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Acta Crystallogr Sect E Struct Rep Online. 2010 May 1; 66(Pt 5): m524.
Published online 2010 April 14. doi:  10.1107/S1600536810012870
PMCID: PMC2979161

Disodium dihydrogen pyridine-2,3,5,6-tetra­carboxyl­ate trihydrate

Abstract

In the title compound, 2Na+·C9H3NO8 2−·3H2O, the asymmetric unit consists of two Na+ cations, one dihydrogen pyridine-2,3,5,6-tetra­carboxyl­ate dianion (H2pdtc2−) and three water mol­ecules coordinated to the Na+ cations. The configuration of the anion is stabilized by intramolecular O—H(...)O hydrogen bonding between vicinal carboxylate/carboxy groups. The Na+ cations are bridged by the H2pdtc2− dianions, generating layers extending infinitely in sheets parallel to (001), and further pillared by the water mol­ecule linkers to build up a three-dimensional framework.

Related literature

For related compounds involving the pyridine-2,3,5,6-tetra­carboxylic acid ligand, see: Zhang et al. (2010 [triangle]); Yang et al. (2008 [triangle]); Sun, Zhou & An (2009 [triangle]); Sun, Zhou & Yan (2009 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0m524-scheme1.jpg

Experimental

Crystal data

  • 2Na+·C9H3NO8 2−·3H2O
  • M r = 353.15
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0m524-efi1.jpg
  • a = 5.5844 (11) Å
  • b = 6.6770 (13) Å
  • c = 18.631 (4) Å
  • α = 81.34 (3)°
  • β = 86.77 (3)°
  • γ = 68.36 (3)°
  • V = 638.4 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.23 mm−1
  • T = 293 K
  • 0.1 × 0.1 × 0.1 mm

Data collection

  • Rigaku R-AXIS RAPID diffractometer
  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995 [triangle]) T min = 0.97, T max = 0.98
  • 5075 measured reflections
  • 2247 independent reflections
  • 1780 reflections with I > 2σ(I)
  • R int = 0.018

Refinement

  • R[F 2 > 2σ(F 2)] = 0.043
  • wR(F 2) = 0.139
  • S = 1.14
  • 2247 reflections
  • 208 parameters
  • H-atom parameters constrained
  • Δρmax = 0.55 e Å−3
  • Δρmin = −0.33 e Å−3

Data collection: RAPID-AUTO (Rigaku, 1998 [triangle]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810012870/ds2024sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810012870/ds2024Isup2.hkl

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

Acknowledgments

This project was supported by the National Natural Science Foundation of China (grant No. 20072022), the Science and Technology Department of Zhejiang Province (grant No. 2006C21105), and the Education Department of Zhejiang Province. The authors also extend grateful thanks to the K. C. Wong Magna Fund of Ningbo University.

supplementary crystallographic information

Comment

A great many metal-polycarboxylate compounds with benzene-1,2,4,5-tetracarboxylic acid (H4btec) as ligands have been designed and characterized (Zhang et al., 2010). Analogous in structure to H4btec, only four complexes [Ni(H2pdtc)(H2O)2].3H2O (Yang et al., 2008), [Zn4(pdtc)2(phen)2(H2O)2].20H2O (Yang et al., 2008), [Cd(H2pdtc)(H2O)3].3H2O (Sun, Zhou & Yan, 2009) and [Ni2(pdtc)(H2O)3(2,2'-bpy)].4H2O (Sun, Zhou & An, 2009) about pyridine-2,3,5,6-tetracarboxylic acid (H4pdtc) have been reported. The four coordination polymers are constructed by linking transition metal centres through the ligands. In this context, we represent a disodium salt of dihydrogen pyridine-2,3,5,6-tetracarboxylate dianion [Na2(H2pdtc)(H2O)3].

