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

Zhu, H.-B.; Hou, X.-S.

doi:10.1107/S1600536810049184

metal-organic compounds

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ISSN: 2056-9890

Volume 66| Part 12| December 2010| Page m1685

https://doi.org/10.1107/S1600536810049184

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

Hai-Bin Zhu ^a ^* and Xian-Shan Hou ^b

^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 Pd^II 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 ). For recent advances in developing of autitumor palladium-based coordination compounds, see: Caires (2007 ).

Experimental

Crystal data

[Pd(C₉H₆N₃O₃S)Cl]
M_r = 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 ) 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[F² > 2σ(F²)] = 0.021
wR(F²) = 0.053
S = 1.06
1522 reflections
107 parameters
H-atom parameters constrained
Δρ_max = 0.60 e Å⁻³
Δρ_min = −0.61 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT-Plus (Bruker, 2007); 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 I, global. DOI: https://doi.org/10.1107/S1600536810049184/cv5004sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810049184/cv5004Isup2.hkl

checkCIF report

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.

Structure description 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).

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

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
M_r = 378.09	D_x = 2.221 Mg m⁻³
Orthorhombic, Pnma	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2n	Cell parameters from 1522 reflections
a = 15.4598 (16) Å	θ = 2.3–25.5°
b = 6.5974 (7) Å	µ = 2.06 mm⁻¹
c = 11.0844 (12) Å	T = 298 K
V = 1130.5 (2) Å³	Block, orange
Z = 4	0.19 × 0.15 × 0.12 mm

Data collection top

Bruker APEXII CCD area-detector diffractometer	1522 independent reflections
Radiation source: fine-focus sealed tube	1433 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.020
φ and ω scans	θ_max = 28.3°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −20→20
T_min = 0.697, T_max = 0.781	k = −8→8
9511 measured reflections	l = −12→14

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.021	H-atom parameters constrained
wR(F²) = 0.053	w = 1/[σ²(F_o²) + (0.0313P)² + 0.4917P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max = 0.002
1522 reflections	Δρ_max = 0.60 e Å⁻³
107 parameters	Δρ_min = −0.61 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0057 (4)

Crystal data top

[Pd(C₉H₆N₃O₃S)Cl]	V = 1130.5 (2) Å³
M_r = 378.09	Z = 4
Orthorhombic, Pnma	Mo Kα radiation
a = 15.4598 (16) Å	µ = 2.06 mm⁻¹
b = 6.5974 (7) Å	T = 298 K
c = 11.0844 (12) Å	0.19 × 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)
T_min = 0.697, T_max = 0.781	R_int = 0.020
9511 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.021	0 restraints
wR(F²) = 0.053	H-atom parameters constrained
S = 1.06	Δρ_max = 0.60 e Å⁻³
1522 reflections	Δρ_min = −0.61 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Pd1	0.026756 (12)	0.2500	0.969638 (16)	0.02762 (9)
Cl1	−0.11601 (4)	0.2500	1.02532 (7)	0.04094 (18)
S1	0.08397 (5)	0.2500	0.70360 (6)	0.03980 (17)
N1	0.08013 (14)	0.2500	1.1342 (2)	0.0307 (4)
N2	0.14834 (13)	0.2500	0.9239 (2)	0.0296 (4)
C6	0.20748 (17)	0.2500	1.0130 (3)	0.0326 (5)
C5	0.16952 (17)	0.2500	1.1331 (3)	0.0333 (6)
C9	0.17219 (18)	0.2500	0.8096 (3)	0.0359 (6)
N3	0.25317 (17)	0.2500	0.7706 (3)	0.0472 (6)
C7	0.29440 (19)	0.2500	0.9801 (3)	0.0446 (7)
H7A	0.3382	0.2500	1.0376	0.053*
C4	0.2151 (2)	0.2500	1.2392 (3)	0.0443 (7)
H4A	0.2753	0.2500	1.2380	0.053*
C1	0.0393 (2)	0.2500	1.2392 (3)	0.0410 (7)
H1A	−0.0209	0.2500	1.2396	0.049*
C8	0.3128 (2)	0.2500	0.8575 (4)	0.0517 (8)
H8A	0.3706	0.2500	0.8344	0.062*
C3	0.1715 (2)	0.2500	1.3479 (3)	0.0509 (8)
H3B	0.2019	0.2500	1.4203	0.061*
C2	0.0826 (2)	0.2500	1.3478 (3)	0.0507 (8)
H2A	0.0521	0.2500	1.4201	0.061*
O1	0.00639 (14)	0.2500	0.78404 (18)	0.0474 (6)
O2	0.09105 (11)	0.0660 (3)	0.63642 (15)	0.0575 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Pd1	0.02287 (12)	0.03579 (13)	0.02421 (12)	0.000	−0.00022 (6)	0.000
Cl1	0.0254 (3)	0.0465 (4)	0.0508 (5)	0.000	0.0048 (3)	0.000
S1	0.0425 (4)	0.0520 (4)	0.0249 (3)	0.000	0.0033 (3)	0.000
N1	0.0315 (11)	0.0333 (11)	0.0273 (10)	0.000	−0.0022 (9)	0.000
N2	0.0256 (10)	0.0309 (11)	0.0322 (11)	0.000	−0.0004 (9)	0.000
C6	0.0267 (12)	0.0322 (13)	0.0389 (14)	0.000	−0.0033 (11)	0.000
C5	0.0319 (12)	0.0324 (13)	0.0356 (14)	0.000	−0.0052 (11)	0.000
C9	0.0347 (13)	0.0384 (14)	0.0347 (14)	0.000	0.0072 (11)	0.000
N3	0.0373 (13)	0.0543 (16)	0.0499 (16)	0.000	0.0166 (12)	0.000
C7	0.0256 (14)	0.0476 (17)	0.060 (2)	0.000	−0.0022 (13)	0.000
C4	0.0425 (16)	0.0455 (16)	0.0449 (17)	0.000	−0.0164 (14)	0.000
C1	0.0433 (16)	0.0487 (17)	0.0309 (14)	0.000	0.0010 (12)	0.000
C8	0.0294 (14)	0.058 (2)	0.068 (2)	0.000	0.0110 (15)	0.000
C3	0.063 (2)	0.0545 (19)	0.0348 (16)	0.000	−0.0199 (16)	0.000
C2	0.063 (2)	0.060 (2)	0.0291 (15)	0.000	−0.0005 (15)	0.000
O1	0.0333 (10)	0.0831 (17)	0.0257 (10)	0.000	−0.0025 (9)	0.000
O2	0.0666 (10)	0.0630 (11)	0.0430 (8)	−0.0049 (8)	0.0037 (8)	−0.0151 (8)

