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ISSN: 2056-9890

Pyridine-2,3-di­amine

aNelson Mandela Metropolitan University, Summerstrand Campus, Department of Chemistry, University Way, Summerstrand, PO Box 77000, Port Elizabeth 6031, South Africa
*Correspondence e-mail: richard.betz@webmail.co.za

(Received 12 July 2011; accepted 20 July 2011; online 30 July 2011)

The mol­ecule of the title pyridine derivative, C5H7N3, shows approximately non-crystallographic Cs symmetry. Intra­cyclic angles cover the range 117.50 (14)–123.03 (15)°. In the crystal, N—H⋯N hydrogen bonds connect mol­ecules into a three-dimensional network. The closest inter­centroid distance between two π-systems occurs with the c-axis repeat at 3.9064 (12) Å.

Related literature

For the crystal structure of the dihydro­chloride of the title compound, see: Hemamalini & Fun (2010[Hemamalini, M. & Fun, H.-K. (2010). Acta Cryst. E66, o513-o514.]). For the crystal structures of Zn complexes of the title compound, see: de Cires-Mejias et al. (2004[Cires-Mejias, C. de, Tanase, S., Reedijk, J., Gonzalez-Vilchez, F., Vilaplana, R., Mills, A. M., Kooijman, H. & Spek, A. L. (2004). Inorg. Chim. Acta, 357, 1494-1498.]). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C5H7N3

  • Mr = 109.14

  • Tetragonal, P 42 b c

  • a = 16.4670 (3) Å

  • c = 3.9064 (12) Å

  • V = 1059.3 (3) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 200 K

  • 0.48 × 0.16 × 0.11 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • 9864 measured reflections

  • 754 independent reflections

  • 706 reflections with I > 2σ(I)

  • Rint = 0.047

Refinement
  • R[F2 > 2σ(F2)] = 0.036

  • wR(F2) = 0.085

  • S = 1.10

  • 754 reflections

  • 89 parameters

  • 1 restraint

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

  • Δρmax = 0.23 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H21⋯N1i 0.87 (2) 2.32 (2) 3.153 (2) 161.2 (19)
N2—H22⋯N2ii 0.85 (2) 2.58 (2) 3.4369 (16) 175.9 (18)
N3—H31⋯N1iii 0.86 (2) 2.32 (2) 3.115 (2) 156 (2)
N3—H32⋯N3iv 0.89 (3) 2.47 (2) 3.359 (2) 175 (2)
Symmetry codes: (i) [-y, x, z+{\script{1\over 2}}]; (ii) [y, -x, z+{\script{1\over 2}}]; (iii) [-y, x, z-{\script{1\over 2}}]; (iv) [-y+{\script{1\over 2}}, -x+{\script{1\over 2}}, z-{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2010[Bruker (2010). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2010[Bruker (2010). APEX2 and SAINT 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: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) 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: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Chelate ligands have found widespread use in coordination chemistry due to the enhanced thermodynamic stability of resultant coordination compounds in relation to coordination compounds exclusively applying comparable monodentate ligands. Combining identical donor atoms in different states of hybridization, a molecular set-up to accomodate a large variety of metal centers of variable Lewis acidity is at hand. In this aspect, the title compound seemed interesting due to its use as strictly neutral or – depending on the pH value – as anionic or cationic ligand. Furthermore, thanks to the presence of three possible donor atoms, the title compound might serve as a building block in the formation of metal-organic framework structures. For the title compound, two zinc-supported polymers have been reported whose crystal structure analysis shows the absence of chelate-type building motifs (de Cires-Mejias et al., 2004). At the beginning of a more comprehensive study to elucidate the formation of coordination polymers exclusively featuring nitrogen-containing ligands, we determined the structure of the title compound to enable comparative studies of metrical parameters in envisioned coordination compounds. Information about the molecular and crystal structure of the dihydrochloride of the title compound is apparent in the literature (Hemamalini & Fun, 2010).

Intracyclic angles cover a range of 117.50 (14)–123.03 (15) ° with the smallest angle found on the carbon atom bearing the amino group in meta position to the intracyclic nitrogen atom and the biggest angle found on the carbon atom bearing a hydrogen atom in ortho position to the intracyclic nitrogen atom. Apart from the hydrogen atoms of the amino groups which point to opposite sides of the plane defined the aromatic system, all atoms are essentially residing in one common plane (r.m.s. deviation of all fitted non-hydrogen atoms = 0.0152 Å). The amino groups are not planar, the least-squares planes defined by the NH2 groups subtend angles of 40.2 (2) ° and 79.5 (2) ° with the least-squares plane defined by the atoms of the heterocycle (Fig. 1).

