Crystal structure of di­chlorido­{4-[(E)-(meth­oxy­imino-κN)meth­yl]-1,3-thia­zol-2-amine-κN ³}palladium(II)

Abstract

In the title compound, [PdCl₂(C₅H₇N₃OS)], the Pd^II atom adopts a distorted square-planar coordination sphere defined by two N atoms of the bidentate ligand and two Cl atoms. The mean deviation from the coordination plane is 0.029 Å. The methyl group is not coplanar with the plane of the metallacycle [torsion angle C—O—N—C = 20.2 (4)°]. Steric repulsion between the methyl group and atoms of the metallacycle is manifested by shortened intra­molecular H⋯C contacts of 2.27, 2.38 and 2.64 Å, as compared with the sum of the van der Waals radii of 2.87 Å. The amino group participates via one H atom in the formation of an intra­molecular N—H⋯Cl hydrogen bond. In the crystal, the other H atom of the amino group links mol­ecules via bifurcated N—H⋯(Cl,O) hydrogen bonds into chains parallel to [001].

Related literature  

4-[(Meth­oxy­imino)­meth­yl]-1,3-thia­zol-2-amine (MIMTA) belongs to the class of polyfunctional oximes that are potential biologically active complexing agents (Dodoff et al., 2009 ▸; Elo, 2004 ▸; Scaffidi-Domianello et al., 2011 ▸; Donde & Patil, 2011 ▸; Kuwar et al., 2006 ▸). Palladium complexes based on MIMTA are thus inter­esting in biomedicine (Orysyk et al., 2013 ▸). For the structures of related complexes, see: Orysyk et al. (2015 ▸); Mokhir et al. (2002 ▸). For van der Waals radii, see: Zefirov (1997 ▸).

Experimental  

Crystal data  

• [PdCl₂(C₅H₇N₃OS)]

• M _r = 334.50

• Orthorhombic,

• a = 4.347 (3) Å

• b = 13.583 (2) Å

• c = 16.411 (3) Å

• V = 969.0 (7) ų

• Z = 4

• Mo Kα radiation

• μ = 2.64 mm⁻¹

• T = 294 K

• 0.4 × 0.3 × 0.2 mm

Data collection  

• Agilent Xcalibur Sapphire3 diffractometer

• Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012 ▸) T _min = 0.742, T _max = 1.000

• 4284 measured reflections

• 2106 independent reflections

• 2028 reflections with I > 2σ(I)

• R _int = 0.019

Refinement  

• R[F ² > 2σ(F ²)] = 0.022

• wR(F ²) = 0.047

• S = 1.04

• 2106 reflections

• 120 parameters

• H-atom parameters constrained

• Δρ_max = 0.37 e Å⁻³

• Δρ_min = −0.36 e Å⁻³

• Absolute structure: Flack (1983), 969 Friedel pairs

• Absolute structure parameter: 0.39 (4)

Data collection: CrysAlis CCD (Agilent, 2012 ▸); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Agilent, 2012 ▸); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▸); molecular graphics: OLEX2 (Dolomanov et al., 2009 ▸); software used to prepare material for publication: OLEX2.

Supplementary Material

CCDC reference: 1037339

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
N3H3ACl2	0.86	2.34	3.124(3)	151
N3H3BCl1i	0.86	2.48	3.280(3)	156
N3H3BO1i	0.86	2.45	3.015(3)	124

Symmetry code: (i) .

supplementary crystallographic information

S1. Experimental

PdCl₂ (0.036 g, 0.2 mmol) was dissolved in 6N HCl (3 ml) at 313–323 K, and ethanol (7 ml) was added. To the resulting light-brown solution was added a hot solution of 4-[(methoxyimino)methyl]-1,3-thiazol-2-amine (0.031 g, 0.2 mmol), dissolved in ethanol (10 ml). The reaction mixture was stirred for one hour under reflux and cooled down to room temperature whereupon orange needle-like single crystals were filtered off, washed with ethanol and diethyl ether and dried in a vacuum desiccator over CaCl₂. Yield: 0.045 g (65%).

S2. Refinement

All hydrogen atoms were located from difference Fourier maps and constrained to ride on their parent atoms, with U_iso = 1.2U_eq (except U_iso = 1.5U_eq for the methyl group). The structure was refined from a crystal twinned by inversion (Flack parameter value 0.39 (4)).

Figures

Fig. 1.

The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.

Fig. 2.

Crystal packing of the title compound with hydrogen bonds shown as dashed lines.

Crystal data

[PdCl2(C5H7N3OS)]	Dx = 2.293 Mg m−3
Mr = 334.50	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 2494 reflections
a = 4.347 (3) Å	θ = 3.8–31.7°
b = 13.583 (2) Å	µ = 2.64 mm−1
c = 16.411 (3) Å	T = 294 K
V = 969.0 (7) Å3	, orange
Z = 4	0.4 × 0.3 × 0.2 mm
F(000) = 648

Data collection

Agilent Xcalibur Sapphire3 diffractometer	2106 independent reflections
Radiation source: Enhance (Mo) X-ray Source	2028 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.019
Detector resolution: 16.1827 pixels mm-1	θmax = 27.5°, θmin = 3.0°
ω scans	h = −5→5
Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012)	k = −17→16
Tmin = 0.742, Tmax = 1.000	l = −21→21
4284 measured reflections

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.022	H-atom parameters constrained
wR(F2) = 0.047	w = 1/[σ2(Fo2) + (0.0225P)2 + 0.1807P] where P = (Fo2 + 2Fc2)/3
S = 1.04	(Δ/σ)max = 0.002
2106 reflections	Δρmax = 0.37 e Å−3
120 parameters	Δρmin = −0.36 e Å−3
0 restraints	Absolute structure: Flack (1983), 969 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.39 (4)

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 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Pd1	0.15497 (6)	0.986930 (16)	0.742144 (12)	0.02751 (7)
Cl1	−0.1238 (2)	1.04846 (7)	0.84901 (5)	0.0396 (2)
Cl2	−0.0192 (2)	1.11559 (6)	0.66418 (5)	0.0411 (2)
S1	0.6968 (2)	0.84020 (7)	0.53414 (5)	0.0394 (2)
O1	0.2794 (6)	0.86291 (19)	0.88793 (12)	0.0379 (6)
N1	0.3271 (7)	0.87185 (19)	0.80514 (14)	0.0306 (6)
N2	0.3996 (6)	0.91712 (19)	0.65287 (15)	0.0291 (6)
N3	0.3636 (8)	1.0058 (2)	0.53113 (15)	0.0489 (8)
H3A	0.2466	1.0498	0.5526	0.059*
H3B	0.4153	1.0104	0.4807	0.059*
C1	0.5024 (9)	0.8046 (3)	0.92925 (18)	0.0389 (8)
H1A	0.4798	0.8132	0.9870	0.058*
H1B	0.7050	0.8249	0.9130	0.058*
H1C	0.4729	0.7366	0.9156	0.058*
C2	0.4954 (8)	0.8100 (2)	0.76650 (18)	0.0328 (7)
H2	0.5819	0.7552	0.7916	0.039*
C3	0.5408 (8)	0.8314 (2)	0.68133 (18)	0.0315 (7)
C4	0.7074 (9)	0.7815 (3)	0.62715 (19)	0.0375 (8)
H4	0.8138	0.7236	0.6379	0.045*
C5	0.4632 (8)	0.9318 (2)	0.57529 (18)	0.0317 (7)

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Pd1	0.03240 (12)	0.02459 (11)	0.02555 (10)	−0.00010 (10)	−0.00195 (9)	0.00015 (8)
Cl1	0.0450 (5)	0.0412 (5)	0.0327 (4)	0.0059 (4)	0.0021 (4)	−0.0055 (3)
Cl2	0.0511 (5)	0.0326 (4)	0.0394 (4)	0.0092 (4)	−0.0021 (4)	0.0062 (4)
S1	0.0506 (6)	0.0390 (5)	0.0286 (4)	0.0037 (5)	0.0042 (4)	−0.0028 (3)
O1	0.0456 (14)	0.0444 (14)	0.0237 (9)	0.0096 (12)	0.0026 (10)	0.0059 (9)
N1	0.0373 (15)	0.0304 (14)	0.0240 (11)	−0.0015 (15)	−0.0013 (12)	0.0048 (10)
N2	0.0361 (16)	0.0239 (13)	0.0273 (12)	−0.0007 (12)	−0.0025 (11)	0.0012 (10)
N3	0.077 (2)	0.0424 (17)	0.0276 (12)	0.014 (2)	0.0087 (14)	0.0054 (12)
C1	0.045 (2)	0.045 (2)	0.0260 (14)	0.006 (2)	−0.0007 (16)	0.0053 (14)
C2	0.0409 (18)	0.0273 (15)	0.0303 (15)	0.0048 (15)	−0.0018 (15)	0.0024 (13)
C3	0.0388 (18)	0.0277 (17)	0.0282 (14)	−0.0013 (15)	−0.0032 (14)	−0.0001 (13)
C4	0.045 (2)	0.0342 (18)	0.0333 (15)	0.0069 (17)	−0.0021 (16)	−0.0014 (13)
C5	0.0385 (18)	0.0316 (18)	0.0251 (14)	−0.0029 (16)	0.0012 (14)	0.0012 (13)

