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Acta Cryst. (2007). E63, o2809    [ doi:10.1107/S1600536807021368 ]

Propane-1,3-diaminium pyridine-2,3-dicarboxylate monohydrate

F. Manteghi, M. Ghadermazi and H. Aghabozorg

Abstract top

The title compound, C3H12N22+·C7H3NO42-·H2O, contains one dicationic fragment, one dianionic fragment and one water molecule. The two carboxylate groups of the pyridine-2,3-dicarboxylate (pydc2-) fragment are almost perpendicular to each other [dihedral angle 83.10 (8)°]. In the crystal structure, intermolecular N-H...O, N-H...N, O-H...O and C-H...O hydrogen bonds and edge-to-face [pi]-[pi] stacking, together with ion pairing, are responsible for extending the structure in three dimensions, resulting in a supramolecular network.

Comment top

Pyridinedicarboxylic acids are applied as proton donors in ion pairs, as ligands in coordination compounds, and as hydrogen donor or acceptor in hydrogen bondings. However, their metal complexes have interesting properties in biological systems (Mendoza-Diaz et al., 2005).

The molecule of the title compound, (I), contains one dicationic and one dianionic fragments and also one water molecule (Fig. 1). The bond lengths and angles are within normal ranges (Allen et al., 1987). The two carboxylate groups of (pydc)2– fragment are perpendicular to each other.

As can be seen from the packing diagram (Fig. 2), the intramolecular N—H···O and intermolecular N—H···O, N—H···N, O—H···O and C—H···O hydrogen bonds (Table 1) and edge to face π-π stacking together with ion pairing are responsible for expanding the structure in three dimension resulting in a supramolecular network.

The bond distances and angles of C–H···π stacking are 2.81 Å (H···π) and 136° (C–H···π), which are within normal range (Chandrasekhar et al., 2001). Another notable feature of the structure as shown in Fig. 2, is that the hydrogen bonds between water molecules, NH3+ tail of diamine and O atom of carboxylate group (i.e. two O5, two N3 and two O3 atoms and the related H atoms) form a 12-membered cyclic arrangement with a centre of symmetry in the middle of the ring.

Related literature top

For general backgroud, see: Allen et al. (1987); Mendoza-Diaz et al. (2005); Chandrasekhar et al. (2001).

Experimental top

The title compound was synthesized by adding pyridine-2,3-dicarboxylic acid (10 mmol) to propane-1,3-diamine (10 mmol) in tetrahydrofuran (40 ml), and refluxing it. After a while, a white precipitate was obtained which was recrystallized to colorless crystals suitable for X-ray analysis.

Refinement top

H atoms were positioned geometrically, with O—H = 0.82 Å (for OH2), N—H = 0.91 Å (for NH3) and C—H = 0.95 and 0.99 Å for aromatic and methylene H, respectively, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C,O,N).

