metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 71| Part 3| March 2015| Pages m63-m64

Crystal structure of bis­­[S-hexyl 3-(4-methyl­benzyl­­idene)di­thio­carbazato-κ2N3,S]palladium(II)

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aDepartment of Chemistry, Rajshahi University, Rajshahi-6205, Bangladesh, bDepartment of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan, cCenter for Environmental Conservation and Research Safety, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan, and dDepartment of Chemical and Pharmaceutical Sciences, via Giorgieri 1, 34127 Trieste, Italy
*Correspondence e-mail: sabina_sust@yahoo.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 20 January 2015; accepted 2 February 2015; online 11 February 2015)

The whole mol­ecule of the title complex, [Pd(C15H21N2S2)2], is generated by twofold rotational symmetry. The palladium(II) atom exhibits a square-planar coordination geometry, and is located on the crystallographic twofold axis that induces a cis configuration of the N,S chelating ligands. In the crystal, mol­ecules stack along the c-axis direction and there are no significant inter­molecular inter­actions present. The structure was refined as an inversion twin with a final BASF parameter of 0.34 (2).

1. Related literature

For the crystal structures of the free Schiff base ligand and of its NiII complex, see: Howlader et al. (2015a[Howlader, M. B. H., Begum, M. S., Sheikh, M. C., Miyatake, R. & Zangrando, E. (2015a). Acta Cryst. E71, o103-o104.],b[Howlader, M. B. H., Begum, M. S., Sheikh, M. C., Miyatake, R. & Zangrando, E. (2015b). Acta Cryst. E71, m26-m27.]). For similar bis­(di­thio­carbazato)Pd complexes with a cis configuration of the azomethine N and thiol­ate S atoms, see: Ali et al. (2002[Ali, M. A., Mirza, A. H., Butcher, R. J., Tarafder, M. T. H., Keat, T. B. & Ali, A. M. (2002). J. Inorg. Biochem. 92, 141-148.]); Liu et al. (2011[Liu, Z.-D., Zhang, X.-J., Wu, J.-Y., Hao, F.-Y., Zhou, H.-P. & Tian, Y.-P. (2011). Polyhedron, 30, 279-283.]); Duan et al. (1998[Duan, C.-Y., Tian, Y.-P., Liu, Z.-H., You, X.-Z. & Mak, T. C. W. (1998). J. Organomet. Chem. 570, 155-162.]); Tampouris et al. (2007[Tampouris, K., Coco, S., Yannopoulos, A. & Koinis, S. (2007). Polyhedron, 26, 4269-4275.]). For complexes with a trans configuration, see: Khaledi & Mohd Ali (2011[Khaledi, H. & Mohd Ali, H. (2011). Acta Cryst. E67, m230.]); Tampouris et al. (2007[Tampouris, K., Coco, S., Yannopoulos, A. & Koinis, S. (2007). Polyhedron, 26, 4269-4275.]); Tarafder et al. (2010[Tarafder, M. T. H., Islam, M. A. A. A. A., Howlader, M. B. H., Guidolin, N. & Zangrando, E. (2010). Acta Cryst. C66, m363-m365.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • [Pd(C15H21N2S2)2]

  • Mr = 693.32

  • Monoclinic, C 2

  • a = 18.3559 (11) Å

  • b = 9.6747 (5) Å

  • c = 10.3368 (6) Å

  • β = 116.810 (2)°

  • V = 1638.37 (16) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 7.14 mm−1

  • T = 173 K

  • 0.25 × 0.16 × 0.11 mm

2.2. Data collection

  • Rigaku R-AXIS RAPID diffractometer

  • Absorption correction: multi-scan (ABSCOR; Rigaku, 1995[Rigaku (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.268, Tmax = 0.507

  • 9318 measured reflections

  • 2710 independent reflections

  • 2121 reflections with I > 2σ(I)

  • Rint = 0.120

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.091

  • wR(F2) = 0.225

  • S = 1.03

  • 2710 reflections

  • 180 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 2.07 e Å−3

  • Δρmin = −1.32 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1218 Friedel pairs

