metal-organic compounds

Transcription

1 metal-organic compounds Acta Crystallographica Section E Structure Reports Online ISSN Bis(3-benzoyl-1,1-di-sec-butylthioureatoj 2 O,S)palladium(II) N. Selvakumaran, a R. Karvembu, a Seik Weng Ng b,c and Edward R. T. Tiekink b * a Department of Chemistry, National Institute of Technology, Tiruchirappalli , India, b Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia, and c Chemistry Department, Faculty of, Science, King Abdulaziz University, PO Box Jeddah, Saudi Arabia Correspondence edward.tiekink@gmail.com Received 11 September 2011; accepted 11 September 2011 Tetragonal, I4 a = (1) Å c = (5) Å V = (9) Å 3 Z =4 Data collection Agilent SuperNova Dual diffractometer with an Atlas detector Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010) T min = 0.819, T max = Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections 186 parameters H-atom parameters constrained Mo K radiation = 0.69 mm 1 T = 100 K mm 4752 measured reflections 3229 independent reflections 3152 reflections with I > 2(I) R int = max = 0.51 e Å 3 min = 0.44 e Å 3 Absolute structure: Flack (1983), 1225 Friedel pairs Flack parameter: 0.02 (2) Key indicators: single-crystal X-ray study; T = 100 K; mean (C C) = Å; R factor = 0.023; wr factor = 0.058; data-to-parameter ratio = The complex molecule of the title complex, [Pd(C 16 H 23 - N 2 OS) 2 ], is completed by crystallographic twofold symmetry with the metal atom lying on the rotation axis. The Pd II atom exists within a slightly distorted square-planar geometry defined by a cis-o 2 S 2 donor set. The dihedral angle formed between the mean planes of the symmetry-related sixmembered chelate rings is (7) and the bond lengths within the rings are indicative of significant electron delocalization. In the crystal, molecules aggregate into dimers linked by four C HO interactions. Related literature For background to the synthesis and cytotoxicity of related Pd II complexes of N,N-di(alkyl/aryl)-N 0 -benzoylthiourea ligands, see: Selvakumaran et al. (2011). Table 1 Selected geometric parameters (Å, ). Pd O (17) Pd S (6) O1 Pd S (5) Table 2 Hydrogen-bond geometry (Å, ). D HA D H HA DA D HA C6 H6O1 i (3) 136 Symmetry code: (i) y þ 1 2 ; x þ 1 2 ; z þ 1 2. Data collection: CrysAlis PRO (Agilent, 2010); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publcif (Westrip, 2010). NS thanks NITT for a Fellowship. The authors thank the University of Malaya for supporting this study. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB6404). Experimental Crystal data [Pd(C 16 H 23 N 2 OS) 2 ] M r = References Agilent (2010). CrysAlis PRO. Agilent Technologies, Yarnton, England. Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany. Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. Flack, H. D. (1983). Acta Cryst. A39, Selvakumaran, N., Ng, S. W., Tiekink, E. R. T. & Karvembu, R. (2011). Inorg. Chim. Acta, 376, Sheldrick, G. M. (2008). Acta Cryst. A64, Westrip, S. P. (2010). J. Appl. Cryst. 43, Additional correspondence author, kar@nitt.edu. m1394 Selvakumaran et al. doi: /s Acta Cryst. (2011). E67, m1394

2

3 Acta Cryst. (2011). E67, m1394 [ doi: /s ] Bis(3-benzoyl-1,1-di-sec-butylthioureato- 2 O,S)palladium(II) N. Selvakumaran, R. Karvembu, S. W. Ng and E. R. T. Tiekink Comment The title complex, (I), was investigated during a study of the synthesis and cytotoxicity profiles of N,N-di(alkyl/aryl)-N'- benzoylthiourea ligands, LH (Selvakumaran et al., 2011). The Pd II atom in (I), Fig. 1, exists in a square planar geometry defined by a cis-o 2 S 2 donor set, Table 1, as found for related PdL 2 species (Selvakumaran et al., 2011). The molecule has crystallographically imposed 2-fold symmetry. There are significant deviations from the least-squares plane through the six-membered chelate ring (r.m.s. deviation = Å) with the maximum deviations being found for the S1 (0.255 (1) Å) and Pd ( (1) Å) atoms. The major twist in the ring is found about the N1 C8 bond as seen in the value of the C7 N1 C8 S1 torsion angle of (4). Nevertheless, the bond distance data, Table 1, are consistent with considerable delocalization of π-electron density over the six atoms; a similar conclusion was made for related species (Selvakumaran et al., 2011). The dihedral angle formed between the symmetry related chelate rings is (7). The most prominent intermolecular interactions in the crystal structure are of the type C H O, Table 2. These involve benzene-h and the coordinated O atoms, and result in the formation of two molecule aggregates sustained, from symmetry, by four such interactions, Fig. 2. Experimental The title complex, (I), was prepared and characterized as in the literature (Selvakumaran et al., 2011). Orange blocks were obtained by slow evaporation of a dichloromethane solution of the complex. Refinement The H-atoms were placed in calculated positions (C H 0.95 to 1.00 Å) and were included in the refinement in the riding model approximation, with U iso (H) set to 1.2 to 1.5U equiv (C). Figures Fig. 1. The molecular structure of (I) showing displacement ellipsoids at the 50% probability level. The molecule has 2-fold symmetry. Unlabelled atoms are related by the symmetry operation 1 - x, -y, z. sup-1

