supplementary materials


fk2069 scheme

Acta Cryst. (2013). E69, m238-m239    [ doi:10.1107/S1600536813008271 ]

Dichlorido{2,6-diisopropyl-N-[(S)-pyrrolidin-2-ylmethyl]aniline-[kappa]2N,N'}palladium(II)

S. Nayab, H.-I. Lee and J. H. Jeong

Abstract top

In the title compound, [PdCl2(C17H28N2)], the PdII atom displays a square-planar coordination involving two N atoms of a 2,6-diisopropyl-N-[(S)-pyrrolidin-2-ylmethyl]aniline ligand and two chloride ligands, with a deviation of 0.090 (1) Å for the PdII atom from the best plane. The absolute configuration of the chiral C atom of the pyrrolidine ring is S, which induces R configurations at the two N atoms of the aniline ligand. Optical isomerism arising from the chelate five-membered ring is configured as [delta]. The Pd-N bond lengths are 2.040 (3) and 2.072 (2) Å, and the Pd-Cl bond lengths are 2.3055 (8) and 2.3160 (8) Å. In the crystal, pairs of N-H...Cl hydrogen bonds link molecules into discrete dimers.

Comment top

Palladium complexes of various types bearing the enantiopure ligands are widely used in modern asymmetric synthesis (Sodeoka et al., 2006). Palladium complexes (Quintard et al., 2008; Tan et al., 2009) containing homochiral diamine ligands derivable from natural amino acids are now well established in the clinical treatment as anticancer drugs (Barnham et al., 1994). In this paper, we describe synthesis and the crystal structure of novel chiral dichloro Pd(II) complex bearing the ligand 2,6-diisopropyl-N-(S-pyrrolidin-2-yl) methyl)benzenamine which was prepared by the reported method (Shifeng et al., 2010). The geometry around the Pd(II) centre is almost square-planar (Fig. 1). The coordination plane composed of Pd, Cl1, Cl2, N1, and N2 is nearly coplanar within 0.090 (1) Å deviation from the best plane. The bite angle of N1—Pd—N2 [84.0 (1) °] is much smaller than the Cl1—Pd—Cl2 [93.10 (3) °] angle. The chiral C atom of the pyrrolidine moiety has S configuration and the induced chiralities at two N atoms of the ligand show R configuration. The orientation of the hydrogen atoms of the chiral C and N atoms is in head-to-head. Optical isomerism arising from the chelate five-membered ring is configured as δ. The bond lengths of Pd—N are 2.040 (3) and 2.072 (2) Å and those of Pd—Cl are 2.3055 (8) and 2.3160 (8) Å. These bond lengths are similar to the known average Pd—N and Pd—Cl lengths of (1R,2R)-(1,2-bisbenzyl)-1,2- diaminocyclohexane palladium dichloride complex (Rafii et al., 2007). There are two intermolecular N—H···Cl between each two molecules to form discrete dimers as shown in Fig. 2. Hydrogen-bond parameters are listed in Table 1.

Related literature top

For background to the use of palladium complexes bearing enantiopure ligands in asymmetric synthesis, see: Sodeoka & Hamashima (2006); Quintard et al. (2008); Tan et al. (2009) and as anticancer drugs, see: Barnham et al. (1994). For the synthesis of the 2,6-diisopropyl-N-[(S)-pyrrolidin-2-ylmethyl]aniline ligand, see: Shifeng et al. (2010). For related structures, see: Rafii et al. (2007). For a description of the Cambridge Structural Database, see: Allen et al. (2002).

