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Acta Cryst. (2007). E63, m2555    [ doi:10.1107/S1600536807044315 ]

Poly[aqua([mu]4-benzene-1,3-dicarboxylato-[kappa]4O:O':O'':O''')bis(imidazole-[kappa]N)palladium(II)]

L.-J. Hao and T.-L. Yu

Abstract top

In the title compound, [Pd(C8H4O4)(C3H4N2)2(H2O)]n, two monodendate imidazole ligands are bonded to the PdII atom, and individual units are linked into chains by 1,3-benzenedicarboxylate anions. The PdII atom is seven-coordinated by two N atoms from two imidazole ligands, four O atoms from two independent 1,3-benzenedicarboxylate anions and one water molecule, exhibiting a distorted pentagonal-bipyramidal coordination environment. One of the carboxylate O atoms at the base of the pyramid is bonded only very loosely, with a Pd-O distance of 2.771 (2) Å [cf. 2.312 (2)-2.488 (3) Å for the other Pd-O distances]. N-H...O and O-H...O hydrogen-bonding interactions link parallel chains together.

Comment top

In recent years, carboxylic acids have been widely used as polydentate ligands, which can coordinate to transition or rare earth ions yielding complexes with interesting properties that are useful in materials science (Church & Halvorson, 1959; Chung et al., 1971) and in biological systems (Okabe & Oya, 2000; Serre et al., 2005; Pocker & Fong, 1980; Scapin et al., 1997). Herein, we report the synthesis and X-ray crystal structure analysis of the title compound, poly[aqua (benzene-1,3-dicarboxylato) bis(imidazole) palladium(II)].

The molecular structure of the title compound is shown in Fig. 1. Pd(II) is seven-coordianted with two N atoms from two imidazole ligands, four O atoms from two independent 1,3-benzene dicarboxylate, and one water molecule. The palladium ion exhibits a distorted pentagonal bipyramidal coordination environment with one of the imidazole ligands and the water molecule being located in the two apical positions, and the N and O atoms of the remaining imidazole and the carboxylate ions in the basal plane. One of the carboxylate ions is coordinated to the Pd(II) ion in an asymmetric fashion with the Pd(1)—O(3) bond being with 2.771 (2) Å much longer than the other Pd—O bonding distances (2.312 (2) to 2.488 (3) Å). The 1,3-benzene dicarboxylate ions bridge neigboring Pd(II) ion to gives rise to one-dimensional zigzag chains (Fig. 2). N—H···O and O—H···O hydrogen bonding interactions connect the parallel chains with each other stabilize the structure (see the hydrogen-bond geometry table for numerical values and Figure 3 for a packing diagram showing the H-bond interactions).

Related literature top

For related literature, see: Church & Halvorson (1959); Chung et al. (1971); Okabe & Oya (2000); Serre et al. (2005); Pocker & Fong (1980); Scapin et al. (1997).

Experimental top

A mixture of palladium acetate (0.5 mmol), imidazole (1.0 mmol), benzene-1,3-dicarboxylic acid (0.5 mmol), H2O (8 ml) and ethanol (8 ml) in a 25 ml Teflon-lined stainless steel autoclave was kept at 413 K for three days. Colorless crystals were obtained after cooling to room temperature with a yield of 27%. Anal. Calc. for C14H14N4O5Pd: C 39.56, H 3.30, N 13.19%; Found: C 39.51, H 3.27, N 13.17%.

Refinement top

O—H and N—H hydrogen atoms were located in difference density maps and were refined with distance restraints of d(O—H) = 0.82 (2) Å, d(N—H) = 0.88 (2) Å. All other H atoms were placed in calculated positions with a C—H bond distance of 0.93 Å. Uiso(H) for the water H atoms was set to 1.5Ueq, all others to 1.2Ueq of the respective carrier atom.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2001); data reduction: SAINT-Plus (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2001); software used to prepare material for publication: SHELXTL (Bruker, 2001).

