Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805027704/hg6238sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536805027704/hg6238Isup2.hkl |
CCDC reference: 287594
Bpy (7 mg, 0.0448 mmol) dissolved in dimethyl formamide (DMF, 1.0 ml) was reacted with palladium acetate, [Pd(CH3COOH)2] (10 mg), dissolved in DMF (2 ml), and then bpy (5 mg) dissolved in DMF (1 ml) was added. The mixture was allowed to stand at room temperature for a number of days to give red plate crystals of the complex.
All H atoms were located in difference Fourier maps, and then were placed at ideal positions and treated as riding, with a C—H distance of 0.93 Å and Uiso(H) = 1.2Ueq(carrier atom).
Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1992); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN (Molecular Structure Corporation, 2000); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: TEXSAN.
Fig. 1. Molecular structure of (I), with the atom-numbering scheme. Displacement ellipsoids for non-H atoms correspond to 50% probability. |
[Pd(C6H4O2)(C10H8N2)] | F(000) = 736.0 |
Mr = 370.70 | Dx = 1.840 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.7107 Å |
Hall symbol: -P 2yn | Cell parameters from 25 reflections |
a = 7.017 (2) Å | θ = 14.8–15.0° |
b = 23.873 (2) Å | µ = 1.39 mm−1 |
c = 8.118 (3) Å | T = 296 K |
β = 100.30 (3)° | Plate, red |
V = 1338.0 (6) Å3 | 0.30 × 0.30 × 0.15 mm |
Z = 4 |
Rigaku AFC-5R diffractometer | Rint = 0.013 |
ω–2θ scans | θmax = 27.5° |
Absorption correction: ψ scan (North et al., 1968) | h = 0→9 |
Tmin = 0.632, Tmax = 0.812 | k = 0→31 |
3414 measured reflections | l = −10→10 |
3079 independent reflections | 3 standard reflections every 150 reflections |
2709 reflections with I > 2σ(I) | intensity decay: 0.1% |
Refinement on F2 | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.043 | w = 1/[σ2(Fo2) + (0.0537P)2 + 6.095P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.136 | (Δ/σ)max < 0.001 |
S = 1.21 | Δρmax = 1.94 e Å−3 |
3079 reflections | Δρmin = −1.62 e Å−3 |
190 parameters |
[Pd(C6H4O2)(C10H8N2)] | V = 1338.0 (6) Å3 |
Mr = 370.70 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 7.017 (2) Å | µ = 1.39 mm−1 |
b = 23.873 (2) Å | T = 296 K |
c = 8.118 (3) Å | 0.30 × 0.30 × 0.15 mm |
β = 100.30 (3)° |
Rigaku AFC-5R diffractometer | 2709 reflections with I > 2σ(I) |
Absorption correction: ψ scan (North et al., 1968) | Rint = 0.013 |