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2005); software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. A packing diagram for (I). Hydrogen bonds are shown as dashed lines.
Propane-1,3-diaminium pyridine-2,3-dicarboxylate monohydrate top
Crystal data top
C3H12N22+·C7H3NO42−·H2OZ = 2
Mr = 259.27F(000) = 276
Triclinic, P1Dx = 1.424 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.4274 (5) ÅCell parameters from 265 reflections
b = 8.6176 (5) Åθ = 3–28°
c = 10.7314 (7) ŵ = 0.12 mm−1
α = 109.989 (1)°T = 100 K
β = 102.225 (1)°Prism, colourless
γ = 100.883 (1)°0.24 × 0.22 × 0.18 mm
V = 604.81 (7) Å3
Data collection top
Bruker APEXII CCD area-detector
diffractometer		2897 independent reflections
Radiation source: fine-focus sealed tube2467 reflections with I > 2σ(I)
graphiteRint = 0.022
ω scansθmax = 28.0°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		h = −9→9
Tmin = 0.970, Tmax = 0.978k = −11→11
6110 measured reflectionsl = −13→14
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)] = 0.036Hydrogen site location: constr
wR(F2) = 0.097H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0478P)2 + 0.1817P]
where P = (Fo2 + 2Fc2)/3
2897 reflections(Δ/σ)max < 0.001
165 parametersΔρmax = 0.38 e Å−3
0 restraintsΔρmin = −0.24 e Å−3
Crystal data top
C3H12N22+·C7H3NO42−·H2Oγ = 100.883 (1)°
Mr = 259.27V = 604.81 (7) Å3
Triclinic, P1Z = 2
a = 7.4274 (5) ÅMo Kα radiation
b = 8.6176 (5) ŵ = 0.12 mm−1
c = 10.7314 (7) ÅT = 100 K
α = 109.989 (1)°0.24 × 0.22 × 0.18 mm
β = 102.225 (1)°
Data collection top
Bruker APEXII CCD area-detector
diffractometer		2897 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		2467 reflections with I > 2σ(I)
Tmin = 0.970, Tmax = 0.978Rint = 0.022
6110 measured reflectionsθmax = 28.0°
Refinement top
R[F2 > 2σ(F2)] = 0.036H-atom parameters constrained
wR(F2) = 0.097Δρmax = 0.38 e Å−3
S = 1.04Δρmin = −0.24 e Å−3
2897 reflectionsAbsolute structure: ?
165 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
O10.97996 (13)0.66664 (11)0.41529 (9)0.01712 (19)
O21.21462 (12)0.91436 (10)0.50032 (8)0.01534 (19)
O31.32210 (12)0.61030 (11)0.31424 (8)0.01571 (19)
O41.39865 (14)0.59160 (13)0.11966 (10)0.0227 (2)
N11.10608 (14)0.71092 (12)0.03480 (10)0.0140 (2)
C10.97376 (17)0.78571 (15)−0.00249 (12)0.0153 (2)
H1A0.94250.7817−0.09430.018*
C20.88011 (17)0.86906 (15)0.08756 (12)0.0163 (2)
H2A0.79080.92490.05880.020*
C30.91878 (17)0.86966 (15)0.21982 (12)0.0150 (2)
H3A0.85570.92490.28290.018*
C41.05220 (16)0.78750 (14)0.25870 (11)0.0119 (2)
C51.14535 (16)0.71214 (14)0.16337 (11)0.0116 (2)
C61.08930 (16)0.78848 (14)0.40348 (12)0.0125 (2)
C71.30215 (17)0.63029 (14)0.20165 (12)0.0135 (2)
N20.69146 (14)0.43762 (12)0.16715 (10)0.0141 (2)