The crystal structure of the title compound is marked by a hydrogen bonding system involving all hydrogen atoms of both amino groups as donors and the intracyclic as well as the exocyclic nitrogen atoms as acceptors. The intracyclic nitrogen atom serves as a twofold acceptor for one of the hydrogen atoms of each of the two different amino groups. The remaining hydrogen atom on each amino group gives rise to a cooperative chain of hydrogen bonds, respectively. The latter ones are antidromic. In terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptor for this hydrogen bonding system on the unitary level is C11(2)C11(2)C11(4)C11(5). In total, the molecules are connected to a three-dimensional network (Fig. 2). The closest intercentroid distance between two aromatic systems follows the c-axis repeat at 3.9064 (12) Å.

The packing of the title compound is shown in Figure 3.

Related literature top

For the crystal structure of the dihydrochloride of the title compound, see: Hemamalini & Fun (2010). For the crystal structures of Zn complexes, see: de Cires-Mejias et al. (2004). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990); Bernstein et al. (1995).

Experimental top

The compound was obtained commercially (Aldrich). Crystals suitable for the X-ray diffraction study were taken directly from the provided compound.

Refinement top

Carbon-bound H atoms were placed in calculated positions (C—H 0.95 Å) and were included in the refinement in the riding model approximation, with U(H) set to 1.2Ueq(C). The H atoms of the amine groups were located on a difference Fourier map and refined with individual thermal parameters. Due to the absence of a strong anomalous scatterer, the Flack parameter is meaningless. Thus, Friedel opposites (2407 pairs) have been merged and the item was removed from the CIF.