The asymmetric unit of the title compound consisits of two crystallographically independent Na cations, one dihydrogen pyridine-2,3,5,6-tetracarboxylate dianion (H2pdtc2-) and three water molecules (Fig. 1). The ligand is deprotonated at 2,5-positioned carboxylate groups. The values of the dihedral angle between the planes of the carboxylic groups and the planar pyridine ring are 3.7 (4)°, 2.0 (5)°, 10.5 (4)°, 2.4 (5)°, respectively. Both Na1 and Na2 ions are seven-coordinated with one N atom, two carboxylate O atoms and four water molecules at Na1 and five carboxylate O atoms and two water molecules at Na2, building highly distorted pentagonal–bipyramidal environment. The average value of the Na—O(water) length [2.494 (2) Å] is closer to the average Na—O (carboxylate) distance [2.498 (2) Å], and both are slightly smaller than the Na—N value [2.654 (2) Å]. The sodium cations are bridged by the (H2pdtc2-) to generate layers extending infinitely in sheets parallel to (001) (Fig. 2), and further pillared by the water molecule linkers (Fig. 3) to build up 3D framework, which is found to be stabilized by hydrogen bonds from water molecules to carboxylate O atoms (Table 1).

Experimental

0.0766 g (0.3 mmol) pyridine-2,3,5,6-tetracarboxylic acid and 0.024 g (0.6 mmol) NaOH were successively added to 10.0 ml H2O and stirred at room temperature for 2 h, and the resulting colorless solution (pH = 3.48) was then transferred to a 50 ml beaker for slow evaporation at room temperature for several months, affording colorless block crystals (yield: 0.05 g).

Refinement

H atoms bonded to C atoms were placed in geometrically calculated positions and were refined using a riding model, with Uiso(H) = 1.2Ueq(C). H atoms attached to O atoms were found in a difference Fourier synthesis and were refined using a riding model, with Uiso(H) values set at 1.2Ueq(O).

Figures

Fig. 1.
ORTEP view of the title compound, Displacement ellipsoids are drawn at the 30% probability level. [Symmetry codes: (i) 2 - x, 1 - y, 1 - z; (ii) 3 - x, 1 - y, 1 - z; (iii) 2 - x, 1 - y, -z; (iv) x - 1, y - 1, z; (v) x, y - 1, z; (vi) 1 - x, -y, -z.]
Fig. 2.
2D layer ∞[Na2(H2pdtc)] parallel to (001) generated from bridging sodium cations and (H2pdtc2-).
Fig. 3.
3D framework built from linking ∞[Na2(H2pdtc)] layers by the water molecules (the water molecule linkers are marked in green)

Crystal data

2Na+·C9H3NO82·3H2OZ = 2
Mr = 353.15F(000) = 360
Triclinic, P1Dx = 1.837 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.5844 (11) ÅCell parameters from 4730 reflections
b = 6.6770 (13) Åθ = 3.3–27.5°
c = 18.631 (4) ŵ = 0.23 mm1
α = 81.34 (3)°T = 293 K
β = 86.77 (3)°Block, colourless
γ = 68.36 (3)°0.1 × 0.1 × 0.1 mm
V = 638.4 (2) Å3

Data collection

Rigaku R-AXIS RAPID diffractometer2247 independent reflections
Radiation source: fine-focus sealed tube1780 reflections with I > 2σ(I)
graphiteRint = 0.018
Detector resolution: 0 pixels mm-1θmax = 25.0°, θmin = 3.3°
ω scansh = −6→6
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)k = −7→7
Tmin = 0.97, Tmax = 0.98l = −22→22
5075 measured reflections