Figures top
[Figure 1] Fig. 1. A view of the structure of (I), showing 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. Chains of the title compound along the [010] direction.
[Figure 3] Fig. 3. Packing diagram, viewed along the [010] direction. Dashed lines indicate hydrogen bonds, hydrogen atoms themselves are omitted for clarity.
Poly[aqua(µ4-benzene-1,3-dicarboxylato-κ4O:O':O'':O''') bis(imidazole-κN)palladium(II)] top
Crystal data top
[Pd(C8H4O4)(C3H4N2)2(H2O)]F(000) = 848
Mr = 424.69Dx = 1.684 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3516 reflections
a = 8.5814 (17) Åθ = 1.7–27.0°
b = 19.426 (4) ŵ = 1.14 mm−1
c = 10.118 (2) ÅT = 293 K
β = 96.62 (3)°Cube, colourless
V = 1675.5 (6) Å30.43 × 0.28 × 0.22 mm
Z = 4
Data collection top
Bruker APEXII CCD area-detector
diffractometer		3280 independent reflections
Radiation source: fine-focus sealed tube2523 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.031
φ and ω scansθmax = 26.0°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		h = −10→9
Tmin = 0.640, Tmax = 0.788k = −23→11
8842 measured reflectionsl = −12→12
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)] = 0.031Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.071H atoms treated by a mixture of independent and constrained refinement
S = 1.00 w = 1/[σ2(Fo2) + (0.0336P)2]
where P = (Fo2 + 2Fc2)/3
3280 reflections(Δ/σ)max = 0.003
229 parametersΔρmax = 0.40 e Å−3
4 restraintsΔρmin = −0.62 e Å−3
Crystal data top
[Pd(C8H4O4)(C3H4N2)2(H2O)]V = 1675.5 (6) Å3
Mr = 424.69Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.5814 (17) ŵ = 1.14 mm−1
b = 19.426 (4) ÅT = 293 K
c = 10.118 (2) Å0.43 × 0.28 × 0.22 mm
β = 96.62 (3)°
Data collection top
Bruker APEXII CCD area-detector
diffractometer		3280 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		2523 reflections with I > 2σ(I)
Tmin = 0.640, Tmax = 0.788Rint = 0.031
8842 measured reflectionsθmax = 26.0°
Refinement top
R[F2 > 2σ(F2)] = 0.031H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.071Δρmax = 0.40 e Å−3
S = 1.00Δρmin = −0.62 e Å−3
3280 reflectionsAbsolute structure: ?
229 parametersFlack parameter: ?
4 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
Pd10.37425 (3)0.126490 (13)1.00522 (2)0.03491 (10)
C10.4890 (4)0.2744 (2)0.8764 (4)0.0612 (10)
H10.44730.26300.79020.073*
C20.5780 (5)0.3305 (2)0.9103 (5)0.0653 (11)
H20.60970.36380.85300.078*
C30.5445 (4)0.2718 (2)1.0866 (4)0.0641 (11)
H30.55040.25881.17550.077*
C40.0640 (5)0.2230 (2)0.9641 (5)0.0741 (13)
H40.12560.26240.96300.089*
C5−0.0908 (5)0.2224 (3)0.9456 (6)0.1025 (19)
H5−0.15650.26010.92720.123*
C6−0.0034 (5)0.1199 (2)0.9826 (6)0.0913 (17)
H6−0.00090.07260.99590.110*
C70.4815 (4)0.09640 (18)0.7491 (3)0.0413 (8)
C80.5730 (3)0.08147 (17)0.6351 (3)0.0368 (7)
C90.7237 (4)0.0550 (2)0.6573 (3)0.0533 (10)
H90.76840.04600.74380.064*
C100.8084 (4)0.0420 (2)0.5512 (4)0.0663 (12)
H100.90910.02380.56650.080*