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: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 50% probability level).
[Figure 2] Fig. 2. Intermolecular contacts, viewed approximately along [0 0 1]. Symmetry operators: i y, -x, z - 1/2; ii y, -x, z + 1/2; iii -y, x, z - 1/2; iv -y, x, z + 1/2; v -y + 1/2, -x + 1/2, z - 1/2; vi -y + 1/2, -x + 1/2, z + 1/2.
[Figure 3] Fig. 3. Molecular packing of the title compound, viewed along [0 0 - 1] (anisotropic displacement ellipsoids drawn at 50% probability level).
Pyridine-2,3-diamine top
Crystal data top
C5H7N3Dx = 1.369 Mg m3
Mr = 109.14Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P42bcCell parameters from 5917 reflections
Hall symbol: P 4c -2abθ = 2.5–28.3°
a = 16.4670 (3) ŵ = 0.09 mm1
c = 3.9064 (12) ÅT = 200 K
V = 1059.3 (3) Å3Needle, brown
Z = 80.48 × 0.16 × 0.11 mm
F(000) = 464
Data collection top
Bruker APEXII CCD
diffractometer
706 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.047
Graphite monochromatorθmax = 28.3°, θmin = 1.8°
ϕ and ω scansh = 2120
9864 measured reflectionsk = 2121
754 independent reflectionsl = 55
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)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.085H atoms treated by a mixture of independent and constrained refinement
S = 1.10 w = 1/[σ2(Fo2) + (0.0428P)2 + 0.2489P]
where P = (Fo2 + 2Fc2)/3
754 reflections(Δ/σ)max < 0.001
89 parametersΔρmax = 0.23 e Å3
1 restraintΔρmin = 0.17 e Å3
Crystal data top
C5H7N3Z = 8
Mr = 109.14Mo Kα radiation
Tetragonal, P42bcµ = 0.09 mm1
a = 16.4670 (3) ÅT = 200 K
c = 3.9064 (12) Å0.48 × 0.16 × 0.11 mm
V = 1059.3 (3) Å3
Data collection top
Bruker APEXII CCD
diffractometer
706 reflections with I > 2σ(I)
9864 measured reflectionsRint = 0.047
754 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0361 restraint
wR(F2) = 0.085H atoms treated by a mixture of independent and constrained refinement
S = 1.10Δρmax = 0.23 e Å3
754 reflectionsΔρmin = 0.17 e Å3
89 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.20596 (8)0.05610 (8)0.9243 (5)0.0268 (3)
N20.11296 (8)0.04458 (9)1.0621 (5)0.0271 (3)
H210.1094 (13)0.0921 (14)1.156 (8)0.040 (6)*
H220.0934 (12)0.0063 (14)1.184 (7)0.037 (6)*
N30.21809 (9)0.16454 (9)0.7974 (5)0.0302 (4)
H310.1677 (13)0.1730 (12)0.757 (7)0.033 (5)*
H320.2471 (12)0.1946 (12)0.652 (8)0.038 (6)*
C10.18758 (9)0.02266 (9)0.9286 (5)0.0225 (4)
C20.23965 (9)0.08211 (9)0.7834 (6)0.0240 (3)
C30.31167 (10)0.05570 (10)0.6425 (5)0.0283 (4)
H30.34780.09380.54170.034*
C40.33173 (10)0.02631 (11)0.6469 (6)0.0307 (4)
H40.38190.04490.55560.037*
C50.27702 (10)0.07971 (10)0.7870 (6)0.0300 (4)
H50.29000.13590.78690.036*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0256 (7)0.0250 (7)0.0298 (8)0.0002 (5)0.0024 (7)0.0000 (7)
N20.0250 (7)0.0249 (7)0.0315 (8)0.0003 (5)0.0025 (6)0.0013 (7)
N30.0276 (7)0.0256 (7)0.0374 (9)0.0023 (5)0.0009 (8)0.0039 (8)
C10.0214 (7)0.0252 (7)0.0209 (8)0.0013 (5)0.0042 (7)0.0005 (7)
C20.0238 (7)0.0267 (7)0.0217 (7)0.0032 (5)0.0040 (7)0.0003 (8)
C30.0261 (8)0.0357 (8)0.0231 (8)0.0065 (6)0.0014 (8)0.0009 (8)
C40.0242 (7)0.0411 (9)0.0268 (9)0.0024 (6)0.0012 (8)0.0044 (9)
C50.0288 (8)0.0278 (8)0.0334 (9)0.0045 (6)0.0023 (10)0.0021 (9)
Geometric parameters (Å, º) top
N1—C11.332 (2)C1—C21.420 (2)
N1—C51.345 (2)C2—C31.378 (2)
N2—C11.383 (2)C3—C41.390 (2)
N2—H210.87 (2)C3—H30.9500
N2—H220.85 (2)C4—C51.373 (3)
N3—C21.404 (2)C4—H40.9500
N3—H310.86 (2)C5—H50.9500
N3—H320.89 (3)
C1—N1—C5118.97 (15)C3—C2—C1117.50 (14)
C1—N2—H21117.1 (15)N3—C2—C1119.89 (16)
C1—N2—H22110.7 (14)C2—C3—C4120.41 (16)
H21—N2—H22114 (2)C2—C3—H3119.8
C2—N3—H31113.3 (13)C4—C3—H3119.8
C2—N3—H32112.2 (14)C5—C4—C3118.11 (16)
H31—N3—H32108 (2)C5—C4—H4120.9
N1—C1—N2117.44 (15)C3—C4—H4120.9
N1—C1—C2121.95 (15)N1—C5—C4123.03 (15)
N2—C1—C2120.49 (14)N1—C5—H5118.5
C3—C2—N3122.57 (16)C4—C5—H5118.5
C5—N1—C1—N2178.05 (17)N3—C2—C3—C4177.43 (19)
C5—N1—C1—C21.9 (3)C1—C2—C3—C40.4 (3)
N1—C1—C2—C31.4 (3)C2—C3—C4—C51.6 (3)
N2—C1—C2—C3177.42 (18)C1—N1—C5—C40.6 (3)
N1—C1—C2—N3179.3 (2)C3—C4—C5—N11.1 (3)
N2—C1—C2—N34.7 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H21···N1i0.87 (2)2.32 (2)3.153 (2)161.2 (19)
N2—H22···N2ii0.85 (2)2.58 (2)3.4369 (16)175.9 (18)
N3—H31···N1iii0.86 (2)2.32 (2)3.115 (2)156 (2)
N3—H32···N3iv0.89 (3)2.47 (2)3.359 (2)175 (2)
Symmetry codes: (i) y, x, z+1/2; (ii) y, x, z+1/2; (iii) y, x, z1/2; (iv) y+1/2, x+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC5H7N3
Mr109.14
Crystal system, space groupTetragonal, P42bc
Temperature (K)200
a, c (Å)16.4670 (3), 3.9064 (12)
V3)1059.3 (3)
Z8
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.48 × 0.16 × 0.11
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
9864, 754, 706
Rint0.047
(sin θ/λ)max1)0.667
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.085, 1.10
No. of reflections754
No. of parameters89
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.23, 0.17

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H21···N1i0.87 (2)2.32 (2)3.153 (2)161.2 (19)
N2—H22···N2ii0.85 (2)2.58 (2)3.4369 (16)175.9 (18)
N3—H31···N1iii0.86 (2)2.32 (2)3.115 (2)156 (2)
N3—H32···N3iv0.89 (3)2.47 (2)3.359 (2)175 (2)
Symmetry codes: (i) y, x, z+1/2; (ii) y, x, z+1/2; (iii) y, x, z1/2; (iv) y+1/2, x+1/2, z1/2.
 

Acknowledgements

The authors thank Mrs Phyllis Atkinson for helpful discussions.

References

First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationBruker (2010). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCires-Mejias, C. de, Tanase, S., Reedijk, J., Gonzalez-Vilchez, F., Vilaplana, R., Mills, A. M., Kooijman, H. & Spek, A. L. (2004). Inorg. Chim. Acta, 357, 1494–1498.  Google Scholar
First citationEtter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256–262.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
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First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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