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)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.139H-atom parameters constrained
S = 1.14w = 1/[σ2(Fo2) + (0.0916P)2 + 0.0526P] where P = (Fo2 + 2Fc2)/3
2247 reflections(Δ/σ)max < 0.001
208 parametersΔρmax = 0.55 e Å3
0 restraintsΔρmin = −0.33 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
Na11.28244 (19)0.41119 (18)0.44136 (5)0.0360 (3)
Na20.70103 (18)0.05082 (15)0.05556 (5)0.0275 (3)
N1.2379 (4)0.4267 (3)0.29938 (10)0.0234 (5)
C11.1039 (4)0.3240 (4)0.27451 (12)0.0222 (5)
C21.0250 (4)0.3696 (4)0.20111 (12)0.0227 (5)
C31.0921 (4)0.5287 (4)0.15822 (12)0.0225 (5)
H3A1.03920.56530.11000.027*
C41.2339 (4)0.6372 (4)0.18300 (12)0.0205 (5)
C51.3080 (4)0.5774 (4)0.25638 (12)0.0213 (5)
C61.0527 (5)0.1626 (4)0.33584 (13)0.0280 (6)
O11.1267 (4)0.1553 (3)0.39697 (9)0.0364 (5)
O20.9322 (4)0.0429 (3)0.32087 (10)0.0408 (5)
C70.8762 (5)0.2689 (4)0.16184 (13)0.0252 (5)
O30.7999 (4)0.1219 (3)0.19559 (9)0.0361 (5)
H30.85430.09540.23960.043*
O40.8325 (3)0.3309 (3)0.09639 (9)0.0299 (4)
C81.2832 (4)0.8074 (4)0.12553 (12)0.0231 (5)
O51.1680 (3)0.8518 (3)0.06780 (9)0.0295 (4)
O61.4448 (3)0.8925 (3)0.13981 (9)0.0335 (5)
C91.4680 (5)0.6635 (4)0.29836 (13)0.0270 (6)
O71.5562 (4)0.8069 (3)0.26636 (10)0.0385 (5)
H71.52600.83590.22050.046*
O81.5129 (4)0.5911 (3)0.36238 (9)0.0437 (5)
O91.6891 (4)0.2384 (3)0.49492 (11)0.0466 (5)
H9A1.81560.20810.46550.056*
H9B1.72510.11170.52020.056*
O100.8582 (4)0.6942 (3)0.43369 (10)0.0363 (5)
H10A0.86160.82050.41310.044*
H10B0.74140.67200.40940.044*
O110.2943 (3)0.2647 (3)0.00399 (9)0.0304 (4)
H11A0.26050.3963−0.02080.037*
H11B0.14550.29490.02720.037*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Na10.0340 (6)0.0478 (6)0.0265 (6)−0.0181 (5)−0.0043 (4)0.0044 (4)
Na20.0285 (5)0.0318 (5)0.0256 (5)−0.0155 (4)−0.0043 (4)−0.0008 (4)
N0.0272 (10)0.0255 (10)0.0180 (10)−0.0103 (9)−0.0006 (8)−0.0027 (8)
C10.0233 (11)0.0233 (12)0.0200 (12)−0.0090 (10)−0.0002 (9)−0.0012 (9)
C20.0238 (11)0.0224 (11)0.0227 (12)−0.0092 (10)−0.0015 (9)−0.0036 (9)
C30.0277 (12)0.0245 (12)0.0150 (11)−0.0092 (10)−0.0040 (9)−0.0018 (9)
C40.0223 (11)0.0206 (11)0.0190 (11)−0.0087 (10)0.0001 (9)−0.0020 (9)
C50.0239 (11)0.0210 (11)0.0189 (11)−0.0087 (10)0.0008 (9)−0.0012 (9)
C60.0314 (13)0.0300 (13)0.0237 (13)−0.0146 (11)0.0001 (10)0.0013 (10)
O10.0510 (12)0.0438 (11)0.0195 (10)−0.0264 (10)−0.0049 (8)0.0057 (8)
O20.0608 (13)0.0453 (11)0.0292 (10)−0.0379 (11)−0.0054 (9)0.0056 (8)
C70.0299 (13)0.0243 (12)0.0228 (13)−0.0113 (11)−0.0018 (10)−0.0031 (10)
O30.0517 (12)0.0412 (10)0.0275 (10)−0.0324 (10)−0.0060 (8)0.0008 (8)
O40.0415 (10)0.0320 (9)0.0227 (9)−0.0210 (8)−0.0068 (7)−0.0009 (7)
C80.0273 (12)0.0261 (12)0.0169 (11)−0.0116 (10)0.0006 (9)−0.0017 (9)
O50.0327 (9)0.0376 (10)0.0201 (9)−0.0176 (8)−0.0049 (7)0.0046 (7)
O60.0455 (11)0.0461 (11)0.0213 (9)−0.0337 (10)−0.0057 (8)0.0040 (8)
C90.0331 (13)0.0292 (13)0.0226 (13)−0.0171 (11)−0.0036 (10)0.0007 (10)
O70.0557 (12)0.0519 (12)0.0234 (9)−0.0394 (11)−0.0088 (8)0.0027 (8)
O80.0642 (14)0.0651 (13)0.0189 (10)−0.0469 (12)−0.0146 (9)0.0090 (9)
O90.0342 (11)0.0582 (13)0.0355 (11)−0.0105 (10)0.0001 (9)0.0132 (10)
O100.0387 (10)0.0452 (11)0.0304 (10)−0.0236 (9)−0.0077 (8)0.0033 (8)
O110.0286 (9)0.0302 (9)0.0296 (9)−0.0098 (8)0.0007 (7)0.0019 (7)