Experimental top

The ligand, 2,6-diisopropyl-N-(S-pyrrolidin-2-yl)methyl) benzenamine, was prepared by the reported method (Shifeng et al., 2010). Ligand (0.30 g, 1.15 mmol) solution in CH3CN (7 ml) was treated with PdCl2(CH3CN)2 (0.30 g, 1.15 mmol) in CH3CN (10 ml) at ambient temperature for overnight. The solvent was removed under reduced pressure to get brown orange reside. Washing the precipitate with cold Et2O afforded orange solid as the final product (0.38 g, 76%). Anal. Calcd. for C17H28Cl2N2Pd: C, 46.64; H, 6.45; N, 6.40. Found: C, 46.60; H, 6.51; N, 6.37%. 1H NMR (400 MHz, CDCl3) δ 7.19 (m, 2H, ArH), 7.05 [m, 1H, ArH], 3.73 (m, 2H, PyCH2), 3.52 (m, 2H, ArCH2), 3.32 (m, 2H, pyH & ArNH), 3.00–2.64 (m, 2H, pyH), 2.60- 2.51 (br s, 1H, PyNH), 1.91 (m, 2H, pyH), 1.63–1.57 (m, 2H, pyH), 1.29 (d, J = 6.8 Hz, 12H, 4 CH3).

Refinement top

All H atoms were positioned geometrically and refined using a riding model with C—H 0.93 - 0.98 Å, N—H 0.86 Å and Uiso = 1.5Ueq(C) for CH3 and 1.2Ueq(C,N).