4 Fig. 2. Two molecule aggregate in (I) mediated by C H O interactions shown as orange dashed lines. Hydrogen atoms not participating in C H O contacts have been omitted for reasons of clarity. Bis(3-benzoyl-1,1-di-sec-butylthioureato- κ 2 O,S)palladium(II) Crystal data [Pd(C 16 H 23 N 2 OS) 2 ] D x = Mg m 3 M r = Mo Kα radiation, λ = Å Tetragonal, I4 Cell parameters from 3599 reflections Hall symbol: I -4 θ = a = (1) Å µ = 0.69 mm 1 c = (5) Å T = 100 K V = (9) Å 3 Block, orange Z = mm F(000) = 1440 Data collection Agilent SuperNova Dual diffractometer with an Atlas detector Radiation source: SuperNova (Mo) X-ray Source Mirror R int = independent reflections 3152 reflections with I > 2σ(I) Detector resolution: pixels mm -1 θ max = 27.5, θ min = 3.0 ω scans Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010) T min = 0.819, T max = measured reflections h = k = l = Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ 2 (F o 2 ) + (0.0272P) P] where P = (F o 2 + 2F c 2 )/3 S = 1.02 (Δ/σ) max < reflections Δρ max = 0.51 e Å parameters Δρ min = 0.44 e Å 3 0 restraints Absolute structure: Flack (1983), 1225 Friedel pairs sup-2

5 Primary atom site location: structure-invariant direct methods Flack parameter: 0.02 (2) 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 F 2 against ALL reflections. The weighted R-factor wr and goodness of fit S are based on F 2, conventional R-factors R are based on F, with F set to zero for negative F 2. The threshold expression of F 2 > σ(f 2 ) is used only for calculating R- factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 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 (Å 2 ) x y z U iso */U eq Pd (11) (7) S (5) (5) (3) (13) O (13) (13) (9) (4) N (18) (17) (10) (5) N (17) (16) (11) (5) C (2) (19) (13) (5) C (2) (2) (14) (6) H * C (2) (2) (15) (6) H * C (2) (2) (14) (6) H * C (2) (2) (13) (6) H * C (2) (19) (13) (5) H * C (19) (19) (13) (5) C (19) (19) (13) (5) C (2) (2) (15) (6) H9A * H9B * C (2) (2) (17) (6) H * C (3) (3) (16) (8) H11A * H11B * H11C * C (3) (3) (18) (8) H12A * H12B * H12C * sup-3

6 C (19) (19) (15) (5) H13A * H13B * C (2) (2) (15) (6) H * C (3) (3) (14) (8) H15A * H15B * H15C * C (3) (3) (17) (10) H16A * H16B * H16C * Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 Pd (15) (15) (11) (12) S (3) (3) (3) (2) (3) (3) O (9) (10) (8) (8) (8) (8) N (11) (11) (11) (9) (8) (8) N (11) (11) (11) (8) (10) (10) C (13) (13) (13) (10) (11) (10) C (14) (14) (15) (11) (12) (12) C (13) (15) (15) (12) (12) (12) C (15) (16) (15) (12) (12) (12) C (15) (15) (14) (12) (11) (11) C (13) (13) (12) (10) (10) (10) C (13) (12) (12) (10) (11) (11) C (12) (13) (12) (10) (10) (11) C (15) (14) (14) (11) (12) (12) C (15) (14) (14) (11) (15) (14) C (2) (18) (16) (15) (15) (14) C (2) (17) (19) (15) (17) (15) C (13) (13) (12) (10) (13) (13) C (16) (17) (14) (13) (13) (13) C (2) (19) (15) (16) (14) (14) C (2) (2) (2) (17) (16) (16) Geometric parameters (Å, ) Pd O1 i (17) C9 H9A Pd O (17) C9 H9B Pd S1 i (6) C10 C (4) Pd S (6) C10 C (5) S1 C (3) C10 H O1 C (3) C11 H11A N1 C (3) C11 H11B sup-4