Geometric parameters (Å, °)

Na1—O92.337 (2)C3—H3A0.9300
Na1—O82.379 (2)C4—C51.406 (3)
Na1—O102.420 (2)C4—C81.531 (3)
Na1—O12.442 (2)C5—C91.528 (3)
Na1—O10i2.498 (2)C6—O11.221 (3)
Na1—N2.654 (2)C6—O21.287 (3)
Na1—O9ii2.835 (3)C7—O41.235 (3)
Na1—Na1i3.657 (2)C7—O31.278 (3)
Na1—Na1ii3.948 (2)O3—H30.8603
Na2—O112.358 (2)C8—O51.225 (3)
Na2—O5iii2.4395 (18)C8—O61.288 (3)
Na2—O6iv2.4477 (19)O5—Na2iii2.4395 (18)
Na2—O5v2.457 (2)O5—Na2viii2.457 (2)
Na2—O42.4738 (18)O6—Na2ix2.4477 (19)
Na2—O11vi2.516 (2)C9—O81.221 (3)
Na2—O32.840 (2)C9—O71.287 (3)
Na2—C73.022 (3)O7—H70.8596
Na2—Na2vi3.444 (2)O9—Na1ii2.835 (3)
Na2—Na2vii3.724 (2)O9—H9A0.8516
N—C11.325 (3)O9—H9B0.8625
N—C51.349 (3)O10—Na1i2.498 (2)
C1—C21.414 (3)O10—H10A0.8790
C1—C61.539 (3)O10—H10B0.8816
C2—C31.382 (3)O11—Na2vi2.516 (2)
C2—C71.519 (3)O11—H11A0.8872
C3—C41.389 (3)O11—H11B0.8833
O9—Na1—O881.23 (8)O11—Na2—Na2vii120.83 (6)
O9—Na1—O10151.17 (9)O5iii—Na2—Na2vii40.67 (5)
O8—Na1—O1099.80 (8)O6iv—Na2—Na2vii146.74 (7)
O9—Na1—O1112.23 (9)O5v—Na2—Na2vii40.31 (4)
O8—Na1—O1120.07 (7)O4—Na2—Na2vii83.00 (6)
O10—Na1—O192.37 (7)O11vi—Na2—Na2vii79.10 (6)
O9—Na1—O10i81.74 (8)O3—Na2—Na2vii108.88 (6)
O8—Na1—O10i150.12 (7)C7—Na2—Na2vii93.42 (6)
O10—Na1—O10i83.92 (8)Na2vi—Na2—Na2vii102.29 (5)
O1—Na1—O10i89.14 (7)C1—N—C5122.15 (19)
O9—Na1—N119.02 (8)C1—N—Na1120.01 (14)
O8—Na1—N62.02 (6)C5—N—Na1116.33 (15)
O10—Na1—N85.55 (8)N—C1—C2121.20 (19)
O1—Na1—N60.81 (6)N—C1—C6110.34 (19)
O10i—Na1—N147.64 (7)C2—C1—C6128.5 (2)
O9—Na1—O9ii80.93 (8)C3—C2—C1116.0 (2)
O8—Na1—O9ii70.80 (7)C3—C2—C7114.6 (2)
O10—Na1—O9ii72.45 (7)C1—C2—C7129.44 (19)
O1—Na1—O9ii163.26 (7)C2—C3—C4123.8 (2)
O10i—Na1—O9ii82.40 (7)C2—C3—H3A118.1
N—Na1—O9ii123.02 (7)C4—C3—H3A118.1
O9—Na1—Na1i118.79 (7)C3—C4—C5116.01 (19)
O8—Na1—Na1i134.81 (8)C3—C4—C8114.27 (19)
O10—Na1—Na1i42.77 (5)C5—C4—C8129.72 (19)
O1—Na1—Na1i90.98 (6)N—C5—C4120.8 (2)
O10i—Na1—Na1i41.15 (5)N—C5—C9111.11 (19)
N—Na1—Na1i121.70 (7)C4—C5—C9128.05 (19)
O9ii—Na1—Na1i73.15 (6)O1—C6—O2122.8 (2)
O9—Na1—Na1ii45.17 (6)O1—C6—C1118.3 (2)
O8—Na1—Na1ii70.94 (5)O2—C6—C1118.9 (2)
O10—Na1—Na1ii107.58 (7)C6—O1—Na1127.72 (16)
O1—Na1—Na1ii155.73 (7)O4—C7—O3120.7 (2)
