Pyridine-2,5-di­amine

In the title mol­ecule, C₅H₇N₃, intra­cyclic angles cover the range 117.15 (10)–124.03 (11)°. The N atoms of the amino groups have trigonal–pyramidal configurations deviating slightly from the pyridine plane by 0.106 (2) and −0.042 (2) Å. In the crystal, the pyridine N atom serves as an acceptor of an N—H⋯N hydrogen bond which links two mol­ecules into a centrosymmetric dimer. Inter­molecular N—H⋯N hydrogen bonds between the amino groups further consolidate the crystal packing, forming a three-dimensional network.

Related literature

For general background, see: Domenicano et al. (1975); Domenicano & Vaciago (1979); Mootz & Wussow (1981); Crawford et al. (2009). For the crystal structures of isomeric diamino­pyridines, see: Schwalbe et al. (1987); Rubin-Preminger & Englert (2007); Al-Dajani et al. (2009); Betz et al. (2011).

Experimental

Crystal data

• C₅H₇N₃

• M_r = 109.14

• Orthorhombic, P b c a

• a = 11.4447 (11) Å

• b = 7.1447 (7) Å

• c = 12.8030 (12) Å

• V = 1046.89 (17) ų

• Z = 8

• Mo Kα radiation

• μ = 0.09 mm⁻¹

• T = 296 K

• 0.30 × 0.25 × 0.20 mm

Data collection

• Bruker APEXII CCD diffractometer

• Absorption correction: multi-scan (SADABS; Sheldrick, 2003) T_min = 0.973, T_max = 0.982

• 13022 measured reflections

• 1595 independent reflections

• 1240 reflections with I > 2σ(I)

• R_int = 0.049

Refinement

• R[F² > 2σ(F²)] = 0.042

• wR(F²) = 0.109

• S = 1.01

• 1595 reflections

• 85 parameters

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

• Δρ_max = 0.36 e Å⁻³

• Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯N1^i	0.874 (17)	2.183 (17)	3.0541 (15)	175.1 (10)
N2—H2B⋯N3^ii	0.879 (17)	2.309 (17)	3.1457 (16)	159.3 (10)
N3—H3A⋯N2^iii	0.894 (16)	2.397 (17)	3.2150 (16)	152.2 (10)
N3—H3B⋯N2^iv	0.898 (17)	2.593 (17)	3.4803 (16)	170.0 (10)
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) ; (iii) ; (iv) .

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

S1. Comment

Polydentate ligands have found widespread use in coordination chemistry due to the increased thermodynamic stability of resultant coordination compounds as compared to that of such compounds with monodentate ligands. In this aspect, the title compound can be considered as a versatile polydentate ligand in metal-organic synthesis. Furthermore, owing to the presence of three donor atoms, the title compound might play a role of the building block in the formation of metal-organic frameworks as well as for cocrystals.

In this work, we determined the crystal structure of the title compound (I), C₅H₇N₃ (Figure 1), to enable comparative studies of its geometrical parameters in metal-organic complexes. Yet, the crystal structure of I can be helpful in the future investigations.

The geometry of aromatic molecules is known to be sensitive to the electronic effects of substituents. Based on the crystallographic analysis of monosubstituted arenes, it was concluded (Domenicano et al., 1975; Domenicano & Vaciago, 1979) that the endocyclic angle at the ipso-C atom is > 120° for a σ-electron-withdrawing substituent and < 120° for a σ-electron-donating substituent. Moreover, in the nitrogen-containing heterocyclic aromatic molecules, the endocyclic angle at the nitrogen atom is < 120°, and those at the carbon atoms in ortho-positions to the heteroatom are > 120° (Mootz & Wussow, 1981; Crawford et al., 2009). Similarly to the related diaminopyridines (Schwalbe et al., 1987; Rubin-Preminger & Englert, 2007; Al-Dajani et al., 2009; Betz et al., 2011), these effects are also manifested in the investigated compound. So, the smallest endocyclic angle in I (117.13 (10)°) is observed at the C5 carbon atom bearing the σ-electron-donating amino group, whereas the largest endocyclic angle in I (124.03 (11)°) is observed at the C6 carbon atom in ortho-position to the N1 heteroatom. The value of the endocyclic angle at the second (C2) carbon atom in ortho-position to the N1 heteroatom (121.83 (11)°) is significantly smaller than that at the C6 carbon atom because the C2 carbon atom bears the σ-electron-donating amino group, i.e., the C2 carbon atom is subjected to the influence of the two opposed electronic effects. The value of the endocyclic angle at the N1 heteroatom (118.15 (10)°) is also in good agreement with the above mentioned electronic effects.