Geometric parameters (Å, º)

Pd1—Cl1	2.2897 (10)	N3—H3A	0.8600
Pd1—Cl2	2.2943 (9)	N3—H3B	0.8600
Pd1—N1	2.018 (3)	N3—C5	1.313 (4)
Pd1—N2	2.044 (3)	C1—H1A	0.9600
S1—C4	1.723 (3)	C1—H1B	0.9600
S1—C5	1.742 (3)	C1—H1C	0.9600
O1—N1	1.380 (3)	C2—H2	0.9300
O1—C1	1.423 (4)	C2—C3	1.441 (4)
N1—C2	1.282 (4)	C3—C4	1.332 (5)
N2—C3	1.397 (4)	C4—H4	0.9300
N2—C5	1.318 (4)
Cl1—Pd1—Cl2	88.54 (4)	O1—C1—H1B	109.5
N1—Pd1—Cl1	94.96 (8)	O1—C1—H1C	109.5
N1—Pd1—Cl2	176.43 (8)	H1A—C1—H1B	109.5
N1—Pd1—N2	79.34 (10)	H1A—C1—H1C	109.5
N2—Pd1—Cl1	173.65 (8)	H1B—C1—H1C	109.5
N2—Pd1—Cl2	97.20 (8)	N1—C2—H2	122.4
C4—S1—C5	90.16 (16)	N1—C2—C3	115.2 (3)
N1—O1—C1	114.6 (2)	C3—C2—H2	122.4
O1—N1—Pd1	121.1 (2)	N2—C3—C2	115.6 (3)
C2—N1—Pd1	117.8 (2)	C4—C3—N2	116.1 (3)
C2—N1—O1	121.0 (3)	C4—C3—C2	128.3 (3)
C3—N2—Pd1	112.1 (2)	S1—C4—H4	125.0
C5—N2—Pd1	137.0 (2)	C3—C4—S1	110.0 (3)
C5—N2—C3	110.9 (3)	C3—C4—H4	125.0
H3A—N3—H3B	120.0	N2—C5—S1	112.9 (2)
C5—N3—H3A	120.0	N3—C5—S1	121.7 (2)
C5—N3—H3B	120.0	N3—C5—N2	125.4 (3)
O1—C1—H1A	109.5
Pd1—N1—C2—C3	0.1 (4)	N1—C2—C3—N2	0.9 (5)
Pd1—N2—C3—C2	−1.4 (4)	N1—C2—C3—C4	178.7 (4)
Pd1—N2—C3—C4	−179.5 (3)	N2—Pd1—N1—O1	175.8 (3)
Pd1—N2—C5—S1	179.58 (19)	N2—Pd1—N1—C2	−0.7 (3)
Pd1—N2—C5—N3	−1.1 (6)	N2—C3—C4—S1	−0.2 (4)
Cl1—Pd1—N1—O1	−7.0 (2)	C1—O1—N1—Pd1	−156.2 (2)
Cl1—Pd1—N1—C2	176.4 (3)	C1—O1—N1—C2	20.2 (4)
Cl1—Pd1—N2—C3	−25.3 (9)	C2—C3—C4—S1	−178.0 (3)
Cl1—Pd1—N2—C5	155.6 (5)	C3—N2—C5—S1	0.5 (4)
Cl2—Pd1—N1—O1	161.6 (12)	C3—N2—C5—N3	179.8 (3)
Cl2—Pd1—N1—C2	−14.9 (15)	C4—S1—C5—N2	−0.5 (3)
Cl2—Pd1—N2—C3	−179.7 (2)	C4—S1—C5—N3	−179.8 (3)
Cl2—Pd1—N2—C5	1.2 (3)	C5—S1—C4—C3	0.4 (3)
O1—N1—C2—C3	−176.4 (3)	C5—N2—C3—C2	177.9 (3)
N1—Pd1—N2—C3	1.1 (2)	C5—N2—C3—C4	−0.2 (4)
N1—Pd1—N2—C5	−178.0 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···Cl2	0.86	2.34	3.124 (3)	151
N3—H3B···Cl1i	0.86	2.48	3.280 (3)	156
N3—H3B···O1i	0.86	2.45	3.015 (3)	124

Symmetry code: (i) −x+1/2, −y+2, z−1/2.