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

Hao, L.; Mu, C.; Wang, R.

doi:10.1107/S1600536808016097

metal-organic compounds

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ISSN: 2056-9890

Volume 64| Part 7| July 2008| Page m896

doi:10.1107/S1600536808016097

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

Lujiang Hao,^a ^* Chunhua Mu ^b and Ridong Wang ^c

^aCollege of Food and Biological Engineering, Shandong Institute of Light Industry, Jinan 250353, People's Republic of China, ^bMaize Research Insitute, Shandong Academy of Agricultural Science, Jinan 250100, People's Republic of China, and ^cDepartment of Clinical Medicine, Medical School, Shandong University, Jinan 250012, People's Republic of China
^*Correspondence e-mail: lujianghao001@yahoo.com.cn

(Received 13 April 2008; accepted 28 May 2008; online 7 June 2008)

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 ). For uses in biological systems, see: Chung et al. (1971 ); Okabe & Oya (2000 ); Serre et al. (2005 ); Pocker & Fong (1980 ); Scapin et al. (1997 ); Kim et al. (2001 ).

Experimental

Crystal data

[Pd(C₁₁H₉N₂O₄)₂(H₂O)₄]·2H₂O
M_r = 680.90
Monoclinic, P 2₁ /n
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 ) 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[F² > 2σ(F²)] = 0.028
wR(F²) = 0.072
S = 1.00
2425 reflections
205 parameters
9 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.49 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O7—H1W⋯O4ⁱ	0.822 (10)	1.985 (14)	2.756 (3)	156 (3)
O7—H2W⋯O5ⁱ	0.821 (10)	1.937 (10)	2.747 (3)	169 (3)
Symmetry code: (i) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2004); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

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

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

checkCIF report

Comment top

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.

Related literature top

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

Experimental top

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%.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2004); data reduction: SAINT-Plus (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	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.

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

Crystal data top

[Pd(C₁₁H₉N₂O₄)₂(H₂O)₄]·2H₂O	F(000) = 696
M_r = 680.90	D_x = 1.685 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 2425 reflections
a = 5.4702 (10) Å	θ = 2.0–25.2°
b = 11.794 (2) Å	µ = 0.77 mm⁻¹
c = 20.886 (3) Å	T = 293 K
β = 95.13 (3)°	Block, colorless
V = 1342.1 (4) Å³	0.43 × 0.28 × 0.22 mm
Z = 2

Data collection top

Bruker APEXII CCD area-detector diffractometer	2425 independent reflections
Radiation source: fine-focus sealed tube	1958 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.032
ϕ and ω scans	θ_max = 25.2°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2004)	h = −6→6
T_min = 0.733, T_max = 0.849	k = −13→14
7075 measured reflections	l = −24→13

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.072	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	w = 1/[σ²(F_o²) + (0.042P)²] where P = (F_o² + 2F_c²)/3
2425 reflections	(Δ/σ)_max = 0.005
205 parameters	Δρ_max = 0.24 e Å⁻³
9 restraints	Δρ_min = −0.49 e Å⁻³

Crystal data top

[Pd(C₁₁H₉N₂O₄)₂(H₂O)₄]·2H₂O	V = 1342.1 (4) Å³
M_r = 680.90	Z = 2
Monoclinic, P2₁/n	Mo Kα radiation
a = 5.4702 (10) Å	µ = 0.77 mm⁻¹
b = 11.794 (2) Å	T = 293 K
c = 20.886 (3) Å	0.43 × 0.28 × 0.22 mm
β = 95.13 (3)°

Data collection top

Bruker APEXII CCD area-detector diffractometer	2425 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2004)	1958 reflections with I > 2σ(I)
T_min = 0.733, T_max = 0.849	R_int = 0.032
7075 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.028	9 restraints
wR(F²) = 0.072	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	Δρ_max = 0.24 e Å⁻³
2425 reflections	Δρ_min = −0.49 e Å⁻³
205 parameters