  • Absolute structure parameter: 0.34 (2)

Data collection: RAPID-AUTO (Rigaku, 2010[Rigaku (2010). RAPID AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Synthesis and crystallization top

A solution of PdCl2 (0.044 g, 0.25 mmol, 25 mL methanol) was added to a solution of the ligand, S-hexyl (E)-3-(4-methyl­benzyl­idene)di­thio­carbazate (0.147 g, 0.5 mmol, 10 mL methanol). The resulting mixture was stirred at room temperature for 3 h. An orange red precipitate was formed, filtered off, washed with methanol and dried in vacuo over anhydrous CaCl2. Orange red single crystals, suitable for X-ray diffraction, of the compound were obtained by slow evaporation from a mixture of chloro­form and aceto­nitrile (1:1) after 5 days (m.p.: 433 K).

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 1. All H atoms were fixed geometrically (C—H = 0.95 - 0.99 Å) and refined as riding, with Uiso(H) =1.2 Ueq(C). The rather high R factor is affected by the small crystal dimensions and consequently by low diffraction at high θ angles. The collected data were cut at a resolution of 0.85 Å. The structure was refined as an inversion twin with a final BASF parameter = 0.34 (2).

Comment top

In the crystal of the title complex, Fig. 1, the PdII atom resides on a crystallographic twofold rotational axis and the two chelating Schiff base ligands, in their deprotonated imino thiolate form, coordinate the metal center via the azomithine nitrogen atom, N1 and thiolate sulfur atom, S1 in a cis-planar configuration (Fig. 1). However, the donor atoms are not coplanar as observed for the corresponding nickel derivative (Howlader et al., 2015b), but the square planar geometry presents a slight tetrahedral distortion with displacement of atoms N1 and S1 of ± 0.121 (14) and 0.134 (6) Å, respectively, from the coordination mean plane. The Pd1–S1 and Pd1—N1 coordination bond distances are of 2.264 (4) and 2.154 (12) Å, respectively, with an N1—Pd1—S1 chelating angle of 83.2 (3)°. These values are in agreement with those observed in similar Pd-bis(dithiocarbazato) complexes, either with a cis configuration (Ali et al., 2002; Liu, et al., 2011; Duan et al., 1998; Tampouris et al., 2007) or with a trans configuration (Khaledi et al., 2011; Tampouris et al., 2007; Tarafder et al., 2010). It is worth noting that the E conformation about the imine bond N1C8 [= 1.207 (17) Å; torsion angle N2—N1—C8—C5 = 172.1 (14)°] is different to that observed in the nickel derivative mentioned above, viz.1.2 (7)°. This allows an approach between the rings of the methylbenzylidene moieties, with a centroid-to-centroid distance of 4.114 (8) Å, indicating a very weak π-π interaction.

In the crystal, there are no significant intermolecular interactions present. The molecules pack along the c axis direction (Fig. 2).

Related literature top

For the crystal structures of the uncoordinated Schiff base ligand and of its NiII complex, see: Howlader et al. (2015a,b). For similar bis(dithiocarbazato)Pd complexes with a cis configuration of the azomethine N and thiolate S atoms, see: Ali et al. (2002); Liu et al. (2011); Duan et al. (1998); Tampouris et al. (2007). For complexes with a trans configuration, see: Khaledi & Mohd Ali (2011); Tampouris et al. (2007); Tarafder et al. (2010).

