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

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ISSN: 2056-9890

Pyridine-2,5-di­amine

aD. Ghitu Institute of Electronic Engineering and Nanotechnologies, 3/3 Academy str., MD-2028 Chisinau, Moldova, bX-Ray Structural Centre, A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov St, B-334, Moscow 119991, Russian Federation, cInstitute of Applied Physics Academy of Sciences of Moldova, 5 Academy str., MD-2028 Chisinau, Moldova, and dDepartment of Chemistry & Biology, New Mexico Highlands University, 803 University Avenue, Las Vegas, NM 87701, USA
*Correspondence e-mail: sergiudraguta@gmail.com

(Received 6 November 2012; accepted 8 November 2012; online 17 November 2012)

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, A., Vaciago, A. & Coulson, C. A. (1975). Acta Cryst. B31, 221-234.]); Domenicano & Vaciago (1979[Domenicano, A. & Vaciago, A. (1979). Acta Cryst. B35, 1382-1388.]); Mootz & Wussow (1981[Mootz, D. & Wussow, H.-G. (1981). J. Chem. Phys. 75, 1517-1522.]); Crawford et al. (2009[Crawford, S., Kirchner, M. T., Blaser, D., Boese, R., David, W. I. F., Dawson, A., Gehrke, A., Ibberson, R. M., Marshall, W. G., Parsons, S. & Yamamuro, O. (2009). Angew. Chem. Int. Ed. 48, 755-757.]). For the crystal structures of isomeric diamino­pyridines, see: Schwalbe et al. (1987[Schwalbe, C. H., Williams, G. J. B. & Koetzle, T. F. (1987). Acta Cryst. C43, 2191-2195.]); Rubin-Preminger & Englert (2007[Rubin-Preminger, J. M. & Englert, U. (2007). Acta Cryst. E63, o757-o758.]); Al-Dajani et al. (2009[Al-Dajani, M. T. M., Salhin, A., Mohamed, N., Loh, W.-S. & Fun, H.-K. (2009). Acta Cryst. E65, o2931-o2932.]); Betz et al. (2011[Betz, R., Gerber, T., Hosten, E. & Schalekamp, H. (2011). Acta Cryst. E67, o2154.]).

[Scheme 1]

Experimental

Crystal data
  • C5H7N3

  • Mr = 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) Å3

  • 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[Sheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.973, Tmax = 0.982

  • 13022 measured reflections

  • 1595 independent reflections

  • 1240 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.36 e Å−3

  • Δρmin = −0.24 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2A⋯N1i 0.874 (17) 2.183 (17) 3.0541 (15) 175.1 (10)
N2—H2B⋯N3ii 0.879 (17) 2.309 (17) 3.1457 (16) 159.3 (10)
N3—H3A⋯N2iii 0.894 (16) 2.397 (17) 3.2150 (16) 152.2 (10)
N3—H3B⋯N2iv 0.898 (17) 2.593 (17) 3.4803 (16) 170.0 (10)
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) [-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]; (iii) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]; (iv) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2001[Bruker (2001). 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.

Supporting information


Comment top

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 top

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 top

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.

Refinement top

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

Computing details top

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 top
[Figure 1] 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.
[Figure 2] Fig. 2. A portion of the crystal packing showing intermolecular N—H···N hydrogen bonds as dashed lines.
Pyridine-2,5-diamine top
Crystal data top
C5H7N3F(000) = 464
Mr = 109.14Dx = 1.385 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 2334 reflections
a = 11.4447 (11) Åθ = 3.2–28.8°
b = 7.1447 (7) ŵ = 0.09 mm1
c = 12.8030 (12) ÅT = 296 K
V = 1046.89 (17) Å3Prism, red
Z = 80.30 × 0.25 × 0.20 mm
Data collection top
Bruker APEXII CCD
diffractometer
1595 independent reflections
Radiation source: fine-focus sealed tube1240 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.049
ϕ and ω scansθmax = 30.5°, θmin = 3.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 1616
Tmin = 0.973, Tmax = 0.982k = 1010
13022 measured reflectionsl = 1818
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)] = 0.042Hydrogen site location: difference Fourier map
wR(F2) = 0.109H atoms treated by a mixture of independent and constrained refinement
S = 1.01 w = 1/[σ2(Fo2) + (0.0475P)2 + 0.63P]
where P = (Fo2 + 2Fc2)/3
1595 reflections(Δ/σ)max < 0.001
85 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.24 e Å3
Crystal data top
C5H7N3V = 1046.89 (17) Å3
Mr = 109.14Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 11.4447 (11) ŵ = 0.09 mm1
b = 7.1447 (7) ÅT = 296 K
c = 12.8030 (12) Å0.30 × 0.25 × 0.20 mm
Data collection top
Bruker APEXII CCD
diffractometer
1595 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
1240 reflections with I > 2σ(I)
Tmin = 0.973, Tmax = 0.982Rint = 0.049
13022 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.109H atoms treated by a mixture of independent and constrained refinement
S = 1.01Δρmax = 0.36 e Å3
1595 reflectionsΔρmin = 0.24 e Å3
85 parameters
Special details top

