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Acta Crystallogr Sect E Struct Rep Online. 2009 July 1; 65(Pt 7): o1511–o1512.
Published online 2009 June 6. doi:  10.1107/S160053680902100X
PMCID: PMC2969435

2,3-Diamino­pyridinium 4-nitro­benzoate

Abstract

In the title salt, C5H8N3 +·C7H4NO4 , the pyridine N atom of the 2,3-diamino­pyridine mol­ecule is protonated. The protonated N atom and one of the two 2-amino groups are hydrogen bonded to the 4-nitro­benzoate anion through a pair of N—H(...)O hydrogen bonds, forming an R 2 2(8) ring motif. The carboxyl­ate mean plane of the 4-nitro­benzoate anion is twisted by 3.77 (5)° from the attached ring and the nitro group is similarly twisted by 2.28 (10)°. In the crystal, the mol­ecules are linked by N—H(...)O and C—H(...)O inter­actions into sheets parallel to (100).

Related literature

For substituted pyridines, see: Pozharski et al. (1997 [triangle]); Katritzky et al. (1996 [triangle]); Jeffrey & Saenger (1991 [triangle]); Jeffrey (1997 [triangle]); Scheiner (1997 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1511-scheme1.jpg

Experimental

Crystal data

  • C5H8N3 +·C7H4NO4
  • M r = 276.26
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1511-efi1.jpg
  • a = 8.0827 (2) Å
  • b = 6.7365 (1) Å
  • c = 11.4489 (3) Å
  • β = 101.967 (1)°
  • V = 609.83 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 100 K
  • 0.25 × 0.17 × 0.10 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.972, T max = 0.988
  • 11659 measured reflections
  • 2808 independent reflections
  • 2155 reflections with I > 2σ(I)
  • R int = 0.045

Refinement

  • R[F 2 > 2σ(F 2)] = 0.052
  • wR(F 2) = 0.116
  • S = 1.04
  • 2808 reflections
  • 229 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.43 e Å−3
  • Δρmin = −0.30 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680902100X/tk2462sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680902100X/tk2462Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

HKF and KBS thank the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/PFIZIK/613312. KBS thanks Universiti Sains Malaysia for a post–doctoral research fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.

supplementary crystallographic information

Comment

Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997; Katritzky et al., 1996). Pyridine and its substituted derivatives are often involved in hydrogen bonding interactions (Jeffrey & Saenger, 1991; Jeffrey, 1997; Scheiner, 1997). In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title salt (I) is presented here.

The asymmetric unit of (I), Fig. 1, contains a protonated 2,3-diaminopyridinium cation and a 4-nitrobenzoate anion. In the 2,3-diaminopyridinium cation, a wide angle (123.62 (17)°) is subtended at the protonated N1 atom. The 2,3-diaminopyridinium cation is planar, with a maximum deviation of 0.005 (2)Å for atom C1. The carboxylate group is twisted slightly from the ring; the dihedral angle between C1—C6 and O3/O4/C7/C6 planes is 5.41 (10)°. The nitro group is also slightly twisted away from its attached benzene ring by 2.28 (10)°.

In the crystal packing, Fig. 2, the protonated N1 atom and the 2-amino group (N2) is hydrogen-bonded to the carboxylate oxygen atoms (O3 and O4) via a pair of N—H···O hydrogen bonds forming a ring motif, R22(8) (Bernstein et al., 1995). The 2-amino groups (N2 and N3) are involved in N—H···O3 hydrogen bonding interactions to form a R12(7) ring motif. One of the amino group hydrogen atoms, H2N3, and the ring hydrogen atom, H10A, are connected to the 4-nitro group oxygen atoms (O1 and O2) to form an R22(8) ring motif (Table 1 and Fig. 2). These molecules are linked by these interactions into sheets parallel to (100). The crystal structure is further stabilized by a π-π stacking interactions between the aminopyridine- and carboxylate-rings with centroid-to-centroid distances of 3.8343 (10) Å.

Experimental

Hot methanol solutions (20 ml) of 2,3-diaminopyridine (27 mg, Aldrich) and 4-nitrobenzoic acid (42 mg, Merck) were mixed and warmed over a heating magnetic stirrer for 5 minutes. The resulting solution was allowed to cool slowly at room temperature. Crystals of (I) appeared from the mother liquor after a few days.