Geometric parameters (Å, º) top

Pd1—N2	1.947 (2)	C5—C4	1.372 (4)
Pd1—N1	2.002 (2)	C9—N3	1.324 (4)
Pd1—O1	2.081 (2)	N3—C8	1.333 (5)
Pd1—Cl1	2.2918 (7)	C7—C8	1.388 (5)
S1—O2	1.4282 (17)	C7—H7A	0.9300
S1—O2ⁱ	1.4282 (17)	C4—C3	1.381 (5)
S1—O1	1.494 (2)	C4—H4A	0.9300
S1—C9	1.800 (3)	C1—C2	1.378 (5)
N1—C1	1.324 (4)	C1—H1A	0.9300
N1—C5	1.382 (3)	C8—H8A	0.9300
N2—C9	1.319 (4)	C3—C2	1.374 (5)
N2—C6	1.346 (4)	C3—H3B	0.9300
C6—C7	1.392 (4)	C2—H2A	0.9300
C6—C5	1.455 (4)

N2—Pd1—N1	80.76 (10)	N2—C9—N3	125.3 (3)
N2—Pd1—O1	83.60 (9)	N2—C9—S1	114.5 (2)
N1—Pd1—O1	164.36 (9)	N3—C9—S1	120.2 (2)
N2—Pd1—Cl1	179.48 (7)	C9—N3—C8	114.7 (3)
N1—Pd1—Cl1	98.72 (7)	C8—C7—C6	117.0 (3)
O1—Pd1—Cl1	96.92 (6)	C8—C7—H7A	121.5
O2—S1—O2ⁱ	116.39 (15)	C6—C7—H7A	121.5
O2—S1—O1	111.87 (8)	C5—C4—C3	119.8 (3)
O2ⁱ—S1—O1	111.87 (8)	C5—C4—H4A	120.1
O2—S1—C9	106.40 (9)	C3—C4—H4A	120.1
O2ⁱ—S1—C9	106.40 (9)	N1—C1—C2	122.4 (3)
O1—S1—C9	102.63 (12)	N1—C1—H1A	118.8
C1—N1—C5	119.0 (2)	C2—C1—H1A	118.8
C1—N1—Pd1	127.17 (19)	N3—C8—C7	124.5 (3)
C5—N1—Pd1	113.83 (18)	N3—C8—H8A	117.8
C9—N2—C6	121.0 (2)	C7—C8—H8A	117.8
C9—N2—Pd1	121.33 (19)	C2—C3—C4	119.2 (3)
C6—N2—Pd1	117.69 (19)	C2—C3—H3B	120.4
N2—C6—C7	117.6 (3)	C4—C3—H3B	120.4
N2—C6—C5	113.4 (2)	C3—C2—C1	119.1 (3)
C7—C6—C5	129.0 (3)	C3—C2—H2A	120.4
C4—C5—N1	120.4 (3)	C1—C2—H2A	120.4
C4—C5—C6	125.3 (3)	S1—O1—Pd1	117.92 (12)
N1—C5—C6	114.3 (2)

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8A···O1ⁱⁱ	0.93	2.48	3.379 (4)	164
C7—H7A···O2ⁱⁱⁱ	0.93	2.60	3.238 (3)	127
C7—H7A···O2^iv	0.93	2.60	3.238 (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]
M_r	378.09
Crystal system, space group	Orthorhombic, Pnma
Temperature (K)	298
a, b, c (Å)	15.4598 (16), 6.5974 (7), 11.0844 (12)
V (Å³)	1130.5 (2)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	2.06
Crystal size (mm)	0.19 × 0.15 × 0.12

Data collection
Diffractometer	Bruker APEXII CCD area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2001)
T_min, T_max	0.697, 0.781
No. of measured, independent and observed [I > 2σ(I)] reflections	9511, 1522, 1433
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.668

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.021, 0.053, 1.06
No. of reflections	1522
No. of parameters	107
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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+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

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