Tmin = 0.632, Tmax = 0.812 | 3 standard reflections every 150 reflections |
3414 measured reflections | intensity decay: 0.1% |
3079 independent reflections |
R[F2 > 2σ(F2)] = 0.043 | 190 parameters |
wR(F2) = 0.136 | H-atom parameters constrained |
S = 1.21 | Δρmax = 1.94 e Å−3 |
3079 reflections | Δρmin = −1.62 e Å−3 |
Refinement. Refinement using reflections with F2 > −10.0 σ(F2). The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R-factor (gt). |
x | y | z | Uiso*/Ueq | ||
Pd1 | 0.76643 (5) | 0.00981 (2) | −0.00121 (4) | 0.0268 (1) | |
O1 | 0.8946 (6) | 0.0700 (2) | 0.1488 (4) | 0.0322 (8) | |
O2 | 0.7077 (5) | 0.0696 (2) | −0.1718 (4) | 0.0327 (8) | |
N1 | 0.8064 (6) | −0.0532 (2) | 0.1643 (5) | 0.0299 (9) | |
N2 | 0.6366 (6) | −0.0518 (2) | −0.1446 (5) | 0.0292 (9) | |
C2 | 0.7272 (7) | −0.1027 (2) | 0.1075 (6) | 0.030 (1) | |
C3 | 0.7401 (8) | −0.1490 (3) | 0.2116 (7) | 0.038 (1) | |
C4 | 0.8380 (9) | −0.1436 (3) | 0.3763 (7) | 0.042 (1) | |
C5 | 0.9177 (9) | −0.0929 (3) | 0.4326 (7) | 0.045 (1) | |
C6 | 0.9021 (9) | −0.0494 (3) | 0.3221 (7) | 0.039 (1) | |
C12 | 0.6294 (7) | −0.1019 (2) | −0.0683 (6) | 0.031 (1) | |
C13 | 0.5358 (8) | −0.1469 (3) | −0.1540 (7) | 0.037 (1) | |
C14 | 0.4500 (9) | −0.1404 (3) | −0.3204 (7) | 0.041 (1) | |
C15 | 0.4604 (9) | −0.0899 (3) | −0.3978 (7) | 0.043 (1) | |
C16 | 0.5546 (9) | −0.0459 (3) | −0.3072 (7) | 0.040 (1) | |
C17 | 0.8803 (7) | 0.1186 (2) | 0.0639 (6) | 0.029 (1) | |
C18 | 0.9567 (8) | 0.1683 (3) | 0.1350 (7) | 0.037 (1) | |
C19 | 0.9308 (9) | 0.2184 (3) | 0.0443 (8) | 0.043 (1) | |
C20 | 0.8272 (9) | 0.2185 (3) | −0.1180 (8) | 0.043 (1) | |
C21 | 0.7530 (8) | 0.1686 (3) | −0.1925 (7) | 0.037 (1) | |
C22 | 0.7783 (7) | 0.1188 (2) | −0.1039 (6) | 0.029 (1) | |
H3 | 0.6847 | −0.1829 | 0.1726 | 0.0455* | |
H4 | 0.8493 | −0.1743 | 0.4481 | 0.0508* | |
H5 | 0.9804 | −0.0885 | 0.5428 | 0.0544* | |
H6 | 0.9606 | −0.0155 | 0.3580 | 0.0465* | |
H13 | 0.5302 | −0.1811 | −0.1006 | 0.0444* | |
H14 | 0.3857 | −0.1703 | −0.3792 | 0.0490* | |
H15 | 0.4049 | −0.0853 | −0.5099 | 0.0514* | |
H16 | 0.5616 | −0.0115 | −0.3593 | 0.0481* | |
H18 | 1.0258 | 0.1684 | 0.2440 | 0.0442* | |
H19 | 0.9830 | 0.2515 | 0.0928 | 0.0521* | |
H20 | 0.8071 | 0.2520 | −0.1773 | 0.0521* | |
H21 | 0.6862 | 0.1687 | −0.3023 | 0.0447* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.0307 (2) | 0.0266 (2) | 0.0221 (2) | 0.0011 (1) | 0.0019 (1) | −0.0011 (1) |