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

	x	y	z	U_iso*/U_eq
Pd1	0.5000	1.0000	0.0000	0.02449 (11)
C1	0.7711 (5)	1.0484 (2)	0.14648 (12)	0.0299 (6)
C2	0.5544 (5)	0.9924 (2)	0.17543 (12)	0.0326 (6)
H2A	0.4065	1.0354	0.1631	0.039*
H2B	0.5316	0.9166	0.1578	0.039*
C3	0.4539 (5)	1.0371 (2)	0.28620 (12)	0.0294 (6)
H3	0.3237	1.0858	0.2745	0.035*
C4	0.7676 (4)	0.9208 (2)	0.28035 (12)	0.0279 (6)
C5	0.9568 (5)	0.8536 (2)	0.26202 (14)	0.0365 (7)
H5	0.9834	0.8433	0.2190	0.044*
C6	1.1029 (6)	0.8030 (3)	0.31070 (17)	0.0480 (8)
H6	1.2346	0.7586	0.3006	0.058*
C7	1.0587 (6)	0.8166 (3)	0.37470 (17)	0.0540 (9)
H7	1.1595	0.7793	0.4062	0.065*
C8	0.8726 (6)	0.8828 (3)	0.39307 (15)	0.0449 (7)
H8	0.8444	0.8916	0.4360	0.054*
C9	0.7282 (5)	0.9361 (2)	0.34427 (12)	0.0299 (6)
C11	0.4355 (5)	1.0558 (3)	0.40327 (13)	0.0369 (7)
H11A	0.4276	0.9955	0.4346	0.044*
H11B	0.2696	1.0831	0.3923	0.044*
C12	0.5910 (5)	1.1527 (2)	0.43369 (13)	0.0347 (6)
H1W	0.545 (5)	0.681 (2)	0.2365 (7)	0.042*
H2W	0.571 (4)	0.693 (2)	0.1719 (9)	0.042*
H3W	0.160 (5)	1.1619 (14)	0.0196 (13)	0.042*
H4W	0.074 (4)	1.078 (2)	0.0568 (12)	0.042*
H5W	0.503 (3)	0.7896 (18)	0.0589 (13)	0.042*
H6W	0.270 (3)	0.799 (2)	0.0290 (13)	0.042*
N1	0.5889 (4)	0.98516 (17)	0.24523 (11)	0.0290 (5)
N2	0.5306 (4)	1.01001 (17)	0.34575 (11)	0.0301 (5)
O1	0.1897 (3)	1.09974 (17)	0.03739 (10)	0.0394 (5)
O2	0.3926 (4)	0.83292 (17)	0.04423 (10)	0.0451 (5)
O3	0.7682 (3)	1.03890 (18)	0.08641 (9)	0.0384 (5)
O4	0.9339 (4)	1.09448 (18)	0.18150 (9)	0.0460 (5)
O5	0.7726 (4)	1.1842 (2)	0.40763 (11)	0.0650 (7)
O6	0.5172 (3)	1.19231 (18)	0.48365 (9)	0.0439 (5)
O7	0.4821 (4)	0.7010 (2)	0.20114 (10)	0.0485 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Pd1	0.02495 (17)	0.02873 (18)	0.01952 (16)	−0.00361 (11)	0.00047 (11)	0.00121 (11)
C1	0.0280 (14)	0.0368 (15)	0.0252 (15)	0.0003 (12)	0.0035 (11)	0.0001 (12)
C2	0.0323 (15)	0.0429 (17)	0.0225 (14)	−0.0058 (12)	0.0013 (12)	−0.0005 (11)
C3	0.0301 (14)	0.0302 (14)	0.0285 (15)	−0.0017 (11)	0.0057 (12)	−0.0005 (11)
C4	0.0297 (14)	0.0259 (14)	0.0280 (14)	−0.0057 (11)	0.0025 (11)	−0.0017 (11)
C5	0.0348 (15)	0.0316 (16)	0.0433 (18)	−0.0014 (12)	0.0053 (13)	−0.0082 (13)
C6	0.0394 (17)	0.0315 (17)	0.072 (2)	0.0073 (13)	−0.0003 (16)	−0.0058 (15)
C7	0.055 (2)	0.042 (2)	0.061 (2)	0.0064 (16)	−0.0148 (17)	0.0110 (16)
C8	0.0555 (19)	0.0411 (18)	0.0369 (17)	−0.0030 (15)	−0.0020 (14)	0.0067 (13)
C9	0.0336 (15)	0.0261 (15)	0.0295 (15)	−0.0037 (12)	0.0007 (11)	0.0001 (11)
C11	0.0397 (16)	0.0461 (18)	0.0264 (15)	−0.0038 (14)	0.0115 (12)	−0.0088 (13)
C12	0.0360 (15)	0.0362 (16)	0.0322 (16)	0.0023 (12)	0.0049 (12)	−0.0056 (12)
N1	0.0282 (12)	0.0365 (14)	0.0227 (12)	−0.0006 (9)	0.0046 (9)	0.0024 (9)
N2	0.0342 (13)	0.0327 (13)	0.0239 (12)	−0.0027 (9)	0.0058 (10)	−0.0037 (9)
O1	0.0368 (11)	0.0391 (12)	0.0445 (13)	−0.0023 (9)	0.0158 (9)	0.0021 (9)
O2	0.0349 (12)	0.0429 (13)	0.0558 (14)	−0.0055 (9)	−0.0058 (10)	0.0164 (10)
O3	0.0353 (11)	0.0585 (13)	0.0212 (11)	−0.0095 (9)	0.0023 (8)	−0.0004 (9)
O4	0.0425 (12)	0.0675 (15)	0.0279 (11)	−0.0240 (10)	0.0021 (9)	−0.0049 (9)
O5	0.0650 (16)	0.0750 (17)	0.0596 (15)	−0.0360 (13)	0.0314 (13)	−0.0339 (13)
O6	0.0475 (13)	0.0510 (14)	0.0339 (11)	0.0038 (9)	0.0067 (9)	−0.0152 (9)
O7	0.0458 (13)	0.0635 (15)	0.0366 (13)	0.0001 (11)	0.0067 (10)	0.0083 (11)

