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

Begum, M.S.; Howlader, M.B.H.; Sheikh, M.C.; Miyatake, R.; Zangrando, E.

doi:10.1107/S2056989015002236

metal-organic compounds

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ISSN: 2056-9890

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

doi:10.1107/S2056989015002236

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

M. Sabina Begum,^a ^* M. Belayet Hossain Howlader,^a M. Chanmiya Sheikh,^b Ryuta Miyatake ^c and Ennio Zangrando ^d

^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).

Keywords: crystal structure; palladium(II) complex; cis-ligand configuration.

CCDC reference: 1046981

1. Related literature

For the crystal structures of the free Schiff base ligand and of its Ni^II 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 ).

2. Experimental

2.1. Crystal data

[Pd(C₁₅H₂₁N₂S₂)₂]
M_r = 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 ) T_min = 0.268, T_max = 0.507
9318 measured reflections
2710 independent reflections
2121 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 2.07 e Å⁻³
Δρ_min = −1.32 e Å⁻³
Absolute structure: Flack (1983 ), 1218 Friedel pairs
Absolute structure parameter: 0.34 (2)

Data collection: RAPID-AUTO (Rigaku, 2010 ); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; 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 ).

Supporting information

CCDC reference: 1046981

Crystal structure: contains datablocks Global, I. DOI: 10.1107/S2056989015002236/su5071sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015002236/su5071Isup2.hkl

checkCIF report

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 U_iso(H) =1.2 U_eq(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 Pd^II 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 N1═C8 [= 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 Ni^II 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

	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.
	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
M_r = 693.32	F(000) = 720
Monoclinic, C2	D_x = 1.405 Mg m⁻³
Hall symbol: C 2y	Cu Kα radiation, λ = 1.54187 Å
a = 18.3559 (11) Å	θ = 4.8–67.0°
b = 9.6747 (5) Å	µ = 7.14 mm⁻¹
c = 10.3368 (6) Å	T = 173 K
β = 116.810 (2)°	Prism, orange
V = 1638.37 (16) Å³	0.25 × 0.16 × 0.11 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	2710 independent reflections
Radiation source: fine-focus sealed tube	2121 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.120
Detector resolution: 10.000 pixels mm^-1	θ_max = 65.1°, θ_min = 4.8°
ω scans	h = −21→21
Absorption correction: multi-scan (ABSCOR; Rigaku, 1995)	k = −11→11
T_min = 0.268, T_max = 0.507	l = −12→12
9318 measured reflections

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)] = 0.091	H-atom parameters constrained
wR(F²) = 0.225	w = 1/[σ²(F_o²) + (0.1251P)²] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max < 0.001
2710 reflections	Δρ_max = 2.07 e Å⁻³
180 parameters	Δρ_min = −1.32 e Å⁻³
1 restraint	Absolute structure: Flack (1983), 1218 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.34 (2)