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell refinement: CAD-4 Software (Enraf–Nonius, 1989); data reduction: XCAD (McArdle, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII(Burnett & Johnson, 1996); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 40% probability level.
[Figure 2] Fig. 2. Packing diagram of the title compound approximately viewed along b-axis. Hydrogen bonds are indicated by dashed lines.
Dichlorido{2,6-diisopropyl-N-[(S)-pyrrolidin-2-ylmethyl]aniline-κ2N,N'}palladium(II) top
Crystal data top
[PdCl2(C17H28N2)]F(000) = 1792
Mr = 437.71Dx = 1.513 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 25 reflections
a = 24.287 (3) Åθ = 9.0–13.0°
b = 8.6534 (12) ŵ = 1.24 mm1
c = 18.355 (2) ÅT = 293 K
β = 94.851 (9)°Brick, orange
V = 3843.7 (8) Å30.45 × 0.40 × 0.40 mm
Z = 8
Data collection top
Enraf–Nonius CAD-4 four-circle
diffractometer
3089 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.018
Graphite monochromatorθmax = 25.5°, θmin = 1.7°
ω/2θ scansh = 029
Absorption correction: ψ scan
(ABSCALC; McArdle & Daly, 1999)
k = 100
Tmin = 0.578, Tmax = 0.608l = 2222
3790 measured reflections3 standard reflections every 60 min
3580 independent reflections intensity decay: 0.2%
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.105H-atom parameters constrained
S = 1.08 w = 1/[σ2(Fo2) + (0.0819P)2 + 0.2845P]
where P = (Fo2 + 2Fc2)/3
3580 reflections(Δ/σ)max = 0.004
199 parametersΔρmax = 1.33 e Å3
0 restraintsΔρmin = 1.56 e Å3
Crystal data top
[PdCl2(C17H28N2)]V = 3843.7 (8) Å3
Mr = 437.71Z = 8
Monoclinic, C2/cMo Kα radiation
a = 24.287 (3) ŵ = 1.24 mm1
b = 8.6534 (12) ÅT = 293 K
c = 18.355 (2) Å0.45 × 0.40 × 0.40 mm
β = 94.851 (9)°
Data collection top
Enraf–Nonius CAD-4 four-circle
diffractometer
3089 reflections with I > 2σ(I)
Absorption correction: ψ scan
(ABSCALC; McArdle & Daly, 1999)
Rint = 0.018
Tmin = 0.578, Tmax = 0.608θmax = 25.5°
3790 measured reflections3 standard reflections every 60 min
3580 independent reflections intensity decay: 0.2%
Refinement top
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.105Δρmax = 1.33 e Å3
S = 1.08Δρmin = 1.56 e Å3
3580 reflectionsAbsolute structure: ?
199 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Pd0.792743 (8)0.79819 (2)0.934349 (11)0.02593 (12)
Cl10.71265 (3)0.92407 (9)0.89218 (4)0.0389 (2)
Cl20.83021 (3)1.01710 (9)0.99173 (5)0.0391 (2)
N10.76098 (10)0.5922 (3)0.89652 (14)0.0320 (5)
H10.73080.57860.91690.038*
N20.86249 (10)0.6681 (3)0.96516 (14)0.0296 (5)
H20.85970.64561.01030.035*
C10.74724 (15)0.5713 (4)0.81664 (19)0.0448 (8)
H1A0.77700.60750.78890.054*
H1B0.71350.62530.80010.054*
C20.74001 (19)0.3971 (4)0.8098 (2)0.0560 (10)
H2A0.70430.36500.82450.067*
H2B0.74360.36290.76010.067*
C30.78631 (16)0.3348 (4)0.8613 (2)0.0518 (10)
H3A0.81890.31560.83560.062*
H3B0.77540.23880.88330.062*
C40.79815 (12)0.4599 (4)0.92021 (18)0.0352 (7)
H40.78880.42110.96780.042*
C50.85712 (12)0.5168 (3)0.92571 (19)0.0362 (7)
H5A0.88080.44090.95150.043*
H5B0.86920.52870.87700.043*
C60.91821 (11)0.7313 (3)0.96309 (17)0.0291 (6)
C70.95576 (13)0.7160 (3)1.02479 (18)0.0327 (7)
C80.93964 (13)0.6498 (4)1.09665 (17)0.0372 (7)