O1 | 0.044 (2) | 0.030 (2) | 0.021 (2) | −0.002 (2) | −0.001 (1) | 0.000 (1) |
O2 | 0.039 (2) | 0.030 (2) | 0.025 (2) | −0.002 (2) | −0.003 (1) | 0.000 (1) |
N1 | 0.030 (2) | 0.035 (2) | 0.024 (2) | 0.001 (2) | 0.004 (2) | −0.001 (2) |
N2 | 0.030 (2) | 0.036 (2) | 0.021 (2) | 0.001 (2) | 0.003 (2) | −0.002 (2) |
C2 | 0.028 (2) | 0.039 (3) | 0.023 (2) | 0.001 (2) | 0.005 (2) | 0.000 (2) |
C3 | 0.040 (3) | 0.041 (3) | 0.029 (3) | −0.004 (2) | −0.001 (2) | 0.004 (2) |
C4 | 0.055 (4) | 0.043 (3) | 0.027 (3) | −0.001 (3) | 0.001 (2) | 0.009 (2) |
C5 | 0.050 (3) | 0.056 (4) | 0.026 (3) | −0.001 (3) | −0.001 (2) | 0.002 (3) |
C6 | 0.046 (3) | 0.039 (3) | 0.028 (3) | −0.004 (2) | −0.001 (2) | −0.004 (2) |
C12 | 0.029 (2) | 0.036 (3) | 0.027 (2) | 0.002 (2) | 0.003 (2) | −0.001 (2) |
C13 | 0.041 (3) | 0.040 (3) | 0.029 (3) | −0.002 (2) | 0.003 (2) | −0.002 (2) |
C14 | 0.050 (3) | 0.042 (3) | 0.028 (3) | −0.007 (3) | 0.000 (2) | −0.008 (2) |
C15 | 0.051 (3) | 0.046 (4) | 0.027 (3) | −0.004 (3) | −0.004 (2) | −0.004 (2) |
C16 | 0.049 (3) | 0.041 (3) | 0.027 (3) | −0.002 (2) | −0.003 (2) | −0.001 (2) |
C17 | 0.028 (2) | 0.033 (3) | 0.024 (2) | 0.002 (2) | 0.001 (2) | −0.002 (2) |
C18 | 0.039 (3) | 0.043 (3) | 0.026 (2) | −0.004 (2) | −0.002 (2) | −0.006 (2) |
C19 | 0.047 (3) | 0.037 (3) | 0.042 (3) | −0.007 (2) | −0.004 (3) | −0.007 (2) |
C20 | 0.052 (3) | 0.034 (3) | 0.041 (3) | 0.000 (2) | −0.002 (3) | 0.008 (2) |
C21 | 0.040 (3) | 0.041 (3) | 0.027 (3) | 0.001 (2) | −0.006 (2) | 0.007 (2) |
C22 | 0.031 (2) | 0.033 (3) | 0.023 (2) | 0.003 (2) | 0.001 (2) | −0.002 (2) |
Pd1—O1 | 1.992 (4) | C12—C13 | 1.380 (8) |
Pd1—O2 | 1.980 (4) | C13—C14 | 1.386 (8) |
Pd1—N1 | 2.003 (4) | C13—H13 | 0.930 |
Pd1—N2 | 1.993 (4) | C14—C15 | 1.367 (9) |
O1—C17 | 1.345 (7) | C14—H14 | 0.930 |
O2—C22 | 1.354 (6) | C15—C16 | 1.381 (9) |
N1—C2 | 1.352 (7) | C15—H15 | 0.930 |
N1—C6 | 1.339 (7) | C16—H16 | 0.930 |
N2—C12 | 1.351 (7) | C17—C18 | 1.385 (8) |
N2—C16 | 1.350 (7) | C17—C22 | 1.421 (7) |
C2—C3 | 1.384 (8) | C18—C19 | 1.398 (9) |
C2—C12 | 1.469 (7) | C18—H18 | 0.930 |
C3—C4 | 1.396 (8) | C19—C20 | 1.386 (8) |
C3—H3 | 0.930 | C19—H19 | 0.930 |
C4—C5 | 1.376 (9) | C20—C21 | 1.395 (9) |
C4—H4 | 0.930 | C20—H20 | 0.930 |
C5—C6 | 1.365 (9) | C21—C22 | 1.384 (8) |
C5—H5 | 0.930 | C21—H21 | 0.930 |
C6—H6 | 0.930 | ||
Pd1···Pd1i | 3.308 (1) | C2···C17i | 3.322 (8) |