O10i—Na1—Na1ii79.63 (5)O4—C7—C2118.50 (19)
N—Na1—Na1ii132.72 (6)O3—C7—C2120.8 (2)
O9ii—Na1—Na1ii35.76 (5)O4—C7—Na252.54 (11)
Na1i—Na1—Na1ii94.41 (5)O3—C7—Na269.52 (13)
O11—Na2—O5iii80.18 (7)C2—C7—Na2164.48 (15)
O11—Na2—O6iv82.71 (7)C7—O3—Na285.55 (14)
O5iii—Na2—O6iv150.56 (7)C7—O3—H3107.5
O11—Na2—O5v161.10 (7)Na2—O3—H3160.1
O5iii—Na2—O5v80.98 (7)C7—O4—Na2104.12 (14)
O6iv—Na2—O5v113.75 (7)O5—C8—O6123.9 (2)
O11—Na2—O4101.38 (7)O5—C8—C4117.35 (19)
O5iii—Na2—O489.54 (6)O6—C8—C4118.8 (2)
O6iv—Na2—O4117.34 (7)C8—O5—Na2iii130.76 (15)
O5v—Na2—O479.82 (7)C8—O5—Na2viii123.43 (15)
O11—Na2—O11vi90.16 (7)Na2iii—O5—Na2viii99.02 (7)
O5iii—Na2—O11vi78.64 (7)C8—O6—Na2ix128.80 (14)
O6iv—Na2—O11vi77.63 (6)O8—C9—O7121.0 (2)
O5v—Na2—O11vi84.77 (7)O8—C9—C5118.5 (2)
O4—Na2—O11vi161.90 (7)O7—C9—C5120.5 (2)
O11—Na2—O3117.19 (7)C9—O7—H7112.8
O5iii—Na2—O3134.97 (6)C9—O8—Na1126.87 (16)
O6iv—Na2—O374.36 (6)Na1—O9—Na1ii99.07 (8)
O5v—Na2—O377.80 (7)Na1—O9—H9A115.5
O4—Na2—O347.92 (6)Na1ii—O9—H9A104.4
O11vi—Na2—O3137.20 (7)Na1—O9—H9B118.8
O11—Na2—C7113.48 (7)Na1ii—O9—H9B120.3
O5iii—Na2—C7110.79 (7)H9A—O9—H9B98.8
O6iv—Na2—C797.96 (7)Na1—O10—Na1i96.08 (8)
O5v—Na2—C774.82 (7)Na1—O10—H10A112.2
O4—Na2—C723.34 (6)Na1i—O10—H10A129.4
O11vi—Na2—C7155.41 (7)Na1—O10—H10B116.3
O3—Na2—C724.93 (6)Na1i—O10—H10B97.7
O11—Na2—Na2vi46.94 (5)H10A—O10—H10B105.2
O5iii—Na2—Na2vi74.89 (5)Na2—O11—Na2vi89.84 (7)
O6iv—Na2—Na2vi75.92 (5)Na2—O11—H11A122.9
O5v—Na2—Na2vi125.55 (7)Na2vi—O11—H11A121.8
O4—Na2—Na2vi146.06 (7)Na2—O11—H11B125.4
O11vi—Na2—Na2vi43.23 (5)Na2vi—O11—H11B100.3
O3—Na2—Na2vi148.10 (6)H11A—O11—H11B96.5
C7—Na2—Na2vi159.59 (7)

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O3—H3···O20.861.552.410175
O7—H7···O60.861.552.402175
O9—H9A···O1x0.852.052.900175
O9—H9B···O1xi0.862.112.945161
O10—H10A···O2viii0.882.213.024153
O10—H10B···O8xii0.881.862.738173
O11—H11A···O4xiii0.892.052.917167
O11—H11B···O4xii0.882.082.949170

Symmetry codes: (x) x+1, y, z; (xi) −x+3, −y, −z+1; (viii) x, y+1, z; (xii) x−1, y, z; (xiii) −x+1, −y+1, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DS2024).

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