7 N1 C (3) C11 H11C N2 C (3) C12 H12A N2 C (3) C12 H12B N2 C (3) C12 H12C C1 C (3) C13 C (4) C1 C (4) C13 H13A C1 C (3) C13 H13B C2 C (4) C14 C (5) C2 H C14 C (4) C3 C (4) C14 H C3 H C15 H15A C4 C (4) C15 H15B C4 H C15 H15C C5 C (4) C16 H16A C5 H C16 H16B C6 H C16 H16C C9 C (4) O1 i Pd O (10) C11 C10 C (3) O1 i Pd S1 i (5) C11 C10 C (2) O1 Pd S1 i (5) C9 C10 C (3) O1 i Pd S (5) C11 C10 H O1 Pd S (5) C9 C10 H S1 i Pd S (3) C12 C10 H C8 S1 Pd (9) C10 C11 H11A C7 O1 Pd (16) C10 C11 H11B C7 N1 C (2) H11A C11 H11B C8 N2 C (2) C10 C11 H11C C8 N2 C (2) H11A C11 H11C C13 N2 C (2) H11B C11 H11C C6 C1 C (2) C10 C12 H12A C6 C1 C (2) C10 C12 H12B C2 C1 C (2) H12A C12 H12B C3 C2 C (3) C10 C12 H12C C3 C2 H H12A C12 H12C C1 C2 H H12B C12 H12C C2 C3 C (3) N2 C13 C (2) C2 C3 H N2 C13 H13A C4 C3 H C14 C13 H13A C3 C4 C (3) N2 C13 H13B C3 C4 H C14 C13 H13B C5 C4 H H13A C13 H13B C6 C5 C (3) C16 C14 C (3) C6 C5 H C16 C14 C (2) C4 C5 H C15 C14 C (3) C1 C6 C (2) C16 C14 H C1 C6 H C15 C14 H C5 C6 H C13 C14 H O1 C7 N (2) C14 C15 H15A sup-5

8 O1 C7 C (2) C14 C15 H15B N1 C7 C (2) H15A C15 H15B N2 C8 N (2) C14 C15 H15C N2 C8 S (2) H15A C15 H15C N1 C8 S (2) H15B C15 H15C N2 C9 C (2) C14 C16 H16A N2 C9 H9A C14 C16 H16B C10 C9 H9A H16A C16 H16B N2 C9 H9B C14 C16 H16C C10 C9 H9B H16A C16 H16C H9A C9 H9B H16B C16 H16C O1 i Pd S1 C (7) C2 C1 C7 O (2) O1 Pd S1 C (10) C6 C1 C7 N (2) S1 i Pd S1 C (10) C2 C1 C7 N (4) O1 i Pd O1 C (2) C13 N2 C8 N (2) S1 i Pd O1 C (6) C9 N2 C8 N1 4.7 (3) S1 Pd O1 C7 6.9 (2) C13 N2 C8 S1 8.0 (3) C6 C1 C2 C3 1.4 (4) C9 N2 C8 S (19) C7 C1 C2 C (2) C7 N1 C8 N (2) C1 C2 C3 C4 1.0 (4) C7 N1 C8 S (4) C2 C3 C4 C5 0.1 (4) Pd S1 C8 N (19) C3 C4 C5 C6 0.6 (4) Pd S1 C8 N (2) C2 C1 C6 C5 0.7 (4) C8 N2 C9 C (3) C7 C1 C6 C (2) C13 N2 C9 C (3) C4 C5 C6 C1 0.2 (4) N2 C9 C10 C (3) Pd O1 C7 N (4) N2 C9 C10 C (3) Pd O1 C7 C (16) C8 N2 C13 C (3) C8 N1 C7 O (4) C9 N2 C13 C (3) C8 N1 C7 C (2) N2 C13 C14 C (3) C6 C1 C7 O1 8.0 (3) N2 C13 C14 C (2) Symmetry codes: (i) x+1, y, z. Hydrogen-bond geometry (Å, ) D H A D H H A D A D H A C6 H6 O1 ii (3) 136 Symmetry codes: (ii) y+1/2, x+1/2, z+1/2. sup-6

9 Fig. 1 sup-7

10 Fig. 2 sup-8