthesis, see: Stibrany et al. (2004); Kia et al. (2008, 2009a,b). For applications, see, for example: Blancafort (1978); Chan (1993); Vizi (1986); Li et al. (1996); Ueno et al. (1995); Corey & Grogan (1999). For the stability of the temperature controller used for data collection, see: Cosier & Glazer (1986). For standard bond-length data, see: Allen et al. (1987).

Experimental top

The synthetic method was based on previous work (Stibrany et al., 2004), except that 10 mmol of 2-cyanopyridine and 40 mmol of ethylenediamine were used. Single crystals suitable for X-ray diffraction were obtained by evaporation of a methanol solution at room temperature.

Refinement top

The N-bound H atom was located in a Fourier difference map and refined freely (Table 1). The other H atoms were positioned geometrically and refined with a riding approximation model; C—H = 0.95–0.99 Å and Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: APEX2 (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with atom labels. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed down the b axis, showing a one-dimensional extended chain along the a axis, formed by intermolecular N—H···N interactions. The intermolecular interactions are shown as dashed lines.
2-(4,5-Dihydro-1H-imidazol-2-yl)pyridine top
Crystal data top
C8H9N3F(000) = 624
Mr = 147.18Dx = 1.389 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 3233 reflections
a = 10.0057 (8) Åθ = 3.1–30.9°
b = 7.9828 (7) ŵ = 0.09 mm1
c = 17.6199 (14) ÅT = 100 K
V = 1407.4 (2) Å3Plate, colourless
Z = 80.48 × 0.46 × 0.09 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
1238 independent reflections
Radiation source: fine-focus sealed tube869 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.094
ϕ and ω scansθmax = 25.0°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
h = 1111
Tmin = 0.959, Tmax = 0.992k = 99
10642 measured reflectionsl = 2020
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)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.146H atoms treated by a mixture of independent and constrained refinement
S = 1.08 w = 1/[σ2(Fo2) + (0.0658P)2 + 1.1427P]
where P = (Fo2 + 2Fc2)/3
1238 reflections(Δ/σ)max < 0.001
104 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
C8H9N3V = 1407.4 (2) Å3
Mr = 147.18Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 10.0057 (8) ŵ = 0.09 mm1
b = 7.9828 (7) ÅT = 100 K
c = 17.6199 (14) Å0.48 × 0.46 × 0.09 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
1238 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
869 reflections with I > 2σ(I)
Tmin = 0.959, Tmax = 0.992Rint = 0.094
10642 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0510 restraints
wR(F2) = 0.146H atoms treated by a mixture of independent and constrained refinement
S = 1.08Δρmax = 0.26 e Å3
1238 reflectionsΔρmin = 0.31 e Å3
104 parameters
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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
N10.4819 (2)0.2650 (3)0.01294 (14)0.0329 (7)
N20.2746 (2)0.1657 (3)0.03211 (12)0.0232 (6)
N30.4811 (2)0.1456 (3)0.13473 (12)0.0225 (6)
C10.3126 (3)0.2543 (4)0.10232 (14)0.0251 (7)
H10.24780.34460.11370.030*
H20.31490.17570.14570.030*
C20.4531 (3)0.3285 (4)0.08783 (14)0.0232 (7)
H30.51880.28770.12560.028*
H40.45160.45250.08860.028*
C30.3763 (2)0.1770 (3)0.01289 (14)0.0195 (6)
C40.3779 (3)0.1036 (3)0.08982 (14)0.0202 (6)
C50.2758 (2)0.0035 (3)0.11365 (15)0.0213 (6)
H50.20500.03260.08030.026*
C60.2797 (3)0.0662 (4)0.18629 (14)0.0231 (7)
H60.21060.13780.20400.028*
C70.3852 (3)0.0238 (3)0.23325 (15)0.0231 (7)
H70.39040.06580.28360.028*
C80.4829 (3)0.0814 (4)0.20475 (15)0.0229 (7)
H80.55560.10970.23690.027*
H1N10.555 (3)0.278 (4)0.0109 (16)0.036 (9)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0146 (14)0.0501 (17)0.0340 (15)0.0094 (12)0.0053 (12)0.0105 (12)
N20.0147 (13)0.0261 (13)0.0289 (12)0.0008 (10)0.0021 (10)0.0009 (9)
N30.0105 (11)0.0244 (13)0.0326 (13)0.0018 (10)0.0013 (10)0.0013 (10)
C10.0138 (14)0.0320 (16)0.0296 (15)0.0004 (12)0.0023 (12)0.0006 (12)
C20.0146 (14)0.0260 (15)0.0290 (15)0.0005 (12)0.0007 (11)0.0008 (11)
C30.0118 (14)0.0173 (14)0.0292 (15)0.0027 (11)0.0018 (11)0.0038 (11)
C40.0108 (13)0.0180 (14)0.0317 (15)0.0048 (11)0.0008 (11)0.0028 (11)
C50.0102 (15)0.0204 (15)0.0334 (15)0.0005 (11)0.0010 (11)0.0056 (11)
C60.0161 (15)0.0205 (15)0.0327 (16)0.0009 (12)0.0048 (12)0.0017 (11)
C70.0204 (15)0.0203 (14)0.0287 (15)0.0029 (12)0.0023 (12)0.0001 (11)
C80.0148 (15)0.0259 (15)0.0278 (15)0.0007 (12)0.0042 (11)0.0040 (12)
Geometric parameters (Å, º) top
N1—C31.349 (3)C2—H40.9900
N1—C21.442 (4)C3—C41.477 (4)
N1—H1N10.85 (3)C4—C51.397 (4)
N2—C31.293 (3)C5—C61.374 (4)
N2—C11.475 (3)C5—H50.9500
N3—C81.336 (3)C6—C71.383 (4)
N3—C41.343 (3)C6—H60.9500
C1—C21.547 (4)C7—C81.383 (4)
C1—H10.9900C7—H70.9500
C1—H20.9900C8—H80.9500
C2—H30.9900
C3—N1—C2109.6 (2)N2—C3—C4122.9 (2)
C3—N1—H1N1125 (2)N1—C3—C4120.5 (2)
C2—N1—H1N1126 (2)N3—C4—C5122.5 (2)
C3—N2—C1106.1 (2)N3—C4—C3116.7 (2)
C8—N3—C4117.3 (2)C5—C4—C3120.7 (2)
N2—C1—C2106.2 (2)C6—C5—C4118.8 (2)
N2—C1—H1110.5C6—C5—H5120.6
C2—C1—H1110.5C4—C5—H5120.6
N2—C1—H2110.5C5—C6—C7119.3 (3)
C2—C1—H2110.5C5—C6—H6120.4
H1—C1—H2108.7C7—C6—H6120.4
N1—C2—C1101.4 (2)C8—C7—C6118.1 (2)
N1—C2—H3111.5C8—C7—H7121.0
C1—C2—H3111.5C6—C7—H7121.0
N1—C2—H4111.5N3—C8—C7124.0 (2)
C1—C2—H4111.5N3—C8—H8118.0
H3—C2—H4109.3C7—C8—H8118.0
N2—C3—N1116.5 (2)
C3—N2—C1—C23.2 (3)N1—C3—C4—N37.7 (4)
C3—N1—C2—C12.3 (3)N2—C3—C4—C59.5 (4)
N2—C1—C2—N13.3 (3)N1—C3—C4—C5172.6 (2)
C1—N2—C3—N11.9 (3)N3—C4—C5—C61.2 (4)
C1—N2—C3—C4179.9 (2)C3—C4—C5—C6178.6 (2)
C2—N1—C3—N20.4 (3)C4—C5—C6—C71.0 (4)
C2—N1—C3—C4177.7 (2)C5—C6—C7—C80.3 (4)
C8—N3—C4—C50.5 (4)C4—N3—C8—C70.4 (4)
C8—N3—C4—C3179.3 (2)C6—C7—C8—N30.5 (4)
N2—C3—C4—N3170.2 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···N2i0.85 (3)2.27 (3)3.084 (3)160 (3)
C2—H3···Cg1ii0.992.873.611 (3)133
C6—H6···Cg1iii0.952.843.561 (3)134
Symmetry codes: (i) x+1/2, y+1/2, z; (ii) x+1, y, z; (iii) x1/2, y3/2, z.

Experimental details

Crystal data
Chemical formulaC8H9N3
Mr147.18
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)100
a, b, c (Å)10.0057 (8), 7.9828 (7), 17.6199 (14)
V3)1407.4 (2)
Z8
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.48 × 0.46 × 0.09
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2005)
Tmin, Tmax0.959, 0.992
No. of measured, independent and
observed [I > 2σ(I)] reflections
10642, 1238, 869
Rint0.094
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.146, 1.08
No. of reflections1238
No. of parameters104
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.26, 0.31

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···N2i0.85 (3)2.27 (3)3.084 (3)160 (3)
C2—H3···Cg1ii0.992.873.611 (3)133
C6—H6···Cg1iii0.952.843.561 (3)134
Symmetry codes: (i) x+1/2, y+1/2, z; (ii) x+1, y, z; (iii) x1/2, y3/2, z.
 

Acknowledgements

HKF and RK thank the Malaysian Government and Universiti Sains Malaysia for a Science Fund Grant (No. 305/PFIZIK/613312). RK thanks Universiti Sains Malaysia for a postdoctoral research fellowship. HK thanks PNU for financial support. HKF also thanks Universiti Sains Malaysia for a Research University Golden Goose Grant (No. 1001/PFIZIK/811012).

References

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