Crystal structure of di­chlorido­{4-[(E)-(meth­oxy­imino-κN)meth­yl]-1,3-thia­zol-2-amine-κN3}palladium(II)

Dyakonenko, V.V.; Zholob, O.O.; Orysyk, S.I.; Pekhnyo, V.I.

doi:10.1107/S2056989014026619

metal-organic compounds

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Crystal structure of dichlorido{4-[(E)-(methoxyimino-κN)methyl]-1,3-thiazol-2-amine-κN³}palladium(II)

Viktorita V. Dyakonenko,^a ^* Olga O. Zholob,^b Svitlana I. Orysyk ^b and Vasily I. Pekhnyo ^b

^aState Scientific "Institution Institute for Single Crystals", National Academy of Science of Ukraine, 60 Lenina ave., Kharkiv 61001, Ukraine, and ^bV.I. Vernadskii Institute of General and Inorganic Chemistry, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine
^*Correspondence e-mail: vika@xray.isc.kharkov.com

Edited by M. Weil, Vienna University of Technology, Austria (Received 25 November 2014; accepted 3 December 2014; online 1 January 2015)

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].

Keywords: crystal structure; palladium; multi-functional ligand; 4-[(methoxyimino)methyl]-1,3-thiazol-2-amine (MIMTA).

CCDC reference: 1037339

1. 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 ).

2. Experimental

2.1. Crystal data

[PdCl₂(C₅H₇N₃OS)]
M_r = 334.50
Orthorhombic, P 2₁ 2₁ 2₁
a = 4.347 (3) Å
b = 13.583 (2) Å
c = 16.411 (3) Å
V = 969.0 (7) Å³
Z = 4
Mo Kα radiation
μ = 2.64 mm⁻¹
T = 294 K
0.4 × 0.3 × 0.2 mm

2.2. 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

2.3. Refinement

R[F² > 2σ(F²)] = 0.022
wR(F²) = 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)

Table 1
Hydrogen-bond geometry (Å, °)

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) $[-x+{\script{1\over 2}}, -y+2, z-{\script{1\over 2}}]$ .

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.

Supporting information

CCDC reference: 1037339

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989014026619/wm5096sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989014026619/wm5096Isup2.hkl

checkCIF report

Related literature top

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 top

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%).

Structure description top

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).

Computing details top

Data collection: CrysAlis CCD (Agilent, 2012); cell refinement: CrysAlis CCD (Agilent, 2012); 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 (Dolomanov et al., 2009).

Figures top

	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.

Dichlorido{4-[(E)-(methoxyimino-κN)methyl]-1,3-thiazol-2-amine-κN³}palladium(II) top

Crystal data top

[PdCl₂(C₅H₇N₃OS)]	D_x = 2.293 Mg m⁻³
M_r = 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 top

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

Refinement top

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(F_o²) + (0.0225P)² + 0.1807P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max = 0.002
2106 reflections	Δρ_max = 0.37 e Å⁻³
120 parameters	Δρ_min = −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)

Crystal data top

[PdCl₂(C₅H₇N₃OS)]	V = 969.0 (7) Å³
M_r = 334.50	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 4.347 (3) Å	µ = 2.64 mm⁻¹
b = 13.583 (2) Å	T = 294 K
c = 16.411 (3) Å	0.4 × 0.3 × 0.2 mm

Data collection top

Agilent Xcalibur Sapphire3 diffractometer	2106 independent reflections
Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012)	2028 reflections with I > 2σ(I)
T_min = 0.742, T_max = 1.000	R_int = 0.019
4284 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.022	H-atom parameters constrained
wR(F²) = 0.047	Δρ_max = 0.37 e Å⁻³
S = 1.04	Δρ_min = −0.36 e Å⁻³
2106 reflections	Absolute structure: Flack (1983), 969 Friedel pairs
120 parameters	Absolute structure parameter: 0.39 (4)
0 restraints

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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) top

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) top

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.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···Cl2	0.86	2.34	3.124 (3)	151.4
N3—H3B···Cl1ⁱ	0.86	2.48	3.280 (3)	155.9
N3—H3B···O1ⁱ	0.86	2.45	3.015 (3)	124.0

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

References

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