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ISSN: 2056-9890

Chlorido[4-(pyridin-2-yl-κN)pyrimidine-2-sulfonato-κ2N3,O]palladium(II)

aSchool of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, People's Republic of China, and bJiangsu Hengrui Pharmaceutical Company, Lianyungang 222002, People's Republic of China
*Correspondence e-mail: zhuhaibin@seu.edu.cn

(Received 20 November 2010; accepted 24 November 2010; online 27 November 2010)

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[Wong, E. & Giandomenico, C. M. (1999). Chem. Rev. 99, 2451-2466.]). For recent advances in developing of autitumor palladium-based coordination compounds, see: Caires (2007[Caires, A. C. F. (2007). Anti-Cancer Agents Med. Chem. 7, 484-498.]).

[Scheme 1]

Experimental

Crystal data
  • [Pd(C9H6N3O3S)Cl]

  • Mr = 378.09

  • Orthorhombic, P n m a

  • 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[Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.697, Tmax = 0.781

  • 9511 measured reflections

  • 1522 independent reflections

  • 1433 reflections with I > 2σ(I)

  • Rint = 0.020

Refinement
  • R[F2 > 2σ(F2)] = 0.021

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C8—H8A⋯O1i 0.93 2.48 3.379 (4) 164
C7—H7A⋯O2ii 0.93 2.60 3.238 (3) 127
C7—H7A⋯O2iii 0.93 2.60 3.238 (3) 127
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [-x+{\script{1\over 2}}, -y, z+{\script{1\over 2}}]; (iii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 2007[Bruker (2007). APEX2 and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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 top

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).

Structure description top

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.

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

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus (Bruker, 2007); 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
[Figure 1] 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].
Chlorido[4-(pyridin-2-yl-κN)pyrimidine-2-sulfonato- κ2N3,O]palladium(II) top
Crystal data top
[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 top
Bruker APEXII CCD area-detector
diffractometer
1522 independent reflections
Radiation source: fine-focus sealed tube1433 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.020
φ and ω scansθmax = 28.3°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 2020
Tmin = 0.697, Tmax = 0.781k = 88
9511 measured reflectionsl = 1214
Refinement top
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) = 0.053 w = 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)
Crystal data top
[Pd(C9H6N3O3S)Cl]V = 1130.5 (2) Å3
Mr = 378.09Z = 4
Orthorhombic, PnmaMo Kα radiation
a = 15.4598 (16) ŵ = 2.06 mm1
b = 6.5974 (7) ÅT = 298 K
c = 11.0844 (12) Å0.19 × 0.15 × 0.12 mm
Data collection top
Bruker APEXII CCD area-detector
diffractometer
1522 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
1433 reflections with I > 2σ(I)
Tmin = 0.697, Tmax = 0.781Rint = 0.020
9511 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0210 restraints
wR(F2) = 0.053H-atom parameters constrained
S = 1.06Δρmax = 0.60 e Å3
1522 reflectionsΔρmin = 0.61 e Å3
107 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
xyzUiso*/Ueq
Pd10.026756 (12)0.25000.969638 (16)0.02762 (9)
Cl10.11601 (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)
H1A0.02090.25001.23960.049*
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) top
U11U22U33U12U13U23
Pd10.02287 (12)0.03579 (13)0.02421 (12)0.0000.00022 (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)0.0000.0022 (9)0.000
N20.0256 (10)0.0309 (11)0.0322 (11)0.0000.0004 (9)0.000
C60.0267 (12)0.0322 (13)0.0389 (14)0.0000.0033 (11)0.000
C50.0319 (12)0.0324 (13)0.0356 (14)0.0000.0052 (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)0.0000.0022 (13)0.000
C40.0425 (16)0.0455 (16)0.0449 (17)0.0000.0164 (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)0.0000.0199 (16)0.000
C20.063 (2)0.060 (2)0.0291 (15)0.0000.0005 (15)0.000
O10.0333 (10)0.0831 (17)0.0257 (10)0.0000.0025 (9)0.000
O20.0666 (10)0.0630 (11)0.0430 (8)0.0049 (8)0.0037 (8)0.0151 (8)
Geometric parameters (Å, º) top
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 code: (i) x, y+1/2, z.
Hydrogen-bond geometry (Å, º) top
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.

Experimental details

Crystal data
Chemical formula[Pd(C9H6N3O3S)Cl]
Mr378.09
Crystal system, space groupOrthorhombic, Pnma
Temperature (K)298
a, b, c (Å)15.4598 (16), 6.5974 (7), 11.0844 (12)
V3)1130.5 (2)
Z4
Radiation typeMo Kα
µ (mm1)2.06
Crystal size (mm)0.19 × 0.15 × 0.12
Data collection
DiffractometerBruker APEXII CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.697, 0.781
No. of measured, independent and
observed [I > 2σ(I)] reflections
9511, 1522, 1433
Rint0.020
(sin θ/λ)max1)0.668
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.021, 0.053, 1.06
No. of reflections1522
No. of parameters107
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.60, 0.61

Computer programs: APEX2 (Bruker, 2007), SAINT-Plus (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C8—H8A···O1i0.932.483.379 (4)164
C7—H7A···O2ii0.932.603.238 (3)127
C7—H7A···O2iii0.932.603.238 (3)127
Symmetry codes: (i) x+1/2, y+1/2, z+3/2; (ii) x+1/2, y, z+1/2; (iii) x+1/2, y+1/2, z+1/2.
 

Acknowledgements

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

References

First citationBruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruker (2007). APEX2 and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCaires, A. C. F. (2007). Anti-Cancer Agents Med. Chem. 7, 484–498.  Web of Science CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWong, E. & Giandomenico, C. M. (1999). Chem. Rev. 99, 2451–2466.  Web of Science CrossRef PubMed CAS Google Scholar

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