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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o300.
Published online 2007 December 18. doi:  10.1107/S1600536807055602
PMCID: PMC2915349

Bis(2,6-diamino­pyridinium)–adipate–adipic acid–water (2/1/1/2)

Abstract

The crystal structure of the title compound, 2C5H8N3 +·C6H8O4 2−·C6H10O4·2H2O, consists of amino­pyridinium cations, adipate dianions, adipic acid mol­ecules and disordered solvent water mol­ecules [occupancies 0.50 (4) and 0.50 (4)]. Both the adipate and adipic acid are located across inversion centres. Eight-membered hydrogen-bonded rings exist involving amino­pyridinium and adipate ions. Adipic acid mol­ecules and adipate anions are linked into zigzag supra­molecular chains by O—H(...)O hydrogen bonds.

Related literature

For general background, see: Lah et al. (2001 [triangle]); Yang et al. (1995 [triangle]); Goswami & Ghosh (1997 [triangle]); Lehn (1990 [triangle]). For related structures, see: Büyükgüngör & Odabaşoğlu (2002 [triangle], 2006 [triangle]); Odabaşoğlu & Büyükgüngör (2006 [triangle]); Shanmuga Sundara Raj et al., (2000 [triangle]). For synthesis, see: Odabaşoğlu & Büyükgüngör (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o300-scheme1.jpg

Experimental

Crystal data

  • 2C5H8N3 +·C6H8O4 2−·C6H10O4·2H2O
  • M r = 546.58
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o300-efi1.jpg
  • a = 5.0645 (7) Å
  • b = 7.6261 (11) Å
  • c = 17.702 (3) Å
  • α = 87.861 (11)°
  • β = 85.169 (11)°
  • γ = 73.323 (11)°
  • V = 652.55 (18) Å3
  • Z = 1
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 296 (2) K
  • 0.60 × 0.48 × 0.08 mm

Data collection

  • Stoe IPDS 2 diffractometer
  • Absorption correction: integration (X-RED32; Stoe & Cie, 2002 [triangle]) T min = 0.949, T max = 0.993
  • 7575 measured reflections
  • 2996 independent reflections
  • 2261 reflections with I > 2σ(I)
  • R int = 0.043

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.118
  • S = 1.05
  • 2996 reflections
  • 192 parameters
  • 17 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.18 e Å−3

Data collection: X-AREA (Stoe & Cie, 2002 [triangle]); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and PLATON (Spek, 2003 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536807055602/xu2332sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807055602/xu2332Isup2.hkl

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

Acknowledgments

The author acknowledges the Faculty of Arts and Sciences, Ondokuz Mayıs University, Turkey, for the use of the Stoe IPDS II diffractometer (purchased under grant F.279 of the University Research Fund). The author also thanks Professor Dr O. Büyükgüngör for collection of the X-ray data and Professor Dr M. Odabaşoğlu for the synthesis of the title compound.

supplementary crystallographic information

Comment

The title crystal is obtained with the reaction of 2-aminopyridine (used in hair and other dyes) and adipic acid (used to esters for plasticizers and as food additive). In addition, The cupper(II) complexes of 2-aminopyridinium carboxylates have important properties in the applications of pharmaceuticals, fungicides, oxygen transfer, oxidative addition, homogenous hydrogenation, gas occlusion compounds, and solvent extractions processes (Lah et al., 2001; Yang et al., 1995). Hydrogen bonding plays a key role in molecular recognition (Goswami & Ghosh, 1997). The design of highly specific solid-state structure is of considerable significance in organic chemistry due to their important applications in the development of new optical, magnetic and electronic systems (Lehn, 1990). This report concerns the x-ray structure analysis of the title complex. In the structure investigations show that the 2-aminopyridinium ions are linked to the adipate ions by N1—H1···O1 and N3—H3···O2 hydrogen bonds through the formation of cyclic eight-membered hydrogen bonded rings.

An ORTEP diagram of (I) with numbering scheme is shown in Fig. 1. The bond lengths and angles in the structure is within the normally expected ranges. Similar C1—N3 and C5—N2 bonds were observed in other 2-aminopyridine containing molecules (Büyükgüngör & Odabaşoğlu, 2002; Odabaşoğlu & Büyükgüngör, 2006; Shanmuga Sundara Raj et al., 2000). Furthermore, these bond angle and length agrees with that similar bond angle and length values of 2,6-diaminopyridinium hydrogen fumarate complex (Büyükgüngör & Odabaşoğlu, 2006).