The N2 and N3 nitrogen atoms of the amino groups have the trigonal-pyramidal configurations. It is worthy to note that these atoms are slightly out of the plane defined the aromatic system (r.m.s. deviation is 0.003 Å) by 0.106 (2) and -0.042 (2) Å, respectively. Apparently, this fact is explained by the developed hydrogen bonding system with the participation of the both amino groups.

In the crystal of I, the amino groups act both as proton donors and proton acceptors upon formation of the intermolecular N—H···N hydrogen bonds (Table 1). The N1 heteroatom serves as the acceptor for a hydrogen atom of one of the two amino groups (Table 1). In total, the molecules of I are linked by the intermolecular N—H···N hydrogen bonds into a three-dimensional network (Figure 2). There are no π-π interactions between the aromatic rings.

Related literature

For general background, see: Domenicano et al. (1975); Domenicano & Vaciago (1979); Mootz & Wussow (1981); Crawford et al. (2009). For the crystal structures of isomeric diaminopyridines, see: Schwalbe et al. (1987); Rubin-Preminger & Englert (2007); Al-Dajani et al. (2009); Betz et al. (2011).

S2. Experimental

The compound I was obtained commercially (Aldrich) as a fine-crystalline powder and purified additionally by filtration. Crystals suitable for the X-ray diffraction study were grown by slow evaporation from chloroform solution.

S3. Refinement

The hydrogen atoms of the amino groups were localized in the difference-Fourier map and refined isotropically with fixed isotropic displacement parameters [U_iso(H) = 1.2U_eq(N)]. C-bound H atoms were placed in calculated positions [C—H = 0.93 Å], and refined as riding, with U_iso(H) = 1.2U_eq(C).

Computing details

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); 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).

Figures

	Fig. 1. Molecular structure of I. Displacement ellipsoids are shown at the 50% probability level. H atoms are presented as small spheres of arbitrary radius.
	Fig. 2. A portion of the crystal packing showing intermolecular N—H···N hydrogen bonds as dashed lines.

Pyridine-2,5-diamine

Crystal data

C5H7N3	F(000) = 464
Mr = 109.14	Dx = 1.385 Mg m^−3
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 2334 reflections
a = 11.4447 (11) Å	θ = 3.2–28.8°
b = 7.1447 (7) Å	µ = 0.09 mm^−1
c = 12.8030 (12) Å	T = 296 K
V = 1046.89 (17) Å^3	Prism, red
Z = 8	0.30 × 0.25 × 0.20 mm

Data collection

Bruker APEXII CCD diffractometer	1595 independent reflections
Radiation source: fine-focus sealed tube	1240 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.049
ϕ and ω scans	θmax = 30.5°, θmin = 3.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −16→16
Tmin = 0.973, Tmax = 0.982	k = −10→10
13022 measured reflections	l = −18→18