H80.90950.57621.08520.045*
C90.9180 (2)0.7757 (5)1.1435 (3)0.0637 (12)
H9A0.94690.84911.15620.096*
H9B0.90580.73111.18730.096*
H9C0.88760.82701.11690.096*
C100.98669 (18)0.5623 (6)1.1401 (2)0.0643 (11)
H10A1.01620.63291.15440.096*
H10B1.00020.48221.11010.096*
H10C0.97320.51731.18290.096*
C111.00930 (14)0.7704 (4)1.0203 (2)0.0406 (8)
H111.03470.76291.06100.049*
C121.02549 (14)0.8350 (5)0.9571 (2)0.0463 (8)
H121.06160.86910.95480.056*
C130.98797 (13)0.8487 (4)0.8975 (2)0.0410 (7)
H130.99930.89270.85500.049*
C140.93362 (13)0.7992 (3)0.89800 (18)0.0319 (7)
C150.89514 (13)0.8238 (4)0.82901 (18)0.0383 (7)
H150.85820.78910.83930.046*
C160.89141 (18)0.9966 (5)0.8104 (3)0.0623 (11)
H16A0.92741.03480.80200.093*
H16B0.87761.05200.85040.093*
H16C0.86681.01130.76720.093*
C170.91266 (18)0.7291 (6)0.7649 (2)0.0580 (11)
H17A0.94960.75720.75520.087*
H17B0.88790.74920.72240.087*
H17C0.91160.62110.77680.087*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd0.02146 (17)0.02124 (17)0.03568 (17)0.00033 (7)0.00598 (10)0.00046 (8)
Cl10.0303 (4)0.0360 (4)0.0503 (5)0.0077 (3)0.0037 (3)0.0045 (3)
Cl20.0330 (4)0.0265 (4)0.0583 (5)0.0053 (3)0.0064 (3)0.0055 (3)
N10.0259 (12)0.0289 (13)0.0417 (14)0.0020 (10)0.0056 (10)0.0027 (11)
N20.0253 (12)0.0252 (11)0.0385 (14)0.0003 (10)0.0048 (10)0.0039 (11)
C10.054 (2)0.0314 (17)0.0469 (19)0.0011 (14)0.0072 (15)0.0049 (14)
C20.077 (3)0.0322 (18)0.057 (2)0.0009 (18)0.0068 (19)0.0135 (17)
C30.053 (2)0.0223 (15)0.079 (3)0.0006 (15)0.0031 (19)0.0053 (17)
C40.0348 (15)0.0246 (15)0.0461 (17)0.0013 (12)0.0030 (13)0.0054 (13)
C50.0317 (15)0.0245 (15)0.0526 (19)0.0015 (12)0.0054 (13)0.0026 (13)
C60.0207 (13)0.0271 (14)0.0399 (16)0.0026 (11)0.0048 (11)0.0020 (12)
C70.0309 (15)0.0262 (15)0.0409 (17)0.0031 (11)0.0027 (13)0.0018 (12)
C80.0385 (17)0.0371 (17)0.0354 (16)0.0002 (14)0.0005 (13)0.0023 (14)
C90.075 (3)0.057 (3)0.063 (3)0.006 (2)0.029 (2)0.005 (2)
C100.063 (3)0.065 (3)0.064 (3)0.013 (2)0.003 (2)0.016 (2)
C110.0279 (15)0.0421 (19)0.050 (2)0.0007 (13)0.0054 (14)0.0020 (16)
C120.0281 (16)0.0480 (19)0.064 (2)0.0051 (15)0.0089 (15)0.0036 (18)
C130.0302 (15)0.0403 (18)0.054 (2)0.0019 (14)0.0116 (14)0.0073 (15)
C140.0289 (15)0.0274 (16)0.0404 (17)0.0013 (10)0.0079 (13)0.0007 (12)
C150.0319 (16)0.0445 (19)0.0402 (18)0.0028 (13)0.0133 (14)0.0112 (15)
C160.056 (2)0.059 (3)0.071 (3)0.0042 (19)0.003 (2)0.028 (2)
C170.048 (2)0.083 (3)0.043 (2)0.006 (2)0.0075 (17)0.004 (2)
Geometric parameters (Å, º) top
Pd—N12.040 (3)C7—C81.519 (5)
Pd—N22.072 (2)C8—C91.510 (5)
Pd—Cl12.3055 (8)C8—C101.536 (5)
Pd—Cl22.3160 (8)C8—H80.9800
N1—C11.487 (4)C9—H9A0.9600
N1—C41.500 (4)C9—H9B0.9600
N1—H10.8600C9—H9C0.9600
N2—C61.463 (4)C10—H10A0.9600
N2—C51.497 (4)C10—H10B0.9600
N2—H20.8600C10—H10C0.9600
C1—C21.521 (5)C11—C121.375 (5)
C1—H1A0.9700C11—H110.9300
C1—H1B0.9700C12—C131.369 (5)
C2—C31.507 (5)C12—H120.9300
C2—H2A0.9700C13—C141.388 (4)
C2—H2B0.9700C13—H130.9300
C3—C41.539 (5)C14—C151.524 (5)
C3—H3A0.9700C15—C171.524 (5)
C3—H3B0.9700C15—C161.535 (5)
C4—C51.510 (4)C15—H150.9800
C4—H40.9800C16—H16A0.9600
C5—H5A0.9700C16—H16B0.9600
C5—H5B0.9700C16—H16C0.9600
C6—C71.399 (4)C17—H17A0.9600