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2010); cell refinement: RAPID-AUTO (Rigaku, 2010); data reduction: RAPID-AUTO (Rigaku, 2010); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of the title complex, with atom labelling (symmetry code: (i) -x + 1, y, -z). Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Crystal packing of the title complex viewed along the b axis.
Bis[S-hexyl 3-(4-methylbenzylidene)dithiocarbazato-κ2N3,S]palladium(II) top
Crystal data top
[Pd(C15H21N2S2)2]Z = 2
Mr = 693.32F(000) = 720
Monoclinic, C2Dx = 1.405 Mg m3
Hall symbol: C 2yCu Kα radiation, λ = 1.54187 Å
a = 18.3559 (11) Åθ = 4.8–67.0°
b = 9.6747 (5) ŵ = 7.14 mm1
c = 10.3368 (6) ÅT = 173 K
β = 116.810 (2)°Prism, orange
V = 1638.37 (16) Å30.25 × 0.16 × 0.11 mm
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2710 independent reflections
Radiation source: fine-focus sealed tube2121 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.120
Detector resolution: 10.000 pixels mm-1θmax = 65.1°, θmin = 4.8°
ω scansh = 2121
Absorption correction: multi-scan
(ABSCOR; Rigaku, 1995)
k = 1111
Tmin = 0.268, Tmax = 0.507l = 1212
9318 measured reflections
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)] = 0.091H-atom parameters constrained
wR(F2) = 0.225 w = 1/[σ2(Fo2) + (0.1251P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max < 0.001
2710 reflectionsΔρmax = 2.07 e Å3
180 parametersΔρmin = 1.32 e Å3
1 restraintAbsolute structure: Flack (1983), 1218 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.34 (2)
Crystal data top
[Pd(C15H21N2S2)2]V = 1638.37 (16) Å3
Mr = 693.32Z = 2
Monoclinic, C2Cu Kα radiation
a = 18.3559 (11) ŵ = 7.14 mm1
b = 9.6747 (5) ÅT = 173 K
c = 10.3368 (6) Å0.25 × 0.16 × 0.11 mm
β = 116.810 (2)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2710 independent reflections
Absorption correction: multi-scan
(ABSCOR; Rigaku, 1995)
2121 reflections with I > 2σ(I)
Tmin = 0.268, Tmax = 0.507Rint = 0.120
9318 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.091H-atom parameters constrained
wR(F2) = 0.225Δρmax = 2.07 e Å3
S = 1.03Δρmin = 1.32 e Å3
2710 reflectionsAbsolute structure: Flack (1983), 1218 Friedel pairs
180 parametersAbsolute structure parameter: 0.34 (2)
1 restraint
Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
Pd10.50000.54950.00000.0607 (4)
S10.4807 (3)0.3802 (4)0.1325 (5)0.0725 (11)
S20.4003 (2)0.3956 (4)0.3156 (4)0.0726 (9)
N10.4949 (7)0.6818 (12)0.1634 (13)0.060 (3)
N20.4526 (9)0.6244 (17)0.2347 (16)0.071 (4)
C10.7185 (10)1.1510 (17)0.0408 (17)0.087 (4)
H1A0.76701.10340.04650.130*
H1B0.73531.23270.10360.130*
H1C0.68391.17960.05940.130*
C20.6712 (6)1.0545 (19)0.0900 (11)0.063 (3)
C30.6745 (8)0.9122 (16)0.0758 (15)0.072 (4)
H30.70830.87460.03690.086*
C40.6290 (7)0.8236 (13)0.1178 (14)0.062 (3)
H40.63390.72620.11240.075*
C50.5759 (7)0.8797 (13)0.1679 (13)0.061 (3)
C60.5741 (8)1.0255 (14)0.1841 (14)0.070 (4)
H60.54121.06560.22340.084*
C70.6196 (8)1.1052 (14)0.1431 (14)0.071 (3)
H70.61611.20250.15090.085*
C80.5215 (8)0.7962 (12)0.2045 (14)0.062 (3)
H80.50480.83780.27000.074*
C90.4449 (11)0.4926 (16)0.2274 (18)0.059 (4)
C100.3742 (9)0.529 (2)0.4125 (15)0.080 (5)
H10A0.42420.57220.48850.096*
H10B0.34060.60250.34490.096*
C110.3247 (9)0.4534 (18)0.4821 (16)0.081 (4)
H11A0.28090.39810.40620.097*
H11B0.36170.38860.55710.097*
C120.2885 (8)0.545 (2)0.5472 (14)0.081 (3)
H12A0.25800.61830.47650.097*
H12B0.33270.59040.63240.097*
C130.2311 (9)0.4735 (19)0.5952 (19)0.091 (5)
H13A0.19510.41120.51610.109*
H13B0.26420.41480.68000.109*