Pd1···N2ii | 3.406 (5) | C2···C22i | 3.496 (7) |
Pd1···O1i | 3.427 (4) | C2···C22ii | 3.563 (7) |
O1···N2i | 3.325 (6) | C2···C18i | 3.579 (8) |
O1···C14ii | 3.437 (8) | C3···C21ii | 3.468 (8) |
O1···C5iii | 3.462 (7) | C4···C21i | 3.514 (9) |
O1···C15ii | 3.509 (8) | C6···C22i | 3.512 (8) |
O1···C13ii | 3.540 (7) | C12···C22ii | 3.426 (8) |
O1···N1i | 3.597 (6) | C12···C18i | 3.436 (8) |
O1···C12i | 3.598 (7) | C12···C17i | 3.457 (7) |
O2···C6i | 3.227 (8) | C13···C17ii | 3.206 (8) |
O2···C2ii | 3.284 (7) | C13···C22ii | 3.368 (8) |
O2···C12ii | 3.412 (7) | C13···C18ii | 3.524 (8) |
O2···N1i | 3.422 (6) | C13···C18i | 3.574 (8) |
O2···C15iv | 3.516 (7) | C14···C17ii | 3.421 (8) |
N1···C22i | 3.420 (7) | C14···C18ii | 3.520 (9) |
N1···C17i | 3.487 (7) | ||
O1—Pd1—O2 | 85.6 (1) | C2—C12—C13 | 125.2 (5) |
O1—Pd1—N1 | 97.9 (2) | C12—C13—C14 | 119.3 (6) |
O1—Pd1—N2 | 178.1 (2) | C12—C13—H13 | 120.4 |
O2—Pd1—N1 | 175.7 (2) | C14—C13—H13 | 120.4 |
O2—Pd1—N2 | 96.2 (2) | C13—C14—C15 | 119.8 (6) |
N1—Pd1—N2 | 80.3 (2) | C13—C14—H14 | 120.1 |
Pd1—O1—C17 | 109.0 (3) | C15—C14—H14 | 120.1 |
Pd1—O2—C22 | 109.0 (3) | C14—C15—C16 | 119.0 (5) |
Pd1—N1—C2 | 115.3 (3) | C14—C15—H15 | 120.5 |
Pd1—N1—C6 | 125.2 (4) | C16—C15—H15 | 120.5 |
C2—N1—C6 | 119.5 (5) | N2—C16—C15 | 121.4 (6) |
Pd1—N2—C12 | 115.9 (3) | N2—C16—H16 | 119.3 |
Pd1—N2—C16 | 124.4 (4) | C15—C16—H16 | 119.3 |
C12—N2—C16 | 119.7 (5) | O1—C17—C18 | 122.6 (4) |
N1—C2—C3 | 120.8 (4) | O1—C17—C22 | 118.2 (5) |
N1—C2—C12 | 114.3 (5) | C18—C17—C22 | 119.2 (5) |
C3—C2—C12 | 124.9 (5) | C17—C18—C19 | 120.6 (5) |
C2—C3—C4 | 118.6 (6) | C17—C18—H18 | 119.7 |
C2—C3—H3 | 120.7 | C19—C18—H18 | 119.7 |
C4—C3—H3 | 120.7 | C18—C19—C20 | 120.0 (6) |
C3—C4—C5 | 120.0 (6) | C18—C19—H19 | 120.0 |
C3—C4—H4 | 120.0 | C20—C19—H19 | 120.0 |
C5—C4—H4 | 120.0 | C19—C20—C21 | 120.1 (6) |
C4—C5—C6 | 118.2 (5) | C19—C20—H20 | 120.0 |
C4—C5—H5 | 120.9 | C21—C20—H20 | 120.0 |
C6—C5—H5 | 120.9 | C20—C21—C22 | 120.3 (5) |
N1—C6—C5 | 123.0 (6) | C20—C21—H21 | 119.8 |
N1—C6—H6 | 118.5 | C22—C21—H21 | 119.8 |
C5—C6—H6 | 118.5 | O2—C22—C17 | 118.2 (5) |
N2—C12—C2 | 114.1 (5) | O2—C22—C21 | 122.0 (4) |
N2—C12—C13 | 120.7 (5) | C17—C22—C21 | 119.8 (5) |
Pd1—O1—C17—C18 | −179.8 (4) | N1—C6—C5—C4 | 2.8 (10) |
Pd1—O1—C17—C22 | 1.9 (6) | N2—PD1—O2—C22 | 178.5 (3) |
Pd1—O2—C22—C17 | 1.9 (6) | N2—PD1—N1—C2 | −2.2 (4) |
Pd1—O2—C22—C21 | −177.8 (4) | N2—PD1—N1—C6 | 178.2 (5) |