2-Aminopyridine and derivatives, are protonated in acidic solution. As for mono-aminopyridinium adipate-adipic acid and in some 2-aminopyridine-containing molecules, the bonding of the H atom to the ring N atom of 2-aminopyridine rather than the amine N atom gives an ion for which an additional resonance structure can be written.

The packing of the molecules is shown in Figure 2. In (I), the 2,6-diaminopyridinium ions are linked to the adipate-adipic ions through N—H···O, O—H···O hydrogen bonds (Table 1). The dihedral angles between the aminopyridinium ring and the O1/O2/C9/C10/C11 and O3/O4/C6/C7/C8 groups are 3.31 (7) and 7.25 (8)° respectively.

The H atoms between the water molecules are distorted because of the mutual repulsive interactions. So, H5B and H5C atoms are the same H-atom in the water molecule, and this H-atom makes a flip-flop motion between the two positions with site occupation factors of 0.50 (4) and 0.50 (4), respectively. The other H-atom (H5A) of the water molecule is localized due to the O5—H5A···O4 intermolecular hydrogen bond between adipic acid molecules (Fig. 3).

Experimental

The title compound was prepared by as described by Odabaşoğlu & Büyükgüngör (2006), using 2,6-diaminopyridine and adipic acid as starting materials. Crystals were obtained by slow evaporation from an aqueous solution.

Refinement

The carboxy H atom was located in a difference Fourier map and refined isotropically. Water H atoms were located in a difference map and refined isotropically with O—H and H···H distances restrained to 0.82 (2) and 1.55 (4) Å, respectively. The site occupancies for disordered H5B and H5C was refined to 0.50 (4) and 0.50 (4), respectively. Other H atoms were refined using the riding model approximation, with C—H = 0.93 (aromatic), 0.97 Å (methylene) and N—H = 0.86 Å, Uiso(H) = 1.2Ueq(C,N).

Figures

Fig. 1.
An ORTEP-3 drawing of the title compound (I) showing the atomic numbering scheme and 50% probability displacement ellipsoids.
Fig. 2.
A perspective view of the packing in (I).
Fig. 3.
The disordered H atoms of water molecules in the crystal structure.

Crystal data

2C5H8N3+·C6H8O42–·C6H10O4·2H2OZ = 1
Mr = 546.58F000 = 292
Triclinic, P1Dx = 1.391 Mg m3
Hall symbol: -P 1Melting point = 428–429 K
a = 5.0645 (7) ÅMo Kα radiation λ = 0.71073 Å
b = 7.6261 (11) ÅCell parameters from 8371 reflections
c = 17.702 (3) Åθ = 2.3–27.9º
α = 87.861 (11)ºµ = 0.11 mm1
β = 85.169 (11)ºT = 296 (2) K
γ = 73.323 (11)ºPlate, colourless
V = 652.55 (18) Å30.60 × 0.48 × 0.08 mm

Data collection

Stoe IPDS 2 diffractometer2996 independent reflections
Radiation source: fine-focus sealed tube2261 reflections with I > 2σ(I)
Monochromator: plane graphiteRint = 0.043
T = 296(2) Kθmax = 27.5º
ω scansθmin = 2.3º
Absorption correction: integration(X-RED32; Stoe & Cie, 2002)h = −6→6
Tmin = 0.949, Tmax = 0.993k = −9→9
7575 measured reflectionsl = −20→22

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.041H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.118  w = 1/[σ2(Fo2) + (0.0653P)2 + 0.039P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
2996 reflectionsΔρmax = 0.21 e Å3
192 parametersΔρmin = −0.18 e Å3
17 restraintsExtinction correction: SHELXL (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.038 (10)

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 (Å2)