C140.1813 (12)0.559 (3)0.632 (2)0.133 (7)
H14A0.15000.62240.55040.160*
H14B0.21650.61680.71700.160*
C150.1205 (10)0.475 (2)0.670 (2)0.110 (6)
H15A0.08880.53910.69820.165*
H15B0.15120.41180.74990.165*
H15C0.08350.42240.58450.165*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.0664 (7)0.0506 (7)0.0761 (7)0.0000.0419 (5)0.000
S10.093 (3)0.051 (2)0.095 (3)0.001 (2)0.062 (2)0.004 (2)
S20.084 (2)0.059 (2)0.092 (2)0.0072 (17)0.0542 (19)0.0009 (17)
N10.055 (6)0.057 (7)0.076 (7)0.011 (5)0.037 (6)0.006 (5)
N20.067 (8)0.072 (9)0.091 (9)0.027 (7)0.050 (7)0.017 (7)
C10.081 (9)0.094 (12)0.096 (11)0.013 (8)0.048 (9)0.004 (8)
C20.063 (6)0.054 (7)0.073 (6)0.014 (9)0.032 (5)0.003 (9)
C30.063 (8)0.084 (11)0.086 (9)0.003 (7)0.048 (7)0.002 (7)
C40.058 (6)0.048 (7)0.082 (8)0.003 (5)0.034 (6)0.003 (6)
C50.060 (7)0.052 (7)0.076 (8)0.000 (6)0.036 (6)0.001 (5)
C60.076 (7)0.053 (10)0.093 (8)0.001 (7)0.048 (7)0.005 (6)
C70.074 (8)0.055 (8)0.080 (9)0.004 (6)0.032 (7)0.011 (6)
C80.079 (8)0.030 (6)0.096 (9)0.006 (6)0.057 (7)0.005 (6)
C90.068 (9)0.052 (9)0.063 (9)0.004 (7)0.034 (7)0.000 (6)
C100.085 (8)0.090 (14)0.081 (8)0.017 (10)0.053 (7)0.007 (9)
C110.084 (9)0.083 (11)0.086 (10)0.009 (8)0.048 (8)0.002 (8)
C120.084 (7)0.088 (9)0.081 (7)0.019 (12)0.047 (6)0.019 (12)
C130.082 (10)0.104 (12)0.109 (12)0.010 (9)0.063 (9)0.002 (9)
C140.162 (16)0.118 (16)0.150 (15)0.043 (19)0.098 (14)0.003 (17)
C150.106 (12)0.112 (14)0.160 (17)0.024 (10)0.102 (13)0.010 (11)
Geometric parameters (Å, º) top
Pd1—N12.154 (12)C6—C71.337 (16)
Pd1—N1i2.154 (12)C6—H60.9500
Pd1—S12.264 (4)C7—H70.9500
Pd1—S1i2.264 (4)C8—H80.9500
S1—C91.777 (17)C10—C111.573 (19)
S2—C91.747 (16)C10—H10A0.9900
S2—C101.829 (18)C10—H10B0.9900
N1—C81.208 (16)C11—C121.44 (2)
N1—N21.404 (17)C11—H11A0.9900
N2—C91.282 (15)C11—H11B0.9900
C1—C21.511 (19)C12—C131.52 (2)
C1—H1A0.9800C12—H12A0.9900
C1—H1B0.9800C12—H12B0.9900
C1—H1C0.9800C13—C141.41 (2)
C2—C71.381 (16)C13—H13A0.9900
C2—C31.39 (2)C13—H13B0.9900
C3—C41.397 (18)C14—C151.56 (3)
C3—H30.9500C14—H14A0.9900
C4—C51.403 (16)C14—H14B0.9900
C4—H40.9500C15—H15A0.9800
C5—C61.423 (17)C15—H15B0.9800
C5—C81.460 (16)C15—H15C0.9800
N1—Pd1—N1i107.1 (6)N2—C9—S2124.7 (15)
N1—Pd1—S183.2 (3)N2—C9—S1125.6 (15)
N1i—Pd1—S1168.1 (3)S2—C9—S1109.6 (9)
N1—Pd1—S1i168.1 (3)C11—C10—S2105.5 (13)
N1i—Pd1—S1i83.2 (3)C11—C10—H10A110.6
S1—Pd1—S1i87.3 (2)S2—C10—H10A110.6
C9—S1—Pd195.1 (5)C11—C10—H10B110.6
C9—S2—C10101.8 (7)S2—C10—H10B110.6
C8—N1—N2114.2 (12)H10A—C10—H10B108.8
C8—N1—Pd1131.8 (10)C12—C11—C10114.0 (15)
N2—N1—Pd1114.0 (9)C12—C11—H11A108.7
C9—N2—N1115.8 (16)C10—C11—H11A108.7
C2—C1—H1A109.5C12—C11—H11B108.7
C2—C1—H1B109.5C10—C11—H11B108.7
H1A—C1—H1B109.5H11A—C11—H11B107.6
C2—C1—H1C109.5C11—C12—C13113.9 (18)
H1A—C1—H1C109.5C11—C12—H12A108.8
H1B—C1—H1C109.5C13—C12—H12A108.8
C7—C2—C3117.7 (14)C11—C12—H12B108.8
C7—C2—C1121.0 (16)C13—C12—H12B108.8
C3—C2—C1121.2 (12)H12A—C12—H12B107.7
C2—C3—C4120.9 (12)C14—C13—C12116.7 (19)
C2—C3—H3119.5C14—C13—H13A108.1
C4—C3—H3119.5C12—C13—H13A108.1
C3—C4—C5119.4 (12)C14—C13—H13B108.1
C3—C4—H4120.3C12—C13—H13B108.1
C5—C4—H4120.3H13A—C13—H13B107.3
C4—C5—C6118.9 (11)C13—C14—C15112 (2)
C4—C5—C8123.5 (11)C13—C14—H14A109.1
C6—C5—C8117.6 (11)C15—C14—H14A109.1
C7—C6—C5118.9 (12)C13—C14—H14B109.1
C7—C6—H6120.5C15—C14—H14B109.1
C5—C6—H6120.5H14A—C14—H14B107.8
C6—C7—C2124.0 (14)C14—C15—H15A109.5
C6—C7—H7118.0C14—C15—H15B109.5
C2—C7—H7118.0H15A—C15—H15B109.5
N1—C8—C5129.2 (12)C14—C15—H15C109.5
N1—C8—H8115.4H15A—C15—H15C109.5
C5—C8—H8115.4H15B—C15—H15C109.5
Symmetry code: (i) x+1, y, z.

