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Acta Crystallogr Sect E Struct Rep Online. 2008 July 1; 64(Pt 7): m896.
Published online 2008 June 7. doi:  10.1107/S1600536808016097
PMCID: PMC2961856

Tetra­aqua­bis[(1-carboxyl­atomethyl-1,3-benzimidazol-3-ium-3-yl)acetato-κO]palladium(II) dihydrate

Abstract

In the title compound, [Pd(C11H9N2O4)2(H2O)4]·2H2O, the palladium(II) cation lies on an inversion centre and is hexa­coordinated by two carboxyl­ate O atoms from two (1-carboxyl­atomethyl-1,3-benzimidazol-3-ium-3-yl)acetate ligands and four water mol­ecules, with a slightly distorted octa­hedral geometry. O—H(...)O hydrogen bonds link the mol­ecules together.

Related literature

For uses of carboxylic acids in materials science, see: Church & Halvorson (1959 [triangle]). For uses in biological systems, see: Chung et al. (1971 [triangle]); Okabe & Oya (2000 [triangle]); Serre et al. (2005 [triangle]); Pocker & Fong (1980 [triangle]); Scapin et al. (1997 [triangle]); Kim et al. (2001 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0m896-scheme1.jpg

Experimental

Crystal data

  • [Pd(C11H9N2O4)2(H2O)4]·2H2O
  • M r = 680.90
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m896-efi1.jpg
  • a = 5.4702 (10) Å
  • b = 11.794 (2) Å
  • c = 20.886 (3) Å
  • β = 95.13 (3)°
  • V = 1342.1 (4) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.77 mm−1
  • T = 293 (2) K
  • 0.43 × 0.28 × 0.22 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2004 [triangle]) T min = 0.733, T max = 0.849
  • 7075 measured reflections
  • 2425 independent reflections
  • 1958 reflections with I > 2σ(I)
  • R int = 0.032

Refinement

  • R[F 2 > 2σ(F 2)] = 0.028
  • wR(F 2) = 0.072
  • S = 1.00
  • 2425 reflections
  • 205 parameters
  • 9 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.24 e Å−3
  • Δρmin = −0.49 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: SAINT-Plus (Bruker, 2004 [triangle]); data reduction: SAINT-Plus; 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: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808016097/cf2196sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808016097/cf2196Isup2.hkl

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

Acknowledgments

This work was supported by the Natural Science Foundation of Shandong Province (grant No. Y2007D39).

supplementary crystallographic information

Comment

In recent years, carboxylates 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). For example, Kim et al. (2001) focused on the syntheses of transition metal complexes containing benzenecarboxylate and rigid aromatic pyridine ligands in order to study their electronic conductivity and magnetic properties. The importance of transition metal dicarboxylate complexes motivated us to pursue synthetic strategies for these compounds, using sodium 1-carboxymethyl-1,3-benzimidazol-3-ium-3-acetate as a polydentate ligand. Here we report the synthesis and X-ray crystal structure analysis of the title compound.

The molecular structure of the title compound is shown in Fig. 1. The palladium(II) cation lies on an inversion center and is hexacoordinated by two carboxylate oxygen atoms from two 1-carboxymethyl-1,3-benzimidazol-3-ium-3-acetato ligands and four water molecules, with a slightly distorted octahedral geometry. The Pd—O bond distances are in the range 2.2608 (19)–2.276 (2) Å. The packing involves hydrogen bonds, shown in Table 1 and Figure 2.

Experimental

A mixture of palladium dichloride (0.5 mmol), imidazole (1.0 mmol), sodium 1-carboxymethyl-1,3-benzimidazol-3-ium-3-acetate (0.5 mmol), water (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 C22H30N4O14Pd: C 38.77, H 4.41, N 8.22%; Found: C 38.68, H 4.37, N 8.14%.