Crystal data top

[Pd(C₁₅H₂₁N₂S₂)₂]	V = 1638.37 (16) Å³
M_r = 693.32	Z = 2
Monoclinic, C2	Cu Kα radiation
a = 18.3559 (11) Å	µ = 7.14 mm⁻¹
b = 9.6747 (5) Å	T = 173 K
c = 10.3368 (6) Å	0.25 × 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)
T_min = 0.268, T_max = 0.507	R_int = 0.120
9318 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.091	H-atom parameters constrained
wR(F²) = 0.225	Δρ_max = 2.07 e Å⁻³
S = 1.03	Δρ_min = −1.32 e Å⁻³
2710 reflections	Absolute structure: Flack (1983), 1218 Friedel pairs
180 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
Pd1	0.5000	0.5495	0.0000	0.0607 (4)
S1	0.4807 (3)	0.3802 (4)	0.1325 (5)	0.0725 (11)
S2	0.4003 (2)	0.3956 (4)	0.3156 (4)	0.0726 (9)
N1	0.4949 (7)	0.6818 (12)	0.1634 (13)	0.060 (3)
N2	0.4526 (9)	0.6244 (17)	0.2347 (16)	0.071 (4)
C1	0.7185 (10)	1.1510 (17)	0.0408 (17)	0.087 (4)
H1A	0.7670	1.1034	0.0465	0.130*
H1B	0.7353	1.2327	0.1036	0.130*
H1C	0.6839	1.1796	−0.0594	0.130*
C2	0.6712 (6)	1.0545 (19)	0.0900 (11)	0.063 (3)
C3	0.6745 (8)	0.9122 (16)	0.0758 (15)	0.072 (4)
H3	0.7083	0.8746	0.0369	0.086*
C4	0.6290 (7)	0.8236 (13)	0.1178 (14)	0.062 (3)
H4	0.6339	0.7262	0.1124	0.075*
C5	0.5759 (7)	0.8797 (13)	0.1679 (13)	0.061 (3)
C6	0.5741 (8)	1.0255 (14)	0.1841 (14)	0.070 (4)
H6	0.5412	1.0656	0.2234	0.084*
C7	0.6196 (8)	1.1052 (14)	0.1431 (14)	0.071 (3)
H7	0.6161	1.2025	0.1509	0.085*
C8	0.5215 (8)	0.7962 (12)	0.2045 (14)	0.062 (3)
H8	0.5048	0.8378	0.2700	0.074*
C9	0.4449 (11)	0.4926 (16)	0.2274 (18)	0.059 (4)
C10	0.3742 (9)	0.529 (2)	0.4125 (15)	0.080 (5)
H10A	0.4242	0.5722	0.4885	0.096*
H10B	0.3406	0.6025	0.3449	0.096*
C11	0.3247 (9)	0.4534 (18)	0.4821 (16)	0.081 (4)
H11A	0.2809	0.3981	0.4062	0.097*
H11B	0.3617	0.3886	0.5571	0.097*
C12	0.2885 (8)	0.545 (2)	0.5472 (14)	0.081 (3)
H12A	0.2580	0.6183	0.4765	0.097*
H12B	0.3327	0.5904	0.6324	0.097*
C13	0.2311 (9)	0.4735 (19)	0.5952 (19)	0.091 (5)
H13A	0.1951	0.4112	0.5161	0.109*
H13B	0.2642	0.4148	0.6800	0.109*
C14	0.1813 (12)	0.559 (3)	0.632 (2)	0.133 (7)
H14A	0.1500	0.6224	0.5504	0.160*
H14B	0.2165	0.6168	0.7170	0.160*
C15	0.1205 (10)	0.475 (2)	0.670 (2)	0.110 (6)
H15A	0.0888	0.5391	0.6982	0.165*
H15B	0.1512	0.4118	0.7499	0.165*
H15C	0.0835	0.4224	0.5845	0.165*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Pd1	0.0664 (7)	0.0506 (7)	0.0761 (7)	0.000	0.0419 (5)	0.000
S1	0.093 (3)	0.051 (2)	0.095 (3)	0.001 (2)	0.062 (2)	0.004 (2)
S2	0.084 (2)	0.059 (2)	0.092 (2)	−0.0072 (17)	0.0542 (19)	0.0009 (17)
N1	0.055 (6)	0.057 (7)	0.076 (7)	−0.011 (5)	0.037 (6)	0.006 (5)
N2	0.067 (8)	0.072 (9)	0.091 (9)	−0.027 (7)	0.050 (7)	−0.017 (7)
C1	0.081 (9)	0.094 (12)	0.096 (11)	−0.013 (8)	0.048 (9)	0.004 (8)
C2	0.063 (6)	0.054 (7)	0.073 (6)	0.014 (9)	0.032 (5)	−0.003 (9)
C3	0.063 (8)	0.084 (11)	0.086 (9)	0.003 (7)	0.048 (7)	−0.002 (7)
C4	0.058 (6)	0.048 (7)	0.082 (8)	0.003 (5)	0.034 (6)	0.003 (6)
C5	0.060 (7)	0.052 (7)	0.076 (8)	0.000 (6)	0.036 (6)	0.001 (5)
C6	0.076 (7)	0.053 (10)	0.093 (8)	0.001 (7)	0.048 (7)	−0.005 (6)
C7	0.074 (8)	0.055 (8)	0.080 (9)	−0.004 (6)	0.032 (7)	0.011 (6)
C8	0.079 (8)	0.030 (6)	0.096 (9)	0.006 (6)	0.057 (7)	0.005 (6)
C9	0.068 (9)	0.052 (9)	0.063 (9)	−0.004 (7)	0.034 (7)	0.000 (6)
C10	0.085 (8)	0.090 (14)	0.081 (8)	−0.017 (10)	0.053 (7)	0.007 (9)
C11	0.084 (9)	0.083 (11)	0.086 (10)	−0.009 (8)	0.048 (8)	0.002 (8)
C12	0.084 (7)	0.088 (9)	0.081 (7)	−0.019 (12)	0.047 (6)	−0.019 (12)
C13	0.082 (10)	0.104 (12)	0.109 (12)	0.010 (9)	0.063 (9)	0.002 (9)
C14	0.162 (16)	0.118 (16)	0.150 (15)	0.043 (19)	0.098 (14)	−0.003 (17)
C15	0.106 (12)	0.112 (14)	0.160 (17)	−0.024 (10)	0.102 (13)	−0.010 (11)