Experimental details

Crystal data
Chemical formula[Pd(C15H21N2S2)2]
Mr693.32
Crystal system, space groupMonoclinic, C2
Temperature (K)173
a, b, c (Å)18.3559 (11), 9.6747 (5), 10.3368 (6)
β (°) 116.810 (2)
V3)1638.37 (16)
Z2
Radiation typeCu Kα
µ (mm1)7.14
Crystal size (mm)0.25 × 0.16 × 0.11
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Rigaku, 1995)
Tmin, Tmax0.268, 0.507
No. of measured, independent and
observed [I > 2σ(I)] reflections
9318, 2710, 2121
Rint0.120
(sin θ/λ)max1)0.588
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.091, 0.225, 1.03
No. of reflections2710
No. of parameters180
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)2.07, 1.32
Absolute structureFlack (1983), 1218 Friedel pairs
Absolute structure parameter0.34 (2)

Computer programs: RAPID-AUTO (Rigaku, 2010), SIR92 (Altomare et al., 1994), SHELXL97 (Sheldrick, 2015), ORTEP-3 for Windows (Farrugia, 2012), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

 

Acknowledgements

MBHH and MSB are grateful to the Department of Chemistry, Rajshahi University, for the provision of laboratory facilities. MCS acknowledges the Department of Applied Chemistry, Toyama University, for providing funds for single-crystal X-ray analyses.

References

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Volume 71| Part 3| March 2015| Pages m63-m64
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