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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2369.
Published online 2010 August 21. doi:  10.1107/S1600536810032617
PMCID: PMC3007997

2,3-Diamino­pyridinium (2E,4E)-hexa-2,4-dienoate

Abstract

In the title salt, C5H8N3 +·C6H7O2 , the pyridine N atom of the 2,3-diamino­pyridine mol­ecule is protonated. The 2,3-diamino­pyridinium cation is essentially planar, with a maximum deviation of 0.068 (2) Å for one of the amino N atoms. The sorbate anion adopts an extended conformation. In the crystal structure, the protonated N atom and one of the two amino-group H atoms are hydrogen bonded to the sorbate anion through a pair of N—H(...)O hydrogen bonds, forming an R 2 2(8) ring motif. The ion pairs are further connected via inter­molecular N—H(...)O and C—H(...)O hydrogen bonds, forming two-dimensional networks parallel to (100).

Related literature

For details of non-covalent inter­actions, see: Desiraju (1995 [triangle]); Moulton & Zaworotko (2001 [triangle]); Biradha & Fujita (2002 [triangle]). For applications of sorbic acid, see: Martindale (1996 [triangle]); Richards (1972 [triangle]). For related structures, see: Cox (1994 [triangle]); Thanigaimani et al. (2007 [triangle]); Raj et al. (2003 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For standard bond-length data, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2369-scheme1.jpg

Experimental

Crystal data

  • C5H8N3 +·C6H7O2
  • M r = 221.26
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2369-efi1.jpg
  • a = 9.0440 (3) Å
  • b = 10.6964 (3) Å
  • c = 12.4632 (4) Å
  • β = 94.947 (2)°
  • V = 1201.18 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 296 K
  • 0.15 × 0.15 × 0.09 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.987, T max = 0.993
  • 8260 measured reflections
  • 2736 independent reflections
  • 1794 reflections with I > 2σ(I)
  • R int = 0.053

Refinement

  • R[F 2 > 2σ(F 2)] = 0.049
  • wR(F 2) = 0.111
  • S = 1.02
  • 2736 reflections
  • 205 parameters
  • All H-atom parameters refined
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [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/S1600536810032617/lh5118sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810032617/lh5118Isup2.hkl

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

Acknowledgments

MH and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

Non-covalent interactions, such as hydrogen bonds, π···π staking and the C—H···π interactions, play important roles in determining the conformation of molecules, crystal packing and molecular assembly in an organized supramolecular structure (Desiraju, 1995; Moulton & Zaworotko, 2001; Biradha & Fujita, 2002). Sorbic acid (2,4-hexadienoic acid) exhibits antibacterial and antifungal properties (Martindale, 1996) and has been used to prevent spoilage of syrup by moulds (Richards, 1972). The crystal structure of sorbic acid (Cox, 1994), 2,4-diamino-6-phenyl-1,3,5-triazine-sorbic acid (Thanigaimani et al., 2007) and trimethoprim sorbate (Raj et al., 2003) have been reported in the literature. Since our aim is to study some interesting hydrogen-bonding interactions, the crystal structure of the title compound is presented herein.

The asymmetric unit of the title compound, (Fig 1), contains one 2,3-diaminopyridinium cation and one sorbate anion. The bond lengths (Allen et al., 1987) and angles are normal. The 2,3-diaminopyridinium cation is planar with a maximum deviation of 0.068 (2) Å for atom N3. Protonation of atom N1 has resulted in a slight increase in the magnitude of angle C1—N1—C5 [122.86 (16)°]. The sorbic acid moiety is in the EE configuration. The extended conformation of the sorbic acid can be described by the torsion angles C6-C7-C8-C9 = -173.77 (16)°, C7-C8-C9-C10 = 176.15 (18)°, C8-C9-C10-C11 = -176.92 (18)° and O2-C6-C7-C8 = 171.14 (16)°. This conformation is similar to that found in the trimethoprim sorbate dihydrate (Raj et al., 2003).

In the crystal structure, (Fig. 2), the protonated N1 atom and the 2-amino group N atom (N2) is hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of N1—H1N1···O2 and N2—H2N2···O1 hydrogen bonds forming a ring motif R22(8) (Bernstein et al., 1995). The ion pairs are further connected via N2—H1N2···O2i; N3—H1N3···O2i; N3—H2N3···O1ii and C10—H10···O1iii hydrogen bonds (see Table 1 for symmetry codes) forming two-dimensional networks parallel to (100).

Experimental

A hot methanol solution (20 ml) of 2,3-diaminopyridine (59 mg, Aldrich) and sorbic acid (56 mg, Merck) were mixed and warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title compound appeared after a few days.

Refinement

All H atoms were located in a difference Fourier map and refined freely [C–H = 0.94 (2)–1.04 (2) Å and N–H = 0.86 (2)–1.00 (2) Å].

Figures

Fig. 1.
The asymmetric unit of the title compound. Displacement ellipsoids are drawn at the 50% probability level. Hydrogen bonds are shown as dashed lines.
Fig. 2.
The crystal packing of (I) showing hydrogen bonds as dashed lines. H atoms not involved in the intermolecular interactions have been omitted for clarity.

