supplementary materials


HTML versionpdf versioncif file3d viewsupplementary materialsCIF check reportsimilar papers Open access

fj2539 scheme

Acta Cryst. (2012). E68, m519    [ doi:10.1107/S1600536812013074 ]

Bis(azido-[kappa]N)(di-2-pyridylamine-[kappa]2N2,N2')palladium(II)

K. Ha

Abstract top

In the title complex, [Pd(N3)2(C10H9N3)], the PdII ion is in a slightly distorted square-planar coordination environment. The ligator atoms comprise the two pyridine N atoms of the chelating di-2-pyridylamine (dpa) ligand and two N atoms from two azide anions. The dpa ligand coordinates the Pd atom in a boat conformation, the dihedral angle between the pyridine rings being 24.4 (1)°. The pyridine rings are somewhat inclined to the least-squares plane of the PdN4 unit, making dihedral angles of 29.02 (9) and 26.47 (9)°. The azide ligands are slightly bent, with N-N-N angles of 173.0 (4) and 174.2 (4)°. In the crystal, molecules are connected by N-H...N and C-H...N hydrogen bonds, forming chains along the c axis. When viewed down the b axis, successive chains are stacked in opposite directions. Intramolecular C-H...N hydrogen bonds are also observed.

Comment top

Crystal structures of PdII complexes with di-2-pyridylamine (dpa; C10H9N3) and halogen ions, [PdX2(dpa)] (X = Cl or Br), have been reported previously (Rauterkus et al., 2003; Yao et al., 2003).

In the title complex, [Pd(N3)2(dpa)], the PdII ion is four-coordinated in a slightly distorted square-planar environment by the two pyridine N atoms of the chelating dpa ligand and two N atoms from two azide anions (Fig. 1). The dpa ligand coordinates the Pd atom in a boat conformation. The dihedral angle between the least-squares planes of the two pyridine rings is 24.4 (1)°. The pyridine rings are somewhat inclined to the least-squares plane of the PdN4 unit [maximum deviation = 0.016 (2) Å], making dihedral angles of 29.02 (9)° and 26.47 (9)°. The Pd—N(azide) and Pd—N(dpa) bond lengths are nearly equivalent [Pd—N: 2.001 (3)–2.046 (3) Å] (Table 1). The azide ligands are slightly bent with the bond angles of <N4—N5—N6 = 173.0 (4)° and <N7—N8—N9 = 174.2 (4)°. But, the N—N bond lengths of the ligands are almost equal [N—N: 1.146 (4)–1.212 (4) Å]. In the crystal, the complex molecules are connected by intermolecular N—H···N and C—H···N hydrogen bonds, forming chains along the c axis (Fig. 2 and Table 2). When viewed down the b axis, successive chains are stacked in opposite directions. Intramolecular C—H···N hydrogen bonds are also observed (Table 2).

Related literature top

For the crystal structures of the related PdII complexes [PdX2(dpa)] (X = Cl or Br), see: Rauterkus et al. (2003); Yao et al. (2003).

Experimental top

To a solution of Na2PdCl4 (0.1451 g, 0.493 mmol) in MeOH (30 ml) were added NaN3 (0.3050 g, 4.692 mmol) and di-2-pyridylamine (0.0860 g, 0.502 mmol), and stirred for 5 h at room temperature. The formed precipitate was separated by filtration and washed with H2O and acetone, and dried at 50 °C, to give a yellow powder (0.1604 g). Crystals suitable for X-ray analysis were obtained by slow evaporation from a CH3CN/acetone solution.

Refinement top

Carbon-bound H atoms were positioned geometrically and allowed to ride on their respective parent atoms: C—H = 0.95 Å with Uiso(H) = 1.2Ueq(C). Nitrogen-bound H atom was located from the difference Fourier map then allowed to ride on its parent atom in the final cycles of refinement with N—H = 0.92 Å and Uiso(H) = 1.5 Ueq(N). The highest peak (0.71 e Å-3) and the deepest hole (-0.41 e Å-3) in the difference Fourier map are located 1.07 Å and 1.54 Å, respectively, from the Pd1 atom.