Refinement

The H atoms of the water molecule were located in a difference density map and were refined with distance restraints H···H = 1.38 (2) Å, O—H = 0.88 (2) Å, and with a fixed Uiso of 0.80 Å2. All other H atoms were placed in calculated positions with a C—H bond distance of 0.93 Å and Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of (I), showing the atomic numbering scheme and 30% probability displacement ellipsoids. [Symmetry code for unlabelled atoms: 1-x, 2-y, -z.]
Fig. 2.
The packing of (I) with hydrogen bonds shown as dashed lines.

Crystal data

[Pd(C11H9N2O4)2(H2O)4]·2H2OF000 = 696
Mr = 680.90Dx = 1.685 Mg m3
Monoclinic, P21/nMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2425 reflections
a = 5.4702 (10) Åθ = 2.0–25.2º
b = 11.794 (2) ŵ = 0.77 mm1
c = 20.886 (3) ÅT = 293 (2) K
β = 95.13 (3)ºBlock, colorless
V = 1342.1 (4) Å30.43 × 0.28 × 0.22 mm
Z = 2

Data collection

Bruker APEXII CCD area-detector diffractometer2425 independent reflections
Radiation source: fine-focus sealed tube1958 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.032
T = 293(2) Kθmax = 25.2º
[var phi] and ω scansθmin = 2.0º
Absorption correction: multi-scan(SADABS; Bruker, 2004)h = −6→6
Tmin = 0.733, Tmax = 0.849k = −13→14
7075 measured reflectionsl = −24→13

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.028H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.072  w = 1/[σ2(Fo2) + (0.042P)2] where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max = 0.005
2425 reflectionsΔρmax = 0.24 e Å3
205 parametersΔρmin = −0.49 e Å3
9 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods

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
Pd10.50001.00000.00000.02449 (11)
C10.7711 (5)1.0484 (2)0.14648 (12)0.0299 (6)
C20.5544 (5)0.9924 (2)0.17543 (12)0.0326 (6)
H2A0.40651.03540.16310.039*
H2B0.53160.91660.15780.039*
C30.4539 (5)1.0371 (2)0.28620 (12)0.0294 (6)
H30.32371.08580.27450.035*
C40.7676 (4)0.9208 (2)0.28035 (12)0.0279 (6)
C50.9568 (5)0.8536 (2)0.26202 (14)0.0365 (7)
H50.98340.84330.21900.044*
C61.1029 (6)0.8030 (3)0.31070 (17)0.0480 (8)
H61.23460.75860.30060.058*
C71.0587 (6)0.8166 (3)0.37470 (17)0.0540 (9)
H71.15950.77930.40620.065*
C80.8726 (6)0.8828 (3)0.39307 (15)0.0449 (7)
H80.84440.89160.43600.054*
C90.7282 (5)0.9361 (2)0.34427 (12)0.0299 (6)
C110.4355 (5)1.0558 (3)0.40327 (13)0.0369 (7)
H11A0.42760.99550.43460.044*
H11B0.26961.08310.39230.044*
C120.5910 (5)1.1527 (2)0.43369 (13)0.0347 (6)
H1W0.545 (5)0.681 (2)0.2365 (7)0.042*
H2W0.571 (4)0.693 (2)0.1719 (9)0.042*
H3W0.160 (5)1.1619 (14)0.0196 (13)0.042*
H4W0.074 (4)1.078 (2)0.0568 (12)0.042*
H5W0.503 (3)0.7896 (18)0.0589 (13)0.042*
H6W0.270 (3)0.799 (2)0.0290 (13)0.042*
N10.5889 (4)0.98516 (17)0.24523 (11)0.0290 (5)
N20.5306 (4)1.01001 (17)0.34575 (11)0.0301 (5)
O10.1897 (3)1.09974 (17)0.03739 (10)0.0394 (5)
O20.3926 (4)0.83292 (17)0.04423 (10)0.0451 (5)
O30.7682 (3)1.03890 (18)0.08641 (9)0.0384 (5)
O40.9339 (4)1.09448 (18)0.18150 (9)0.0460 (5)
O50.7726 (4)1.1842 (2)0.40763 (11)0.0650 (7)
O60.5172 (3)1.19231 (18)0.48365 (9)0.0439 (5)
O70.4821 (4)0.7010 (2)0.20114 (10)0.0485 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Pd10.02495 (17)0.02873 (18)0.01952 (16)−0.00361 (11)0.00047 (11)0.00121 (11)
C10.0280 (14)0.0368 (15)0.0252 (15)0.0003 (12)0.0035 (11)0.0001 (12)
C20.0323 (15)0.0429 (17)0.0225 (14)−0.0058 (12)0.0013 (12)−0.0005 (11)
C30.0301 (14)0.0302 (14)0.0285 (15)−0.0017 (11)0.0057 (12)−0.0005 (11)
C40.0297 (14)0.0259 (14)0.0280 (14)−0.0057 (11)0.0025 (11)−0.0017 (11)
C50.0348 (15)0.0316 (16)0.0433 (18)−0.0014 (12)0.0053 (13)−0.0082 (13)
C60.0394 (17)0.0315 (17)0.072 (2)0.0073 (13)−0.0003 (16)−0.0058 (15)
C70.055 (2)0.042 (2)0.061 (2)0.0064 (16)−0.0148 (17)0.0110 (16)
C80.0555 (19)0.0411 (18)0.0369 (17)−0.0030 (15)−0.0020 (14)0.0067 (13)
C90.0336 (15)0.0261 (15)0.0295 (15)−0.0037 (12)0.0007 (11)0.0001 (11)
C110.0397 (16)0.0461 (18)0.0264 (15)−0.0038 (14)0.0115 (12)−0.0088 (13)
C120.0360 (15)0.0362 (16)0.0322 (16)0.0023 (12)0.0049 (12)−0.0056 (12)
N10.0282 (12)0.0365 (14)0.0227 (12)−0.0006 (9)0.0046 (9)0.0024 (9)
N20.0342 (13)0.0327 (13)0.0239 (12)−0.0027 (9)0.0058 (10)−0.0037 (9)
O10.0368 (11)0.0391 (12)0.0445 (13)−0.0023 (9)0.0158 (9)0.0021 (9)
O20.0349 (12)0.0429 (13)0.0558 (14)−0.0055 (9)−0.0058 (10)0.0164 (10)
O30.0353 (11)0.0585 (13)0.0212 (11)−0.0095 (9)0.0023 (8)−0.0004 (9)
O40.0425 (12)0.0675 (15)0.0279 (11)−0.0240 (10)0.0021 (9)−0.0049 (9)
O50.0650 (16)0.0750 (17)0.0596 (15)−0.0360 (13)0.0314 (13)−0.0339 (13)
O60.0475 (13)0.0510 (14)0.0339 (11)0.0038 (9)0.0067 (9)−0.0152 (9)
O70.0458 (13)0.0635 (15)0.0366 (13)0.0001 (11)0.0067 (10)0.0083 (11)

Geometric parameters (Å, °)

