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Acta Crystallogr Sect E Struct Rep Online. 2010 December 1; 66(Pt 12): m1685.
Published online 2010 November 27. doi:  10.1107/S1600536810049184
PMCID: PMC3011378

Chlorido[4-(pyridin-2-yl-κN)pyrimidine-2-sulfonato-κ2 N 3,O]palladium(II)

Abstract

In the title compound, [Pd(C9H6N3O3S)Cl], the PdII ion is coordinated by one O and two N atoms from a 4-(pyridin-2-yl)pyrimidine-2-sulfonate ligand and one chloride anion in a distorted square-planar geometry. In the crystal, all mol­ecules are situated on mirror planes and inter­act through weak inter­molecular C—H(...)O hydrogen bonds.

Related literature

For anti­tumor drugs with platinum, see: Wong (1999 [triangle]). For recent advances in developing of autitumor palladium-based coordination compounds, see: Caires (2007 [triangle]).

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Object name is e-66-m1685-scheme1.jpg

Experimental

Crystal data

  • [Pd(C9H6N3O3S)Cl]
  • M r = 378.09
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-m1685-efi2.jpg
  • a = 15.4598 (16) Å
  • b = 6.5974 (7) Å
  • c = 11.0844 (12) Å
  • V = 1130.5 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 2.06 mm−1
  • T = 298 K
  • 0.19 × 0.15 × 0.12 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.697, T max = 0.781
  • 9511 measured reflections
  • 1522 independent reflections
  • 1433 reflections with I > 2σ(I)
  • R int = 0.020

Refinement

  • R[F 2 > 2σ(F 2)] = 0.021
  • wR(F 2) = 0.053
  • S = 1.06
  • 1522 reflections
  • 107 parameters
  • H-atom parameters constrained
  • Δρmax = 0.60 e Å−3
  • Δρmin = −0.61 e Å−3

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT-Plus (Bruker, 2007 [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 I, global. DOI: 10.1107/S1600536810049184/cv5004sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810049184/cv5004Isup2.hkl

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

Acknowledgments

The authors acknowledge finanical support from the China Postdoctoral Reseach Fund (20070411010).

supplementary crystallographic information

Comment

In order to overcome the drawbacks of antitumor platinum drugs in clinical treatment (Wong et al., 1999), design and screening of anticancer palladium-based coordination compounds have been actively pursued in recent years (Caires, 2007). In this paper, we report a new palladium (II) coordination compound based on 2-ppsa ligand (2-ppsa = 4-(pyridin-2-yl)pyrimidine-2-sulfonate).

In the title compound (Fig. 1), each palladium(II) atom in a distorted square-planar enviroment is coordinated by one O and two N atoms, and one chloro anion (Pd1—N1 = 2.002 (2) Å; Pd1—N2 = 1.947 (2) Å; Pd1—O1= 2.081 (2) Å; Pd1—Cl1 = 2.2918 (7) Å.). 2-ppsa ligand offers two N atoms and one sulfonato O atom in NNO-chelation manner (N1—Pd1—N2 80.8 (1)°; N2—Pd1—O1 83.60 (9)°). In sulfonato group, the S1—O1 bond distance (1.494 (2) Å) is slightly longer than that for S1—O2(O2i) bond (1.428 (2) Å) due to the O1—Pd1 coordinaiton. Weak C—H···O hydrogen bonds (Table 1) are involved into intermolecular interactions.

Experimental

The CH3CN solution of PdCl2 (0.1 mmol) was layered above the aqueous solution of 2-ppsa sodium salt (0.1 mmol). Orange crystals suitable for X-ray diffraction analysis were obtained after one week.

Refinement

All H atoms were positioned geometrically and allowed to ride on their parent atoms, with C—H = 0.93 \%A and Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound showing the atomic numbering and 30% probability displacement ellipsoids [symmetry code: (i) x, -y + 1/2, z].

Crystal data

[Pd(C9H6N3O3S)Cl]F(000) = 736
Mr = 378.09Dx = 2.221 Mg m3
Orthorhombic, PnmaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2nCell parameters from 1522 reflections
a = 15.4598 (16) Åθ = 2.3–25.5°
b = 6.5974 (7) ŵ = 2.06 mm1
c = 11.0844 (12) ÅT = 298 K
V = 1130.5 (2) Å3Block, orange
Z = 40.19 × 0.15 × 0.12 mm

Data collection

Bruker APEXII CCD area-detector diffractometer1522 independent reflections
Radiation source: fine-focus sealed tube1433 reflections with I > 2σ(I)
graphiteRint = 0.020
[var phi] and ω scansθmax = 28.3°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −20→20
Tmin = 0.697, Tmax = 0.781k = −8→8
9511 measured reflectionsl = −12→14

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.053w = 1/[σ2(Fo2) + (0.0313P)2 + 0.4917P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.002
1522 reflectionsΔρmax = 0.60 e Å3
107 parametersΔρmin = −0.61 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0057 (4)

