Retracted: Poly[aqua(μ4-benzene-1,3-dicarboxylato-κ4O:O′:O′′:O′′′)bis(imidazole-κN)palladium(II)]
Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807044315/zl2039sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807044315/zl2039Isup2.hkl |
CCDC reference: 1259340
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%.
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.
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).
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).
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).
[Pd(C8H4O4)(C3H4N2)2(H2O)] | F(000) = 848 |
Mr = 424.69 | Dx = 1.684 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 3516 reflections |
a = 8.5814 (17) Å | θ = 1.7–27.0° |
b = 19.426 (4) Å | µ = 1.14 mm−1 |
c = 10.118 (2) Å | T = 293 K |
β = 96.62 (3)° | Cube, colourless |
V = 1675.5 (6) Å3 | 0.43 × 0.28 × 0.22 mm |
Z = 4 |
Bruker APEXII CCD area-detector diffractometer | 3280 independent reflections |
Radiation source: fine-focus sealed tube | 2523 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
φ and ω scans | θmax = 26.0°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −10→9 |
Tmin = 0.640, Tmax = 0.788 | k = −23→11 |
8842 measured reflections | l = −12→12 |
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)] = 0.031 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.071 | H 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 parameters | Δρmax = 0.40 e Å−3 |
4 restraints | Δρmin = −0.63 e Å−3 |
[Pd(C8H4O4)(C3H4N2)2(H2O)] | V = 1675.5 (6) Å3 |
Mr = 424.69 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 8.5814 (17) Å | µ = 1.14 mm−1 |
b = 19.426 (4) Å | T = 293 K |
c = 10.118 (2) Å | 0.43 × 0.28 × 0.22 mm |
β = 96.62 (3)° |
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 = 0.788 | Rint = 0.031 |
8842 measured reflections |
R[F2 > 2σ(F2)] = 0.031 | 4 restraints |
wR(F2) = 0.071 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | Δρmax = 0.40 e Å−3 |
3280 reflections | Δρmin = −0.63 e Å−3 |
229 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Pd1 | 0.37425 (3) | 0.126490 (13) | 1.00522 (2) | 0.03491 (10) | |
C1 | 0.4890 (4) | 0.2744 (2) | 0.8764 (4) | 0.0612 (10) | |
H1 | 0.4473 | 0.2630 | 0.7902 | 0.073* | |
C2 | 0.5780 (5) | 0.3305 (2) | 0.9103 (5) | 0.0653 (11) | |
H2 | 0.6097 | 0.3638 | 0.8530 | 0.078* | |
C3 | 0.5445 (4) | 0.2718 (2) | 1.0866 (4) | 0.0641 (11) | |
H3 | 0.5504 | 0.2588 | 1.1755 | 0.077* | |
C4 | 0.0640 (5) | 0.2230 (2) | 0.9641 (5) | 0.0741 (13) | |
H4 | 0.1256 | 0.2624 | 0.9630 | 0.089* | |
C5 | −0.0908 (5) | 0.2224 (3) | 0.9456 (6) | 0.1025 (19) | |