Pd1—N1—C2—C3 | −178.1 (4) | N2—C12—C2—C3 | −179.8 (5) |
Pd1—N1—C2—C12 | 1.5 (6) | N2—C12—C13—C14 | 0.6 (9) |
Pd1—N1—C6—C5 | 176.9 (5) | N2—C16—C15—C14 | 0.2 (10) |
Pd1—N2—C12—C2 | −2.5 (6) | C2—N1—C6—C5 | −2.7 (9) |
Pd1—N2—C12—C13 | 177.3 (4) | C2—C3—C4—C5 | 0.6 (10) |
Pd1—N2—C16—C15 | −177.5 (5) | C2—C12—N2—C16 | 179.0 (5) |
O1—PD1—O2—C22 | −0.7 (3) | C2—C12—C13—C14 | −179.7 (6) |
O1—PD1—N1—C2 | 177.0 (4) | C3—C2—N1—C6 | 1.5 (8) |
O1—PD1—N1—C6 | −2.6 (5) | C3—C2—C12—C13 | 0.5 (9) |
O1—C17—C18—C19 | −177.1 (5) | C3—C4—C5—C6 | −1.6 (10) |
O1—C17—C22—O2 | −2.7 (7) | C4—C3—C2—C12 | 179.9 (6) |
O1—C17—C22—C21 | 177.0 (5) | C6—N1—C2—C12 | −178.8 (5) |
O2—PD1—O1—C17 | −0.7 (3) | C12—N2—C16—C15 | 0.9 (9) |
O2—PD1—N2—C12 | −174.9 (4) | C12—C13—C14—C15 | 0.5 (9) |
O2—PD1—N2—C16 | 3.6 (5) | C13—C12—N2—C16 | −1.3 (8) |
O2—C22—C17—C18 | 178.9 (5) | C13—C14—C15—C16 | −0.9 (10) |
O2—C22—C21—C20 | 179.7 (5) | C17—C18—C19—C20 | 0.3 (10) |
N1—PD1—O1—C17 | −178.1 (3) | C17—C22—C21—C20 | 0.0 (9) |
N1—PD1—N2—C12 | 2.6 (4) | C18—C17—C22—C21 | −1.4 (8) |
N1—PD1—N2—C16 | −178.9 (5) | C18—C19—C20—C21 | −1 (1) |
N1—C2—C3—C4 | −0.5 (9) | C19—C18—C17—C22 | 1.3 (9) |
N1—C2—C12—N2 | 0.6 (7) | C19—C20—C21—C22 | 1.5 (10) |
N1—C2—C12—C13 | −179.1 (5) | C19—C20—C21—C22 | 1.5 (10) |
Symmetry codes: (i) −x+2, −y, −z; (ii) −x+1, −y, −z; (iii) −x+2, −y, −z+1; (iv) −x+1, −y, −z−1. |
Experimental details
Crystal data | |
Chemical formula | [Pd(C6H4O2)(C10H8N2)] |
Mr | 370.70 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 296 |
a, b, c (Å) | 7.017 (2), 23.873 (2), 8.118 (3) |
β (°) | 100.30 (3) |
V (Å3) | 1338.0 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 1.39 |
Crystal size (mm) | 0.30 × 0.30 × 0.15 |
Data collection | |
Diffractometer | Rigaku AFC-5R diffractometer |
Absorption correction | ψ scan (North et al., 1968) |
Tmin, Tmax | 0.632, 0.812 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3414, 3079, 2709 |
Rint | 0.013 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.043, 0.136, 1.21 |
No. of reflections | 3079 |
No. of parameters | 190 |
No. of restraints | ? |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 1.94, −1.62 |
Computer programs: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1992), MSC/AFC Diffractometer Control Software, TEXSAN (Molecular Structure Corporation, 2000), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1976), TEXSAN.