C110.5089 (4)0.09436 (17)0.5050 (3)0.0388 (7)
H110.40720.11140.48890.047*
C120.7429 (4)0.0560 (2)0.4226 (3)0.0555 (10)
H120.80020.04760.35160.067*
C130.5931 (4)0.08233 (17)0.3994 (3)0.0397 (8)
C140.5215 (5)0.09758 (19)0.2596 (3)0.0505 (9)
N10.4694 (3)0.23673 (16)0.9882 (3)0.0532 (8)
N20.6116 (4)0.32854 (18)1.0435 (4)0.0638 (9)
H210.682 (4)0.3538 (18)1.096 (3)0.077*
N30.1206 (3)0.15876 (16)0.9847 (3)0.0482 (7)
N4−0.1346 (4)0.1571 (3)0.9587 (6)0.1079 (16)
H20−0.229 (3)0.140 (3)0.935 (6)0.129*
O10.2779 (3)0.01164 (13)0.9913 (2)0.0496 (6)
O20.5538 (3)0.09052 (13)0.8661 (2)0.0489 (6)
O30.3421 (3)0.11470 (14)0.7305 (2)0.0593 (7)
O40.3885 (3)0.12419 (16)0.2416 (2)0.0722 (8)
O50.5971 (4)0.08483 (16)0.1641 (2)0.0753 (9)
H220.296 (6)−0.006 (2)0.920 (3)0.113*
H230.327 (5)−0.013 (2)1.048 (4)0.113*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02806 (14)0.04265 (16)0.03440 (14)0.00380 (12)0.00523 (9)0.00091 (12)
C10.055 (2)0.061 (3)0.065 (3)−0.003 (2)−0.0070 (19)0.006 (2)
C20.054 (2)0.062 (3)0.079 (3)−0.008 (2)0.004 (2)0.011 (2)
C30.059 (2)0.074 (3)0.061 (2)−0.016 (2)0.012 (2)−0.013 (2)
C40.046 (2)0.051 (3)0.126 (4)0.010 (2)0.011 (2)−0.004 (3)
C50.046 (3)0.066 (3)0.193 (6)0.021 (2)0.003 (3)−0.021 (4)
C60.034 (2)0.057 (3)0.181 (5)0.002 (2)0.008 (3)−0.004 (3)
C70.044 (2)0.047 (2)0.0327 (17)0.0011 (17)0.0051 (14)0.0022 (15)
C80.0366 (17)0.0414 (19)0.0331 (16)−0.0007 (15)0.0074 (13)0.0008 (14)
C90.042 (2)0.080 (3)0.0361 (18)0.010 (2)−0.0005 (15)0.0035 (18)
C100.044 (2)0.109 (4)0.048 (2)0.018 (2)0.0117 (17)0.000 (2)
C110.0363 (17)0.0436 (19)0.0364 (17)0.0022 (16)0.0031 (14)0.0011 (15)
C120.051 (2)0.080 (3)0.0386 (19)0.004 (2)0.0174 (16)−0.0040 (19)
C130.0437 (19)0.0415 (19)0.0339 (17)−0.0019 (16)0.0050 (14)−0.0011 (15)
C140.069 (3)0.048 (2)0.0343 (19)−0.003 (2)0.0053 (18)−0.0017 (16)
N10.0498 (18)0.0557 (19)0.0534 (18)−0.0094 (16)0.0024 (14)−0.0037 (16)
N20.0489 (19)0.061 (2)0.082 (3)−0.0150 (17)0.0069 (17)−0.0165 (19)
N30.0309 (15)0.0496 (18)0.064 (2)0.0047 (14)0.0043 (13)−0.0022 (15)
N40.036 (2)0.076 (3)0.210 (5)0.001 (2)0.011 (3)−0.020 (3)
O10.0518 (15)0.0479 (15)0.0500 (15)0.0053 (12)0.0090 (12)0.0011 (12)
O20.0502 (14)0.0645 (16)0.0324 (12)0.0089 (13)0.0065 (10)0.0026 (11)
O30.0444 (14)0.089 (2)0.0459 (14)0.0201 (14)0.0101 (11)0.0048 (13)
O40.0713 (19)0.103 (2)0.0404 (14)0.0198 (18)−0.0011 (13)0.0079 (14)
O50.109 (2)0.086 (2)0.0328 (13)0.0261 (19)0.0157 (14)−0.0034 (14)
Geometric parameters (Å, º) top
Pd1—N32.252 (3)C7—O31.242 (4)
Pd1—N12.305 (3)C7—O21.276 (4)
Pd1—O22.311 (2)C7—C81.497 (4)
Pd1—O12.378 (3)C8—C91.386 (4)
Pd1—O4i2.382 (2)C8—C111.390 (4)
Pd1—O5i2.487 (3)C9—C101.387 (4)
C1—C21.353 (5)C9—H90.9300
C1—N11.374 (5)C10—C121.383 (5)
C1—H10.9300C10—H100.9300
C2—N21.346 (5)C11—C131.377 (4)
C2—H20.9300C11—H110.9300
C3—N11.312 (4)C12—C131.379 (4)
C3—N21.340 (5)C12—H120.9300
C3—H30.9300C13—C141.505 (4)
C4—C51.321 (6)C14—O41.247 (4)