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A structure detail of the title complex, with displacement ellipsoids drawn at the 50% probability level for non-H atoms.
[Figure 2] Fig. 2. A partial view of the unit-cell contents of the title complex. Intermolecular N—H···N and C—H···N hydrogen-bond interactions are drawn with dashed lines.
Bis(azido-κN)(di-2-pyridylamine- κ2N2,N2')palladium(II) top
Crystal data top
[Pd(N3)2(C10H9N3)]F(000) = 1424
Mr = 361.66Dx = 2.021 Mg m−3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 3353 reflections
a = 17.5552 (15) Åθ = 2.4–26.0°
b = 6.9773 (6) ŵ = 1.57 mm−1
c = 19.6654 (17) ÅT = 200 K
β = 99.206 (2)°Block, yellow
V = 2377.7 (4) Å30.20 × 0.14 × 0.09 mm
Z = 8
Data collection top
Bruker SMART 1000 CCD
diffractometer		2322 independent reflections
Radiation source: fine-focus sealed tube1751 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
φ and ω scansθmax = 26.0°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		h = −21→17
Tmin = 0.901, Tmax = 1.000k = −8→8
7041 measured reflectionsl = −20→24
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)] = 0.029Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.073H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0309P)2 + 3.0994P]
where P = (Fo2 + 2Fc2)/3
2322 reflections(Δ/σ)max = 0.001
181 parametersΔρmax = 0.71 e Å−3
0 restraintsΔρmin = −0.41 e Å−3
Crystal data top
[Pd(N3)2(C10H9N3)]V = 2377.7 (4) Å3
Mr = 361.66Z = 8
Monoclinic, C2/cMo Kα radiation
a = 17.5552 (15) ŵ = 1.57 mm−1
b = 6.9773 (6) ÅT = 200 K
c = 19.6654 (17) Å0.20 × 0.14 × 0.09 mm
β = 99.206 (2)°
Data collection top
Bruker SMART 1000 CCD
diffractometer		2322 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		1751 reflections with I > 2σ(I)
Tmin = 0.901, Tmax = 1.000Rint = 0.029
7041 measured reflectionsθmax = 26.0°
Refinement top
R[F2 > 2σ(F2)] = 0.029H-atom parameters constrained
wR(F2) = 0.073Δρmax = 0.71 e Å−3
S = 1.06Δρmin = −0.41 e Å−3
2322 reflectionsAbsolute structure: ?
181 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.

