Literature DB >> 21577418

cis-Bis[1-allyl-3-(2-pyrid-yl-κN)thio-ureato-κS]palladium(II).

Svitlana Orysyk1, Volodimir Bon, Vasily Pekhnyo.   

Abstract

Yellow plate-like shaped crystals of the title compound, [Pd(C(9)H(10)N(3)S)(2)], were obtained by ligand-exchange reaction between palladium(II) acetyl-acetonate and the corresponding organic reagent at room temperature. The Pd(II) atom shows a slightly distorted square-planar coordination geometry consisting of two ligand mol-ecules in a cis conformation that bind in their thio-lic tautomeric form. Weak inter-molecular Pd⋯H inter-actions with Pd-H distances of 3.328 (2) Å were observed in the crystal structure. The three-dimensional network of the crystal structure is realized by weak inter-molecular C-H⋯N, N-H⋯N and C-H⋯S hydrogen bonds.

Entities:  

Year:  2009        PMID: 21577418      PMCID: PMC2970023          DOI: 10.1107/S1600536809029262

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For a related structure, see: Bon et al. (2007 ▶). For the anti­tumoral properties of Pd compounds, see: Upadhayaya et al. (2009 ▶), Hernández et al. (2008 ▶).

Experimental

Crystal data

[Pd(C9H10N3S)2] M = 490.96 Monoclinic, a = 10.8976 (6) Å b = 8.9730 (5) Å c = 21.798 (1) Å β = 113.624 (2)° V = 1952.9 (2) Å3 Z = 4 Mo Kα radiation μ = 1.18 mm−1 T = 173 K 0.51 × 0.21 × 0.05 mm

Data collection

Bruker APEXII CCD diffractometer Absorption correction: numerical (SADABS; Bruker, 2005 ▶) T min = 0.583, T max = 0.941 17417 measured reflections 4010 independent reflections 3522 reflections with I > 2σ(I) R int = 0.026

