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Acta Crystallogr Sect E Struct Rep Online. 2009 July 1; 65(Pt 7): o1531–o1532.
Published online 2009 June 10. doi:  10.1107/S1600536809021205
PMCID: PMC2969464

3,4-Diamino­pyridinium hydrogen succinate

Abstract

In the title compound, C5H8N3 +·C4H5O4 , the pyridine N atom of the 3,4-diamino­pyridine mol­ecule is protonated. The protonated N atom participates in an N—H(...)O hydrogen bond to a succinate O atom of the singly deprotonated succinate anion. Each of the two amino groups are hydrogen-bonded to the O atoms of two different sets of succinate groups.. The crystal structure is further stabilized by O—H(...)O and C—H(...)O hydrogen bonds.

Related literature

For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997 [triangle]); Katritzky et al. (1996 [triangle]). For the use of 3,4-diamino­pyridine in Schiff base reactions, see: Opozda et al. (2006 [triangle]). For related structures, see: Opozda et al. (2006 [triangle]); Rubin-Preminger & Englert (2007 [triangle]); Koleva et al. (2007 [triangle], 2008 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]) and 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-o1531-scheme1.jpg

Experimental

Crystal data

  • C5H8N3 +·C4H5O4
  • M r = 227.22
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1531-efi1.jpg
  • a = 4.9862 (2) Å
  • b = 9.5028 (3) Å
  • c = 10.4775 (3) Å
  • β = 93.653 (2)°
  • V = 495.45 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 100 K
  • 0.41 × 0.13 × 0.08 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.929, T max = 0.991
  • 9518 measured reflections
  • 2280 independent reflections
  • 2119 reflections with I > 2σ(I)
  • R int = 0.028

Refinement

  • R[F 2 > 2σ(F 2)] = 0.036
  • wR(F 2) = 0.104
  • S = 1.18
  • 2280 reflections
  • 197 parameters
  • 1 restraint
  • All H-atom parameters refined
  • Δρmax = 0.41 e Å−3
  • Δρmin = −0.24 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: SHELXTL; software 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/S1600536809021205/sj2630sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809021205/sj2630Isup2.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). 3,4-diaminopyridine is used as a component in Schiff base reactions (Opozda et al. 2006). The crystal structure of 3,4-diaminopyridine (Rubin-Preminger & Englert, 2007), 3,4-diaminopyridinium hydrogen squarate (Koleva et al., 2007) and 3,4-diaminopyridinium hydrogen tartarate (Koleva et al., 2008) have been reported in the literature. Since our aim is to study some interesting hydrogen-bonding interactions, the synthesis and structure of the title compound (I) is presented here.

The asymmetric unit of (I) (Fig 1), contains a protonated 3,4-diaminopyridinium cation and a hydrogen succinate anion. The bond lengths (Allen et al., 1987) and angles are normal. In the 3,4-diaminopyridinium cation, protonation of the N1 atom leads to a slight increase in the C1—N1—C5 angle to 121.56 (12)°, compared to 115.69 (19)° in 3,4-diaminopyridine (Rubin-Preminger & Englert, 2007). The 3,4-diaminopyridinium cation is planar, with a maximum deviation of 0.0070 (15)Å for atom C4.

In the crystal packing (Fig. 2), the protonated N1 atom is hydrogen bonded to the carboxylate oxygen atom of O3 through N—H···O hydrogen bonds. The two amino groups (N2 and N3) are involved in the hydrogen bonding via N—H···O H-bonds with hydrogen succinate oxygen atom (O1) to form an R12(7) ring motif (Bernstein et al., 1995). The N3 amino group and ring carbon atom (C2) are both hydrogen-bonded to the carboxylate oxygen atom (O3) to form an R12(6) ring motif. The molecules are further connected via O—H···O hydrogen bonds forming a 3-D network (Table 1 and Fig 2).

Experimental

Hot methanol solutions (20 ml) of 3,4-diaminopyridine (27 mg, Aldrich) and succinic acid (29 mg, Merck) were mixed and warmed 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 aroms were located from the difference Fourier map [N–H = 0.93 (3)–0.97 (3) Å, C–H = 0.84 (2)–1.13 (3)Å & O–H = 0.99 (4) Å] and allowed to refine freely. In the absence of significant anomalous scattering effects, 1862 Friedel pairs were merged.

Figures

Fig. 1.
The molecular structure of (I), showing 50% probability displacement ellipsoids and the atom numbering scheme.
Fig. 2.
The overall three-dimensional network of (I). Dashed lines indicate hydrogen bonds.