xyzUiso*/UeqOcc. (<1)
O31.2490 (2)0.92346 (16)0.72447 (6)0.0543 (3)
O41.5316 (2)0.79673 (16)0.62672 (5)0.0512 (3)
C61.3110 (3)0.89651 (18)0.65252 (7)0.0374 (3)
N31.1687 (3)0.4528 (2)0.91704 (7)0.0546 (4)
H3A1.00500.52650.92430.066*
H3B1.26010.40510.95520.066*
C21.5414 (3)0.2937 (2)0.82983 (8)0.0460 (3)
H21.65160.23740.86830.055*
C71.0880 (3)1.00201 (19)0.60401 (7)0.0418 (3)
H7A1.08181.13030.60470.050*
H7B0.91200.99160.62670.050*
C11.2800 (3)0.41269 (18)0.84710 (7)0.0378 (3)
C110.1384 (3)0.92888 (18)0.99095 (7)0.0382 (3)
H11A0.12730.81071.01080.046*
H11B0.27980.96131.01640.046*
O20.6439 (2)0.69564 (16)0.93768 (6)0.0543 (3)
C31.6345 (3)0.2603 (2)0.75544 (9)0.0501 (4)
H31.80950.18090.74380.060*
C81.1183 (3)0.94351 (18)0.52225 (7)0.0388 (3)
H8A1.12440.81540.52070.047*
H8B1.29160.95620.49850.047*
C90.5041 (3)0.77673 (18)0.88646 (7)0.0364 (3)
C100.2239 (3)0.91266 (19)0.90622 (7)0.0388 (3)
H10A0.08490.87640.88120.047*
H10B0.22731.03220.88620.047*
N11.1255 (2)0.49227 (15)0.78902 (6)0.0370 (3)
H10.96400.56620.79970.044*
C41.4745 (3)0.3419 (2)0.69719 (8)0.0498 (4)
H41.54020.31770.64690.060*
O10.58652 (19)0.75241 (14)0.81637 (5)0.0438 (3)
C51.2154 (3)0.45998 (19)0.71505 (7)0.0396 (3)
N21.0457 (3)0.5462 (2)0.66285 (7)0.0553 (4)
H2A0.88620.61890.67670.066*
H2B1.09600.52890.61540.066*
O51.2848 (3)0.4164 (2)0.50152 (7)0.0631 (4)
H4A1.373 (4)0.865 (3)0.7510 (13)0.094 (8)*
H5A1.335 (4)0.338 (3)0.4684 (11)0.076 (6)*
H5B1.114 (4)0.448 (7)0.506 (3)0.089 (15)*0.50 (4)
H5C1.416 (7)0.457 (6)0.507 (3)0.083 (15)*0.50 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O30.0458 (6)0.0706 (7)0.0278 (5)0.0149 (5)−0.0071 (4)−0.0044 (5)
O40.0367 (5)0.0684 (7)0.0338 (5)0.0096 (4)−0.0053 (4)−0.0049 (4)
C60.0346 (6)0.0427 (7)0.0292 (6)−0.0012 (5)−0.0052 (5)−0.0017 (5)
N30.0456 (7)0.0723 (8)0.0295 (6)0.0086 (6)−0.0002 (5)0.0004 (5)
C20.0378 (7)0.0526 (8)0.0361 (7)0.0061 (6)−0.0075 (5)0.0038 (6)
C70.0372 (7)0.0470 (7)0.0322 (6)0.0043 (5)−0.0076 (5)−0.0020 (5)
C10.0358 (6)0.0415 (7)0.0310 (6)−0.0029 (5)−0.0029 (5)0.0011 (5)
C110.0341 (6)0.0455 (7)0.0288 (6)−0.0018 (5)−0.0010 (5)−0.0020 (5)
O20.0410 (5)0.0729 (7)0.0315 (5)0.0124 (5)−0.0062 (4)0.0011 (5)
C30.0370 (7)0.0570 (8)0.0419 (7)0.0092 (6)−0.0005 (6)−0.0042 (6)
C80.0343 (6)0.0441 (7)0.0309 (6)0.0016 (5)−0.0079 (5)0.0001 (5)
C90.0322 (6)0.0426 (6)0.0292 (6)−0.0021 (5)−0.0027 (5)−0.0017 (5)
C100.0335 (6)0.0443 (7)0.0311 (6)0.0006 (5)−0.0013 (5)−0.0006 (5)
N10.0298 (5)0.0424 (6)0.0312 (5)0.0016 (4)−0.0012 (4)−0.0001 (4)
C40.0418 (7)0.0618 (9)0.0324 (7)0.0056 (6)0.0021 (6)−0.0043 (6)
O10.0373 (5)0.0547 (6)0.0274 (5)0.0052 (4)0.0000 (4)−0.0023 (4)
C50.0366 (6)0.0456 (7)0.0311 (6)−0.0032 (5)−0.0031 (5)0.0016 (5)
N20.0421 (7)0.0760 (9)0.0331 (6)0.0073 (6)−0.0075 (5)0.0038 (6)
O50.0483 (7)0.0801 (9)0.0503 (7)0.0009 (6)−0.0029 (6)−0.0218 (6)

Geometric parameters (Å, °)