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
Pd10.251934 (14)0.29162 (4)0.249235 (13)0.02012 (11)
N10.31748 (16)0.2924 (4)0.17242 (15)0.0204 (6)
N20.21863 (17)0.4333 (4)0.09167 (16)0.0283 (8)
H2N0.21040.49690.05020.042*
N30.15471 (16)0.2919 (4)0.17634 (15)0.0216 (7)
N40.35049 (17)0.2861 (5)0.31632 (16)0.0299 (8)
N50.36249 (16)0.3271 (4)0.37610 (17)0.0266 (7)
N60.38160 (18)0.3598 (6)0.43357 (18)0.0409 (9)
N70.18386 (17)0.2944 (5)0.32278 (15)0.0266 (7)
N80.19687 (16)0.3593 (5)0.38063 (16)0.0258 (7)
N90.20315 (19)0.4148 (5)0.43611 (17)0.0386 (9)
C10.3921 (2)0.2266 (6)0.18546 (19)0.0285 (9)
H10.40830.15740.22690.034*
C20.4441 (2)0.2556 (6)0.1421 (2)0.0334 (10)
H20.49520.20770.15300.040*
C30.4206 (2)0.3575 (6)0.0812 (2)0.0336 (9)
H30.45640.38590.05120.040*
C40.3451 (2)0.4161 (6)0.06515 (19)0.0293 (9)
H40.32750.48160.02330.035*
C50.2950 (2)0.3771 (5)0.11182 (18)0.0239 (8)
C60.1522 (2)0.3672 (5)0.11384 (18)0.0237 (8)
C70.0833 (2)0.3866 (6)0.06780 (19)0.0306 (9)
H70.08290.44540.02420.037*
C80.0162 (2)0.3195 (6)0.0865 (2)0.0375 (10)
H8−0.03120.32970.05570.045*
C90.0183 (2)0.2366 (6)0.1508 (2)0.0349 (10)
H9−0.02750.18980.16490.042*
C100.0877 (2)0.2234 (6)0.1935 (2)0.0309 (9)
H100.08930.16360.23710.037*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02099 (16)0.02298 (17)0.01673 (16)0.00000 (12)0.00408 (10)0.00056 (12)
N10.0239 (15)0.0216 (16)0.0162 (16)−0.0020 (12)0.0047 (12)−0.0003 (13)
N20.0321 (18)0.0315 (19)0.0216 (18)−0.0010 (14)0.0052 (14)0.0068 (14)
N30.0223 (15)0.0254 (17)0.0177 (16)0.0004 (12)0.0052 (12)−0.0014 (13)
N40.0252 (17)0.048 (2)0.0152 (17)0.0007 (15)0.0007 (13)−0.0011 (15)
N50.0199 (16)0.0304 (19)0.030 (2)0.0012 (13)0.0061 (14)0.0027 (15)
N60.0316 (19)0.064 (3)0.026 (2)0.0045 (18)0.0017 (15)−0.0128 (19)
N70.0278 (17)0.036 (2)0.0168 (17)−0.0026 (14)0.0066 (13)−0.0029 (14)
N80.0219 (16)0.0279 (18)0.029 (2)0.0031 (13)0.0086 (13)0.0072 (15)
N90.043 (2)0.055 (3)0.0188 (19)0.0027 (17)0.0069 (15)−0.0075 (17)
C10.028 (2)0.033 (2)0.024 (2)0.0014 (17)0.0032 (16)−0.0021 (17)
C20.025 (2)0.044 (3)0.033 (2)0.0013 (17)0.0092 (17)−0.008 (2)
C30.031 (2)0.044 (3)0.028 (2)−0.0066 (19)0.0133 (17)−0.009 (2)
C40.041 (2)0.030 (2)0.016 (2)−0.0032 (17)0.0063 (16)0.0008 (16)
C50.0278 (19)0.0212 (19)0.023 (2)−0.0016 (16)0.0038 (15)−0.0058 (17)
C60.032 (2)0.0182 (19)0.022 (2)0.0030 (16)0.0066 (15)−0.0053 (16)
C70.038 (2)0.030 (2)0.022 (2)0.0006 (19)−0.0013 (16)0.0027 (18)
C80.030 (2)0.043 (3)0.037 (3)0.0045 (18)−0.0019 (18)−0.005 (2)
C90.024 (2)0.044 (3)0.037 (3)−0.0038 (18)0.0063 (17)−0.005 (2)
C100.033 (2)0.036 (2)0.025 (2)−0.0019 (18)0.0094 (17)−0.0033 (18)
Geometric parameters (Å, º) top
Pd1—N42.001 (3)C1—H10.9500
Pd1—N72.018 (3)C2—C31.397 (5)
Pd1—N12.040 (3)C2—H20.9500
Pd1—N32.046 (3)C3—C41.374 (5)
N1—C51.332 (4)C3—H30.9500
N1—C11.373 (4)C4—C51.396 (5)
N2—C61.387 (4)C4—H40.9500
N2—C51.393 (4)C6—C71.398 (5)