Crystal data

C5H8N3+·C4H5O4F(000) = 240
Mr = 227.22Dx = 1.523 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 4153 reflections
a = 4.9862 (2) Åθ = 2.9–38.4°
b = 9.5028 (3) ŵ = 0.12 mm1
c = 10.4775 (3) ÅT = 100 K
β = 93.653 (2)°Block, colourless
V = 495.45 (3) Å30.41 × 0.13 × 0.08 mm
Z = 2

Data collection

Bruker APEXII CCD area-detector diffractometer2280 independent reflections
Radiation source: fine-focus sealed tube2119 reflections with I > 2σ(I)
graphiteRint = 0.028
[var phi] and ω scansθmax = 35.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −8→8
Tmin = 0.929, Tmax = 0.991k = −15→15
9518 measured reflectionsl = −16→16

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)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.104All H-atom parameters refined
S = 1.18w = 1/[σ2(Fo2) + (0.0624P)2 + 0.022P] where P = (Fo2 + 2Fc2)/3
2280 reflections(Δ/σ)max < 0.001
197 parametersΔρmax = 0.41 e Å3
1 restraintΔρmin = −0.24 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems 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
O10.2865 (2)−0.15266 (13)0.23443 (10)0.0166 (2)
O20.2994 (2)−0.04711 (12)0.04363 (10)0.0145 (2)
O31.0339 (2)0.20905 (12)0.27633 (10)0.0148 (2)
O41.0369 (2)0.31053 (11)0.08455 (10)0.01284 (19)
C60.3844 (3)−0.06666 (14)0.16351 (13)0.0109 (2)
C70.6179 (3)0.02567 (15)0.20940 (13)0.0127 (2)
C80.7020 (3)0.13495 (15)0.11407 (13)0.0120 (2)
C90.9402 (3)0.22422 (14)0.16284 (12)0.0100 (2)
N10.4164 (2)0.40451 (13)0.33423 (12)0.0123 (2)
N20.8257 (3)0.65927 (15)0.17427 (12)0.0172 (2)
N31.0198 (3)0.68665 (15)0.43411 (12)0.0148 (2)
C10.5088 (3)0.41464 (15)0.45697 (13)0.0128 (2)
C20.7131 (3)0.50705 (15)0.49097 (13)0.0123 (2)
C30.8247 (3)0.59224 (14)0.39891 (13)0.0108 (2)
C40.7264 (3)0.57828 (14)0.26856 (13)0.0113 (2)
C50.5199 (3)0.48313 (15)0.24195 (13)0.0121 (2)
H90.149 (6)−0.108 (4)0.012 (3)0.059 (11)*
H1N10.270 (6)0.343 (4)0.329 (3)0.039 (8)*
H1N20.801 (5)0.635 (3)0.105 (3)0.026 (7)*
H2N20.992 (6)0.706 (4)0.202 (3)0.036 (7)*
H1N31.097 (5)0.734 (3)0.382 (2)0.019 (6)*
H2N31.073 (4)0.697 (3)0.520 (2)0.018 (6)*
H1A0.426 (4)0.362 (3)0.516 (2)0.020 (6)*
H2A0.770 (4)0.517 (3)0.574 (2)0.018 (5)*
H5A0.458 (5)0.465 (3)0.167 (2)0.015 (5)*
H7A0.570 (5)0.073 (3)0.304 (3)0.029 (7)*
H7B0.758 (6)−0.037 (4)0.247 (3)0.043 (8)*
H8A0.757 (5)0.094 (3)0.043 (3)0.025 (6)*
H8B0.570 (4)0.203 (3)0.097 (2)0.017 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0190 (5)0.0174 (5)0.0134 (4)−0.0080 (4)0.0009 (4)0.0021 (4)
O20.0170 (4)0.0147 (4)0.0111 (4)−0.0043 (4)−0.0033 (3)0.0011 (3)
O30.0168 (4)0.0152 (5)0.0118 (4)−0.0047 (4)−0.0039 (3)0.0026 (4)
O40.0121 (4)0.0130 (4)0.0132 (4)−0.0020 (3)−0.0006 (3)0.0040 (3)
C60.0115 (5)0.0107 (5)0.0107 (5)−0.0012 (4)0.0015 (4)−0.0015 (4)
C70.0130 (5)0.0131 (5)0.0116 (5)−0.0046 (4)−0.0015 (4)0.0019 (4)
C80.0113 (5)0.0129 (5)0.0113 (5)−0.0038 (4)−0.0020 (4)0.0006 (4)
C90.0094 (5)0.0095 (5)0.0109 (5)0.0000 (4)−0.0006 (4)0.0004 (4)
N10.0129 (5)0.0114 (5)0.0124 (5)−0.0025 (4)−0.0001 (4)0.0000 (4)
N20.0227 (6)0.0187 (6)0.0103 (5)−0.0088 (5)0.0012 (4)0.0007 (4)
N30.0164 (5)0.0160 (5)0.0119 (5)−0.0066 (4)0.0002 (4)−0.0018 (4)
C10.0143 (5)0.0130 (5)0.0112 (5)−0.0027 (4)0.0016 (4)0.0014 (4)
C20.0142 (5)0.0128 (5)0.0100 (5)−0.0015 (4)0.0005 (4)0.0003 (4)
C30.0110 (5)0.0105 (5)0.0108 (5)−0.0013 (4)0.0000 (4)−0.0013 (4)
C40.0129 (5)0.0105 (5)0.0104 (5)−0.0016 (4)0.0003 (4)−0.0005 (4)
C50.0127 (5)0.0130 (5)0.0105 (5)−0.0022 (4)−0.0004 (4)−0.0003 (4)