Pd1—O12.2608 (19)C6—C71.389 (4)
Pd1—O1i2.2608 (19)C6—H60.930
Pd1—O32.2687 (19)C7—C81.364 (5)
Pd1—O3i2.2687 (19)C7—H70.930
Pd1—O2i2.276 (2)C8—C91.383 (4)
Pd1—O22.276 (2)C8—H80.930
C1—O41.227 (3)C9—N21.392 (3)
C1—O31.258 (3)C11—N21.455 (3)
C1—C21.529 (4)C11—C121.528 (4)
C2—N11.456 (3)C11—H11A0.970
C2—H2A0.970C11—H11B0.970
C2—H2B0.970C12—O51.232 (3)
C3—N21.316 (4)C12—O61.243 (3)
C3—N11.329 (3)O1—H3W0.832 (10)
C3—H30.930O1—H4W0.823 (10)
C4—C91.383 (3)O2—H5W0.828 (10)
C4—C51.384 (4)O2—H6W0.824 (10)
C4—N11.394 (3)O7—H1W0.822 (10)
C5—C61.373 (4)O7—H2W0.821 (10)
C5—H50.930
O1—Pd1—O1i180.00 (9)C5—C6—H6119.2
O1—Pd1—O394.14 (7)C7—C6—H6119.2
O1i—Pd1—O385.86 (8)C8—C7—C6122.4 (3)
O1—Pd1—O3i85.86 (8)C8—C7—H7118.8
O1i—Pd1—O3i94.14 (7)C6—C7—H7118.8
O3—Pd1—O3i180.0C7—C8—C9116.3 (3)
O1—Pd1—O2i85.34 (7)C7—C8—H8121.8
O1i—Pd1—O2i94.66 (7)C9—C8—H8121.8
O3—Pd1—O2i88.61 (7)C8—C9—C4121.6 (3)
O3i—Pd1—O2i91.39 (7)C8—C9—N2131.4 (3)
O1—Pd1—O294.66 (7)C4—C9—N2106.9 (2)
O1i—Pd1—O285.34 (7)N2—C11—C12113.2 (2)
O3—Pd1—O291.39 (7)N2—C11—H11A108.9
O3i—Pd1—O288.61 (7)C12—C11—H11A108.9
O2i—Pd1—O2180.00 (10)N2—C11—H11B108.9
O4—C1—O3125.3 (2)C12—C11—H11B108.9
O4—C1—C2120.2 (2)H11A—C11—H11B107.7
O3—C1—C2114.5 (2)O5—C12—O6126.3 (3)
N1—C2—C1112.7 (2)O5—C12—C11118.9 (2)
N1—C2—H2A109.1O6—C12—C11114.8 (2)
C1—C2—H2A109.1C3—N1—C4108.4 (2)
N1—C2—H2B109.1C3—N1—C2126.0 (2)
C1—C2—H2B109.1C4—N1—C2125.5 (2)
H2A—C2—H2B107.8C3—N2—C9108.3 (2)
N2—C3—N1110.3 (2)C3—N2—C11125.6 (2)
N2—C3—H3124.8C9—N2—C11125.9 (2)
N1—C3—H3124.8Pd1—O1—H3W115.2 (18)
C9—C4—C5121.8 (2)Pd1—O1—H4W130.4 (18)
C9—C4—N1106.0 (2)H3W—O1—H4W111 (2)
C5—C4—N1132.3 (2)Pd1—O2—H5W118.6 (19)
C6—C5—C4116.4 (3)Pd1—O2—H6W120.1 (19)
C6—C5—H5121.8H5W—O2—H6W112 (2)
C4—C5—H5121.8C1—O3—Pd1139.53 (17)
C5—C6—C7121.5 (3)H1W—O7—H2W114 (2)

Symmetry codes: (i) −x+1, −y+2, −z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O7—H1W···O4ii0.822 (10)1.985 (14)2.756 (3)156 (3)
O7—H2W···O5ii0.821 (10)1.937 (10)2.747 (3)169 (3)

Symmetry codes: (ii) −x+3/2, y−1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CF2196).

References

  • Bruker (2004). APEX2, SAINT-Plus and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
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  • Church, B. S. & Halvorson, H. (1959). Nature (London), 183, 124–125. [PubMed]
  • Kim, Y., Lee, E. & Jung, D. Y. (2001). Chem. Mater.13, 2684–2690.
  • Okabe, N. & Oya, N. (2000). Acta Cryst. C56, 1416–1417. [PubMed]
  • Pocker, Y. & Fong, C. T. O. (1980). Biochemistry, 19, 2045–2049. [PubMed]
  • Scapin, G., Reddy, S. G., Zheng, R. & Blanchard, J. S. (1997). Biochemistry, 36, 15081–15088. [PubMed]
  • Serre, C., Marrot, J. & Férey, G. (2005). Inorg. Chem.44, 654–658. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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