Geometric parameters (Å, º) top

Pd1—O1	2.2608 (19)	C6—C7	1.389 (4)
Pd1—O1ⁱ	2.2608 (19)	C6—H6	0.930
Pd1—O3	2.2687 (19)	C7—C8	1.364 (5)
Pd1—O3ⁱ	2.2687 (19)	C7—H7	0.930
Pd1—O2ⁱ	2.276 (2)	C8—C9	1.383 (4)
Pd1—O2	2.276 (2)	C8—H8	0.930
C1—O4	1.227 (3)	C9—N2	1.392 (3)
C1—O3	1.258 (3)	C11—N2	1.455 (3)
C1—C2	1.529 (4)	C11—C12	1.528 (4)
C2—N1	1.456 (3)	C11—H11A	0.970
C2—H2A	0.970	C11—H11B	0.970
C2—H2B	0.970	C12—O5	1.232 (3)
C3—N2	1.316 (4)	C12—O6	1.243 (3)
C3—N1	1.329 (3)	O1—H3W	0.832 (10)
C3—H3	0.930	O1—H4W	0.823 (10)
C4—C9	1.383 (3)	O2—H5W	0.828 (10)
C4—C5	1.384 (4)	O2—H6W	0.824 (10)
C4—N1	1.394 (3)	O7—H1W	0.822 (10)
C5—C6	1.373 (4)	O7—H2W	0.821 (10)
C5—H5	0.930