Refinement

All the H atoms were located from the difference Fourier map [N–H = 0.82 (3)–0.99 (3)Å and C–H = 0.91 (2)–0.99 (2) Å] and allowed to refine freely. In the absence of significant anomalous scattering effects, 2144 Friedel pairs were merged.

Figures

Fig. 1.
The molecular structures of the ions in (I), illustrating the primary mode of association between them, showing 50% probability displacement ellipsoids and the atom numbering scheme. Dashed lines indicate the hydrogen bonding.
Fig. 2.
The crystal packing of (I). Dashed lines indicate the hydrogen bondings.

Crystal data

C5H8N3+·C7H4NO4F(000) = 288
Mr = 276.26Dx = 1.504 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 2526 reflections
a = 8.0827 (2) Åθ = 2.8–31.7°
b = 6.7365 (1) ŵ = 0.12 mm1
c = 11.4489 (3) ÅT = 100 K
β = 101.967 (1)°Block, brown
V = 609.83 (2) Å30.25 × 0.17 × 0.10 mm
Z = 2

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2808 independent reflections
Radiation source: fine-focus sealed tube2155 reflections with I > 2σ(I)
graphiteRint = 0.045
[var phi] and ω scansθmax = 34.9°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −12→12
Tmin = 0.972, Tmax = 0.988k = −10→10
11659 measured reflectionsl = −17→18

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.116H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0571P)2 + 0.026P] where P = (Fo2 + 2Fc2)/3
2808 reflections(Δ/σ)max < 0.001
229 parametersΔρmax = 0.43 e Å3
1 restraintΔρmin = −0.30 e Å3

Special details

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 s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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)