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
N10.46050 (8)0.50612 (15)0.35845 (8)0.0150 (2)
N20.36236 (10)0.66538 (15)0.49098 (8)0.0167 (2)
H2A0.4111 (14)0.610 (2)0.5333 (13)0.020*
H2B0.2925 (15)0.674 (2)0.5190 (12)0.020*
N30.38898 (10)0.41571 (15)0.07954 (8)0.0164 (2)
H3A0.3841 (13)0.510 (2)0.0337 (12)0.020*
H3B0.4559 (15)0.352 (2)0.0701 (12)0.020*
C20.36402 (10)0.59703 (16)0.38919 (9)0.0139 (2)
C30.27102 (10)0.63298 (17)0.32018 (9)0.0148 (2)
H30.20450.69520.34330.018*
C40.28001 (10)0.57463 (16)0.21780 (9)0.0150 (2)
H40.21920.59710.17120.018*
C50.38092 (10)0.48140 (16)0.18414 (9)0.0139 (2)
C60.46769 (10)0.45101 (17)0.25771 (9)0.0148 (2)
H60.53500.38890.23640.018*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0139 (5)0.0159 (5)0.0154 (5)0.0001 (4)0.0006 (4)0.0002 (4)
N20.0162 (5)0.0189 (5)0.0150 (5)0.0022 (4)0.0009 (4)0.0008 (4)
N30.0163 (5)0.0190 (5)0.0137 (5)0.0027 (4)0.0005 (4)0.0003 (4)
C20.0148 (5)0.0120 (5)0.0148 (5)0.0018 (4)0.0007 (4)0.0006 (4)
C30.0130 (5)0.0138 (5)0.0176 (5)0.0010 (4)0.0003 (4)0.0012 (4)
C40.0134 (5)0.0138 (5)0.0177 (5)0.0001 (4)0.0024 (4)0.0018 (4)
C50.0148 (5)0.0124 (5)0.0143 (5)0.0013 (4)0.0008 (4)0.0008 (4)
C60.0122 (5)0.0154 (5)0.0169 (5)0.0007 (4)0.0009 (4)0.0003 (4)
Geometric parameters (Å, º) top
N1—C21.3401 (15)C2—C31.4069 (16)
N1—C61.3510 (15)C3—C41.3793 (16)
N2—C21.3919 (15)C3—H30.9300
N2—H2A0.874 (17)C4—C51.4011 (16)
N2—H2B0.879 (17)C4—H40.9300
N3—C51.4221 (15)C5—C61.3859 (16)
N3—H3A0.894 (16)C6—H60.9300
N3—H3B0.898 (17)
C2—N1—C6118.15 (10)C4—C3—H3120.5
C2—N2—H2A114.3 (11)C2—C3—H3120.5
C2—N2—H2B114.8 (10)C3—C4—C5119.83 (11)
H2A—N2—H2B111.2 (14)C3—C4—H4120.1
C5—N3—H3A111.4 (10)C5—C4—H4120.1
C5—N3—H3B110.4 (10)C6—C5—C4117.13 (10)
H3A—N3—H3B110.2 (14)C6—C5—N3122.81 (11)
N1—C2—N2117.15 (10)C4—C5—N3120.01 (10)
N1—C2—C3121.83 (11)N1—C6—C5124.03 (11)
N2—C2—C3120.90 (11)N1—C6—H6118.0
C4—C3—C2119.02 (11)C5—C6—H6118.0
C6—N1—C2—N2175.08 (11)C3—C4—C5—C60.54 (16)
C6—N1—C2—C30.96 (17)C3—C4—C5—N3177.98 (11)
N1—C2—C3—C40.66 (17)C2—N1—C6—C50.51 (17)
N2—C2—C3—C4175.23 (11)C4—C5—C6—N10.23 (17)
C2—C3—C4—C50.12 (17)N3—C5—C6—N1177.60 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.874 (17)2.183 (17)3.0541 (15)175.1 (10)
N2—H2B···N3ii0.879 (17)2.309 (17)3.1457 (16)159.3 (10)
N3—H3A···N2iii0.894 (16)2.397 (17)3.2150 (16)152.2 (10)
N3—H3B···N2iv0.898 (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, z1/2; (iv) x+1, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC5H7N3
Mr109.14
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)296
a, b, c (Å)11.4447 (11), 7.1447 (7), 12.8030 (12)
V3)1046.89 (17)
Z8
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.30 × 0.25 × 0.20
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.973, 0.982
No. of measured, independent and
observed [I > 2σ(I)] reflections
13022, 1595, 1240
Rint0.049
(sin θ/λ)max1)0.714
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.109, 1.01
No. of reflections1595
No. of parameters85
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.36, 0.24

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2001), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.874 (17)2.183 (17)3.0541 (15)175.1 (10)
N2—H2B···N3ii0.879 (17)2.309 (17)3.1457 (16)159.3 (10)
N3—H3A···N2iii0.894 (16)2.397 (17)3.2150 (16)152.2 (10)
N3—H3B···N2iv0.898 (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, z1/2; (iv) x+1, y1/2, z+1/2.
 

Acknowledgements

The authors are grateful for NSF support via DMR grant 0934212 (PREM) and CHE 0832622.

References

First citationAl-Dajani, M. T. M., Salhin, A., Mohamed, N., Loh, W.-S. & Fun, H.-K. (2009). Acta Cryst. E65, o2931–o2932.  Web of Science CSD CrossRef IUCr Journals
First citationBetz, R., Gerber, T., Hosten, E. & Schalekamp, H. (2011). Acta Cryst. E67, o2154.  Web of Science CSD CrossRef IUCr Journals
First citationBruker (2001). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationBruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationCrawford, S., Kirchner, M. T., Blaser, D., Boese, R., David, W. I. F., Dawson, A., Gehrke, A., Ibberson, R. M., Marshall, W. G., Parsons, S. & Yamamuro, O. (2009). Angew. Chem. Int. Ed. 48, 755–757.  Web of Science CSD CrossRef CAS
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First citationMootz, D. & Wussow, H.-G. (1981). J. Chem. Phys. 75, 1517–1522.  CSD CrossRef CAS Web of Science
First citationRubin-Preminger, J. M. & Englert, U. (2007). Acta Cryst. E63, o757–o758.  Web of Science CSD CrossRef IUCr Journals
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First citationSheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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