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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): m1274.
Published online 2009 October 3. doi:  10.1107/S1600536809039270
PMCID: PMC2971183

Tetra­kis(pyridine-2-carboxyl­ato-κ2 N,O)palladium(IV) dihydrate

Abstract

The asymmetric unit of the title compound, [Pd(C6H4NO2)4]·2H2O, consists of a quarter of a neutral PdIV complex and half of a solvent water mol­ecule. In the complex, the PdIV ion is located on a fourfold inversion axis and eight-coordinated in a distorted dodeca­hedral environment by four N and four O atoms from four symmetry-related pyridine-2-carboxyl­ate (pic) anionic ligands. In the crystal, the water mol­ecule is involved in O—H(...)O hydrogen bonding, and weak inter­molecular C—H(...)O hydrogen bonds occur. There are also inter­molecular π–π inter­actions between adjacent pyridine rings, with a centroid–centroid distance of 3.715 (3) Å.

Related literature

For details of polyhedra with coordination number eight, see: Lippard & Russ (1968 [triangle]); Muetterties & Guggenberger (1974 [triangle]). For the synthesis and structure of the Pd(II)–pic complex, [Pd(pic)2], see: Qin et al. (2002 [triangle]). For the crystal structures of eight-coordinated M(III, IV)–pic complexes (M = Nb, Er or Bi), see: Ooi et al. (1996 [triangle]); Soares-Santos et al. (2003 [triangle]); Callens et al. (2008 [triangle]). For the crystal structures of Pd(II) in an environment of eight O atoms, see: Izarova et al. (2009 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-m1274-scheme1.jpg

Experimental

Crystal data

  • [Pd(C6H4NO2)4]·2H2O
  • M r = 630.84
  • Tetragonal, An external file that holds a picture, illustration, etc.
Object name is e-65-m1274-efi7.jpg
  • a = 11.1621 (5) Å
  • c = 9.5880 (9) Å
  • V = 1194.59 (14) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.85 mm−1
  • T = 296 K
  • 0.23 × 0.14 × 0.07 mm

Data collection

  • Bruker SMART 1000 CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2000 [triangle]) T min = 0.804, T max = 0.942
  • 8399 measured reflections
  • 1485 independent reflections
  • 1074 reflections with I > 2σ(I)
  • R int = 0.045

Refinement

  • R[F 2 > 2σ(F 2)] = 0.034
  • wR(F 2) = 0.104
  • S = 1.21
  • 1485 reflections
  • 89 parameters
  • H-atom parameters constrained
  • Δρmax = 0.76 e Å−3
  • Δρmin = −1.00 e Å−3

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [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/S1600536809039270/is2464sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809039270/is2464Isup2.hkl

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

Acknowledgments

This study was supported financially by the Special Research Program of Chonnam National University, 2009.

supplementary crystallographic information

Comment

The asymmetric unit of the title compound, [Pd(C6H4NO2)4].2H2O, contains a quarter of a neutral PdIV complex and one half of a solvent water molecule (Fig. 1). In the crystal, the complex has the symmetry elements C2 and S4, and its point group is S4 and the Pd atom lies on the special position at (1/4, 1/4, 1/4) (Wyckoff letter a). The water molecule is disposed about a twofold rotation axis through O atom with the special position at (3/4, 1/4, z) (Wyckoff letter e). In the complex, the Pd4+ ion is eight-coordinated in a distorted dodecahedral environment (Fig. 2) by four N and four O atoms from four distinct pyridine-2-carboxylate (pic) anionic ligands. All four ligands are coordinated in an N,O-chelation mode with the considerably different Pd—O and Pd—N bond lengths [Pd—O = 2.097 (3) Å, Pd—N = 2.373 (3) Å] and the five-membered chelate ring has an O—Pd—N bite angle of 72.07 (12)°. On the contrary, the Pd—O and Pd—N bond lengths in the Pd(II)-pic complex, [Pd(pic)2], are almost equal [Pd—O = 2.003 (2) Å, Pd—N = 1.998 (2) Å] and the bite angle of the chelate ring is 82.36 (9)° (Qin et al., 2002). The C═O bond length [1.215 (5) Å] and the C—O bond length [1.314 (5) Å] are typical and similar to values in the complex [Pd(pic)2] (Qin et al., 2002). In the crystal structure, the water molecule is involved in O—H···O hydrogen bonding and weak intermolecular C—H···O hydrogen bonds occur (Table 1 and Fig. 3). There are also intermolecular π-π interactions between adjacent pyridine rings, with a centroid-centroid distance of 3.715 (3) Å.

Experimental

Single crystals of the title compound were unexpectedly obtained by reacting pyridine-2-carboxylic acid (0.721 g, 5.86 mmol), 1,6-diaminohexane (0.160 g, 1.38 mmol) and Na2PdCl4 (0.200 g, 0.68 mmol) in H2O (10 ml) for 24 h at room temperature. Crystals suitable for X-ray analysis were obtained by slow evaporation from a CH3CN solution of the white reaction product.

