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

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

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 PdII 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].

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[Dodoff, N. I., Kubiak, M., Kuduk-Jaworska, J., Mastalarz, A., Kochel, A., Vassilieva, V., Vassilev, N., Trendafilova, N., Georgieva, I., Lalia-Kantouri, M. & Apostolova, M. (2009). Chemija, 4, 208-217.]; Elo, 2004[Elo, H. (2004). Chemotherapy, 50, 229-233.]; Scaffidi-Domianello et al., 2011[Scaffidi-Domianello, Yu. Yu., Legin, A. A., Jakupec, M. A., Arion, V. B., Kukushkin, V. Yu., Galanski, M. & Keppler, B. K. (2011). Inorg. Chem. 21, 10673-10681.]; Donde & Patil, 2011[Donde, K. J. & Patil, V. R. (2011). J. Pharm. Res. 1, 206-209.]; Kuwar et al., 2006[Kuwar, A. S., Shimpi, S. R., Mahulikar, P. P. & Bendre, R. S. (2006). J. Sci. Ind. Res. 8, 665-669.]). Palladium complexes based on MIMTA are thus inter­esting in biomedicine (Orysyk et al., 2013[Orysyk, S. I., Bon, V. V., Zholob, O. O., Pekhnyo, V. I., Orysyk, V. V., Zborovskii, Yu. L. & Vovk, M. V. (2013). Polyhedron, 51, 211-221.]). For the structures of related complexes, see: Orysyk et al. (2015[Orysyk, S. I., Zholob, O. O., Bon, V. V., Nikulina, V. V., Orysyk, V. V., Nikolaienko, T. V., Garmanchuk, L. V., Zborovskii, Yu. L., Tolstanova, G. M., Khranovska, N. M., Pekhnyo, V. I. & Vovk, M. V. (2015). Polyhedron, 85, 208-220.]); Mokhir et al. (2002[Mokhir, A. A., Gumienna-Kontecka, E., Świątek-Kozlowska, J., Petkova, E. G., Fritsky, I. O., Jerzykiewicz, L., Kapshuk, A. A., Sliva, T. Yu. & Yu, (2002). Inorg. Chim. Acta, 329, 113-121.]). For van der Waals radii, see: Zefirov (1997[Zefirov, Yu. V. (1997). Kristallografiya, 42, 936-958.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • [PdCl2(C5H7N3OS)]

  • Mr = 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[Agilent (2012). CrysAlis RED and CrysAlis CCD. Agilent Technologies, Yarnton, England.]) Tmin = 0.742, Tmax = 1.000

  • 4284 measured reflections

  • 2106 independent reflections

  • 2028 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.37 e Å−3

  • Δρmin = −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 DA 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[Agilent (2012). CrysAlis RED and CrysAlis CCD. Agilent Technologies, Yarnton, England.]); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Agilent, 2012[Agilent (2012). CrysAlis RED and CrysAlis CCD. Agilent Technologies, Yarnton, England.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]); software used to prepare material for publication: OLEX2.

Supporting information


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%).