Geometric parameters (Å, °)

O1—C61.2265 (18)N1—H1N10.93 (3)
O2—C61.3130 (17)N2—C41.3695 (19)
O2—H90.99 (4)N2—H1N20.77 (3)
O3—C91.2578 (16)N2—H2N20.97 (3)
O4—C91.2760 (16)N3—C31.3569 (18)
C6—C71.5118 (19)N3—H1N30.82 (3)
C7—C81.5183 (19)N3—H2N30.93 (2)
C7—H7A1.13 (3)C1—C21.3749 (19)
C7—H7B0.98 (3)C1—H1A0.91 (2)
C8—C91.5213 (18)C2—C31.4013 (19)
C8—H8A0.90 (3)C2—H2A0.91 (2)
C8—H8B0.93 (2)C3—C41.4275 (18)
N1—C11.3414 (18)C4—C51.3853 (18)
N1—C51.3501 (18)C5—H5A0.84 (2)
C6—O2—H9116 (2)C4—N2—H1N2118 (2)
O1—C6—O2123.87 (13)C4—N2—H2N2112.4 (17)
O1—C6—C7121.47 (12)H1N2—N2—H2N2121 (2)
O2—C6—C7114.66 (12)C3—N3—H1N3122.4 (17)
C6—C7—C8115.28 (11)C3—N3—H2N3119.1 (16)
C6—C7—H7A107.9 (14)H1N3—N3—H2N3119 (2)
C8—C7—H7A113.1 (15)N1—C1—C2119.84 (13)
C6—C7—H7B107 (2)N1—C1—H1A117.7 (15)
C8—C7—H7B117.4 (18)C2—C1—H1A122.4 (15)
H7A—C7—H7B94 (2)C1—C2—C3120.72 (12)
C7—C8—C9113.76 (10)C1—C2—H2A119.8 (16)
C7—C8—H8A111.0 (18)C3—C2—H2A119.4 (16)
C9—C8—H8A104.5 (17)N3—C3—C2120.27 (12)
C7—C8—H8B112.4 (14)N3—C3—C4121.19 (12)
C9—C8—H8B101.8 (15)C2—C3—C4118.54 (11)
H8A—C8—H8B113 (2)N2—C4—C5121.32 (12)
O3—C9—O4123.29 (12)N2—C4—C3121.34 (12)
O3—C9—C8119.24 (12)C5—C4—C3117.30 (12)
O4—C9—C8117.47 (11)N1—C5—C4122.02 (12)
C1—N1—C5121.56 (12)N1—C5—H5A114.7 (16)
C1—N1—H1N1108.8 (17)C4—C5—H5A123.1 (16)
C5—N1—H1N1129.4 (17)
O1—C6—C7—C8−175.22 (13)C1—C2—C3—C4−1.6 (2)
O2—C6—C7—C85.09 (18)N3—C3—C4—N20.2 (2)
C6—C7—C8—C9−179.08 (12)C2—C3—C4—N2179.47 (13)
C7—C8—C9—O3−4.90 (18)N3—C3—C4—C5−177.55 (14)
C7—C8—C9—O4174.38 (12)C2—C3—C4—C51.74 (19)
C5—N1—C1—C20.1 (2)C1—N1—C5—C40.0 (2)
N1—C1—C2—C30.7 (2)N2—C4—C5—N1−178.70 (13)
C1—C2—C3—N3177.65 (14)C3—C4—C5—N1−1.0 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H9···O4i0.99 (4)1.53 (4)2.4815 (14)159 (3)
N1—H1N1···O3ii0.93 (3)1.80 (3)2.7036 (16)163 (3)
N2—H1N2···O2iii0.77 (3)2.36 (3)3.0440 (17)150 (3)
N2—H2N2···O1iv0.97 (3)2.00 (3)2.9473 (17)164 (3)
N3—H1N3···O1iv0.82 (3)2.15 (3)2.9720 (18)176 (2)
N3—H2N3···O3v0.93 (2)2.23 (2)3.0699 (17)149.7 (18)
C2—H2A···O3v0.91 (2)2.56 (3)3.2907 (17)138 (2)
C5—H5A···O2iii0.84 (2)2.59 (2)3.1923 (18)129.7 (19)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ2630).

References

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