xyzUiso*/Ueq
O1−0.0506 (2)−0.7085 (2)0.85306 (17)0.0306 (4)
O2−0.04637 (19)−0.7831 (2)0.66897 (16)0.0269 (4)
O30.35100 (19)0.1109 (2)0.60686 (14)0.0223 (3)
O40.35695 (19)0.1713 (2)0.79972 (14)0.0210 (3)
N4−0.0141 (2)−0.6717 (3)0.75606 (18)0.0213 (4)
C10.1816 (2)−0.1740 (3)0.82546 (19)0.0178 (4)
C20.1021 (2)−0.3532 (3)0.8391 (2)0.0183 (4)
C30.0723 (2)−0.4824 (3)0.7432 (2)0.0178 (4)
C40.1172 (2)−0.4421 (3)0.6355 (2)0.0196 (4)
C50.1973 (2)−0.2624 (3)0.6234 (2)0.0180 (4)
C60.2309 (2)−0.1287 (3)0.71862 (19)0.0162 (4)
C70.3201 (2)0.0666 (3)0.70675 (18)0.0169 (4)
N10.5459 (2)0.4983 (2)0.80784 (16)0.0179 (3)
N20.5600 (2)0.4619 (3)0.60992 (18)0.0213 (4)
N30.7324 (2)0.8308 (3)0.62077 (18)0.0212 (4)
C80.5959 (2)0.5681 (3)0.71027 (19)0.0166 (4)
C90.6873 (2)0.7522 (3)0.72040 (19)0.0168 (4)
C100.7217 (2)0.8451 (3)0.8301 (2)0.0197 (4)
C110.6717 (2)0.7629 (3)0.9295 (2)0.0213 (4)
C120.5820 (2)0.5895 (3)0.91644 (19)0.0199 (4)
H1A0.201 (3)−0.084 (4)0.887 (2)0.020 (6)*
H2A0.068 (3)−0.384 (4)0.914 (2)0.020 (6)*
H4A0.089 (3)−0.535 (5)0.569 (2)0.033 (7)*
H5A0.232 (3)−0.233 (4)0.547 (2)0.021 (6)*
H10A0.782 (3)0.972 (5)0.834 (2)0.029 (7)*
H11A0.711 (3)0.821 (4)1.010 (2)0.027 (7)*
H12A0.540 (3)0.527 (4)0.978 (2)0.021 (6)*
H1N10.478 (3)0.375 (5)0.793 (3)0.038 (8)*
H1N20.497 (4)0.353 (5)0.608 (3)0.038 (8)*
H2N20.579 (3)0.496 (4)0.542 (2)0.017 (6)*
H1N30.735 (3)0.759 (5)0.560 (2)0.025 (7)*
H2N30.806 (4)0.917 (5)0.635 (3)0.037 (8)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0374 (9)0.0213 (8)0.0368 (10)−0.0086 (6)0.0162 (8)0.0038 (7)
O20.0274 (7)0.0170 (7)0.0348 (10)−0.0058 (6)0.0027 (7)−0.0027 (7)
O30.0293 (7)0.0175 (6)0.0226 (8)−0.0035 (5)0.0109 (6)0.0002 (6)
O40.0281 (7)0.0164 (6)0.0199 (8)−0.0056 (5)0.0083 (6)−0.0023 (6)
N40.0165 (7)0.0146 (7)0.0320 (10)−0.0015 (6)0.0030 (7)0.0026 (8)
C10.0213 (8)0.0139 (8)0.0187 (10)−0.0012 (7)0.0053 (7)−0.0008 (8)
C20.0185 (8)0.0155 (8)0.0215 (10)−0.0007 (6)0.0054 (7)0.0030 (8)
C30.0166 (8)0.0116 (7)0.0255 (11)−0.0015 (6)0.0053 (7)0.0010 (7)
C40.0216 (8)0.0132 (8)0.0249 (11)−0.0008 (6)0.0067 (8)−0.0015 (8)
C50.0205 (8)0.0146 (8)0.0196 (10)−0.0010 (7)0.0056 (7)−0.0018 (8)
C60.0176 (8)0.0111 (8)0.0201 (10)0.0012 (6)0.0043 (7)0.0032 (7)
C70.0180 (8)0.0128 (8)0.0208 (10)0.0003 (6)0.0058 (7)0.0008 (8)
N10.0188 (7)0.0161 (7)0.0191 (9)−0.0021 (6)0.0048 (6)0.0004 (7)
N20.0300 (9)0.0176 (8)0.0182 (9)−0.0056 (6)0.0094 (7)−0.0014 (7)
N30.0273 (8)0.0178 (7)0.0201 (9)−0.0061 (7)0.0089 (7)−0.0003 (8)
C80.0158 (7)0.0136 (8)0.0208 (10)−0.0012 (6)0.0046 (7)0.0007 (8)
C90.0157 (7)0.0161 (8)0.0189 (9)0.0003 (6)0.0042 (6)0.0023 (8)
C100.0199 (8)0.0168 (8)0.0228 (11)−0.0021 (7)0.0055 (7)−0.0018 (8)
C110.0210 (8)0.0225 (9)0.0206 (11)−0.0001 (7)0.0051 (7)−0.0028 (8)
C120.0201 (8)0.0223 (9)0.0176 (10)−0.0010 (7)0.0045 (7)0.0004 (8)

Geometric parameters (Å, °)