Refinement

H atoms were positioned geometrically and allowed to ride on their respective parent atoms [C—H = 0.93 Å, O—H = 0.87 Å and Uiso(H) = 1.2Ueq(C) or 1.5Ueq(O)]].

Figures

Fig. 1.
The structure of the title compound, with displacement ellipsoids drawn at the 30% probability level for non-H atoms [Symmetry codes: (a) 1/2 - x, 1/2 - y, z, (b) y, 1/2 - x, 1/2 - z, (c) 1/2 - y, x, 1/2 - z]. H atoms are omitted.
Fig. 2.
View of the distorted dodecahedral geometry around the Pd atom.
Fig. 3.
View of the unit-cell contents of the title compound. Hydrogen-bond interactions are drawn with dashed lines.

Crystal data

[Pd(C6H4NO2)4]·2H2ODx = 1.754 Mg m3
Mr = 630.84Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P42/nCell parameters from 3500 reflections
Hall symbol: -P 4bcθ = 2.6–28.3°
a = 11.1621 (5) ŵ = 0.85 mm1
c = 9.5880 (9) ÅT = 296 K
V = 1194.59 (14) Å3Block, colorless
Z = 20.23 × 0.14 × 0.07 mm
F(000) = 636

Data collection

Bruker SMART 1000 CCD diffractometer1485 independent reflections
Radiation source: fine-focus sealed tube1074 reflections with I > 2σ(I)
graphiteRint = 0.045
[var phi] and ω scansθmax = 28.3°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2000)h = −14→14
Tmin = 0.804, Tmax = 0.942k = −14→10
8399 measured reflectionsl = −12→12

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)] = 0.034Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.104H-atom parameters constrained
S = 1.21w = 1/[σ2(Fo2) + (0.031P)2 + 2.1364P] where P = (Fo2 + 2Fc2)/3
1485 reflections(Δ/σ)max < 0.001
89 parametersΔρmax = 0.76 e Å3
0 restraintsΔρmin = −1.00 e Å3

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*/Ueq
Pd10.25000.25000.25000.02277 (17)
O10.0856 (2)0.3186 (3)0.3193 (3)0.0380 (7)
O2−0.0577 (3)0.3299 (3)0.4796 (4)0.0570 (10)
N10.1892 (3)0.1367 (3)0.4471 (4)0.0334 (8)
C10.2408 (4)0.0371 (4)0.4990 (5)0.0416 (10)
H10.31080.00870.45810.050*
C20.1927 (4)−0.0243 (4)0.6114 (5)0.0449 (11)
H20.2298−0.09300.64540.054*
C30.0889 (4)0.0180 (5)0.6722 (5)0.0491 (12)
H30.0561−0.02100.74890.059*
C40.0343 (4)0.1187 (4)0.6182 (4)0.0406 (10)
H4−0.03600.14820.65740.049*
C50.0863 (4)0.1755 (4)0.5038 (5)0.0366 (10)
C60.0317 (4)0.2821 (4)0.4335 (5)0.0371 (9)
O30.75000.25000.1567 (7)0.092 (2)
H3O0.71830.31480.12150.137*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Pd10.02072 (19)0.02072 (19)0.0269 (3)0.0000.0000.000
O10.0315 (15)0.0398 (17)0.0426 (17)0.0077 (12)−0.0017 (14)0.0034 (14)
O20.0388 (19)0.066 (2)0.066 (2)0.0183 (16)0.0149 (17)0.0011 (19)
N10.0312 (18)0.0364 (19)0.0326 (18)0.0020 (14)0.0007 (15)0.0005 (15)
C10.040 (3)0.035 (2)0.049 (3)0.0050 (18)0.000 (2)0.003 (2)
C20.053 (3)0.040 (3)0.042 (3)−0.004 (2)−0.007 (2)0.006 (2)
C30.052 (3)0.056 (3)0.040 (3)−0.006 (2)0.001 (2)0.006 (2)
C40.039 (2)0.056 (3)0.027 (2)−0.004 (2)0.0044 (18)−0.006 (2)
C50.035 (2)0.034 (2)0.041 (2)−0.0023 (17)−0.0010 (18)−0.0059 (19)
C60.032 (2)0.038 (2)0.041 (2)−0.0005 (18)0.0022 (19)−0.006 (2)
O30.121 (6)0.064 (4)0.090 (5)0.002 (4)0.0000.000

Geometric parameters (Å, °)