C4—N31.347 (5)C14—O51.249 (4)
C4—H40.9300N2—H210.901 (19)
C5—N41.335 (7)N4—H200.88 (2)
C5—H50.9300O1—H220.83 (3)
C6—N31.302 (5)O1—H230.83 (4)
C6—N41.336 (5)O4—Pd1ii2.382 (2)
C6—H60.9300O5—Pd1ii2.487 (3)
N3—Pd1—N194.67 (11)C11—C8—C7120.6 (3)
N3—Pd1—O2137.15 (9)C8—C9—C10120.3 (3)
N1—Pd1—O288.21 (10)C8—C9—H9119.9
N3—Pd1—O185.99 (10)C10—C9—H9119.9
N1—Pd1—O1172.26 (9)C12—C10—C9120.0 (3)
O2—Pd1—O186.09 (9)C12—C10—H10120.0
N3—Pd1—O4i92.00 (10)C9—C10—H10120.0
N1—Pd1—O4i96.59 (11)C13—C11—C8121.2 (3)
O2—Pd1—O4i130.19 (9)C13—C11—H11119.4
O1—Pd1—O4i91.10 (9)C8—C11—H11119.4
N3—Pd1—O5i144.39 (9)C13—C12—C10120.2 (3)
N1—Pd1—O5i95.63 (11)C13—C12—H12119.9
O2—Pd1—O5i77.22 (8)C10—C12—H12119.9
O1—Pd1—O5i88.23 (10)C11—C13—C12119.6 (3)
O4i—Pd1—O5i52.98 (9)C11—C13—C14120.1 (3)
C2—C1—N1109.8 (4)C12—C13—C14120.3 (3)
C2—C1—H1125.1O4—C14—O5121.1 (3)
N1—C1—H1125.1O4—C14—C13119.1 (3)
N2—C2—C1106.3 (4)O5—C14—C13119.7 (4)
N2—C2—H2126.8C3—N1—C1104.6 (3)
C1—C2—H2126.8C3—N1—Pd1124.9 (3)
N1—C3—N2111.8 (4)C1—N1—Pd1129.3 (3)
N1—C3—H3124.1C3—N2—C2107.4 (3)
N2—C3—H3124.1C3—N2—H21123 (3)
C5—C4—N3110.6 (4)C2—N2—H21129 (3)
C5—C4—H4124.7C6—N3—C4104.8 (3)
N3—C4—H4124.7C6—N3—Pd1128.3 (3)
C4—C5—N4106.5 (4)C4—N3—Pd1126.8 (3)
C4—C5—H5126.7C5—N4—C6106.9 (4)
N4—C5—H5126.7C5—N4—H20126 (4)
N3—C6—N4111.1 (4)C6—N4—H20125 (4)
N3—C6—H6124.4Pd1—O1—H22110 (4)
N4—C6—H6124.4Pd1—O1—H23111 (4)
O3—C7—O2121.5 (3)H22—O1—H23103 (5)
O3—C7—C8121.4 (3)C7—O2—Pd1104.5 (2)
O2—C7—C8117.1 (3)C14—O4—Pd1ii95.4 (2)
C9—C8—C11118.7 (3)C14—O5—Pd1ii90.4 (2)
C9—C8—C7120.6 (3)
Symmetry codes: (i) x, y, z+1; (ii) x, y, z−1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H22···O5iii0.83 (3)2.02 (3)2.743 (4)145 (5)
O1—H23···O2iv0.83 (4)1.97 (4)2.762 (3)162 (5)
N2—H21···O3v0.90 (2)1.92 (2)2.801 (4)165 (4)
N4—H20···O2vi0.88 (2)2.14 (2)3.020 (5)173 (5)
Symmetry codes: (iii) −x+1, −y, −z+1; (iv) −x+1, −y, −z+2; (v) x+1/2, −y+1/2, z+1/2; (vi) x−1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H22···O5i0.83 (3)2.02 (3)2.743 (4)145 (5)
O1—H23···O2ii0.83 (4)1.97 (4)2.762 (3)162 (5)
N2—H21···O3iii0.901 (19)1.92 (2)2.801 (4)165 (4)
N4—H20···O2iv0.88 (2)2.14 (2)3.020 (5)173 (5)
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, −y, −z+2; (iii) x+1/2, −y+1/2, z+1/2; (iv) x−1, y, z.
references
References top

Bruker (2001). SAINT-Plus and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.

Bruker (2004). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.

Chung, L., Rajan, K. S., Merdinger, E. & Crecz, N. (1971). Biophys. J. 11, 469–475.

Church, B. S. & Halvorson, H. (1959). Nature, 183, 124–125.

Okabe, N. & Oya, N. (2000). Acta Cryst. C56, 1416–1417.

Pocker, Y. & Fong, C. T. O. (1980). Biochemistry, 19, 2045–2049.

Scapin, G., Reddy, S. G., Zheng, R. & Blanchard, J. S. (1997). Biochemistry, 36, 15081–15088.

Serre, C., Marrot, J. & Ferey, G. (2005). Inorg. Chem. 44, 654–658.

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