Refinement

R[F 2 > 2σ(F 2)] = 0.022 wR(F 2) = 0.055 S = 1.03 4010 reflections 272 parameters 3 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.58 e Å−3 Δρmin = −0.37 e Å−3 Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; 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: publCIF (Westrip, 2009 ▶). Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809029262/im2129sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809029262/im2129Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
[Pd(C9H10N3S)2]F(000) = 992
Mr = 490.96Dx = 1.670 Mg m3
Monoclinic, P21/cMelting point: 343 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 10.8976 (6) ÅCell parameters from 8451 reflections
b = 8.9730 (5) Åθ = 3.0–26.4°
c = 21.798 (1) ŵ = 1.18 mm1
β = 113.624 (2)°T = 173 K
V = 1952.9 (2) Å3Plate, yellow
Z = 40.51 × 0.21 × 0.05 mm
Bruker APEXII CCD diffractometer4010 independent reflections
Radiation source: fine-focus sealed tube3522 reflections with I > 2σ(I)
graphiteRint = 0.026
Detector resolution: 8.26 pixels mm-1θmax = 26.4°, θmin = 2.0°
φ and ω scansh = −13→13
Absorption correction: numerical (SADABS; Bruker, 2005)k = −11→11
Tmin = 0.583, Tmax = 0.941l = −26→27
17417 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.022Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.055H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.02P)2 + 1.8761P] where P = (Fo2 + 2Fc2)/3
4010 reflections(Δ/σ)max = 0.001
272 parametersΔρmax = 0.58 e Å3
3 restraintsΔρmin = −0.37 e Å3
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.
xyzUiso*/UeqOcc. (<1)
Pd10.504182 (15)0.273165 (18)0.331038 (7)0.02144 (6)
S10.48920 (6)0.26120 (8)0.43136 (3)0.03554 (15)
S20.72854 (5)0.24180 (7)0.38621 (3)0.02877 (13)
N10.30161 (17)0.3217 (2)0.28592 (8)0.0226 (4)
N20.22927 (17)0.1688 (2)0.35666 (9)0.0246 (4)
N30.3409 (2)0.0682 (3)0.45961 (10)0.0356 (5)
N40.52967 (17)0.26693 (19)0.24180 (8)0.0216 (4)
N50.73705 (17)0.4037 (2)0.27993 (8)0.0238 (4)
N60.88430 (19)0.4612 (2)0.38499 (10)0.0330 (5)
C10.2066 (2)0.2704 (2)0.30613 (10)0.0231 (4)
C20.0738 (2)0.3203 (3)0.27361 (11)0.0282 (5)
H2A0.00670.28030.28620.034*
C30.0396 (2)0.4252 (3)0.22420 (11)0.0303 (5)
H3A−0.05000.46000.20330.036*
C40.1382 (2)0.4802 (3)0.20512 (11)0.0299 (5)
H4A0.11770.55360.17100.036*
C50.2656 (2)0.4259 (2)0.23664 (11)0.0268 (5)
H5A0.33270.46330.22330.032*
C60.3393 (2)0.1622 (3)0.41056 (10)0.0262 (5)
C70.2192 (3)0.0080 (3)0.46317 (13)0.0396 (6)
H7A0.2445−0.06450.50050.048*
H7B0.1673−0.04610.42110.048*
C8A0.1310 (4)0.1276 (5)0.4737 (2)0.0501 (10)0.711 (5)
H8AA0.08850.19630.43830.060*0.711 (5)
C9A0.1099 (12)0.1423 (10)0.5274 (5)0.0819 (19)0.711 (5)
H9AA0.15070.07550.56380.098*0.711 (5)
H9AB0.05340.21980.53070.098*0.711 (5)
C8B0.1993 (11)0.0863 (13)0.5186 (6)0.0501 (10)0.289 (5)
H8BA0.26300.06960.56300.060*0.289 (5)
C9B0.103 (3)0.173 (3)0.5105 (16)0.0819 (19)0.289 (5)
H9BA0.03770.19240.46680.098*0.289 (5)
H9BB0.09620.21990.54810.098*0.289 (5)
C100.6369 (2)0.3219 (2)0.23255 (10)0.0230 (4)
C110.6465 (2)0.3015 (3)0.17078 (11)0.0332 (5)
H11A0.71890.34520.16350.040*
C120.5531 (3)0.2197 (3)0.12094 (12)0.0377 (6)
H12A0.56130.20410.07970.045*
C130.4457 (2)0.1597 (3)0.13180 (11)0.0350 (5)
H13A0.37980.10130.09840.042*
C140.4373 (2)0.1868 (3)0.19154 (11)0.0289 (5)
H14A0.36280.14760.19840.035*
C150.7807 (2)0.3775 (2)0.34392 (10)0.0240 (4)
C160.9495 (2)0.5766 (3)0.36190 (13)0.0380 (6)
H16A0.90160.67150.35980.046*
H16B0.93750.55150.31560.046*
C17A1.0931 (6)0.6027 (8)0.4014 (4)0.0486 (15)0.700 (9)
H17A1.12960.69140.39180.058*0.700 (9)
C18A1.1731 (5)0.5195 (7)0.4466 (3)0.0540 (13)0.700 (9)
H18A1.14190.42940.45810.065*0.700 (9)
H18B1.26450.54730.46910.065*0.700 (9)
C17B1.0811 (14)0.6032 (17)0.4263 (6)0.037 (3)0.300 (9)
H17B1.07450.64690.46450.044*0.300 (9)
C18B1.2000 (13)0.5671 (16)0.4290 (7)0.0540 (13)0.300 (9)
H18C1.20850.52330.39120.065*0.300 (9)
H18D1.27750.58470.46870.065*0.300 (9)
H6N0.904 (2)0.452 (3)0.4237 (13)0.027 (7)*
H3N0.404 (3)0.072 (3)0.4936 (13)0.038 (8)*
U11U22U33U12U13U23
Pd10.01747 (9)0.02785 (10)0.01790 (9)−0.00036 (7)0.00594 (6)0.00161 (6)
S10.0235 (3)0.0626 (4)0.0191 (3)−0.0085 (3)0.0070 (2)−0.0001 (3)
S20.0197 (3)0.0401 (3)0.0239 (3)0.0029 (2)0.0061 (2)0.0081 (2)
N10.0208 (9)0.0246 (9)0.0209 (9)0.0000 (7)0.0067 (7)0.0016 (7)
N20.0226 (9)0.0260 (9)0.0244 (9)−0.0010 (8)0.0086 (7)0.0030 (7)
N30.0307 (11)0.0493 (13)0.0246 (10)0.0025 (10)0.0089 (9)0.0118 (9)
N40.0207 (9)0.0228 (9)0.0203 (9)−0.0008 (7)0.0071 (7)0.0007 (7)
N50.0204 (9)0.0259 (10)0.0247 (9)−0.0012 (7)0.0084 (7)0.0003 (7)
N60.0257 (11)0.0419 (12)0.0250 (11)−0.0068 (9)0.0035 (9)−0.0041 (9)
C10.0230 (11)0.0212 (10)0.0240 (10)−0.0029 (9)0.0082 (9)−0.0029 (8)
C20.0198 (11)0.0314 (12)0.0317 (12)−0.0025 (9)0.0086 (9)0.0007 (9)
C30.0205 (11)0.0319 (13)0.0320 (12)0.0035 (9)0.0038 (9)0.0020 (10)
C40.0302 (12)0.0273 (12)0.0272 (11)0.0008 (10)0.0064 (9)0.0053 (9)
C50.0253 (11)0.0292 (12)0.0253 (11)−0.0022 (9)0.0093 (9)0.0022 (9)
C60.0241 (11)0.0323 (12)0.0244 (11)0.0032 (9)0.0120 (9)0.0011 (9)
C70.0474 (16)0.0395 (14)0.0343 (13)−0.0108 (12)0.0188 (12)0.0048 (11)
C8A0.042 (2)0.068 (3)0.049 (2)0.0008 (19)0.0275 (18)0.005 (2)
C9A0.133 (4)0.060 (5)0.081 (7)0.006 (4)0.072 (5)0.018 (3)
C8B0.042 (2)0.068 (3)0.049 (2)0.0008 (19)0.0275 (18)0.005 (2)
C9B0.133 (4)0.060 (5)0.081 (7)0.006 (4)0.072 (5)0.018 (3)
C100.0230 (11)0.0209 (10)0.0247 (10)0.0013 (8)0.0091 (9)0.0024 (8)
C110.0315 (13)0.0446 (15)0.0269 (12)−0.0040 (11)0.0153 (10)0.0024 (10)
C120.0433 (15)0.0479 (15)0.0233 (12)−0.0028 (12)0.0148 (11)−0.0041 (10)
C130.0388 (14)0.0365 (14)0.0238 (11)−0.0081 (11)0.0064 (10)−0.0074 (10)
C140.0263 (12)0.0299 (12)0.0275 (11)−0.0055 (10)0.0077 (9)−0.0019 (9)
C150.0191 (10)0.0245 (11)0.0281 (11)0.0034 (9)0.0094 (9)−0.0023 (9)
C160.0321 (13)0.0382 (14)0.0427 (14)−0.0109 (11)0.0139 (11)−0.0101 (11)
C17A0.033 (3)0.045 (3)0.063 (4)−0.013 (2)0.014 (3)−0.002 (3)
C18A0.038 (3)0.059 (4)0.054 (3)−0.009 (2)0.0074 (19)0.005 (2)
C17B0.039 (6)0.035 (5)0.045 (7)−0.015 (4)0.026 (6)−0.011 (5)
C18B0.038 (3)0.059 (4)0.054 (3)−0.009 (2)0.0074 (19)0.005 (2)
Pd1—N12.0713 (17)C7—H7A0.9900
Pd1—N42.0730 (17)C7—H7B0.9900
Pd1—S12.2598 (6)C8A—C9A1.288 (7)
Pd1—S22.2686 (6)C8A—H8AA0.9500
S1—C61.752 (2)C9A—H9AA0.9500
S2—C151.753 (2)C9A—H9AB0.9500
N1—C11.358 (3)C8B—C9B1.261 (17)
N1—C51.358 (3)C8B—H8BA0.9500
N2—C61.301 (3)C9B—H9BA0.9500
N2—C11.374 (3)C9B—H9BB0.9500
N3—C61.357 (3)C10—C111.404 (3)
N3—C71.463 (3)C11—C121.367 (3)
N3—H3N0.78 (3)C11—H11A0.9500
N4—C101.355 (3)C12—C131.392 (4)
N4—C141.359 (3)C12—H12A0.9500
N5—C151.302 (3)C13—C141.363 (3)
N5—C101.376 (3)C13—H13A0.9500
N6—C151.353 (3)C14—H14A0.9500
N6—C161.455 (3)C16—C17A1.471 (7)
N6—H6N0.79 (2)C16—C17B1.572 (13)
C1—C21.405 (3)C16—H16A0.9900
C2—C31.365 (3)C16—H16B0.9900
C2—H2A0.9500C17A—C18A1.265 (9)
C3—C41.389 (3)C17A—H17A0.9500
C3—H3A0.9500C18A—H18A0.9500
C4—C51.368 (3)C18A—H18B0.9500
C4—H4A0.9500C17B—C18B1.31 (2)
C5—H5A0.9500C17B—H17B0.9500
C7—C8B1.487 (11)C18B—H18C0.9500
C7—C8A1.519 (5)C18B—H18D0.9500
N1—Pd1—N494.48 (7)C9A—C8A—H8AA117.8
N1—Pd1—S189.59 (5)C7—C8A—H8AA117.8
N4—Pd1—S1174.63 (5)C8A—C9A—H9AA120.0
N1—Pd1—S2174.24 (5)C8A—C9A—H9AB120.0
N4—Pd1—S288.44 (5)H9AA—C9A—H9AB120.0
S1—Pd1—S287.80 (2)C9B—C8B—C7124.2 (18)
C6—S1—Pd1101.25 (7)C9B—C8B—H8BA117.9
C15—S2—Pd198.20 (7)C7—C8B—H8BA117.9
C1—N1—C5118.27 (18)C8B—C9B—H9BA120.0
C1—N1—Pd1125.52 (14)C8B—C9B—H9BB120.0
C5—N1—Pd1115.82 (14)H9BA—C9B—H9BB120.0
C6—N2—C1123.98 (19)N4—C10—N5123.65 (18)
C6—N3—C7123.1 (2)N4—C10—C11119.71 (19)
C6—N3—H3N116 (2)N5—C10—C11116.58 (19)
C7—N3—H3N116 (2)C12—C11—C10120.9 (2)
C10—N4—C14118.47 (18)C12—C11—H11A119.5
C10—N4—Pd1125.27 (14)C10—C11—H11A119.5
C14—N4—Pd1115.87 (14)C11—C12—C13118.8 (2)
C15—N5—C10123.16 (18)C11—C12—H12A120.6
C15—N6—C16124.1 (2)C13—C12—H12A120.6
C15—N6—H6N116.6 (18)C14—C13—C12118.5 (2)
C16—N6—H6N118.9 (18)C14—C13—H13A120.8
N1—C1—N2124.70 (19)C12—C13—H13A120.8
N1—C1—C2119.55 (19)N4—C14—C13123.6 (2)
N2—C1—C2115.73 (19)N4—C14—H14A118.2
C3—C2—C1121.2 (2)C13—C14—H14A118.2
C3—C2—H2A119.4N5—C15—N6117.3 (2)
C1—C2—H2A119.4N5—C15—S2129.22 (17)
C2—C3—C4118.8 (2)N6—C15—S2113.46 (16)
C2—C3—H3A120.6N6—C16—C17A117.6 (3)
C4—C3—H3A120.6N6—C16—C17B101.3 (5)
C5—C4—C3118.3 (2)N6—C16—H16A107.9
C5—C4—H4A120.8C17A—C16—H16A107.9
C3—C4—H4A120.8C17B—C16—H16A100.7
N1—C5—C4123.8 (2)N6—C16—H16B107.9
N1—C5—H5A118.1C17A—C16—H16B107.9
C4—C5—H5A118.1C17B—C16—H16B130.2
N2—C6—N3117.1 (2)H16A—C16—H16B107.2
N2—C6—S1129.58 (17)C18A—C17A—C16127.0 (6)
N3—C6—S1113.29 (17)C18A—C17A—H17A116.5
N3—C7—C8B107.4 (4)C16—C17A—H17A116.5
N3—C7—C8A112.9 (2)C17A—C18A—H18A120.0
N3—C7—H7A109.0C17A—C18A—H18B120.0
C8B—C7—H7A74.1H18A—C18A—H18B120.0
C8A—C7—H7A109.0C18B—C17B—C16122.2 (12)
N3—C7—H7B109.0C18B—C17B—H17B118.9
C8B—C7—H7B140.3C16—C17B—H17B118.9
C8A—C7—H7B109.0C17B—C18B—H18C120.0
H7A—C7—H7B107.8C17B—C18B—H18D120.0
C9A—C8A—C7124.3 (5)H18C—C18B—H18D120.0
N1—Pd1—S1—C642.71 (9)C6—N3—C7—C8B−106.2 (5)
S2—Pd1—S1—C6−142.43 (8)C6—N3—C7—C8A−63.7 (3)
N4—Pd1—S2—C1547.84 (9)N3—C7—C8A—C9A−112.2 (8)
S1—Pd1—S2—C15−136.00 (7)C8B—C7—C8A—C9A−22.0 (10)
N4—Pd1—N1—C1143.98 (17)N3—C7—C8B—C9B113.5 (19)
S1—Pd1—N1—C1−32.53 (17)C8A—C7—C8B—C9B8.4 (18)
N4—Pd1—N1—C5−43.35 (16)C14—N4—C10—N5−179.6 (2)
S1—Pd1—N1—C5140.15 (15)Pd1—N4—C10—N5−7.2 (3)
N1—Pd1—N4—C10140.26 (17)C14—N4—C10—C113.2 (3)
S2—Pd1—N4—C10−34.78 (16)Pd1—N4—C10—C11175.61 (16)
N1—Pd1—N4—C14−47.14 (16)C15—N5—C10—N436.3 (3)
S2—Pd1—N4—C14137.82 (15)C15—N5—C10—C11−146.4 (2)
C5—N1—C1—N2−177.9 (2)N4—C10—C11—C12−3.8 (4)
Pd1—N1—C1—N2−5.4 (3)N5—C10—C11—C12178.9 (2)
C5—N1—C1—C23.2 (3)C10—C11—C12—C131.7 (4)
Pd1—N1—C1—C2175.69 (15)C11—C12—C13—C140.8 (4)
C6—N2—C1—N135.3 (3)C10—N4—C14—C13−0.7 (3)
C6—N2—C1—C2−145.8 (2)Pd1—N4—C14—C13−173.80 (19)
N1—C1—C2—C3−3.3 (3)C12—C13—C14—N4−1.4 (4)
N2—C1—C2—C3177.6 (2)C10—N5—C15—N6176.7 (2)
C1—C2—C3—C41.5 (3)C10—N5—C15—S2−0.6 (3)
C2—C3—C4—C50.3 (3)C16—N6—C15—N5−0.5 (3)
C1—N1—C5—C4−1.4 (3)C16—N6—C15—S2177.21 (18)
Pd1—N1—C5—C4−174.65 (18)Pd1—S2—C15—N5−45.9 (2)
C3—C4—C5—N1−0.4 (4)Pd1—S2—C15—N6136.77 (15)
C1—N2—C6—N3172.1 (2)C15—N6—C16—C17A−148.5 (4)
C1—N2—C6—S1−6.3 (3)C15—N6—C16—C17B−165.4 (6)
C7—N3—C6—N2−17.4 (3)N6—C16—C17A—C18A13.5 (10)
C7—N3—C6—S1161.29 (19)C17B—C16—C17A—C18A61.2 (18)
Pd1—S1—C6—N2−37.2 (2)N6—C16—C17B—C18B112.2 (14)
Pd1—S1—C6—N3144.37 (16)C17A—C16—C17B—C18B−25.9 (13)
D—H···AD—HH···AD···AD—H···A
C3—H3A···N2i0.952.643.511 (3)152
C14—H14A···N5ii0.952.573.376 (3)143
N3—H3N···N3iii0.78 (3)2.84 (3)3.425 (4)133 (2)
C4—H4A···S2iv0.952.983.728 (2)136
C12—H12A···S1v0.953.023.910 (2)156
C18B—H18D···S1vi0.952.953.85 (1)160
C7—H7A···S2iii0.992.853.825 (3)167
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
C3—H3A⋯N2i0.952.643.511 (3)152
C14—H14A⋯N5ii0.952.573.376 (3)143
N3—H3N⋯N3iii0.78 (3)2.84 (3)3.425 (4)133 (2)
C4—H4A⋯S2iv0.952.983.728 (2)136
C12—H12A⋯S1v0.953.023.910 (2)156
C18B—H18D⋯S1vi0.952.953.85 (1)160
C7—H7A⋯S2iii0.992.853.825 (3)167

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) .

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