H5 | −0.1565 | 0.2601 | 0.9272 | 0.123* | |
C6 | −0.0034 (5) | 0.1199 (2) | 0.9826 (6) | 0.0913 (17) | |
H6 | −0.0009 | 0.0726 | 0.9959 | 0.110* | |
C7 | 0.4815 (4) | 0.09640 (18) | 0.7491 (3) | 0.0413 (8) | |
C8 | 0.5730 (3) | 0.08147 (17) | 0.6351 (3) | 0.0368 (7) | |
C9 | 0.7237 (4) | 0.0550 (2) | 0.6573 (3) | 0.0533 (10) | |
H9 | 0.7684 | 0.0460 | 0.7438 | 0.064* | |
C10 | 0.8084 (4) | 0.0420 (2) | 0.5512 (4) | 0.0663 (12) | |
H10 | 0.9091 | 0.0238 | 0.5665 | 0.080* | |
C11 | 0.5089 (4) | 0.09436 (17) | 0.5050 (3) | 0.0388 (7) | |
H11 | 0.4072 | 0.1114 | 0.4889 | 0.047* | |
C12 | 0.7429 (4) | 0.0560 (2) | 0.4226 (3) | 0.0555 (10) | |
H12 | 0.8002 | 0.0476 | 0.3516 | 0.067* | |
C13 | 0.5931 (4) | 0.08233 (17) | 0.3994 (3) | 0.0397 (8) | |
C14 | 0.5215 (5) | 0.09758 (19) | 0.2596 (3) | 0.0505 (9) | |
N1 | 0.4694 (3) | 0.23673 (16) | 0.9882 (3) | 0.0532 (8) | |
N2 | 0.6116 (4) | 0.32854 (18) | 1.0435 (4) | 0.0638 (9) | |
H21 | 0.682 (4) | 0.3538 (18) | 1.096 (3) | 0.077* | |
N3 | 0.1206 (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* | |
O1 | 0.2779 (3) | 0.01164 (13) | 0.9913 (2) | 0.0496 (6) | |
O2 | 0.5538 (3) | 0.09052 (13) | 0.8661 (2) | 0.0489 (6) | |
O3 | 0.3421 (3) | 0.11470 (14) | 0.7305 (2) | 0.0593 (7) | |
O4 | 0.3885 (3) | 0.12419 (16) | 0.2416 (2) | 0.0722 (8) | |
O5 | 0.5971 (4) | 0.08483 (16) | 0.1641 (2) | 0.0753 (9) | |
H22 | 0.296 (6) | −0.006 (2) | 0.920 (3) | 0.113* | |
H23 | 0.327 (5) | −0.013 (2) | 1.048 (4) | 0.113* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.02806 (14) | 0.04265 (16) | 0.03440 (14) | 0.00380 (12) | 0.00523 (9) | 0.00091 (12) |
C1 | 0.055 (2) | 0.061 (3) | 0.065 (3) | −0.003 (2) | −0.0070 (19) | 0.006 (2) |
C2 | 0.054 (2) | 0.062 (3) | 0.079 (3) | −0.008 (2) | 0.004 (2) | 0.011 (2) |
C3 | 0.059 (2) | 0.074 (3) | 0.061 (2) | −0.016 (2) | 0.012 (2) | −0.013 (2) |
C4 | 0.046 (2) | 0.051 (3) | 0.126 (4) | 0.010 (2) | 0.011 (2) | −0.004 (3) |
C5 | 0.046 (3) | 0.066 (3) | 0.193 (6) | 0.021 (2) | 0.003 (3) | −0.021 (4) |
C6 | 0.034 (2) | 0.057 (3) | 0.181 (5) | 0.002 (2) | 0.008 (3) | −0.004 (3) |
C7 | 0.044 (2) | 0.047 (2) | 0.0327 (17) | 0.0011 (17) | 0.0051 (14) | 0.0022 (15) |
C8 | 0.0366 (17) | 0.0414 (19) | 0.0331 (16) | −0.0007 (15) | 0.0074 (13) | 0.0008 (14) |
C9 | 0.042 (2) | 0.080 (3) | 0.0361 (18) | 0.010 (2) | −0.0005 (15) | 0.0035 (18) |
C10 | 0.044 (2) | 0.109 (4) | 0.048 (2) | 0.018 (2) | 0.0117 (17) | 0.000 (2) |
C11 | 0.0363 (17) | 0.0436 (19) | 0.0364 (17) | 0.0022 (16) | 0.0031 (14) | 0.0011 (15) |
C12 | 0.051 (2) | 0.080 (3) | 0.0386 (19) | 0.004 (2) | 0.0174 (16) | −0.0040 (19) |