Crystal data

C5H8N3+·C6H7O2F(000) = 472
Mr = 221.26Dx = 1.224 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1444 reflections
a = 9.0440 (3) Åθ = 3.3–28.9°
b = 10.6964 (3) ŵ = 0.09 mm1
c = 12.4632 (4) ÅT = 296 K
β = 94.947 (2)°Block, red
V = 1201.18 (6) Å30.15 × 0.15 × 0.09 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2736 independent reflections
Radiation source: fine-focus sealed tube1794 reflections with I > 2σ(I)
graphiteRint = 0.053
[var phi] and ω scansθmax = 27.5°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −11→8
Tmin = 0.987, Tmax = 0.993k = −13→11
8260 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)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.111All H-atom parameters refined
S = 1.02w = 1/[σ2(Fo2) + (0.0417P)2 + 0.1735P] where P = (Fo2 + 2Fc2)/3
2736 reflections(Δ/σ)max < 0.001
205 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.22 e Å3

Special details

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 > 2σ(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
O1−0.19667 (13)0.14636 (12)0.53361 (8)0.0233 (3)
O2−0.04642 (13)0.18916 (12)0.40526 (8)0.0241 (3)
C6−0.14500 (18)0.12200 (17)0.44625 (11)0.0180 (4)
H7−0.148 (2)−0.0069 (18)0.3182 (13)0.026 (5)*
H8−0.364 (2)−0.0391 (18)0.4703 (14)0.030 (5)*
H9−0.317 (2)−0.1811 (18)0.2736 (14)0.028 (5)*
H10−0.545 (2)−0.2085 (19)0.4233 (15)0.037 (6)*
H11A−0.672 (3)−0.307 (2)0.2669 (16)0.050 (6)*
H11B−0.556 (2)−0.407 (2)0.3260 (14)0.031 (5)*
H11C−0.507 (2)−0.3389 (19)0.2230 (15)0.034 (5)*
C7−0.1975 (2)0.01064 (18)0.38280 (12)0.0224 (4)
C8−0.3120 (2)−0.06038 (18)0.40571 (12)0.0209 (4)
C9−0.3730 (2)−0.16160 (17)0.33880 (13)0.0219 (4)
C10−0.4924 (2)−0.22749 (18)0.35940 (14)0.0252 (4)
C11−0.5606 (2)−0.3280 (2)0.28818 (17)0.0309 (5)
H2N30.224 (2)0.516 (2)0.8425 (15)0.035 (6)*
N10.09874 (16)0.36086 (15)0.52745 (10)0.0212 (4)
N20.00087 (17)0.28443 (16)0.67865 (12)0.0236 (4)
N30.1886 (2)0.44680 (19)0.80698 (11)0.0286 (4)
C10.1867 (2)0.43933 (19)0.47441 (14)0.0278 (5)
C20.2698 (2)0.5265 (2)0.52935 (15)0.0324 (5)
C30.2682 (2)0.53273 (19)0.64186 (14)0.0276 (5)
C40.18421 (19)0.45140 (18)0.69625 (12)0.0222 (4)
C50.09207 (18)0.36429 (17)0.63493 (12)0.0193 (4)
H10.178 (2)0.4288 (18)0.3983 (14)0.027 (5)*
H20.324 (2)0.586 (2)0.4933 (15)0.038 (6)*
H30.326 (2)0.599 (2)0.6825 (14)0.032 (5)*
H1N10.039 (2)0.297 (2)0.4839 (15)0.037 (6)*
H1N2−0.021 (2)0.291 (2)0.7442 (17)0.038 (6)*
H2N2−0.065 (2)0.236 (2)0.6330 (16)0.036 (6)*
H1N30.113 (3)0.407 (2)0.8330 (16)0.049 (7)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0270 (7)0.0241 (8)0.0191 (5)−0.0026 (6)0.0040 (5)−0.0010 (5)
O20.0274 (7)0.0258 (8)0.0193 (5)−0.0058 (6)0.0023 (5)0.0002 (5)
C60.0193 (9)0.0172 (11)0.0170 (7)0.0011 (8)−0.0020 (6)0.0033 (7)
C70.0238 (10)0.0241 (12)0.0190 (7)0.0022 (9)0.0005 (7)−0.0010 (7)
C80.0206 (9)0.0205 (12)0.0211 (7)0.0050 (8)−0.0006 (7)0.0010 (7)
C90.0237 (10)0.0191 (12)0.0225 (8)0.0016 (8)0.0002 (7)−0.0009 (7)
C100.0243 (10)0.0218 (12)0.0295 (9)0.0013 (9)0.0023 (7)0.0001 (8)
C110.0272 (11)0.0276 (14)0.0373 (10)−0.0041 (10)−0.0007 (9)−0.0009 (10)
N10.0237 (8)0.0201 (9)0.0197 (6)−0.0022 (7)0.0010 (6)−0.0009 (6)
N20.0252 (9)0.0272 (11)0.0187 (7)−0.0052 (8)0.0034 (6)−0.0046 (7)
N30.0309 (10)0.0300 (11)0.0246 (7)−0.0088 (8)0.0012 (7)−0.0094 (7)
C10.0320 (11)0.0280 (13)0.0235 (8)−0.0025 (9)0.0033 (8)0.0042 (8)
C20.0346 (12)0.0280 (14)0.0351 (9)−0.0075 (10)0.0053 (9)0.0068 (9)
C30.0293 (11)0.0183 (12)0.0346 (9)−0.0039 (9)−0.0001 (8)−0.0032 (8)
C40.0207 (9)0.0206 (11)0.0249 (8)0.0029 (8)0.0003 (7)−0.0029 (8)
C50.0185 (9)0.0167 (11)0.0223 (7)0.0030 (8)0.0006 (6)−0.0012 (7)