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.042	Hydrogen site location: difference Fourier map
wR(F^2) = 0.109	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0475P)^2 + 0.63P] where P = (Fo^2 + 2Fc^2)/3
1595 reflections	(Δ/σ)max < 0.001
85 parameters	Δρmax = 0.36 e Å^−3
0 restraints	Δρmin = −0.24 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.46050 (8)	0.50612 (15)	0.35845 (8)	0.0150 (2)
N2	0.36236 (10)	0.66538 (15)	0.49098 (8)	0.0167 (2)
H2A	0.4111 (14)	0.610 (2)	0.5333 (13)	0.020*
H2B	0.2925 (15)	0.674 (2)	0.5190 (12)	0.020*
N3	0.38898 (10)	0.41571 (15)	0.07954 (8)	0.0164 (2)
H3A	0.3841 (13)	0.510 (2)	0.0337 (12)	0.020*
H3B	0.4559 (15)	0.352 (2)	0.0701 (12)	0.020*
C2	0.36402 (10)	0.59703 (16)	0.38919 (9)	0.0139 (2)
C3	0.27102 (10)	0.63298 (17)	0.32018 (9)	0.0148 (2)
H3	0.2045	0.6952	0.3433	0.018*
C4	0.28001 (10)	0.57463 (16)	0.21780 (9)	0.0150 (2)
H4	0.2192	0.5971	0.1712	0.018*
C5	0.38092 (10)	0.48140 (16)	0.18414 (9)	0.0139 (2)
C6	0.46769 (10)	0.45101 (17)	0.25771 (9)	0.0148 (2)
H6	0.5350	0.3889	0.2364	0.018*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0139 (5)	0.0159 (5)	0.0154 (5)	−0.0001 (4)	−0.0006 (4)	0.0002 (4)
N2	0.0162 (5)	0.0189 (5)	0.0150 (5)	0.0022 (4)	−0.0009 (4)	−0.0008 (4)
N3	0.0163 (5)	0.0190 (5)	0.0137 (5)	0.0027 (4)	0.0005 (4)	0.0003 (4)
C2	0.0148 (5)	0.0120 (5)	0.0148 (5)	−0.0018 (4)	0.0007 (4)	0.0006 (4)
C3	0.0130 (5)	0.0138 (5)	0.0176 (5)	0.0010 (4)	0.0003 (4)	0.0012 (4)
C4	0.0134 (5)	0.0138 (5)	0.0177 (5)	0.0001 (4)	−0.0024 (4)	0.0018 (4)
C5	0.0148 (5)	0.0124 (5)	0.0143 (5)	−0.0013 (4)	0.0008 (4)	0.0008 (4)
C6	0.0122 (5)	0.0154 (5)	0.0169 (5)	0.0007 (4)	0.0009 (4)	0.0003 (4)

Geometric parameters (Å, º)

N1—C2	1.3401 (15)	C2—C3	1.4069 (16)
N1—C6	1.3510 (15)	C3—C4	1.3793 (16)
N2—C2	1.3919 (15)	C3—H3	0.9300
N2—H2A	0.874 (17)	C4—C5	1.4011 (16)
N2—H2B	0.879 (17)	C4—H4	0.9300
N3—C5	1.4221 (15)	C5—C6	1.3859 (16)
N3—H3A	0.894 (16)	C6—H6	0.9300
N3—H3B	0.898 (17)
C2—N1—C6	118.15 (10)	C4—C3—H3	120.5
C2—N2—H2A	114.3 (11)	C2—C3—H3	120.5
C2—N2—H2B	114.8 (10)	C3—C4—C5	119.83 (11)
H2A—N2—H2B	111.2 (14)	C3—C4—H4	120.1
C5—N3—H3A	111.4 (10)	C5—C4—H4	120.1
C5—N3—H3B	110.4 (10)	C6—C5—C4	117.13 (10)
H3A—N3—H3B	110.2 (14)	C6—C5—N3	122.81 (11)
N1—C2—N2	117.15 (10)	C4—C5—N3	120.01 (10)
N1—C2—C3	121.83 (11)	N1—C6—C5	124.03 (11)
N2—C2—C3	120.90 (11)	N1—C6—H6	118.0
C4—C3—C2	119.02 (11)	C5—C6—H6	118.0
C6—N1—C2—N2	−175.08 (11)	C3—C4—C5—C6	0.54 (16)
C6—N1—C2—C3	0.96 (17)	C3—C4—C5—N3	177.98 (11)
N1—C2—C3—C4	−0.66 (17)	C2—N1—C6—C5	−0.51 (17)
N2—C2—C3—C4	175.23 (11)	C4—C5—C6—N1	−0.23 (17)
C2—C3—C4—C5	−0.12 (17)	N3—C5—C6—N1	−177.60 (11)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1^i	0.874 (17)	2.183 (17)	3.0541 (15)	175.1 (10)
N2—H2B···N3^ii	0.879 (17)	2.309 (17)	3.1457 (16)	159.3 (10)
N3—H3A···N2^iii	0.894 (16)	2.397 (17)	3.2150 (16)	152.2 (10)
N3—H3B···N2^iv	0.898 (17)	2.593 (17)	3.4803 (16)	170.0 (10)

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1/2, −y+1, z+1/2; (iii) x, −y+3/2, z−1/2; (iv) −x+1, y−1/2, −z+1/2.