H2B0.73420.41600.09120.017*
H2C0.78980.50990.24450.017*
H2D0.59480.48760.15720.017*
N30.37974 (15)0.18365 (13)0.44053 (10)0.0153 (2)
H3B0.32670.08460.44840.018*
H3C0.29090.24250.43410.018*
H3D0.48250.24980.51670.018*
C80.61920 (17)0.27374 (15)0.18108 (12)0.0151 (2)
H8A0.72230.21620.18690.018*
H8B0.51020.19610.09800.018*
C90.55396 (17)0.30690 (15)0.31028 (12)0.0152 (2)
H9A0.47090.38460.31330.018*
H9B0.66770.36550.39370.018*
C100.44394 (17)0.14129 (15)0.31345 (12)0.0151 (2)
H10A0.33100.08060.22950.018*
H10B0.52750.06450.31410.018*
O50.09016 (13)0.32465 (11)0.34573 (9)0.0181 (2)
H5A0.05140.34000.41390.022*
H5B0.12450.42040.34480.022*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0195 (4)0.0172 (4)0.0141 (4)0.0004 (3)0.0058 (3)0.0077 (3)
O20.0180 (4)0.0143 (4)0.0116 (4)0.0020 (3)0.0033 (3)0.0045 (3)
O30.0190 (4)0.0167 (4)0.0132 (4)0.0066 (3)0.0045 (3)0.0074 (3)
O40.0254 (5)0.0335 (5)0.0210 (5)0.0182 (4)0.0135 (4)0.0155 (4)
N10.0170 (5)0.0128 (5)0.0113 (5)0.0027 (4)0.0043 (4)0.0047 (4)
C10.0183 (6)0.0151 (5)0.0113 (5)0.0031 (4)0.0019 (4)0.0060 (4)
C20.0152 (6)0.0165 (6)0.0174 (6)0.0054 (5)0.0027 (5)0.0079 (5)
C30.0159 (6)0.0146 (5)0.0146 (5)0.0044 (4)0.0059 (4)0.0052 (4)
C40.0128 (5)0.0100 (5)0.0112 (5)0.0003 (4)0.0033 (4)0.0040 (4)
C50.0129 (5)0.0100 (5)0.0107 (5)0.0007 (4)0.0033 (4)0.0043 (4)
C60.0145 (5)0.0136 (5)0.0121 (5)0.0066 (4)0.0059 (4)0.0056 (4)
C70.0144 (5)0.0106 (5)0.0136 (5)0.0023 (4)0.0035 (4)0.0038 (4)
N20.0152 (5)0.0150 (5)0.0123 (5)0.0031 (4)0.0053 (4)0.0056 (4)
N30.0165 (5)0.0147 (5)0.0150 (5)0.0024 (4)0.0038 (4)0.0079 (4)
C80.0165 (6)0.0131 (5)0.0143 (5)0.0027 (4)0.0044 (4)0.0048 (4)
C90.0170 (6)0.0133 (5)0.0148 (5)0.0025 (4)0.0053 (4)0.0057 (4)
C100.0155 (5)0.0149 (5)0.0142 (5)0.0033 (4)0.0033 (4)0.0062 (4)
O50.0245 (5)0.0168 (4)0.0158 (4)0.0061 (4)0.0098 (4)0.0077 (3)
Geometric parameters (Å, °) top
O1—C61.2612 (14)N2—H2C0.9100
O2—C61.2495 (14)N2—H2D0.9100
O3—C71.2601 (14)N3—C101.4905 (15)
O4—C71.2473 (15)N3—H3B0.9100
N1—C11.3380 (15)N3—H3C0.9100
N1—C51.3444 (14)N3—H3D0.9100
C1—C21.3902 (17)C8—C91.5181 (16)
C1—H1A0.9500C8—H8A0.9900
C2—C31.3853 (16)C8—H8B0.9900
C2—H2A0.9500C9—C101.5199 (16)
C3—C41.3961 (16)C9—H9A0.9900
C3—H3A0.9500C9—H9B0.9900
C4—C51.4008 (15)C10—H10A0.9900
C4—C61.5162 (15)C10—H10B0.9900
C5—C71.5258 (15)O5—H5A0.8200
N2—C81.4822 (15)O5—H5B0.8200
N2—H2B0.9100
C1—N1—C5118.43 (10)H2C—N2—H2D109.5
N1—C1—C2122.72 (11)C10—N3—H3B109.5
N1—C1—H1A118.6C10—N3—H3C109.5
C2—C1—H1A118.6H3B—N3—H3C109.5
C3—C2—C1119.13 (11)C10—N3—H3D109.5
C3—C2—H2A120.4H3B—N3—H3D109.5
C1—C2—H2A120.4H3C—N3—H3D109.5
C2—C3—C4118.75 (11)N2—C8—C9110.58 (9)
C2—C3—H3A120.6N2—C8—H8A109.5
C4—C3—H3A120.6C9—C8—H8A109.5
C3—C4—C5118.43 (10)N2—C8—H8B109.5