N2—H2N0.9200C7—C81.370 (5)
N3—C61.331 (4)C7—H70.9500
N3—C101.361 (5)C8—C91.386 (6)
N4—N51.195 (4)C8—H80.9500
N5—N61.149 (4)C9—C101.368 (5)
N7—N81.212 (4)C9—H90.9500
N8—N91.146 (4)C10—H100.9500
C1—C21.360 (5)
N4—Pd1—N794.38 (12)C4—C3—C2119.3 (4)
N4—Pd1—N187.57 (12)C4—C3—H3120.3
N7—Pd1—N1177.94 (11)C2—C3—H3120.3
N4—Pd1—N3176.68 (11)C3—C4—C5118.5 (4)
N7—Pd1—N388.79 (12)C3—C4—H4120.8
N1—Pd1—N389.28 (11)C5—C4—H4120.8
C5—N1—C1116.9 (3)N1—C5—N2120.9 (3)
C5—N1—Pd1122.9 (2)N1—C5—C4123.2 (3)
C1—N1—Pd1119.7 (2)N2—C5—C4116.0 (3)
C6—N2—C5129.5 (3)N3—C6—N2121.1 (3)
C6—N2—H2N114.8N3—C6—C7122.2 (3)
C5—N2—H2N113.3N2—C6—C7116.6 (3)
C6—N3—C10117.8 (3)C8—C7—C6119.0 (4)
C6—N3—Pd1123.2 (2)C8—C7—H7120.5
C10—N3—Pd1118.9 (2)C6—C7—H7120.5
N5—N4—Pd1129.9 (3)C7—C8—C9119.2 (4)
N6—N5—N4173.0 (4)C7—C8—H8120.4
N8—N7—Pd1129.2 (2)C9—C8—H8120.4
N9—N8—N7174.2 (4)C10—C9—C8118.7 (4)
C2—C1—N1123.3 (4)C10—C9—H9120.7
C2—C1—H1118.4C8—C9—H9120.7
N1—C1—H1118.4N3—C10—C9123.0 (4)
C1—C2—C3118.6 (4)N3—C10—H10118.5
C1—C2—H2120.7C9—C10—H10118.5
C3—C2—H2120.7
N4—Pd1—N1—C5−149.3 (3)C1—N1—C5—C4−5.9 (5)
N3—Pd1—N1—C531.7 (3)Pd1—N1—C5—C4165.2 (3)
N4—Pd1—N1—C121.6 (3)C6—N2—C5—N1−22.4 (6)
N3—Pd1—N1—C1−157.4 (3)C6—N2—C5—C4157.9 (4)
N7—Pd1—N3—C6151.4 (3)C3—C4—C5—N12.7 (6)
N1—Pd1—N3—C6−27.9 (3)C3—C4—C5—N2−177.7 (3)
N7—Pd1—N3—C10−24.3 (3)C10—N3—C6—N2−177.5 (3)
N1—Pd1—N3—C10156.4 (3)Pd1—N3—C6—N26.8 (5)
N7—Pd1—N4—N5−18.7 (4)C10—N3—C6—C73.5 (5)
N1—Pd1—N4—N5160.7 (4)Pd1—N3—C6—C7−172.2 (3)
N4—Pd1—N7—N829.4 (3)C5—N2—C6—N326.7 (6)
N3—Pd1—N7—N8−151.6 (3)C5—N2—C6—C7−154.3 (4)
C5—N1—C1—C24.6 (5)N3—C6—C7—C8−2.5 (6)
Pd1—N1—C1—C2−166.9 (3)N2—C6—C7—C8178.5 (4)
N1—C1—C2—C30.1 (6)C6—C7—C8—C90.9 (6)
C1—C2—C3—C4−3.5 (6)C7—C8—C9—C10−0.4 (6)
C2—C3—C4—C52.2 (6)C6—N3—C10—C9−3.1 (6)
C1—N1—C5—N2174.4 (3)Pd1—N3—C10—C9172.8 (3)
Pd1—N1—C5—N2−14.4 (5)C8—C9—C10—N31.5 (6)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···N9i0.922.313.208 (4)165
C1—H1···N40.952.352.816 (5)110
C4—H4···N6i0.952.403.175 (5)138
C10—H10···N70.952.352.861 (5)113
Symmetry code: (i) x, −y+1, z−1/2.
Selected bond lengths (Å) top
Pd1—N42.001 (3)Pd1—N12.040 (3)
Pd1—N72.018 (3)Pd1—N32.046 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···N9i0.922.313.208 (4)165
C1—H1···N40.952.352.816 (5)110.0
C4—H4···N6i0.952.403.175 (5)138
C10—H10···N70.952.352.861 (5)113.0
Symmetry code: (i) x, −y+1, z−1/2.
Acknowledgements top

This work was supported by the Priority Research Centers Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2011–0030747).

references
References top

Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.

Rauterkus, M. J., Fakih, S., Mock, C., Puscasu, I. & Krebs, B. (2003). Inorg. Chim. Acta, 350, 355–365.

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

Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Yao, W.-R., Liu, Z.-H. & Zhang, Q.-F. (2003). Acta Cryst. C59, m139–m140.