O1—N41.232 (2)N1—C81.349 (3)
O2—N41.232 (2)N1—C121.363 (3)
O3—C71.256 (2)N1—H1N10.99 (3)
O4—C71.260 (2)N2—C81.333 (3)
N4—C31.476 (2)N2—H1N20.89 (3)
C1—C21.391 (3)N2—H2N20.85 (3)
C1—C61.397 (3)N3—C91.373 (3)
C1—H1A0.92 (3)N3—H1N30.85 (3)
C2—C31.383 (3)N3—H2N30.82 (3)
C2—H2A0.98 (3)C8—C91.435 (3)
C3—C41.382 (3)C9—C101.379 (3)
C4—C51.394 (3)C10—C111.399 (3)
C4—H4A0.98 (3)C10—H10A0.98 (3)
C5—C61.396 (3)C11—C121.367 (3)
C5—H5A0.99 (3)C11—H11A0.99 (3)
C6—C71.520 (3)C12—H12A0.94 (3)
O2—N4—O1123.84 (17)C8—N1—C12123.62 (17)
O2—N4—C3118.06 (18)C8—N1—H1N1113.8 (17)
O1—N4—C3118.10 (18)C12—N1—H1N1122.6 (17)
C2—C1—C6120.69 (19)C8—N2—H1N2119.0 (19)
C2—C1—H1A119.4 (17)C8—N2—H2N2126.1 (17)
C6—C1—H1A119.9 (17)H1N2—N2—H2N2114 (2)
C3—C2—C1117.7 (2)C9—N3—H1N3121 (2)
C3—C2—H2A122.2 (16)C9—N3—H2N3114 (2)
C1—C2—H2A120.1 (16)H1N3—N3—H2N3115 (3)
C4—C3—C2123.38 (18)N2—C8—N1118.49 (17)
C4—C3—N4118.44 (18)N2—C8—C9123.34 (19)
C2—C3—N4118.18 (18)N1—C8—C9118.16 (18)
C3—C4—C5118.21 (19)N3—C9—C10122.90 (18)
C3—C4—H4A120.7 (17)N3—C9—C8119.10 (19)
C5—C4—H4A121.1 (17)C10—C9—C8117.97 (18)
C4—C5—C6120.13 (19)C9—C10—C11121.58 (18)
C4—C5—H5A118.6 (16)C9—C10—H10A116.5 (16)
C6—C5—H5A121.2 (16)C11—C10—H10A121.9 (16)
C5—C6—C1119.87 (17)C12—C11—C10119.1 (2)
C5—C6—C7120.51 (17)C12—C11—H11A120.1 (16)
C1—C6—C7119.62 (17)C10—C11—H11A120.5 (16)
O3—C7—O4125.37 (18)N1—C12—C11119.6 (2)
O3—C7—C6118.35 (18)N1—C12—H12A115.8 (16)
O4—C7—C6116.28 (17)C11—C12—H12A124.6 (16)
C6—C1—C2—C3−0.8 (3)C1—C6—C7—O3−174.40 (17)
C1—C2—C3—C4−0.1 (3)C5—C6—C7—O4−174.72 (17)
C1—C2—C3—N4−179.16 (16)C1—C6—C7—O45.6 (2)
O2—N4—C3—C4−1.9 (3)C12—N1—C8—N2177.00 (18)
O1—N4—C3—C4178.55 (18)C12—N1—C8—C9−2.2 (3)
O2—N4—C3—C2177.21 (18)N2—C8—C9—N33.9 (3)
O1—N4—C3—C2−2.3 (3)N1—C8—C9—N3−176.90 (17)
C2—C3—C4—C50.4 (3)N2—C8—C9—C10−177.88 (18)
N4—C3—C4—C5179.44 (17)N1—C8—C9—C101.3 (2)
C3—C4—C5—C60.2 (3)N3—C9—C10—C11178.94 (19)
C4—C5—C6—C1−1.0 (3)C8—C9—C10—C110.8 (3)
C4—C5—C6—C7179.32 (16)C9—C10—C11—C12−2.1 (3)
C2—C1—C6—C51.3 (3)C8—N1—C12—C110.9 (3)
C2—C1—C6—C7−179.02 (17)C10—C11—C12—N11.3 (3)
C5—C6—C7—O35.3 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···O40.99 (3)1.70 (3)2.671 (2)167 (3)
N2—H1N2···O30.89 (3)2.01 (3)2.901 (2)178 (5)
N2—H2N2···O3i0.86 (2)2.06 (2)2.903 (2)171 (2)
N3—H1N3···O3i0.85 (3)2.14 (3)2.951 (3)159 (2)
N3—H2N3···O2ii0.82 (3)2.34 (3)3.140 (2)165 (3)
C10—H10A···O1ii0.98 (3)2.53 (3)3.507 (2)176.9 (16)
C11—H11A···O4iii0.99 (2)2.56 (2)3.216 (3)123.5 (19)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2462).

References

  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • Jeffrey, G. A. (1997). In An Introduction to Hydrogen Bonding Oxford University Press.
  • Jeffrey, G. A. & Saenger, W. (1991). In Hydrogen Bonding in Biological Structures Berlin: Springer.
  • Katritzky, A. R., Rees, C. W. & Scriven, E. F. V. (1996). In Comprehensive Heterocyclic Chemistry II Oxford: Pergamon Press.
  • Pozharski, A. F., Soldatenkov, A. T. & Katritzky, A. R. (1997). In Heterocycles in Life and Society New York: Wiley.
  • Scheiner, S. (1997). In Hydrogen Bonding, A Theoretical Perspective Oxford University Press.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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