C3—C4—C6117.43 (10)C9—C8—H8B109.5
C5—C4—C6124.13 (10)H8A—C8—H8B108.1
N1—C5—C4122.47 (10)C8—C9—C10112.02 (9)
N1—C5—C7116.06 (10)C8—C9—H9A109.2
C4—C5—C7121.45 (10)C10—C9—H9A109.2
O2—C6—O1126.29 (11)C8—C9—H9B109.2
O2—C6—C4117.55 (10)C10—C9—H9B109.2
O1—C6—C4115.97 (10)H9A—C9—H9B107.9
O4—C7—O3126.58 (11)N3—C10—C9109.16 (9)
O4—C7—C5117.09 (10)N3—C10—H10A109.8
O3—C7—C5116.33 (10)C9—C10—H10A109.8
C8—N2—H2B109.5N3—C10—H10B109.8
C8—N2—H2C109.5C9—C10—H10B109.8
H2B—N2—H2C109.5H10A—C10—H10B108.3
C8—N2—H2D109.5H5A—O5—H5B105.4
H2B—N2—H2D109.5
C5—N1—C1—C22.11 (17)C3—C4—C6—O2−87.25 (13)
N1—C1—C2—C3−2.61 (18)C5—C4—C6—O291.67 (14)
C1—C2—C3—C40.55 (17)C3—C4—C6—O187.95 (13)
C2—C3—C4—C51.79 (17)C5—C4—C6—O1−93.12 (13)
C2—C3—C4—C6−179.22 (10)N1—C5—C7—O49.82 (15)
C1—N1—C5—C40.43 (17)C4—C5—C7—O4−168.65 (11)
C1—N1—C5—C7−178.02 (10)N1—C5—C7—O3−170.88 (10)
C3—C4—C5—N1−2.37 (17)C4—C5—C7—O310.65 (16)
C6—C4—C5—N1178.71 (10)N2—C8—C9—C10168.92 (9)
C3—C4—C5—C7176.00 (10)C8—C9—C10—N3−178.42 (9)
C6—C4—C5—C7−2.92 (17)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2B···O4i0.912.242.918 (1)131
N2—H2B···N1i0.912.142.967 (2)150
N2—H2C···O10.911.922.823 (1)175
N2—H2D···O4ii0.911.892.798 (2)174
N3—H3B···O2iii0.911.862.752 (2)168
N3—H3C···O50.911.972.836 (2)158
N3—H3D···O3iv0.911.892.799 (1)174
O5—H5A···O1v0.821.912.702 (1)161
O5—H5B···O1ii0.822.523.094 (1)128
O5—H5B···O3ii0.822.152.890 (1)151
C10—H10B···O2iv0.992.383.102 (2)129
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) x−1, y−1, z; (iv) −x+2, −y+1, −z+1; (v) −x+1, −y+1, −z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2B···O4i0.912.242.918 (1)131
N2—H2B···N1i0.912.142.967 (2)150
N2—H2C···O10.911.922.823 (1)175
N2—H2D···O4ii0.911.892.798 (2)174
N3—H3B···O2iii0.911.862.752 (2)168
N3—H3C···O50.911.972.836 (2)158
N3—H3D···O3iv0.911.892.799 (1)174
O5—H5A···O1v0.821.912.702 (1)161
O5—H5B···O1ii0.822.523.094 (1)128
O5—H5B···O3ii0.822.152.890 (1)151
C10—H10B···O2iv0.992.383.102 (2)129
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) x−1, y−1, z; (iv) −x+2, −y+1, −z+1; (v) −x+1, −y+1, −z+1.
Acknowledgements top

The authors are grateful to Iran University of Science and Technology for financial support of this work.

references
References top

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.

Bruker (2005). APEX2 (Version 2.0-1), SAINT (Version 7.23a), SADABS (Version 2004/1) and SHELXTL (Version 6.1). Bruker AXS Inc., Madison, Wisconsin, USA.

Chandrasekhar, V., Baskar, V., Kingsley, S., Nagendrana, S. & Butcher, R. J. (2001). CrystEngComm, 17, 1–3.

Mendoza-Diaz, G., Rigotti, G., Piro, O. E. & Sileo, E. E. (2005). Polyhedron, 24, 777–783.

Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.