O1—Pd1—O1ⁱ	180.00 (9)	C5—C6—H6	119.2
O1—Pd1—O3	94.14 (7)	C7—C6—H6	119.2
O1ⁱ—Pd1—O3	85.86 (8)	C8—C7—C6	122.4 (3)
O1—Pd1—O3ⁱ	85.86 (8)	C8—C7—H7	118.8
O1ⁱ—Pd1—O3ⁱ	94.14 (7)	C6—C7—H7	118.8
O3—Pd1—O3ⁱ	180.0	C7—C8—C9	116.3 (3)
O1—Pd1—O2ⁱ	85.34 (7)	C7—C8—H8	121.8
O1ⁱ—Pd1—O2ⁱ	94.66 (7)	C9—C8—H8	121.8
O3—Pd1—O2ⁱ	88.61 (7)	C8—C9—C4	121.6 (3)
O3ⁱ—Pd1—O2ⁱ	91.39 (7)	C8—C9—N2	131.4 (3)
O1—Pd1—O2	94.66 (7)	C4—C9—N2	106.9 (2)
O1ⁱ—Pd1—O2	85.34 (7)	N2—C11—C12	113.2 (2)
O3—Pd1—O2	91.39 (7)	N2—C11—H11A	108.9
O3ⁱ—Pd1—O2	88.61 (7)	C12—C11—H11A	108.9
O2ⁱ—Pd1—O2	180.00 (10)	N2—C11—H11B	108.9
O4—C1—O3	125.3 (2)	C12—C11—H11B	108.9
O4—C1—C2	120.2 (2)	H11A—C11—H11B	107.7
O3—C1—C2	114.5 (2)	O5—C12—O6	126.3 (3)
N1—C2—C1	112.7 (2)	O5—C12—C11	118.9 (2)
N1—C2—H2A	109.1	O6—C12—C11	114.8 (2)
C1—C2—H2A	109.1	C3—N1—C4	108.4 (2)
N1—C2—H2B	109.1	C3—N1—C2	126.0 (2)
C1—C2—H2B	109.1	C4—N1—C2	125.5 (2)
H2A—C2—H2B	107.8	C3—N2—C9	108.3 (2)
N2—C3—N1	110.3 (2)	C3—N2—C11	125.6 (2)
N2—C3—H3	124.8	C9—N2—C11	125.9 (2)
N1—C3—H3	124.8	Pd1—O1—H3W	115.2 (18)
C9—C4—C5	121.8 (2)	Pd1—O1—H4W	130.4 (18)
C9—C4—N1	106.0 (2)	H3W—O1—H4W	111 (2)
C5—C4—N1	132.3 (2)	Pd1—O2—H5W	118.6 (19)
C6—C5—C4	116.4 (3)	Pd1—O2—H6W	120.1 (19)
C6—C5—H5	121.8	H5W—O2—H6W	112 (2)
C4—C5—H5	121.8	C1—O3—Pd1	139.53 (17)
C5—C6—C7	121.5 (3)	H1W—O7—H2W	114 (2)

Symmetry code: (i) −x+1, −y+2, −z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O7—H1W···O4ⁱⁱ	0.82 (1)	1.99 (1)	2.756 (3)	156 (3)
O7—H2W···O5ⁱⁱ	0.82 (1)	1.94 (1)	2.747 (3)	169 (3)

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

Experimental details

Crystal data
Chemical formula	[Pd(C₁₁H₉N₂O₄)₂(H₂O)₄]·2H₂O
M_r	680.90
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	5.4702 (10), 11.794 (2), 20.886 (3)
β (°)	95.13 (3)
V (Å³)	1342.1 (4)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.77
Crystal size (mm)	0.43 × 0.28 × 0.22

Data collection
Diffractometer	Bruker APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2004)
T_min, T_max	0.733, 0.849
No. of measured, independent and observed [I > 2σ(I)] reflections	7075, 2425, 1958
R_int	0.032
(sin θ/λ)_max (Å⁻¹)	0.599

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.028, 0.072, 1.00
No. of reflections	2425
No. of parameters	205
No. of restraints	9
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.24, −0.49

Computer programs: APEX2 (Bruker, 2004), SAINT-Plus (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O7—H1W···O4ⁱ	0.822 (10)	1.985 (14)	2.756 (3)	156 (3)
O7—H2W···O5ⁱ	0.821 (10)	1.937 (10)	2.747 (3)	169 (3)

Symmetry code: (i) −x+3/2, y−1/2, −z+1/2.

Acknowledgements

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

References

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Volume 64| Part 7| July 2008| Page m896

doi:10.1107/S1600536808016097

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metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

metal-organic compounds

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