C13 | 0.0437 (19) | 0.0415 (19) | 0.0339 (17) | −0.0019 (16) | 0.0050 (14) | −0.0011 (15) |
C14 | 0.069 (3) | 0.048 (2) | 0.0343 (19) | −0.003 (2) | 0.0053 (18) | −0.0017 (16) |
N1 | 0.0498 (18) | 0.0557 (19) | 0.0534 (18) | −0.0094 (16) | 0.0024 (14) | −0.0037 (16) |
N2 | 0.0489 (19) | 0.061 (2) | 0.082 (3) | −0.0150 (17) | 0.0069 (17) | −0.0165 (19) |
N3 | 0.0309 (15) | 0.0496 (18) | 0.064 (2) | 0.0047 (14) | 0.0043 (13) | −0.0022 (15) |
N4 | 0.036 (2) | 0.076 (3) | 0.210 (5) | 0.001 (2) | 0.011 (3) | −0.020 (3) |
O1 | 0.0518 (15) | 0.0479 (15) | 0.0500 (15) | 0.0053 (12) | 0.0090 (12) | 0.0011 (12) |
O2 | 0.0502 (14) | 0.0645 (16) | 0.0324 (12) | 0.0089 (13) | 0.0065 (10) | 0.0026 (11) |
O3 | 0.0444 (14) | 0.089 (2) | 0.0459 (14) | 0.0201 (14) | 0.0101 (11) | 0.0048 (13) |
O4 | 0.0713 (19) | 0.103 (2) | 0.0404 (14) | 0.0198 (18) | −0.0011 (13) | 0.0079 (14) |
O5 | 0.109 (2) | 0.086 (2) | 0.0328 (13) | 0.0261 (19) | 0.0157 (14) | −0.0034 (14) |
Pd1—N3 | 2.252 (3) | C7—O3 | 1.242 (4) |
Pd1—N1 | 2.305 (3) | C7—O2 | 1.276 (4) |
Pd1—O2 | 2.311 (2) | C7—C8 | 1.497 (4) |
Pd1—O1 | 2.378 (3) | C8—C9 | 1.386 (4) |
Pd1—O4i | 2.382 (2) | C8—C11 | 1.390 (4) |
Pd1—O5i | 2.487 (3) | C9—C10 | 1.387 (4) |
C1—C2 | 1.353 (5) | C9—H9 | 0.9300 |
C1—N1 | 1.374 (5) | C10—C12 | 1.383 (5) |
C1—H1 | 0.9300 | C10—H10 | 0.9300 |
C2—N2 | 1.346 (5) | C11—C13 | 1.377 (4) |
C2—H2 | 0.9300 | C11—H11 | 0.9300 |
C3—N1 | 1.312 (4) | C12—C13 | 1.379 (4) |
C3—N2 | 1.340 (5) | C12—H12 | 0.9300 |
C3—H3 | 0.9300 | C13—C14 | 1.505 (4) |
C4—C5 | 1.321 (6) | C14—O4 | 1.247 (4) |
C4—N3 | 1.347 (5) | C14—O5 | 1.249 (4) |
C4—H4 | 0.9300 | N2—H21 | 0.901 (19) |
C5—N4 | 1.335 (7) | N4—H20 | 0.88 (2) |
C5—H5 | 0.9300 | O1—H22 | 0.83 (3) |
C6—N3 | 1.302 (5) | O1—H23 | 0.83 (4) |
C6—N4 | 1.336 (5) | O4—Pd1ii | 2.382 (2) |
C6—H6 | 0.9300 | O5—Pd1ii | 2.487 (3) |
N3—Pd1—N1 | 94.67 (11) | C11—C8—C7 | 120.6 (3) |
N3—Pd1—O2 | 137.15 (9) | C8—C9—C10 | 120.3 (3) |
N1—Pd1—O2 | 88.21 (10) | C8—C9—H9 | 119.9 |
N3—Pd1—O1 | 85.99 (10) | C10—C9—H9 | 119.9 |
N1—Pd1—O1 | 172.26 (9) | C12—C10—C9 | 120.0 (3) |
O2—Pd1—O1 | 86.09 (9) | C12—C10—H10 | 120.0 |
N3—Pd1—O4i | 92.00 (10) | C9—C10—H10 | 120.0 |
N1—Pd1—O4i | 96.59 (11) | C13—C11—C8 | 121.2 (3) |
O2—Pd1—O4i | 130.19 (9) | C13—C11—H11 | 119.4 |
O1—Pd1—O4i | 91.10 (9) | C8—C11—H11 | 119.4 |
N3—Pd1—O5i | 144.39 (9) | C13—C12—C10 | 120.2 (3) |
N1—Pd1—O5i | 95.63 (11) | C13—C12—H12 | 119.9 |
O2—Pd1—O5i | 77.22 (8) | C10—C12—H12 | 119.9 |
O1—Pd1—O5i | 88.23 (10) | C11—C13—C12 | 119.6 (3) |
O4i—Pd1—O5i | 52.98 (9) | C11—C13—C14 | 120.1 (3) |