C6—C141.410 (4)C17—H17B0.9600
C7—C111.392 (5)C17—H17C0.9600
N1—Pd—N283.98 (10)C11—C7—C6117.9 (3)
N1—Pd—Cl190.83 (7)C11—C7—C8119.3 (3)
N2—Pd—Cl1174.45 (7)C6—C7—C8122.7 (3)
N1—Pd—Cl2172.72 (7)C9—C8—C7110.5 (3)
N2—Pd—Cl292.27 (8)C9—C8—C10109.8 (3)
Cl1—Pd—Cl293.10 (3)C7—C8—C10113.6 (3)
C1—N1—C4105.8 (2)C9—C8—H8107.5
C1—N1—Pd119.3 (2)C7—C8—H8107.5
C4—N1—Pd111.56 (18)C10—C8—H8107.5
C1—N1—H1106.5C8—C9—H9A109.5
C4—N1—H1106.5C8—C9—H9B109.5
Pd—N1—H1106.5H9A—C9—H9B109.5
C6—N2—C5111.0 (2)C8—C9—H9C109.5
C6—N2—Pd121.74 (19)H9A—C9—H9C109.5
C5—N2—Pd107.90 (18)H9B—C9—H9C109.5
C6—N2—H2104.9C8—C10—H10A109.5
C5—N2—H2104.9C8—C10—H10B109.5
Pd—N2—H2104.9H10A—C10—H10B109.5
N1—C1—C2102.5 (3)C8—C10—H10C109.5
N1—C1—H1A111.3H10A—C10—H10C109.5
C2—C1—H1A111.3H10B—C10—H10C109.5
N1—C1—H1B111.3C12—C11—C7121.5 (3)
C2—C1—H1B111.3C12—C11—H11119.3
H1A—C1—H1B109.2C7—C11—H11119.3
C3—C2—C1103.2 (3)C13—C12—C11119.4 (3)
C3—C2—H2A111.1C13—C12—H12120.3
C1—C2—H2A111.1C11—C12—H12120.3
C3—C2—H2B111.1C12—C13—C14122.5 (3)
C1—C2—H2B111.1C12—C13—H13118.8
H2A—C2—H2B109.1C14—C13—H13118.8
C2—C3—C4105.9 (3)C13—C14—C6117.1 (3)
C2—C3—H3A110.6C13—C14—C15117.9 (3)
C4—C3—H3A110.6C6—C14—C15125.0 (3)
C2—C3—H3B110.6C17—C15—C14112.0 (3)
C4—C3—H3B110.6C17—C15—C16111.6 (3)
H3A—C3—H3B108.7C14—C15—C16110.0 (3)
N1—C4—C5108.3 (2)C17—C15—H15107.7
N1—C4—C3105.2 (3)C14—C15—H15107.7
C5—C4—C3113.3 (3)C16—C15—H15107.7
N1—C4—H4110.0C15—C16—H16A109.5
C5—C4—H4110.0C15—C16—H16B109.5
C3—C4—H4110.0H16A—C16—H16B109.5
N2—C5—C4111.2 (2)C15—C16—H16C109.5
N2—C5—H5A109.4H16A—C16—H16C109.5
C4—C5—H5A109.4H16B—C16—H16C109.5
N2—C5—H5B109.4C15—C17—H17A109.5
C4—C5—H5B109.4C15—C17—H17B109.5
H5A—C5—H5B108.0H17A—C17—H17B109.5
C7—C6—C14121.6 (3)C15—C17—H17C109.5
C7—C6—N2119.0 (3)H17A—C17—H17C109.5
C14—C6—N2119.4 (3)H17B—C17—H17C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl2i0.862.473.283 (3)158
N2—H2···Cl1i0.862.683.410 (3)144
Symmetry code: (i) x+3/2, y+3/2, z+2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl2i0.862.4713.283 (3)157.49
N2—H2···Cl1i0.862.6813.410 (3)143.47
Symmetry code: (i) x+3/2, y+3/2, z+2.
Acknowledgements top

This research was supported by the Kyungpook National University Research Fund, 2012.

references
References top

Allen, F. H. (2002). Acta Cryst. B58, 380–388.

Barnham, K. J., Djuran, M. I., Frey, U., Mazid, M. A. & Sadler, P. J. (1994). J. Chem. Soc. Chem. Commun. pp. 65–66.

Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory. Tennessee, USA.

Enraf–Nonius (1989). CAD-4 Software. Enraf–Nonius, Delft, Netherland.

McArdle, P. (1999). XCAD. National University of Ireland, Galway, Ireland.

McArdle, P. & Daly, P. (1999). ABSCALC. National University of Ireland, Galway, Ireland.

Quintard, A., Bournaud, C. & Alexakis, A. (2008). Chem. Eur. J. 14, 7504–7507.

Rafii, E., Dassonneville, B. & Heumann, A. (2007). Chem. Commun. pp. 583–585.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Shifeng, M., Jinjin, B., Jin, Y. & Yawen, Z. (2010). Chirality, 22, 855–862.

Sodeoka, M. & Hamashima, Y. (2006). Pure Appl. Chem. 78, 477–494.

Tan, B., Zeng, X., Lu, Y., Chua, P. J. & Zhong, G. (2009). Org. Lett. 11, 1927–1930.