O3—C61.2955 (15)C3—C41.382 (2)
O3—H4A0.829 (17)C3—H30.9300
O4—C61.2196 (16)C8—C8ii1.521 (2)
C6—C71.5001 (18)C8—H8A0.9700
N3—C11.3252 (17)C8—H8B0.9700
N3—H3A0.8600C9—O11.2781 (15)
N3—H3B0.8600C9—C101.5199 (16)
C2—C31.369 (2)C10—H10A0.9700
C2—C11.3901 (18)C10—H10B0.9700
C2—H20.9300N1—C51.3572 (16)
C7—C81.5129 (17)N1—H10.8600
C7—H7A0.9700C4—C51.3806 (18)
C7—H7B0.9700C4—H40.9300
C1—N11.3617 (17)C5—N21.3375 (17)
C11—C11i1.524 (2)N2—H2A0.8600
C11—C101.5253 (17)N2—H2B0.8600
C11—H11A0.9700O5—H5A0.824 (16)
C11—H11B0.9700O5—H5B0.824 (19)
O2—C91.2332 (16)O5—H5C0.823 (19)
C6—O3—H4A113.2 (17)C7—C8—H8A109.2
O4—C6—O3123.06 (12)C8ii—C8—H8A109.2
O4—C6—C7123.27 (11)C7—C8—H8B109.2
O3—C6—C7113.66 (11)C8ii—C8—H8B109.2
C1—N3—H3A120.0H8A—C8—H8B107.9
C1—N3—H3B120.0O2—C9—O1122.48 (11)
H3A—N3—H3B120.0O2—C9—C10119.63 (11)
C3—C2—C1119.16 (13)O1—C9—C10117.89 (11)
C3—C2—H2120.4C9—C10—C11114.35 (11)
C1—C2—H2120.4C9—C10—H10A108.7
C6—C7—C8115.81 (10)C11—C10—H10A108.7
C6—C7—H7A108.3C9—C10—H10B108.7
C8—C7—H7A108.3C11—C10—H10B108.7
C6—C7—H7B108.3H10A—C10—H10B107.6
C8—C7—H7B108.3C5—N1—C1122.82 (11)
H7A—C7—H7B107.4C5—N1—H1118.6
N3—C1—N1117.35 (12)C1—N1—H1118.6
N3—C1—C2124.09 (13)C5—C4—C3118.80 (13)
N1—C1—C2118.55 (12)C5—C4—H4120.6
C11i—C11—C10113.06 (13)C3—C4—H4120.6
C11i—C11—H11A109.0N2—C5—N1117.53 (12)
C10—C11—H11A109.0N2—C5—C4123.31 (12)
C11i—C11—H11B109.0N1—C5—C4119.16 (12)
C10—C11—H11B109.0C5—N2—H2A120.0
H11A—C11—H11B107.8C5—N2—H2B120.0
C2—C3—C4121.51 (13)H2A—N2—H2B120.0
C2—C3—H3119.2H5A—O5—H5B108 (4)
C4—C3—H3119.2H5A—O5—H5C107 (4)
C7—C8—C8ii112.10 (13)H5B—O5—H5C140 (5)
O4—C6—C7—C814.8 (2)C11i—C11—C10—C9177.91 (14)
O3—C6—C7—C8−166.16 (13)N3—C1—N1—C5−179.08 (13)
C3—C2—C1—N3179.15 (16)C2—C1—N1—C50.2 (2)
C3—C2—C1—N1−0.1 (2)C2—C3—C4—C50.2 (3)
C1—C2—C3—C4−0.1 (3)C1—N1—C5—N2−179.90 (13)
C6—C7—C8—C8ii179.37 (15)C1—N1—C5—C4−0.1 (2)
O2—C9—C10—C11−2.29 (19)C3—C4—C5—N2179.70 (16)
O1—C9—C10—C11178.28 (12)C3—C4—C5—N1−0.1 (2)

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O10.862.032.8917 (14)175
N2—H2A···O4iii0.862.152.8589 (16)139
N2—H2B···O50.862.253.0892 (18)166
N3—H3A···O20.861.912.7729 (16)178
N3—H3B···O2iv0.862.062.8936 (17)162
O3—H4A···O1v0.829 (17)1.688 (17)2.5099 (15)171 (3)
O5—H5A···O4vi0.824 (16)1.972 (17)2.7773 (15)165 (2)
O5—H5B···O5vii0.824 (19)2.00 (2)2.804 (3)164 (5)
O5—H5C···O5vi0.823 (19)2.01 (2)2.819 (3)168 (5)

Symmetry codes: (iii) x−1, y, z; (iv) −x+2, −y+1, −z+2; (v) x+1, y, z; (vi) −x+3, −y+1, −z+1; (vii) −x+2, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU2332).

References

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