C2—C1—N1 | 109.8 (4) | C12—C13—C14 | 120.3 (3) |
C2—C1—H1 | 125.1 | O4—C14—O5 | 121.1 (3) |
N1—C1—H1 | 125.1 | O4—C14—C13 | 119.1 (3) |
N2—C2—C1 | 106.3 (4) | O5—C14—C13 | 119.7 (4) |
N2—C2—H2 | 126.8 | C3—N1—C1 | 104.6 (3) |
C1—C2—H2 | 126.8 | C3—N1—Pd1 | 124.9 (3) |
N1—C3—N2 | 111.8 (4) | C1—N1—Pd1 | 129.3 (3) |
N1—C3—H3 | 124.1 | C3—N2—C2 | 107.4 (3) |
N2—C3—H3 | 124.1 | C3—N2—H21 | 123 (3) |
C5—C4—N3 | 110.6 (4) | C2—N2—H21 | 129 (3) |
C5—C4—H4 | 124.7 | C6—N3—C4 | 104.8 (3) |
N3—C4—H4 | 124.7 | C6—N3—Pd1 | 128.3 (3) |
C4—C5—N4 | 106.5 (4) | C4—N3—Pd1 | 126.8 (3) |
C4—C5—H5 | 126.7 | C5—N4—C6 | 106.9 (4) |
N4—C5—H5 | 126.7 | C5—N4—H20 | 126 (4) |
N3—C6—N4 | 111.1 (4) | C6—N4—H20 | 125 (4) |
N3—C6—H6 | 124.4 | Pd1—O1—H22 | 110 (4) |
N4—C6—H6 | 124.4 | Pd1—O1—H23 | 111 (4) |
O3—C7—O2 | 121.5 (3) | H22—O1—H23 | 103 (5) |
O3—C7—C8 | 121.4 (3) | C7—O2—Pd1 | 104.5 (2) |
O2—C7—C8 | 117.1 (3) | C14—O4—Pd1ii | 95.4 (2) |
C9—C8—C11 | 118.7 (3) | C14—O5—Pd1ii | 90.4 (2) |
C9—C8—C7 | 120.6 (3) |
Symmetry codes: (i) x, y, z+1; (ii) x, y, z−1. |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H22···O5iii | 0.83 (3) | 2.02 (3) | 2.743 (4) | 145 (5) |
O1—H23···O2iv | 0.83 (4) | 1.97 (4) | 2.762 (3) | 162 (5) |
N2—H21···O3v | 0.90 (2) | 1.92 (2) | 2.801 (4) | 165 (4) |
N4—H20···O2vi | 0.88 (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. |
Experimental details
Crystal data | |
Chemical formula | [Pd(C8H4O4)(C3H4N2)2(H2O)] |
Mr | 424.69 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 293 |
a, b, c (Å) | 8.5814 (17), 19.426 (4), 10.118 (2) |
β (°) | 96.62 (3) |
V (Å3) | 1675.5 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 1.14 |
Crystal size (mm) | 0.43 × 0.28 × 0.22 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.640, 0.788 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8842, 3280, 2523 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.617 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.031, 0.071, 1.00 |
No. of reflections | 3280 |
No. of parameters | 229 |
No. of restraints | 4 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.40, −0.63 |
Computer programs: APEX2 (Bruker, 2004), SAINT-Plus (Bruker, 2001), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 2001).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H22···O5i | 0.83 (3) | 2.02 (3) | 2.743 (4) | 145 (5) |
O1—H23···O2ii | 0.83 (4) | 1.97 (4) | 2.762 (3) | 162 (5) |
N2—H21···O3iii | 0.901 (19) | 1.92 (2) | 2.801 (4) | 165 (4) |
N4—H20···O2iv | 0.88 (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. |
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).