Geometric parameters (Å, °)

O1—C61.2488 (18)N1—C11.366 (2)
O2—C61.285 (2)N1—H1N11.00 (2)
C6—C71.485 (2)N2—C51.336 (2)
C7—C81.335 (2)N2—H1N20.86 (2)
C7—H70.974 (17)N2—H2N20.95 (2)
C8—C91.446 (2)N3—C41.378 (2)
C8—H80.993 (18)N3—H2N30.91 (2)
C9—C101.333 (3)N3—H1N30.89 (3)
C9—H91.017 (18)C1—C21.347 (3)
C10—C111.493 (3)C1—H10.952 (16)
C10—H100.982 (19)C2—C31.405 (2)
C11—H11A1.04 (2)C2—H20.94 (2)
C11—H11B0.97 (2)C3—C41.372 (3)
C11—H11C0.99 (2)C3—H30.99 (2)
N1—C51.3466 (19)C4—C51.427 (2)
O1—C6—O2123.69 (16)C1—N1—H1N1117.8 (11)
O1—C6—C7120.34 (15)C5—N2—H1N2122.4 (14)
O2—C6—C7115.97 (14)C5—N2—H2N2119.2 (12)
C8—C7—C6124.12 (15)H1N2—N2—H2N2115.5 (18)
C8—C7—H7119.4 (11)C4—N3—H2N3116.1 (12)
C6—C7—H7116.4 (11)C4—N3—H1N3115.1 (14)
C7—C8—C9124.52 (16)H2N3—N3—H1N3117.3 (19)
C7—C8—H8118.2 (11)C2—C1—N1120.15 (16)
C9—C8—H8117.1 (11)C2—C1—H1125.5 (12)
C10—C9—C8124.02 (16)N1—C1—H1114.3 (12)
C10—C9—H9121.0 (11)C1—C2—C3119.12 (19)
C8—C9—H9114.9 (11)C1—C2—H2121.0 (12)
C9—C10—C11124.47 (17)C3—C2—H2119.8 (12)
C9—C10—H10120.1 (12)C4—C3—C2121.12 (19)
C11—C10—H10115.3 (12)C4—C3—H3119.4 (11)
C10—C11—H11A109.4 (13)C2—C3—H3119.5 (11)
C10—C11—H11B110.0 (11)C3—C4—N3123.23 (17)
H11A—C11—H11B108.2 (17)C3—C4—C5118.16 (15)
C10—C11—H11C111.7 (11)N3—C4—C5118.57 (17)
H11A—C11—H11C110.2 (16)N2—C5—N1118.07 (16)
H11B—C11—H11C107.3 (16)N2—C5—C4123.47 (15)
C5—N1—C1122.86 (16)N1—C5—C4118.45 (16)
C5—N1—H1N1119.3 (11)
O1—C6—C7—C88.5 (3)C2—C3—C4—N3174.29 (19)
O2—C6—C7—C8−171.14 (16)C2—C3—C4—C5−3.3 (3)
C6—C7—C8—C9173.77 (16)C1—N1—C5—N2179.13 (17)
C7—C8—C9—C10−176.15 (18)C1—N1—C5—C4−1.8 (3)
C8—C9—C10—C11176.92 (18)C3—C4—C5—N2−177.03 (18)
C5—N1—C1—C2−1.2 (3)N3—C4—C5—N25.3 (3)
N1—C1—C2—C32.0 (3)C3—C4—C5—N14.0 (3)
C1—C2—C3—C40.3 (3)N3—C4—C5—N1−173.69 (16)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···O21.00 (2)1.66 (2)2.6591 (19)174.7 (18)
N2—H1N2···O2i0.86 (2)2.05 (2)2.9065 (18)173.1 (17)
N2—H2N2···O10.94 (2)1.90 (2)2.8432 (19)176.2 (18)
N3—H1N3···O2i0.89 (2)2.04 (2)2.930 (2)174 (2)
N3—H2N3···O1ii0.91 (2)2.11 (2)2.913 (2)146.9 (16)
C10—H10···O1iii0.983 (19)2.531 (18)3.330 (2)138.2 (14)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5118).

References

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