Refinement top

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

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
[Figure 1] Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] 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)]Dx = 2.293 Mg m3
Mr = 334.50Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 2494 reflections
a = 4.347 (3) Åθ = 3.8–31.7°
b = 13.583 (2) ŵ = 2.64 mm1
c = 16.411 (3) ÅT = 294 K
V = 969.0 (7) Å3, orange
Z = 40.4 × 0.3 × 0.2 mm
F(000) = 648
Data collection top
Agilent Xcalibur Sapphire3
diffractometer
2106 independent reflections
Radiation source: Enhance (Mo) X-ray Source2028 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
Detector resolution: 16.1827 pixels mm-1θmax = 27.5°, θmin = 3.0°
ω scansh = 55
Absorption correction: multi-scan
(CrysAlis RED; Agilent, 2012)
k = 1716
Tmin = 0.742, Tmax = 1.000l = 2121
4284 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.022H-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 reflectionsΔρmax = 0.37 e Å3
120 parametersΔρmin = 0.36 e Å3
0 restraintsAbsolute structure: Flack (1983), 969 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.39 (4)
Crystal data top
[PdCl2(C5H7N3OS)]V = 969.0 (7) Å3
Mr = 334.50Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 4.347 (3) ŵ = 2.64 mm1
b = 13.583 (2) ÅT = 294 K
c = 16.411 (3) Å0.4 × 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)
Tmin = 0.742, Tmax = 1.000Rint = 0.019
4284 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.022H-atom parameters constrained
wR(F2) = 0.047Δρmax = 0.37 e Å3
S = 1.04Δρmin = 0.36 e Å3
2106 reflectionsAbsolute structure: Flack (1983), 969 Friedel pairs
120 parametersAbsolute 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
xyzUiso*/Ueq
Pd10.15497 (6)0.986930 (16)0.742144 (12)0.02751 (7)
Cl10.1238 (2)1.04846 (7)0.84901 (5)0.0396 (2)
Cl20.0192 (2)1.11559 (6)0.66418 (5)0.0411 (2)
S10.6968 (2)0.84020 (7)0.53414 (5)0.0394 (2)
O10.2794 (6)0.86291 (19)0.88793 (12)0.0379 (6)
N10.3271 (7)0.87185 (19)0.80514 (14)0.0306 (6)
N20.3996 (6)0.91712 (19)0.65287 (15)0.0291 (6)
N30.3636 (8)1.0058 (2)0.53113 (15)0.0489 (8)
H3A0.24661.04980.55260.059*
H3B0.41531.01040.48070.059*
C10.5024 (9)0.8046 (3)0.92925 (18)0.0389 (8)
H1A0.47980.81320.98700.058*
H1B0.70500.82490.91300.058*
H1C0.47290.73660.91560.058*
C20.4954 (8)0.8100 (2)0.76650 (18)0.0328 (7)
H20.58190.75520.79160.039*
C30.5408 (8)0.8314 (2)0.68133 (18)0.0315 (7)
C40.7074 (9)0.7815 (3)0.62715 (19)0.0375 (8)
H40.81380.72360.63790.045*
C50.4632 (8)0.9318 (2)0.57529 (18)0.0317 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.03240 (12)0.02459 (11)0.02555 (10)0.00010 (10)0.00195 (9)0.00015 (8)
Cl10.0450 (5)0.0412 (5)0.0327 (4)0.0059 (4)0.0021 (4)0.0055 (3)
Cl20.0511 (5)0.0326 (4)0.0394 (4)0.0092 (4)0.0021 (4)0.0062 (4)
S10.0506 (6)0.0390 (5)0.0286 (4)0.0037 (5)0.0042 (4)0.0028 (3)
O10.0456 (14)0.0444 (14)0.0237 (9)0.0096 (12)0.0026 (10)0.0059 (9)
N10.0373 (15)0.0304 (14)0.0240 (11)0.0015 (15)0.0013 (12)0.0048 (10)
N20.0361 (16)0.0239 (13)0.0273 (12)0.0007 (12)0.0025 (11)0.0012 (10)
N30.077 (2)0.0424 (17)0.0276 (12)0.014 (2)0.0087 (14)0.0054 (12)
C10.045 (2)0.045 (2)0.0260 (14)0.006 (2)0.0007 (16)0.0053 (14)
C20.0409 (18)0.0273 (15)0.0303 (15)0.0048 (15)0.0018 (15)0.0024 (13)
C30.0388 (18)0.0277 (17)0.0282 (14)0.0013 (15)0.0032 (14)0.0001 (13)
C40.045 (2)0.0342 (18)0.0333 (15)0.0069 (17)0.0021 (16)0.0014 (13)
C50.0385 (18)0.0316 (18)0.0251 (14)0.0029 (16)0.0012 (14)0.0012 (13)
Geometric parameters (Å, º) top
Pd1—Cl12.2897 (10)N3—H3A0.8600
Pd1—Cl22.2943 (9)N3—H3B0.8600
Pd1—N12.018 (3)N3—C51.313 (4)
Pd1—N22.044 (3)C1—H1A0.9600
S1—C41.723 (3)C1—H1B0.9600
S1—C51.742 (3)C1—H1C0.9600
O1—N11.380 (3)C2—H20.9300
O1—C11.423 (4)C2—C31.441 (4)
N1—C21.282 (4)C3—C41.332 (5)
N2—C31.397 (4)C4—H40.9300
N2—C51.318 (4)
Cl1—Pd1—Cl288.54 (4)O1—C1—H1B109.5
N1—Pd1—Cl194.96 (8)O1—C1—H1C109.5
N1—Pd1—Cl2176.43 (8)H1A—C1—H1B109.5
N1—Pd1—N279.34 (10)H1A—C1—H1C109.5
N2—Pd1—Cl1173.65 (8)H1B—C1—H1C109.5
N2—Pd1—Cl297.20 (8)N1—C2—H2122.4
C4—S1—C590.16 (16)N1—C2—C3115.2 (3)
N1—O1—C1114.6 (2)C3—C2—H2122.4
O1—N1—Pd1121.1 (2)N2—C3—C2115.6 (3)
C2—N1—Pd1117.8 (2)C4—C3—N2116.1 (3)
C2—N1—O1121.0 (3)C4—C3—C2128.3 (3)
C3—N2—Pd1112.1 (2)S1—C4—H4125.0
C5—N2—Pd1137.0 (2)C3—C4—S1110.0 (3)
C5—N2—C3110.9 (3)C3—C4—H4125.0
H3A—N3—H3B120.0N2—C5—S1112.9 (2)
C5—N3—H3A120.0N3—C5—S1121.7 (2)
C5—N3—H3B120.0N3—C5—N2125.4 (3)
O1—C1—H1A109.5
Pd1—N1—C2—C30.1 (4)N1—C2—C3—N20.9 (5)
Pd1—N2—C3—C21.4 (4)N1—C2—C3—C4178.7 (4)
Pd1—N2—C3—C4179.5 (3)N2—Pd1—N1—O1175.8 (3)
Pd1—N2—C5—S1179.58 (19)N2—Pd1—N1—C20.7 (3)
Pd1—N2—C5—N31.1 (6)N2—C3—C4—S10.2 (4)
Cl1—Pd1—N1—O17.0 (2)C1—O1—N1—Pd1156.2 (2)
Cl1—Pd1—N1—C2176.4 (3)C1—O1—N1—C220.2 (4)
Cl1—Pd1—N2—C325.3 (9)C2—C3—C4—S1178.0 (3)
Cl1—Pd1—N2—C5155.6 (5)C3—N2—C5—S10.5 (4)
Cl2—Pd1—N1—O1161.6 (12)C3—N2—C5—N3179.8 (3)
Cl2—Pd1—N1—C214.9 (15)C4—S1—C5—N20.5 (3)
Cl2—Pd1—N2—C3179.7 (2)C4—S1—C5—N3179.8 (3)
Cl2—Pd1—N2—C51.2 (3)C5—S1—C4—C30.4 (3)
O1—N1—C2—C3176.4 (3)C5—N2—C3—C2177.9 (3)
N1—Pd1—N2—C31.1 (2)C5—N2—C3—C40.2 (4)
N1—Pd1—N2—C5178.0 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···Cl20.862.343.124 (3)151
N3—H3B···Cl1i0.862.483.280 (3)156
N3—H3B···O1i0.862.453.015 (3)124
Symmetry code: (i) x+1/2, y+2, z1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···Cl20.862.343.124 (3)151.4
N3—H3B···Cl1i0.862.483.280 (3)155.9
N3—H3B···O1i0.862.453.015 (3)124.0
Symmetry code: (i) x+1/2, y+2, z1/2.
 

