Pyridine-2,3-diamine

Betz, R.; Gerber, T.; Hosten, E.; Schalekamp, H.

doi:10.1107/S1600536811029412

organic compounds

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ISSN: 2056-9890

Volume 67| Part 8| August 2011| Page o2154

doi:10.1107/S1600536811029412

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Pyridine-2,3-diamine

Richard Betz,^a ^* Thomas Gerber,^a Eric Hosten ^a and Henk Schalekamp ^a

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

Experimental

Crystal data

C₅H₇N₃
M_r = 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)
R_int = 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
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯N3^iv	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 ); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT; 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 and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811029412/om2449sup1.cif

Supporting information file. DOI: 10.1107/S1600536811029412/om2449Isup2.cdx

Structure factors: contains datablock I. DOI: 10.1107/S1600536811029412/om2449Isup3.hkl

Supporting information file. DOI: 10.1107/S1600536811029412/om2449Isup4.cml

checkCIF report

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.

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

	Fig. 1. The molecular structure of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 50% probability level).
	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.
	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

C₅H₇N₃	D_x = 1.369 Mg m⁻³
M_r = 109.14	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P4₂bc	Cell parameters from 5917 reflections
Hall symbol: P 4c -2ab	θ = 2.5–28.3°
a = 16.4670 (3) Å	µ = 0.09 mm⁻¹
c = 3.9064 (12) Å	T = 200 K
V = 1059.3 (3) Å³	Needle, brown
Z = 8	0.48 × 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 tube	R_int = 0.047
Graphite monochromator	θ_max = 28.3°, θ_min = 1.8°
ϕ and ω scans	h = −21→20
9864 measured reflections	k = −21→21
754 independent reflections	l = −5→5

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.085	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0428P)² + 0.2489P] where P = (F_o² + 2F_c²)/3
754 reflections	(Δ/σ)_max < 0.001
89 parameters	Δρ_max = 0.23 e Å⁻³
1 restraint	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₅H₇N₃	Z = 8
M_r = 109.14	Mo Kα radiation
Tetragonal, P4₂bc	µ = 0.09 mm⁻¹
a = 16.4670 (3) Å	T = 200 K
c = 3.9064 (12) Å	0.48 × 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 reflections	R_int = 0.047
754 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	1 restraint
wR(F²) = 0.085	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.23 e Å⁻³
754 reflections	Δρ_min = −0.17 e Å⁻³
89 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.20596 (8)	−0.05610 (8)	0.9243 (5)	0.0268 (3)
N2	0.11296 (8)	0.04458 (9)	1.0621 (5)	0.0271 (3)
H21	0.1094 (13)	0.0921 (14)	1.156 (8)	0.040 (6)*
H22	0.0934 (12)	0.0063 (14)	1.184 (7)	0.037 (6)*
N3	0.21809 (9)	0.16454 (9)	0.7974 (5)	0.0302 (4)
H31	0.1677 (13)	0.1730 (12)	0.757 (7)	0.033 (5)*
H32	0.2471 (12)	0.1946 (12)	0.652 (8)	0.038 (6)*
C1	0.18758 (9)	0.02266 (9)	0.9286 (5)	0.0225 (4)
C2	0.23965 (9)	0.08211 (9)	0.7834 (6)	0.0240 (3)
C3	0.31167 (10)	0.05570 (10)	0.6425 (5)	0.0283 (4)
H3	0.3478	0.0938	0.5417	0.034*
C4	0.33173 (10)	−0.02631 (11)	0.6469 (6)	0.0307 (4)
H4	0.3819	−0.0449	0.5556	0.037*
C5	0.27702 (10)	−0.07971 (10)	0.7870 (6)	0.0300 (4)
H5	0.2900	−0.1359	0.7869	0.036*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0256 (7)	0.0250 (7)	0.0298 (8)	0.0002 (5)	−0.0024 (7)	0.0000 (7)
N2	0.0250 (7)	0.0249 (7)	0.0315 (8)	−0.0003 (5)	0.0025 (6)	−0.0013 (7)
N3	0.0276 (7)	0.0256 (7)	0.0374 (9)	−0.0023 (5)	−0.0009 (8)	0.0039 (8)
C1	0.0214 (7)	0.0252 (7)	0.0209 (8)	−0.0013 (5)	−0.0042 (7)	−0.0005 (7)
C2	0.0238 (7)	0.0267 (7)	0.0217 (7)	−0.0032 (5)	−0.0040 (7)	0.0003 (8)
C3	0.0261 (8)	0.0357 (8)	0.0231 (8)	−0.0065 (6)	−0.0014 (8)	0.0009 (8)
C4	0.0242 (7)	0.0411 (9)	0.0268 (9)	0.0024 (6)	0.0012 (8)	−0.0044 (9)
C5	0.0288 (8)	0.0278 (8)	0.0334 (9)	0.0045 (6)	−0.0023 (10)	−0.0021 (9)

Geometric parameters (Å, º) top

N1—C1	1.332 (2)	C1—C2	1.420 (2)
N1—C5	1.345 (2)	C2—C3	1.378 (2)
N2—C1	1.383 (2)	C3—C4	1.390 (2)
N2—H21	0.87 (2)	C3—H3	0.9500
N2—H22	0.85 (2)	C4—C5	1.373 (3)
N3—C2	1.404 (2)	C4—H4	0.9500
N3—H31	0.86 (2)	C5—H5	0.9500
N3—H32	0.89 (3)

C1—N1—C5	118.97 (15)	C3—C2—C1	117.50 (14)
C1—N2—H21	117.1 (15)	N3—C2—C1	119.89 (16)
C1—N2—H22	110.7 (14)	C2—C3—C4	120.41 (16)
H21—N2—H22	114 (2)	C2—C3—H3	119.8
C2—N3—H31	113.3 (13)	C4—C3—H3	119.8
C2—N3—H32	112.2 (14)	C5—C4—C3	118.11 (16)
H31—N3—H32	108 (2)	C5—C4—H4	120.9
N1—C1—N2	117.44 (15)	C3—C4—H4	120.9
N1—C1—C2	121.95 (15)	N1—C5—C4	123.03 (15)
N2—C1—C2	120.49 (14)	N1—C5—H5	118.5
C3—C2—N3	122.57 (16)	C4—C5—H5	118.5

C5—N1—C1—N2	178.05 (17)	N3—C2—C3—C4	177.43 (19)
C5—N1—C1—C2	1.9 (3)	C1—C2—C3—C4	−0.4 (3)
N1—C1—C2—C3	−1.4 (3)	C2—C3—C4—C5	1.6 (3)
N2—C1—C2—C3	−177.42 (18)	C1—N1—C5—C4	−0.6 (3)
N1—C1—C2—N3	−179.3 (2)	C3—C4—C5—N1	−1.1 (3)
N2—C1—C2—N3	4.7 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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···N3^iv	0.89 (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, z−1/2; (iv) −y+1/2, −x+1/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₅H₇N₃
M_r	109.14
Crystal system, space group	Tetragonal, P4₂bc
Temperature (K)	200
a, c (Å)	16.4670 (3), 3.9064 (12)
V (Å³)	1059.3 (3)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.48 × 0.16 × 0.11

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	9864, 754, 706
R_int	0.047
(sin θ/λ)_max (Å⁻¹)	0.667

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.085, 1.10
No. of reflections	754
No. of parameters	89
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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···N3^iv	0.89 (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, z−1/2; (iv) −y+1/2, −x+1/2, z−1/2.

Acknowledgements

The authors thank Mrs Phyllis Atkinson for helpful discussions.

References

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