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
Pd10.026756 (12)0.25000.969638 (16)0.02762 (9)
Cl1−0.11601 (4)0.25001.02532 (7)0.04094 (18)
S10.08397 (5)0.25000.70360 (6)0.03980 (17)
N10.08013 (14)0.25001.1342 (2)0.0307 (4)
N20.14834 (13)0.25000.9239 (2)0.0296 (4)
C60.20748 (17)0.25001.0130 (3)0.0326 (5)
C50.16952 (17)0.25001.1331 (3)0.0333 (6)
C90.17219 (18)0.25000.8096 (3)0.0359 (6)
N30.25317 (17)0.25000.7706 (3)0.0472 (6)
C70.29440 (19)0.25000.9801 (3)0.0446 (7)
H7A0.33820.25001.03760.053*
C40.2151 (2)0.25001.2392 (3)0.0443 (7)
H4A0.27530.25001.23800.053*
C10.0393 (2)0.25001.2392 (3)0.0410 (7)
H1A−0.02090.25001.23960.049*
C80.3128 (2)0.25000.8575 (4)0.0517 (8)
H8A0.37060.25000.83440.062*
C30.1715 (2)0.25001.3479 (3)0.0509 (8)
H3B0.20190.25001.42030.061*
C20.0826 (2)0.25001.3478 (3)0.0507 (8)
H2A0.05210.25001.42010.061*
O10.00639 (14)0.25000.78404 (18)0.0474 (6)
O20.09105 (11)0.0660 (3)0.63642 (15)0.0575 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Pd10.02287 (12)0.03579 (13)0.02421 (12)0.000−0.00022 (6)0.000
Cl10.0254 (3)0.0465 (4)0.0508 (5)0.0000.0048 (3)0.000
S10.0425 (4)0.0520 (4)0.0249 (3)0.0000.0033 (3)0.000
N10.0315 (11)0.0333 (11)0.0273 (10)0.000−0.0022 (9)0.000
N20.0256 (10)0.0309 (11)0.0322 (11)0.000−0.0004 (9)0.000
C60.0267 (12)0.0322 (13)0.0389 (14)0.000−0.0033 (11)0.000
C50.0319 (12)0.0324 (13)0.0356 (14)0.000−0.0052 (11)0.000
C90.0347 (13)0.0384 (14)0.0347 (14)0.0000.0072 (11)0.000
N30.0373 (13)0.0543 (16)0.0499 (16)0.0000.0166 (12)0.000
C70.0256 (14)0.0476 (17)0.060 (2)0.000−0.0022 (13)0.000
C40.0425 (16)0.0455 (16)0.0449 (17)0.000−0.0164 (14)0.000
C10.0433 (16)0.0487 (17)0.0309 (14)0.0000.0010 (12)0.000
C80.0294 (14)0.058 (2)0.068 (2)0.0000.0110 (15)0.000
C30.063 (2)0.0545 (19)0.0348 (16)0.000−0.0199 (16)0.000
C20.063 (2)0.060 (2)0.0291 (15)0.000−0.0005 (15)0.000
O10.0333 (10)0.0831 (17)0.0257 (10)0.000−0.0025 (9)0.000
O20.0666 (10)0.0630 (11)0.0430 (8)−0.0049 (8)0.0037 (8)−0.0151 (8)

Geometric parameters (Å, °)

Pd1—N21.947 (2)C5—C41.372 (4)
Pd1—N12.002 (2)C9—N31.324 (4)
Pd1—O12.081 (2)N3—C81.333 (5)
Pd1—Cl12.2918 (7)C7—C81.388 (5)
S1—O21.4282 (17)C7—H7A0.9300
S1—O2i1.4282 (17)C4—C31.381 (5)
S1—O11.494 (2)C4—H4A0.9300
S1—C91.800 (3)C1—C21.378 (5)
N1—C11.324 (4)C1—H1A0.9300
N1—C51.382 (3)C8—H8A0.9300
N2—C91.319 (4)C3—C21.374 (5)
N2—C61.346 (4)C3—H3B0.9300
C6—C71.392 (4)C2—H2A0.9300
C6—C51.455 (4)
N2—Pd1—N180.76 (10)N2—C9—N3125.3 (3)
N2—Pd1—O183.60 (9)N2—C9—S1114.5 (2)
N1—Pd1—O1164.36 (9)N3—C9—S1120.2 (2)
N2—Pd1—Cl1179.48 (7)C9—N3—C8114.7 (3)
N1—Pd1—Cl198.72 (7)C8—C7—C6117.0 (3)
O1—Pd1—Cl196.92 (6)C8—C7—H7A121.5
O2—S1—O2i116.39 (15)C6—C7—H7A121.5
O2—S1—O1111.87 (8)C5—C4—C3119.8 (3)
O2i—S1—O1111.87 (8)C5—C4—H4A120.1
O2—S1—C9106.40 (9)C3—C4—H4A120.1
O2i—S1—C9106.40 (9)N1—C1—C2122.4 (3)
O1—S1—C9102.63 (12)N1—C1—H1A118.8
C1—N1—C5119.0 (2)C2—C1—H1A118.8
C1—N1—Pd1127.17 (19)N3—C8—C7124.5 (3)
C5—N1—Pd1113.83 (18)N3—C8—H8A117.8
C9—N2—C6121.0 (2)C7—C8—H8A117.8
C9—N2—Pd1121.33 (19)C2—C3—C4119.2 (3)
C6—N2—Pd1117.69 (19)C2—C3—H3B120.4
N2—C6—C7117.6 (3)C4—C3—H3B120.4
N2—C6—C5113.4 (2)C3—C2—C1119.1 (3)
C7—C6—C5129.0 (3)C3—C2—H2A120.4
C4—C5—N1120.4 (3)C1—C2—H2A120.4
C4—C5—C6125.3 (3)S1—O1—Pd1117.92 (12)
N1—C5—C6114.3 (2)

Symmetry codes: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C8—H8A···O1ii0.932.483.379 (4)164
C7—H7A···O2iii0.932.603.238 (3)127
C7—H7A···O2iv0.932.603.238 (3)127

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV5004).

References

  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2007). APEX2 and SAINT-Plus Bruker AXS Inc., Madison, Wisconsin, USA.
  • Caires, A. C. F. (2007). Anti-Cancer Agents Med. Chem.7, 484–498. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Wong, E. & Giandomenico, C. M. (1999). Chem. Rev.99, 2451–2466. [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography