Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805041681/sj6164sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536805041681/sj6164Isup2.hkl |
CCDC reference: 296654
Key indicators
- Single-crystal X-ray study
- T = 233 K
- Mean (C-C) = 0.004 Å
- H-atom completeness 91%
- Disorder in solvent or counterion
- R factor = 0.033
- wR factor = 0.074
- Data-to-parameter ratio = 18.4
checkCIF/PLATON results
No syntax errors found
Alert level B ABSTM02_ALERT_3_B The ratio of Tmax/Tmin expected RT(exp) is > 1.20 Absorption corrections should be applied. Tmin and Tmax expected: 0.717 0.913 RT(exp) = 1.274 PLAT057_ALERT_3_B Correction for Absorption Required RT(exp) ... 1.27
Alert level C PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.96 PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ? PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ? PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............ 0.50 Ratio PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)... ? PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.57 Ratio PLAT302_ALERT_4_C Anion/Solvent Disorder ......................... 33.00 Perc. PLAT430_ALERT_2_C Short Inter D...A Contact O1A .. O1A .. 2.88 Ang.
Alert level G FORMU01_ALERT_2_G There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_site* data. Atom count from _chemical_formula_sum:C22.5 H20 Cl1 N2 O0.5 P1 Pd1 S Atom count from the _atom_site data: C22.5 H18 Cl1 N2 O0.5 P1 Pd1 S CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected. CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional? From the CIF: _cell_formula_units_Z 8 From the CIF: _chemical_formula_sum C22.50 H20 Cl N2 O0.50 P Pd S TEST: Compare cell contents of formula and atom_site data atom Z*formula cif sites diff C 180.00 180.00 0.00 H 160.00 144.00 16.00 Cl 8.00 8.00 0.00 N 16.00 16.00 0.00 O 4.00 4.00 0.00 P 8.00 8.00 0.00 Pd 8.00 8.00 0.00 S 8.00 8.00 0.00
0 ALERT level A = In general: serious problem 2 ALERT level B = Potentially serious problem 8 ALERT level C = Check and explain 3 ALERT level G = General alerts; check 6 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion
Pyrimidine-2-thione (0.16 g, 1.14 mmol) dissolved in CH2Cl2 (10 ml) was added dropwise to a suspension of [PdCl2(PPh3)] (0.5 g, 1.14 mmol) (Kitano et al., 1983) in CH2Cl2 (20 ml). The resulting solution was refluxed for 2–3 h and a clear solution was obtained. Yellow crystals were obtained by slow evaporation of the solvent at room temperature.
All C-bound H atoms were refined using a riding model, with C—H = 0.94 Å and Uiso(H) = 1.2Ueq(C). A disordered methanol solvent molecule is located in the asymmetric unit. The disorder, with fixed occupancy of 0.75 for O1 and 0.25 for O1A, was solved by varying the occupancy factors of both O-atom positions until their isotropic displacement parameters refined to a similar value. A final refinement was accomplished with fixed occupancy factors and anisotropic displacement parameters for the O-atom positions. H atoms of this solvent, that would have poor resolution and large displacement parameters, were not investigated in this refinement.
Data collection: COLLECT (Nonius, 1998); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO (Otwinowski & Minor, 1997) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXL97.
Fig. 1. The structures of of the two unique molecules of (I), showing the atom-numbering scheme. Displacement elipsoids are drawn at the 50% probability level |
[Pd(C4H3N2S)Cl(C18H15P)]·0.5CH4O | F(000) = 2136 |
Mr = 531.29 | Dx = 1.591 Mg m−3 |
Monoclinic, P21/c | Melting point: 398 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 16.1340 (2) Å | Cell parameters from 26420 reflections |
b = 9.7020 (1) Å | θ = 1.0–27.5° |
c = 29.0480 (4) Å | µ = 1.14 mm−1 |
β = 102.617 (1)° | T = 233 K |
V = 4437.14 (10) Å3 | Prism, yellow |
Z = 8 | 0.35 × 0.25 × 0.08 mm |
Nonius KappaCCD diffractometer | 8231 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.033 |
Graphite monochromator | θmax = 27.5°, θmin = 2.1° |
ϕ and ω scans | h = −20→20 |
26420 measured reflections | k = −12→12 |
9812 independent reflections | l = −37→36 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.033 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.074 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0217P)2 + 4.762P] where P = (Fo2 + 2Fc2)/3 |
9812 reflections | (Δ/σ)max = 0.002 |
532 parameters | Δρmax = 0.39 e Å−3 |
0 restraints | Δρmin = −0.63 e Å−3 |
[Pd(C4H3N2S)Cl(C18H15P)]·0.5CH4O | V = 4437.14 (10) Å3 |
Mr = 531.29 | Z = 8 |
Monoclinic, P21/c | Mo Kα radiation |
a = 16.1340 (2) Å | µ = 1.14 mm−1 |
b = 9.7020 (1) Å | T = 233 K |
c = 29.0480 (4) Å | 0.35 × 0.25 × 0.08 mm |
β = 102.617 (1)° |
Nonius KappaCCD diffractometer | 8231 reflections with I > 2σ(I) |
26420 measured reflections | Rint = 0.033 |
9812 independent reflections |
R[F2 > 2σ(F2)] = 0.033 | 0 restraints |
wR(F2) = 0.074 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.39 e Å−3 |
9812 reflections | Δρmin = −0.63 e Å−3 |
532 parameters |
Experimental. The data set was not corrected for absorption. A number of redundant reflections were measured. Using these additional scans, a ϕ scan-like absorption correction will be achieved by the normal scaling process. Such a data set has a similar quality as corrected data based on procedures described by Blessing (1995). |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
Pd1 | 0.240964 (11) | 0.66465 (2) | 0.398828 (7) | 0.03162 (6) | |
Pd2 | 0.199587 (12) | 0.83808 (2) | 0.246817 (7) | 0.03306 (6) | |
S1 | 0.31967 (4) | 0.58844 (8) | 0.34683 (3) | 0.04655 (18) | |
S2 | 0.10400 (4) | 0.65839 (8) | 0.24137 (3) | 0.04725 (18) | |
P1 | 0.33454 (4) | 0.82233 (7) | 0.43539 (2) | 0.03084 (14) | |
P2 | 0.25733 (4) | 0.79040 (7) | 0.18507 (2) | 0.03063 (14) | |
Cl1 | 0.14491 (5) | 0.68449 (9) | 0.44749 (3) | 0.0582 (2) | |
Cl2 | 0.27507 (5) | 1.04153 (7) | 0.26184 (3) | 0.04819 (17) | |
N1 | 0.17786 (13) | 0.5047 (2) | 0.35862 (8) | 0.0359 (5) | |
N2 | 0.22709 (15) | 0.3745 (2) | 0.30065 (9) | 0.0441 (6) | |
N3 | 0.12661 (15) | 0.8617 (3) | 0.29720 (8) | 0.0430 (6) | |
N4 | 0.00779 (16) | 0.7263 (3) | 0.30479 (12) | 0.0673 (8) | |
C1 | 0.23438 (16) | 0.4739 (3) | 0.33231 (10) | 0.0374 (6) | |
C2 | 0.10702 (17) | 0.4311 (3) | 0.35238 (11) | 0.0450 (7) | |
H2 | 0.0667 | 0.4496 | 0.3705 | 0.054* | |
C3 | 0.09274 (19) | 0.3273 (3) | 0.31920 (12) | 0.0519 (8) | |
H3 | 0.0425 | 0.2749 | 0.3138 | 0.062* | |
C4 | 0.15472 (19) | 0.3032 (3) | 0.29433 (11) | 0.0489 (7) | |
H4 | 0.1456 | 0.2326 | 0.2716 | 0.059* | |
C5 | 0.42434 (16) | 0.8379 (2) | 0.40719 (9) | 0.0340 (5) | |
C6 | 0.40771 (17) | 0.8749 (3) | 0.35961 (10) | 0.0400 (6) | |
H6 | 0.3521 | 0.8983 | 0.3441 | 0.048* | |
C7 | 0.4722 (2) | 0.8775 (3) | 0.33511 (11) | 0.0490 (7) | |
H7 | 0.4604 | 0.9033 | 0.3031 | 0.059* | |
C8 | 0.5531 (2) | 0.8426 (3) | 0.35745 (13) | 0.0559 (9) | |
H8 | 0.5967 | 0.8425 | 0.3406 | 0.067* | |
C9 | 0.57100 (18) | 0.8072 (3) | 0.40484 (13) | 0.0536 (8) | |
H9 | 0.6269 | 0.7846 | 0.4201 | 0.064* | |
C10 | 0.50693 (17) | 0.8050 (3) | 0.42981 (11) | 0.0410 (6) | |
H10 | 0.5194 | 0.7813 | 0.4620 | 0.049* | |
C11 | 0.29712 (17) | 0.9976 (3) | 0.44036 (9) | 0.0371 (6) | |
C12 | 0.3377 (2) | 1.1097 (3) | 0.42695 (14) | 0.0606 (9) | |
H12 | 0.3853 | 1.0965 | 0.4137 | 0.073* | |
C13 | 0.3095 (3) | 1.2425 (3) | 0.43262 (15) | 0.0720 (11) | |
H13 | 0.3386 | 1.3182 | 0.4236 | 0.086* | |
C14 | 0.2403 (2) | 1.2640 (3) | 0.45110 (13) | 0.0622 (9) | |
H14 | 0.2212 | 1.3540 | 0.4549 | 0.075* | |
C15 | 0.1988 (3) | 1.1532 (4) | 0.46412 (16) | 0.0740 (11) | |
H15 | 0.1507 | 1.1674 | 0.4768 | 0.089* | |
C16 | 0.2264 (2) | 1.0204 (3) | 0.45894 (14) | 0.0613 (9) | |
H16 | 0.1969 | 0.9452 | 0.4681 | 0.074* | |
C17 | 0.38092 (15) | 0.7669 (3) | 0.49519 (9) | 0.0325 (5) | |
C18 | 0.40159 (19) | 0.8585 (3) | 0.53233 (10) | 0.0445 (7) | |
H18 | 0.3871 | 0.9521 | 0.5276 | 0.053* | |
C19 | 0.4437 (2) | 0.8127 (4) | 0.57652 (11) | 0.0535 (8) | |
H19 | 0.4574 | 0.8753 | 0.6018 | 0.064* | |
C20 | 0.4653 (2) | 0.6773 (4) | 0.58341 (11) | 0.0545 (8) | |
H20 | 0.4948 | 0.6471 | 0.6132 | 0.065* | |
C21 | 0.4441 (2) | 0.5849 (3) | 0.54702 (12) | 0.0537 (8) | |
H21 | 0.4587 | 0.4915 | 0.5521 | 0.064* | |
C22 | 0.40118 (19) | 0.6287 (3) | 0.50283 (10) | 0.0430 (6) | |
H22 | 0.3859 | 0.5648 | 0.4781 | 0.052* | |
C23 | 0.07384 (17) | 0.7542 (3) | 0.28565 (11) | 0.0461 (7) | |
C24 | 0.1146 (2) | 0.9486 (4) | 0.33024 (11) | 0.0575 (8) | |
H24 | 0.1516 | 1.0237 | 0.3388 | 0.069* | |
C25 | 0.0481 (3) | 0.9292 (5) | 0.35205 (13) | 0.0720 (11) | |
H25 | 0.0381 | 0.9898 | 0.3755 | 0.086* | |
C26 | −0.0030 (2) | 0.8174 (5) | 0.33807 (15) | 0.0779 (13) | |
H26 | −0.0489 | 0.8032 | 0.3527 | 0.094* | |
C27 | 0.24255 (15) | 0.6118 (3) | 0.16526 (10) | 0.0355 (6) | |
C28 | 0.2221 (2) | 0.5751 (3) | 0.11794 (11) | 0.0557 (8) | |
H28 | 0.2147 | 0.6433 | 0.0944 | 0.067* | |
C29 | 0.2125 (2) | 0.4364 (4) | 0.10564 (13) | 0.0666 (10) | |
H29 | 0.1983 | 0.4113 | 0.0736 | 0.080* | |
C30 | 0.2235 (2) | 0.3358 (3) | 0.13968 (15) | 0.0595 (9) | |
H30 | 0.2169 | 0.2426 | 0.1309 | 0.071* | |
C31 | 0.24404 (19) | 0.3711 (3) | 0.18638 (13) | 0.0501 (8) | |
H31 | 0.2522 | 0.3021 | 0.2097 | 0.060* | |
C32 | 0.25279 (17) | 0.5088 (3) | 0.19923 (10) | 0.0400 (6) | |
H32 | 0.2658 | 0.5327 | 0.2314 | 0.048* | |
C33 | 0.20889 (16) | 0.8957 (3) | 0.13472 (9) | 0.0353 (6) | |
C34 | 0.24838 (18) | 0.9160 (3) | 0.09736 (10) | 0.0480 (7) | |
H34 | 0.3028 | 0.8792 | 0.0988 | 0.058* | |
C35 | 0.2083 (2) | 0.9901 (4) | 0.05790 (11) | 0.0577 (8) | |
H35 | 0.2354 | 1.0033 | 0.0327 | 0.069* | |
C36 | 0.1289 (2) | 1.0442 (4) | 0.05577 (11) | 0.0567 (8) | |
H36 | 0.1012 | 1.0929 | 0.0288 | 0.068* | |
C37 | 0.08991 (19) | 1.0274 (3) | 0.09281 (12) | 0.0544 (8) | |
H37 | 0.0360 | 1.0660 | 0.0913 | 0.065* | |
C38 | 0.12933 (17) | 0.9540 (3) | 0.13243 (10) | 0.0439 (7) | |
H38 | 0.1023 | 0.9435 | 0.1578 | 0.053* | |
C39 | 0.37140 (15) | 0.8203 (2) | 0.19397 (8) | 0.0302 (5) | |
C40 | 0.40287 (17) | 0.9534 (3) | 0.19145 (9) | 0.0369 (6) | |
H40 | 0.3650 | 1.0279 | 0.1841 | 0.044* | |
C41 | 0.48946 (17) | 0.9761 (3) | 0.19975 (10) | 0.0389 (6) | |
H41 | 0.5102 | 1.0660 | 0.1976 | 0.047* | |
C42 | 0.54576 (16) | 0.8679 (3) | 0.21116 (10) | 0.0403 (6) | |
H42 | 0.6046 | 0.8840 | 0.2170 | 0.048* | |
C43 | 0.51539 (16) | 0.7363 (3) | 0.21387 (10) | 0.0411 (6) | |
H43 | 0.5536 | 0.6624 | 0.2216 | 0.049* | |
C44 | 0.42877 (16) | 0.7120 (3) | 0.20532 (10) | 0.0375 (6) | |
H44 | 0.4086 | 0.6217 | 0.2072 | 0.045* | |
O1 | −0.0032 (5) | 0.8323 (10) | 0.4912 (4) | 0.211 (4) | 0.75 |
O1A | 0.0008 (17) | 0.934 (3) | 0.5445 (14) | 0.31 (2) | 0.25 |
C45 | 0.0398 (7) | 0.8312 (14) | 0.5332 (4) | 0.259 (7) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.02951 (10) | 0.03379 (11) | 0.03160 (11) | −0.00387 (7) | 0.00678 (7) | −0.00325 (8) |
Pd2 | 0.03246 (10) | 0.03445 (11) | 0.03351 (11) | 0.00380 (8) | 0.00989 (8) | 0.00369 (8) |
S1 | 0.0391 (4) | 0.0477 (4) | 0.0578 (5) | −0.0126 (3) | 0.0214 (3) | −0.0192 (4) |
S2 | 0.0342 (3) | 0.0464 (4) | 0.0609 (5) | −0.0010 (3) | 0.0097 (3) | 0.0043 (4) |
P1 | 0.0326 (3) | 0.0305 (3) | 0.0297 (3) | −0.0032 (3) | 0.0074 (3) | −0.0026 (3) |
P2 | 0.0285 (3) | 0.0319 (3) | 0.0316 (3) | 0.0025 (2) | 0.0069 (2) | 0.0022 (3) |
Cl1 | 0.0558 (4) | 0.0709 (5) | 0.0564 (5) | −0.0127 (4) | 0.0308 (4) | −0.0112 (4) |
Cl2 | 0.0544 (4) | 0.0373 (4) | 0.0571 (4) | −0.0035 (3) | 0.0214 (3) | −0.0063 (3) |
N1 | 0.0303 (11) | 0.0389 (12) | 0.0378 (12) | −0.0044 (9) | 0.0061 (9) | −0.0048 (10) |
N2 | 0.0465 (13) | 0.0378 (13) | 0.0482 (14) | −0.0028 (10) | 0.0108 (11) | −0.0119 (11) |
N3 | 0.0436 (13) | 0.0498 (14) | 0.0404 (13) | 0.0118 (11) | 0.0194 (11) | 0.0098 (11) |
N4 | 0.0399 (14) | 0.088 (2) | 0.080 (2) | 0.0100 (14) | 0.0264 (14) | 0.0254 (18) |
C1 | 0.0331 (13) | 0.0353 (14) | 0.0429 (15) | −0.0015 (11) | 0.0065 (11) | −0.0018 (12) |
C2 | 0.0315 (14) | 0.0507 (17) | 0.0524 (17) | −0.0076 (12) | 0.0081 (12) | −0.0037 (15) |
C3 | 0.0410 (16) | 0.0479 (18) | 0.063 (2) | −0.0124 (13) | 0.0040 (14) | −0.0089 (16) |
C4 | 0.0505 (17) | 0.0385 (16) | 0.0534 (19) | −0.0053 (13) | 0.0020 (14) | −0.0092 (14) |
C5 | 0.0390 (13) | 0.0270 (12) | 0.0375 (14) | −0.0069 (10) | 0.0118 (11) | −0.0038 (11) |
C6 | 0.0433 (15) | 0.0387 (14) | 0.0394 (15) | −0.0101 (12) | 0.0122 (12) | −0.0009 (12) |
C7 | 0.065 (2) | 0.0427 (16) | 0.0449 (17) | −0.0137 (14) | 0.0249 (15) | −0.0017 (14) |
C8 | 0.061 (2) | 0.0495 (18) | 0.070 (2) | −0.0061 (15) | 0.0406 (18) | −0.0021 (17) |
C9 | 0.0380 (16) | 0.0508 (18) | 0.075 (2) | −0.0002 (13) | 0.0195 (15) | 0.0055 (17) |
C10 | 0.0357 (14) | 0.0388 (15) | 0.0495 (17) | −0.0041 (11) | 0.0115 (12) | 0.0002 (13) |
C11 | 0.0415 (14) | 0.0338 (14) | 0.0353 (14) | 0.0006 (11) | 0.0071 (11) | −0.0013 (12) |
C12 | 0.063 (2) | 0.0357 (16) | 0.090 (3) | 0.0004 (14) | 0.0323 (19) | 0.0029 (17) |
C13 | 0.091 (3) | 0.0345 (17) | 0.097 (3) | 0.0035 (17) | 0.034 (2) | 0.0065 (19) |
C14 | 0.089 (3) | 0.0402 (18) | 0.055 (2) | 0.0181 (17) | 0.0120 (18) | −0.0076 (16) |
C15 | 0.080 (3) | 0.060 (2) | 0.093 (3) | 0.0155 (19) | 0.043 (2) | −0.012 (2) |
C16 | 0.068 (2) | 0.0443 (18) | 0.082 (3) | 0.0028 (16) | 0.0389 (19) | −0.0043 (18) |
C17 | 0.0305 (12) | 0.0363 (14) | 0.0315 (13) | −0.0053 (10) | 0.0084 (10) | −0.0014 (11) |
C18 | 0.0519 (17) | 0.0434 (16) | 0.0359 (15) | −0.0075 (13) | 0.0045 (12) | −0.0024 (13) |
C19 | 0.0606 (19) | 0.064 (2) | 0.0334 (16) | −0.0155 (16) | 0.0056 (14) | −0.0044 (15) |
C20 | 0.0497 (17) | 0.079 (2) | 0.0343 (16) | −0.0061 (16) | 0.0084 (13) | 0.0155 (16) |
C21 | 0.0617 (19) | 0.0511 (18) | 0.0506 (19) | 0.0103 (15) | 0.0176 (15) | 0.0190 (16) |
C22 | 0.0515 (16) | 0.0378 (15) | 0.0412 (16) | 0.0000 (12) | 0.0133 (13) | −0.0003 (13) |
C23 | 0.0344 (14) | 0.0553 (18) | 0.0494 (17) | 0.0108 (13) | 0.0107 (12) | 0.0177 (15) |
C24 | 0.070 (2) | 0.062 (2) | 0.0463 (18) | 0.0176 (17) | 0.0248 (16) | 0.0086 (16) |
C25 | 0.079 (3) | 0.092 (3) | 0.057 (2) | 0.031 (2) | 0.040 (2) | 0.016 (2) |
C26 | 0.054 (2) | 0.117 (4) | 0.074 (3) | 0.029 (2) | 0.039 (2) | 0.033 (3) |
C27 | 0.0282 (12) | 0.0374 (14) | 0.0405 (15) | 0.0007 (10) | 0.0067 (10) | −0.0036 (12) |
C28 | 0.066 (2) | 0.0540 (19) | 0.0429 (17) | 0.0018 (16) | 0.0035 (15) | −0.0080 (16) |
C29 | 0.074 (2) | 0.064 (2) | 0.057 (2) | −0.0027 (18) | 0.0018 (17) | −0.0275 (19) |
C30 | 0.0504 (18) | 0.0431 (18) | 0.087 (3) | −0.0072 (14) | 0.0191 (17) | −0.0211 (19) |
C31 | 0.0437 (16) | 0.0377 (15) | 0.073 (2) | −0.0027 (12) | 0.0223 (15) | −0.0042 (16) |
C32 | 0.0374 (14) | 0.0340 (14) | 0.0501 (17) | −0.0029 (11) | 0.0127 (12) | −0.0028 (13) |
C33 | 0.0325 (13) | 0.0360 (14) | 0.0360 (14) | 0.0029 (10) | 0.0045 (10) | 0.0039 (12) |
C34 | 0.0438 (16) | 0.0603 (19) | 0.0419 (16) | 0.0119 (14) | 0.0138 (13) | 0.0095 (15) |
C35 | 0.063 (2) | 0.073 (2) | 0.0389 (16) | 0.0088 (17) | 0.0150 (14) | 0.0149 (17) |
C36 | 0.059 (2) | 0.063 (2) | 0.0426 (17) | 0.0089 (16) | 0.0007 (14) | 0.0175 (16) |
C37 | 0.0393 (16) | 0.062 (2) | 0.060 (2) | 0.0128 (14) | 0.0072 (14) | 0.0178 (17) |
C38 | 0.0360 (14) | 0.0499 (17) | 0.0465 (16) | 0.0057 (12) | 0.0106 (12) | 0.0104 (14) |
C39 | 0.0290 (12) | 0.0341 (13) | 0.0279 (12) | 0.0016 (10) | 0.0067 (9) | 0.0006 (10) |
C40 | 0.0424 (14) | 0.0308 (13) | 0.0392 (15) | 0.0032 (11) | 0.0126 (11) | −0.0005 (12) |
C41 | 0.0417 (14) | 0.0394 (15) | 0.0377 (15) | −0.0096 (12) | 0.0135 (11) | −0.0041 (12) |
C42 | 0.0296 (13) | 0.0561 (17) | 0.0347 (14) | −0.0051 (12) | 0.0059 (10) | −0.0010 (13) |
C43 | 0.0313 (13) | 0.0453 (16) | 0.0462 (16) | 0.0061 (11) | 0.0073 (11) | 0.0082 (13) |
C44 | 0.0371 (14) | 0.0338 (13) | 0.0412 (15) | 0.0018 (11) | 0.0077 (11) | 0.0045 (12) |
O1 | 0.115 (5) | 0.258 (10) | 0.263 (11) | 0.002 (5) | 0.049 (6) | −0.087 (8) |
O1A | 0.18 (2) | 0.27 (3) | 0.51 (6) | −0.02 (2) | 0.15 (3) | −0.26 (4) |
C45 | 0.164 (9) | 0.344 (16) | 0.224 (12) | 0.086 (9) | −0.057 (8) | −0.138 (11) |
Pd1—N1 | 2.071 (2) | C16—H16 | 0.9400 |
Pd1—P1 | 2.2467 (7) | C17—C18 | 1.381 (4) |
Pd1—S1 | 2.2975 (7) | C17—C22 | 1.387 (4) |
Pd1—Cl1 | 2.3225 (8) | C18—C19 | 1.388 (4) |
Pd1—N3 | 3.660 (2) | C18—H18 | 0.9400 |
Pd2—N3 | 2.082 (2) | C19—C20 | 1.363 (5) |
Pd2—P2 | 2.2424 (7) | C19—H19 | 0.9400 |
Pd2—S2 | 2.3100 (7) | C20—C21 | 1.371 (5) |
Pd2—Cl2 | 2.3104 (7) | C20—H20 | 0.9400 |
Pd2—S1 | 3.9498 (9) | C21—C22 | 1.385 (4) |
S1—C1 | 1.747 (3) | C21—H21 | 0.9400 |
S2—C23 | 1.740 (3) | C22—H22 | 0.9400 |
P1—C17 | 1.816 (3) | C24—C25 | 1.374 (5) |
P1—C5 | 1.820 (3) | C24—H24 | 0.9400 |
P1—C11 | 1.821 (3) | C25—C26 | 1.369 (6) |
P2—C33 | 1.815 (3) | C25—H25 | 0.9400 |
P2—C39 | 1.825 (2) | C26—H26 | 0.9400 |
P2—C27 | 1.825 (3) | C27—C28 | 1.388 (4) |
N1—C2 | 1.326 (3) | C27—C32 | 1.389 (4) |
N1—C1 | 1.345 (3) | C28—C29 | 1.393 (5) |
N2—C1 | 1.320 (3) | C28—H28 | 0.9400 |
N2—C4 | 1.335 (4) | C29—C30 | 1.373 (5) |
N3—C24 | 1.323 (4) | C29—H29 | 0.9400 |
N3—C23 | 1.342 (4) | C30—C31 | 1.368 (5) |
N4—C23 | 1.333 (4) | C30—H30 | 0.9400 |
N4—C26 | 1.349 (5) | C31—C32 | 1.386 (4) |
C2—C3 | 1.378 (4) | C31—H31 | 0.9400 |
C2—H2 | 0.9400 | C32—H32 | 0.9400 |
C3—C4 | 1.375 (5) | C33—C34 | 1.387 (4) |
C3—H3 | 0.9400 | C33—C38 | 1.391 (4) |
C4—H4 | 0.9400 | C34—C35 | 1.388 (4) |
C5—C10 | 1.388 (4) | C34—H34 | 0.9400 |
C5—C6 | 1.396 (4) | C35—C36 | 1.373 (5) |
C6—C7 | 1.383 (4) | C35—H35 | 0.9400 |
C6—H6 | 0.9400 | C36—C37 | 1.369 (5) |
C7—C8 | 1.367 (5) | C36—H36 | 0.9400 |
C7—H7 | 0.9400 | C37—C38 | 1.384 (4) |
C8—C9 | 1.387 (5) | C37—H37 | 0.9400 |
C8—H8 | 0.9400 | C38—H38 | 0.9400 |
C9—C10 | 1.387 (4) | C39—C44 | 1.391 (3) |
C9—H9 | 0.9400 | C39—C40 | 1.396 (3) |
C10—H10 | 0.9400 | C40—C41 | 1.383 (4) |
C11—C12 | 1.369 (4) | C40—H40 | 0.9400 |
C11—C16 | 1.383 (4) | C41—C42 | 1.381 (4) |
C12—C13 | 1.388 (5) | C41—H41 | 0.9400 |
C12—H12 | 0.9400 | C42—C43 | 1.376 (4) |
C13—C14 | 1.356 (5) | C42—H42 | 0.9400 |
C13—H13 | 0.9400 | C43—C44 | 1.385 (4) |
C14—C15 | 1.363 (5) | C43—H43 | 0.9400 |
C14—H14 | 0.9400 | C44—H44 | 0.9400 |
C15—C16 | 1.382 (5) | O1—C45 | 1.266 (12) |
C15—H15 | 0.9400 | O1A—C45 | 1.26 (2) |
N1—Pd1—P1 | 166.81 (6) | C14—C15—H15 | 119.5 |
N1—Pd1—S1 | 70.26 (6) | C16—C15—H15 | 119.5 |
P1—Pd1—S1 | 96.84 (2) | C15—C16—C11 | 120.3 (3) |
N1—Pd1—Cl1 | 95.41 (6) | C15—C16—H16 | 119.9 |
P1—Pd1—Cl1 | 97.16 (3) | C11—C16—H16 | 119.9 |
S1—Pd1—Cl1 | 164.78 (3) | C18—C17—C22 | 119.3 (3) |
N1—Pd1—N3 | 80.66 (7) | C18—C17—P1 | 122.3 (2) |
P1—Pd1—N3 | 101.18 (4) | C22—C17—P1 | 118.2 (2) |
S1—Pd1—N3 | 83.77 (4) | C17—C18—C19 | 120.2 (3) |
Cl1—Pd1—N3 | 99.31 (4) | C17—C18—H18 | 119.9 |
N3—Pd2—P2 | 169.30 (7) | C19—C18—H18 | 119.9 |
N3—Pd2—S2 | 70.10 (7) | C20—C19—C18 | 120.1 (3) |
P2—Pd2—S2 | 100.22 (3) | C20—C19—H19 | 119.9 |
N3—Pd2—Cl2 | 97.40 (7) | C18—C19—H19 | 119.9 |
P2—Pd2—Cl2 | 91.91 (3) | C19—C20—C21 | 120.3 (3) |
S2—Pd2—Cl2 | 166.96 (3) | C19—C20—H20 | 119.9 |
N3—Pd2—S1 | 79.19 (6) | C21—C20—H20 | 119.9 |
P2—Pd2—S1 | 103.83 (2) | C20—C21—C22 | 120.3 (3) |
S2—Pd2—S1 | 78.49 (2) | C20—C21—H21 | 119.9 |
Cl2—Pd2—S1 | 103.38 (2) | C22—C21—H21 | 119.9 |
C1—S1—Pd1 | 81.03 (9) | C21—C22—C17 | 119.8 (3) |
C1—S1—Pd2 | 88.77 (9) | C21—C22—H22 | 120.1 |
Pd1—S1—Pd2 | 91.92 (2) | C17—C22—H22 | 120.1 |
C23—S2—Pd2 | 80.59 (10) | N4—C23—N3 | 125.1 (3) |
C17—P1—C5 | 104.65 (12) | N4—C23—S2 | 125.3 (3) |
C17—P1—C11 | 105.99 (12) | N3—C23—S2 | 109.6 (2) |
C5—P1—C11 | 105.58 (12) | N3—C24—C25 | 120.0 (4) |
C17—P1—Pd1 | 110.14 (8) | N3—C24—H24 | 120.0 |
C5—P1—Pd1 | 111.26 (8) | C25—C24—H24 | 120.0 |
C11—P1—Pd1 | 118.24 (9) | C26—C25—C24 | 116.9 (4) |
C33—P2—C39 | 105.56 (12) | C26—C25—H25 | 121.5 |
C33—P2—C27 | 106.07 (12) | C24—C25—H25 | 121.5 |
C39—P2—C27 | 104.69 (11) | N4—C26—C25 | 124.6 (3) |
C33—P2—Pd2 | 110.32 (9) | N4—C26—H26 | 117.7 |
C39—P2—Pd2 | 115.87 (8) | C25—C26—H26 | 117.7 |
C27—P2—Pd2 | 113.55 (9) | C28—C27—C32 | 119.0 (3) |
C2—N1—C1 | 118.3 (2) | C28—C27—P2 | 122.8 (2) |
C2—N1—Pd1 | 141.6 (2) | C32—C27—P2 | 118.2 (2) |
C1—N1—Pd1 | 100.12 (16) | C27—C28—C29 | 119.4 (3) |
C1—N2—C4 | 114.6 (2) | C27—C28—H28 | 120.3 |
C24—N3—C23 | 119.4 (3) | C29—C28—H28 | 120.3 |
C24—N3—Pd2 | 140.8 (2) | C30—C29—C28 | 120.8 (3) |
C23—N3—Pd2 | 99.43 (18) | C30—C29—H29 | 119.6 |
C24—N3—Pd1 | 82.85 (18) | C28—C29—H29 | 119.6 |
C23—N3—Pd1 | 88.62 (16) | C31—C30—C29 | 120.1 (3) |
Pd2—N3—Pd1 | 104.27 (8) | C31—C30—H30 | 119.9 |
C23—N4—C26 | 113.9 (3) | C29—C30—H30 | 119.9 |
N2—C1—N1 | 126.1 (2) | C30—C31—C32 | 119.7 (3) |
N2—C1—S1 | 125.3 (2) | C30—C31—H31 | 120.1 |
N1—C1—S1 | 108.54 (19) | C32—C31—H31 | 120.1 |
N1—C2—C3 | 119.8 (3) | C31—C32—C27 | 120.9 (3) |
N1—C2—H2 | 120.1 | C31—C32—H32 | 119.6 |
C3—C2—H2 | 120.1 | C27—C32—H32 | 119.6 |
C4—C3—C2 | 117.5 (3) | C34—C33—C38 | 118.8 (2) |
C4—C3—H3 | 121.2 | C34—C33—P2 | 121.3 (2) |
C2—C3—H3 | 121.2 | C38—C33—P2 | 119.9 (2) |
N2—C4—C3 | 123.6 (3) | C33—C34—C35 | 120.6 (3) |
N2—C4—H4 | 118.2 | C33—C34—H34 | 119.7 |
C3—C4—H4 | 118.2 | C35—C34—H34 | 119.7 |
C10—C5—C6 | 119.0 (2) | C36—C35—C34 | 119.8 (3) |
C10—C5—P1 | 123.0 (2) | C36—C35—H35 | 120.1 |
C6—C5—P1 | 117.9 (2) | C34—C35—H35 | 120.1 |
C7—C6—C5 | 120.7 (3) | C37—C36—C35 | 120.2 (3) |
C7—C6—H6 | 119.7 | C37—C36—H36 | 119.9 |
C5—C6—H6 | 119.7 | C35—C36—H36 | 119.9 |
C8—C7—C6 | 119.9 (3) | C36—C37—C38 | 120.5 (3) |
C8—C7—H7 | 120.0 | C36—C37—H37 | 119.7 |
C6—C7—H7 | 120.0 | C38—C37—H37 | 119.7 |
C7—C8—C9 | 120.2 (3) | C37—C38—C33 | 120.0 (3) |
C7—C8—H8 | 119.9 | C37—C38—H38 | 120.0 |
C9—C8—H8 | 119.9 | C33—C38—H38 | 120.0 |
C8—C9—C10 | 120.4 (3) | C44—C39—C40 | 118.7 (2) |
C8—C9—H9 | 119.8 | C44—C39—P2 | 120.79 (19) |
C10—C9—H9 | 119.8 | C40—C39—P2 | 120.44 (18) |
C9—C10—C5 | 119.8 (3) | C41—C40—C39 | 120.3 (2) |
C9—C10—H10 | 120.1 | C41—C40—H40 | 119.9 |
C5—C10—H10 | 120.1 | C39—C40—H40 | 119.9 |
C12—C11—C16 | 118.1 (3) | C42—C41—C40 | 120.5 (2) |
C12—C11—P1 | 122.1 (2) | C42—C41—H41 | 119.8 |
C16—C11—P1 | 119.8 (2) | C40—C41—H41 | 119.8 |
C11—C12—C13 | 120.9 (3) | C43—C42—C41 | 119.7 (2) |
C11—C12—H12 | 119.5 | C43—C42—H42 | 120.1 |
C13—C12—H12 | 119.5 | C41—C42—H42 | 120.1 |
C14—C13—C12 | 120.6 (3) | C42—C43—C44 | 120.4 (2) |
C14—C13—H13 | 119.7 | C42—C43—H43 | 119.8 |
C12—C13—H13 | 119.7 | C44—C43—H43 | 119.8 |
C13—C14—C15 | 119.0 (3) | C43—C44—C39 | 120.5 (2) |
C13—C14—H14 | 120.5 | C43—C44—H44 | 119.8 |
C15—C14—H14 | 120.5 | C39—C44—H44 | 119.8 |
C14—C15—C16 | 121.1 (3) | O1A—C45—O1 | 93 (2) |
S1—Pd1—P1—C5 | 5.44 (10) | S2—Pd2—P2—C27 | −19.90 (9) |
Experimental details
Crystal data | |
Chemical formula | [Pd(C4H3N2S)Cl(C18H15P)]·0.5CH4O |
Mr | 531.29 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 233 |
a, b, c (Å) | 16.1340 (2), 9.7020 (1), 29.0480 (4) |
β (°) | 102.617 (1) |
V (Å3) | 4437.14 (10) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 1.14 |
Crystal size (mm) | 0.35 × 0.25 × 0.08 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 26420, 9812, 8231 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.033, 0.074, 1.03 |
No. of reflections | 9812 |
No. of parameters | 532 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.39, −0.63 |
Computer programs: COLLECT (Nonius, 1998), SCALEPACK (Otwinowski & Minor, 1997), DENZO (Otwinowski & Minor, 1997) and SCALEPACK, SHELXS97 (Sheldrick, 1997a), SHELXL97 (Sheldrick, 1997a), SHELXTL (Sheldrick, 1997b), SHELXL97.
Pd1—N1 | 2.071 (2) | Pd2—Cl2 | 2.3104 (7) |
Pd1—P1 | 2.2467 (7) | S1—C1 | 1.747 (3) |
Pd1—S1 | 2.2975 (7) | S2—C23 | 1.740 (3) |
Pd1—Cl1 | 2.3225 (8) | N1—C1 | 1.345 (3) |
Pd2—N3 | 2.082 (2) | N2—C1 | 1.320 (3) |
Pd2—P2 | 2.2424 (7) | N3—C23 | 1.342 (4) |
Pd2—S2 | 2.3100 (7) | N4—C23 | 1.333 (4) |
N1—Pd1—P1 | 166.81 (6) | S2—Pd2—Cl2 | 166.96 (3) |
N1—Pd1—S1 | 70.26 (6) | C1—S1—Pd1 | 81.03 (9) |
P1—Pd1—S1 | 96.84 (2) | C23—S2—Pd2 | 80.59 (10) |
N1—Pd1—Cl1 | 95.41 (6) | C1—N1—Pd1 | 100.12 (16) |
P1—Pd1—Cl1 | 97.16 (3) | C23—N3—Pd1 | 88.62 (16) |
S1—Pd1—Cl1 | 164.78 (3) | N2—C1—N1 | 126.1 (2) |
N3—Pd2—P2 | 169.30 (7) | N2—C1—S1 | 125.3 (2) |
N3—Pd2—S2 | 70.10 (7) | N1—C1—S1 | 108.54 (19) |
P2—Pd2—S2 | 100.22 (3) | N4—C23—N3 | 125.1 (3) |
N3—Pd2—Cl2 | 97.40 (7) | N4—C23—S2 | 125.3 (3) |
P2—Pd2—Cl2 | 91.91 (3) | N3—C23—S2 | 109.6 (2) |
Palladium(II) complexes with heterocylic thione ligands are of current interest for the synthesis of clinically useful drugs (Raper et al., 1985). The crystal structures of four-coordinate palladium(II) complexes with N– and S-donor hetrocyclic 2-thionate ligands, such as Pd2[2-Me2NCH2C6H4]2(µ-OH)(µ-Br) (Ruiz et al., 1996) and (2-benzolpyridinethiosemicarbazone)palladium(II) have been extensively investigated (Rebolledo et al., 2005). The title compound, (I), exhibits antibacterial and antitumor activity (Krischner et al., 1966) due to the N—C—S group generated by deprotonation of the hetrocyclic thione (Santana et al., 2000). It has also been used as a pesticide (Fackler, 2002) and an antimicrobial agent (Ronconi et al.; 2005).
In the title compound, each Pd atom of the two unique molecules in the asymmetric unit is four coordinate and exhibits a slightly distorted square-planar geometry (Fig. 1). The two molecules are similar except for the conformational orientation of the triphenylphosphine ligand, shown by the torsion angles S1—Pd1—P1—C5 [5.4 (1)°] and S2—Pd2—P2—C27 [−19.9 (1)°]. The pyrimidine-2-thiolate ligand acts as a bidentate chelate, coordinating to Pd via the S1 atom and the adjacent pyrimidine N1 atom. Atom S1 is trans to the chloride anion and N1 is trans to the triphenylphosphine ligand (Table 1). The slightly distorted square-planar geometry of the Pd atoms is also revealed by the displacements of the Pd atoms from the mean plane through the ligand donor atoms of 0.0876 (7) Å for Pd1 and 0.0893 (6) Å for Pd2. These deviations may be related to weak intermolecular interactions between Pd1 and N3 [3.660 (2) Å], and between Pd2 and S1 [3.9498 (9) Å].