Pd1—O1i2.097 (3)N1—C11.347 (5)
Pd1—O1ii2.097 (3)C1—C21.386 (6)
Pd1—O1iii2.097 (3)C1—H10.9300
Pd1—O12.097 (3)C2—C31.380 (7)
Pd1—N1ii2.373 (3)C2—H20.9300
Pd1—N1iii2.373 (3)C3—C41.380 (7)
Pd1—N1i2.373 (3)C3—H30.9300
Pd1—N12.373 (3)C4—C51.393 (6)
O1—C61.314 (5)C4—H40.9300
O2—C61.215 (5)C5—C61.497 (6)
N1—C51.343 (5)O3—H3O0.87
O1i—Pd1—O1ii95.77 (5)N1ii—Pd1—N174.42 (17)
O1i—Pd1—O1iii143.04 (17)N1iii—Pd1—N1129.37 (10)
O1ii—Pd1—O1iii95.77 (5)N1i—Pd1—N1129.37 (10)
O1i—Pd1—O195.77 (5)C6—O1—Pd1123.4 (3)
O1ii—Pd1—O1143.04 (17)C5—N1—C1118.8 (4)
O1iii—Pd1—O195.77 (5)C5—N1—Pd1113.3 (3)
O1i—Pd1—N1ii71.43 (12)C1—N1—Pd1127.7 (3)
O1ii—Pd1—N1ii72.07 (12)N1—C1—C2122.0 (4)
O1iii—Pd1—N1ii145.42 (12)N1—C1—H1119.0
O1—Pd1—N1ii78.64 (12)C2—C1—H1119.0
O1i—Pd1—N1iii78.64 (12)C3—C2—C1118.9 (4)
O1ii—Pd1—N1iii71.43 (12)C3—C2—H2120.5
O1iii—Pd1—N1iii72.07 (12)C1—C2—H2120.5
O1—Pd1—N1iii145.42 (12)C2—C3—C4119.5 (5)
N1ii—Pd1—N1iii129.37 (10)C2—C3—H3120.3
O1i—Pd1—N1i72.07 (12)C4—C3—H3120.3
O1ii—Pd1—N1i145.42 (12)C3—C4—C5118.8 (4)
O1iii—Pd1—N1i78.64 (12)C3—C4—H4120.6
O1—Pd1—N1i71.43 (12)C5—C4—H4120.6
N1ii—Pd1—N1i129.37 (10)N1—C5—C4121.9 (4)
N1iii—Pd1—N1i74.42 (17)N1—C5—C6115.0 (4)
O1i—Pd1—N1145.42 (12)C4—C5—C6123.1 (4)
O1ii—Pd1—N178.64 (12)O2—C6—O1122.9 (4)
O1iii—Pd1—N171.43 (12)O2—C6—C5121.3 (4)
O1—Pd1—N172.07 (12)O1—C6—C5115.8 (4)
O1i—Pd1—O1—C6−141.3 (3)N1iii—Pd1—N1—C124.3 (4)
O1ii—Pd1—O1—C6−33.7 (3)N1i—Pd1—N1—C1127.2 (4)
O1iii—Pd1—O1—C673.9 (3)C5—N1—C1—C2−1.9 (7)
N1ii—Pd1—O1—C6−71.6 (3)Pd1—N1—C1—C2−176.7 (3)
N1iii—Pd1—O1—C6140.4 (3)N1—C1—C2—C3−0.1 (7)
N1i—Pd1—O1—C6149.9 (3)C1—C2—C3—C41.3 (7)
N1—Pd1—O1—C65.6 (3)C2—C3—C4—C5−0.4 (7)
O1i—Pd1—N1—C571.4 (4)C1—N1—C5—C42.8 (6)
O1ii—Pd1—N1—C5155.0 (3)Pd1—N1—C5—C4178.3 (3)
O1iii—Pd1—N1—C5−104.9 (3)C1—N1—C5—C6−176.3 (4)
O1—Pd1—N1—C5−2.2 (3)Pd1—N1—C5—C6−0.7 (4)
N1ii—Pd1—N1—C580.7 (3)C3—C4—C5—N1−1.6 (7)
N1iii—Pd1—N1—C5−150.8 (3)C3—C4—C5—C6177.4 (4)
N1i—Pd1—N1—C5−47.9 (3)Pd1—O1—C6—O2173.0 (3)
O1i—Pd1—N1—C1−113.6 (4)Pd1—O1—C6—C5−7.9 (5)
O1ii—Pd1—N1—C1−29.9 (4)N1—C5—C6—O2−175.7 (4)
O1iii—Pd1—N1—C170.2 (4)C4—C5—C6—O25.2 (7)
O1—Pd1—N1—C1172.9 (4)N1—C5—C6—O15.1 (6)
N1ii—Pd1—N1—C1−104.3 (4)C4—C5—C6—O1−173.9 (4)

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O3—H3O···O2iv0.872.042.879 (5)161
C1—H1···O2v0.932.553.233 (5)131
C2—H2···O3vi0.932.593.420 (6)149

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2464).

References

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