References

First citationAgilent (2012). CrysAlis RED and CrysAlis CCD. Agilent Technologies, Yarnton, England.  Google Scholar
First citationDodoff, N. I., Kubiak, M., Kuduk-Jaworska, J., Mastalarz, A., Kochel, A., Vassilieva, V., Vassilev, N., Trendafilova, N., Georgieva, I., Lalia-Kantouri, M. & Apostolova, M. (2009). Chemija, 4, 208–217.  Google Scholar
First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
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First citationElo, H. (2004). Chemotherapy, 50, 229–233.  Web of Science CrossRef PubMed CAS Google Scholar
First citationKuwar, A. S., Shimpi, S. R., Mahulikar, P. P. & Bendre, R. S. (2006). J. Sci. Ind. Res. 8, 665–669.  Google Scholar
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First citationOrysyk, S. I., Zholob, O. O., Bon, V. V., Nikulina, V. V., Orysyk, V. V., Nikolaienko, T. V., Garmanchuk, L. V., Zborovskii, Yu. L., Tolstanova, G. M., Khranovska, N. M., Pekhnyo, V. I. & Vovk, M. V. (2015). Polyhedron, 85, 208–220.  CSD CrossRef CAS Google Scholar
First citationScaffidi-Domianello, Yu. Yu., Legin, A. A., Jakupec, M. A., Arion, V. B., Kukushkin, V. Yu., Galanski, M. & Keppler, B. K. (2011). Inorg. Chem. 21, 10673–10681.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationZefirov, Yu. V. (1997). Kristallografiya, 42, 936–958.  CAS Google Scholar

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