Geometric parameters (Å, º) top

Pd1—N1	2.154 (12)	C6—C7	1.337 (16)
Pd1—N1ⁱ	2.154 (12)	C6—H6	0.9500
Pd1—S1	2.264 (4)	C7—H7	0.9500
Pd1—S1ⁱ	2.264 (4)	C8—H8	0.9500
S1—C9	1.777 (17)	C10—C11	1.573 (19)
S2—C9	1.747 (16)	C10—H10A	0.9900
S2—C10	1.829 (18)	C10—H10B	0.9900
N1—C8	1.208 (16)	C11—C12	1.44 (2)
N1—N2	1.404 (17)	C11—H11A	0.9900
N2—C9	1.282 (15)	C11—H11B	0.9900
C1—C2	1.511 (19)	C12—C13	1.52 (2)
C1—H1A	0.9800	C12—H12A	0.9900
C1—H1B	0.9800	C12—H12B	0.9900
C1—H1C	0.9800	C13—C14	1.41 (2)
C2—C7	1.381 (16)	C13—H13A	0.9900
C2—C3	1.39 (2)	C13—H13B	0.9900
C3—C4	1.397 (18)	C14—C15	1.56 (3)
C3—H3	0.9500	C14—H14A	0.9900
C4—C5	1.403 (16)	C14—H14B	0.9900
C4—H4	0.9500	C15—H15A	0.9800
C5—C6	1.423 (17)	C15—H15B	0.9800
C5—C8	1.460 (16)	C15—H15C	0.9800

N1—Pd1—N1ⁱ	107.1 (6)	N2—C9—S2	124.7 (15)
N1—Pd1—S1	83.2 (3)	N2—C9—S1	125.6 (15)
N1ⁱ—Pd1—S1	168.1 (3)	S2—C9—S1	109.6 (9)
N1—Pd1—S1ⁱ	168.1 (3)	C11—C10—S2	105.5 (13)
N1ⁱ—Pd1—S1ⁱ	83.2 (3)	C11—C10—H10A	110.6
S1—Pd1—S1ⁱ	87.3 (2)	S2—C10—H10A	110.6
C9—S1—Pd1	95.1 (5)	C11—C10—H10B	110.6
C9—S2—C10	101.8 (7)	S2—C10—H10B	110.6
C8—N1—N2	114.2 (12)	H10A—C10—H10B	108.8
C8—N1—Pd1	131.8 (10)	C12—C11—C10	114.0 (15)
N2—N1—Pd1	114.0 (9)	C12—C11—H11A	108.7
C9—N2—N1	115.8 (16)	C10—C11—H11A	108.7
C2—C1—H1A	109.5	C12—C11—H11B	108.7
C2—C1—H1B	109.5	C10—C11—H11B	108.7
H1A—C1—H1B	109.5	H11A—C11—H11B	107.6
C2—C1—H1C	109.5	C11—C12—C13	113.9 (18)
H1A—C1—H1C	109.5	C11—C12—H12A	108.8
H1B—C1—H1C	109.5	C13—C12—H12A	108.8
C7—C2—C3	117.7 (14)	C11—C12—H12B	108.8
C7—C2—C1	121.0 (16)	C13—C12—H12B	108.8
C3—C2—C1	121.2 (12)	H12A—C12—H12B	107.7
C2—C3—C4	120.9 (12)	C14—C13—C12	116.7 (19)
C2—C3—H3	119.5	C14—C13—H13A	108.1
C4—C3—H3	119.5	C12—C13—H13A	108.1
C3—C4—C5	119.4 (12)	C14—C13—H13B	108.1
C3—C4—H4	120.3	C12—C13—H13B	108.1
C5—C4—H4	120.3	H13A—C13—H13B	107.3
C4—C5—C6	118.9 (11)	C13—C14—C15	112 (2)
C4—C5—C8	123.5 (11)	C13—C14—H14A	109.1
C6—C5—C8	117.6 (11)	C15—C14—H14A	109.1
C7—C6—C5	118.9 (12)	C13—C14—H14B	109.1
C7—C6—H6	120.5	C15—C14—H14B	109.1
C5—C6—H6	120.5	H14A—C14—H14B	107.8
C6—C7—C2	124.0 (14)	C14—C15—H15A	109.5
C6—C7—H7	118.0	C14—C15—H15B	109.5
C2—C7—H7	118.0	H15A—C15—H15B	109.5
N1—C8—C5	129.2 (12)	C14—C15—H15C	109.5
N1—C8—H8	115.4	H15A—C15—H15C	109.5
C5—C8—H8	115.4	H15B—C15—H15C	109.5

Symmetry code: (i) −x+1, y, −z.

Experimental details

Crystal data
Chemical formula	[Pd(C₁₅H₂₁N₂S₂)₂]
M_r	693.32
Crystal system, space group	Monoclinic, C2
Temperature (K)	173
a, b, c (Å)	18.3559 (11), 9.6747 (5), 10.3368 (6)
β (°)	116.810 (2)
V (Å³)	1638.37 (16)
Z	2
Radiation type	Cu Kα
µ (mm⁻¹)	7.14
Crystal size (mm)	0.25 × 0.16 × 0.11

Data collection
Diffractometer	Rigaku R-AXIS RAPID diffractometer
Absorption correction	Multi-scan (ABSCOR; Rigaku, 1995)
T_min, T_max	0.268, 0.507
No. of measured, independent and observed [I > 2σ(I)] reflections	9318, 2710, 2121
R_int	0.120
(sin θ/λ)_max (Å⁻¹)	0.588

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.091, 0.225, 1.03
No. of reflections	2710
No. of parameters	180
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	2.07, −1.32
Absolute structure	Flack (1983), 1218 Friedel pairs
Absolute structure parameter	0.34 (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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