Pd1—O1 | 1.992 (4) | Pd1—N2 | 1.993 (4) |
Pd1—O2 | 1.980 (4) | O1—C17 | 1.345 (7) |
Pd1—N1 | 2.003 (4) | O2—C22 | 1.354 (6) |
O1—Pd1—O2 | 85.6 (1) | O2—Pd1—N1 | 175.7 (2) |
O1—Pd1—N1 | 97.9 (2) | O2—Pd1—N2 | 96.2 (2) |
O1—Pd1—N2 | 178.1 (2) | N1—Pd1—N2 | 80.3 (2) |
The palladium complex [Pd(bpy)(cbdca)] (where bpy is 2,2'-bipyridine, and cbdca is 1,1-cyclobutanedicarboxylate ligand), with an aromatic ligand and a cis-square planar coordination geometry, has been shown to have better cytotoxic activity than cisplatin, cis-diamminedichloroplatinum(II), against P388 lymphocytic leukemia cells (Mansuri-Torshizi et al., 2001).
The planar aromatic ligands may interact easily with DNA, which is the principal target in the chemotherapy of tumors (Shehata, 2001; Cusumano & Giannetto,1997; Neidle et al., 1987).
We have synthesized and determined the crystal structures of several cis-coordinated palladium complexes with aromatic ligands, viz. [Pd(bpy)(cbdca)], [Pb(phen)(cbdca)] (where phen is 1,10-phenanthroline; Muranishi & Okabe, 2004), [Pd(bpy)(nad)], [Pd(biq)(nad)] (where nad is 2,3-naphthalenediol and biq is biquinoline; Okabe et al., 2004) and [Pd(phen)(ca)] (where ca is catechol is 1,2-benzenediol; Okabe et al., 2003). In this study, [Pd(bpy)(ca)], (I), has been synthesized and its structure determined.
In complex (I), the central Pd atom has a distorted cis-square planar coordination geometry with the two N atoms of the heterocycle and the two O atoms of the dianion of the ca ligand (Fig. 1). The overall structure resembles the structures of [Pd(byp)(nad)], (II), and [Pd(phen)(ca)], (III), which have similar bypyridyl and catecholate groups to (I).
The coordinate bond lengths and angles of (I) (Table 1) may be compared with those of (II) and (III), as well as those of other palladium complexes with non-aromatic ligands, suc as [Pd(en)M], (IV), and [Pd(en)C], (V) (where en is ethylenediamine, M is methymalonate and C is 1,1-cyclobutanedicarboxylate; Tercero et al., 2003). The Pd—O and Pd—N bond lengths of (I) resemble those of (II) and (III), in which the Pd—O bond lengths lie in the range 1.981 (2)–1.989 (2) Å and Pd—N in the range 2.001 (3)–2.019 (2) Å, but are slightly shorter than those of (IV) and (V), in which the Pd—O bond lengths lie in the range 1.995 (10)–2.027 (10) Å and Pd—N in the range 2.009 (11)–2.030 (2) Å. The O—Pd—O and N—Pd—N bond angles also resemble to those of (II) and (III), for which O—Pd—O lie in the range 84.84 (9)–85.09 (7)° and N—Pd—N in the range 80.78 (9)–81.69 (8)°, but are a little smaller than those of (IV) and (V), for which O—Pd—O lie in the range 89.51 (17)–92.69 (7)° and N—Pd—N in the range 84.09 (18)–84.15 (8)°. These differences may be explained by the difference in intramolecular mobility of the O and N atoms between the complexes with aromatic ligands and those with non-aromatic ligands, as explained by Okabe et al. (2003).