Bis(dipyridin-2-yl­amine-κ² N ²,N ^2′)palladium(II) dinitrate

Abstract

The asymmetric unit of the title compound, [Pd(C₁₀H₉N₃)₂](NO₃)₂, contains one half of a cationic Pd^II complex and one NO₃ ⁻ anion. In the complex, the Pd^II ion is four-coordinated by four pyridine N atoms derived from the two chelating dipyridin-2-yl­amine (dpa) ligands. The Pd^II atom is located on an inversion centre, and thus the PdN₄ unit is exactly planar. The dpa ligand itself is not planar, showing a dihedral angle between the pyridine rings of 39.9 (1)°. The anions are connected to the complex by inter­molecular N—H⋯O hydrogen bonds between the two O atoms of the anion and the N—H group of the cation. Weak inter­molecular C—H⋯O hydrogen bonds additionally link the constituents in the crystal structure. The NO₃ ⁻ anion was found to be disordered over two sites with a site-occupancy factor of 0.55 (10) for the major component.

Related literature  

For the crystal structures of the related cationic Pd^II complexes [Pd(dpa)₂](X)₂ (X = Cl or PF₆), see: Živković et al. (2007 ▶); Antonioli et al. (2008 ▶).

Experimental  

Crystal data  

• [Pd(C₁₀H₉N₃)₂](NO₃)₂

• M _r = 572.82

• Monoclinic,

• a = 8.5760 (8) Å

• b = 16.8916 (16) Å

• c = 7.4893 (7) Å

• β = 96.296 (2)°

• V = 1078.37 (18) ų

• Z = 2

• Mo Kα radiation

• μ = 0.92 mm⁻¹

• T = 200 K

• 0.29 × 0.23 × 0.14 mm

Data collection  

• Bruker SMART 1000 CCD diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2000 ▶) T _min = 0.890, T _max = 1.000

• 7678 measured reflections

• 2626 independent reflections

• 1932 reflections with I > 2σ(I)

• R _int = 0.025

Refinement  

• R[F ² > 2σ(F ²)] = 0.032

• wR(F ²) = 0.086

• S = 1.16

• 2626 reflections

• 170 parameters

• H-atom parameters constrained

• Δρ_max = 0.91 e Å⁻³

• Δρ_min = −0.94 e Å⁻³

Data collection: SMART (Bruker, 2000 ▶); cell refinement: SAINT (Bruker, 2000 ▶); data reduction: SAINT; 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.

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2N⋯O2i	0.92	2.08	2.964 (4)	160
N2—H2N⋯O3Ai	0.92	2.49	3.274 (17)	144
C2—H2⋯O1ii	0.95	2.57	3.409 (5)	148
C3—H3⋯O3A	0.95	2.55	3.23 (4)	129
C4—H4⋯O2i	0.95	2.37	3.152 (5)	140
C7—H7⋯O3Ai	0.95	2.25	3.07 (2)	144
C10—H10⋯O2iii	0.95	2.53	3.334 (5)	142

Symmetry codes: (i) ; (ii) ; (iii) .

supplementary crystallographic information

Comment

Crystal structures of related cationic Pd^II complexes, [Pd(dpa)₂](X)₂ (dpa = dipyridyl-2-ylamine, C₁₀H₉N₃; X = Cl or PF₆), have been reported previously (Živković et al., 2007; Antonioli et al., 2008).

The asymmetric unit of the title compound, [Pd(C₁₀H₉N₃)₂](NO₃)₂, contains one half of a cationic Pd^II complex and one NO₃^- anion (Fig. 1). In the complex, the Pd^II ion is four-coordinated by four pyridine N atoms derived from the two chelating dipyridin-2-ylamine (dpa) ligands. The Pd atom is located on an inversion centre, and thus the PdN₄ unit is exactly planar. The dpa ligand itself is not planar, showing a dihedral angle between the pyridine rings of 39.9 (1)°. The two Pd—N bond lengths are almost equivalent [Pd—N: 2.021 (3) and 2.030 (3) Å]. The anions are connected to the complex by intermolecular N—H···O hydrogen bonds between the two O atoms of the anion and the N—H group of the cation (Fig. 2 and Table 1). Weak intermolecular C—H···O hydrogen bonds additionally link the constituents in the crystal structure (Table 1). The complex molecules are stacked into columns along the a axis. In the columns, several intermolecular π-π interactions between the pyridine rings are present, the shortest ring centroid-centroid distance being 3.771 (2) Å.

Experimental

To a solution of Pd(NO₃)₂.2H₂O (0.1315 g, 0.494 mmol) in acetone (30 ml) was added dipyridin-2-pyridylamine (0.0858 g, 0.501 mmol) and stirred for 3 h at room temperature. The formed precipitate was separated by filtration and washed with ether, and dried under vacuum, to give a yellow powder (0.1110 g). Crystals suitable for X-ray analysis were obtained by slow evaporation from a CH₃CN solution at room temperature.

Refinement

Carbon-bound H atoms were positioned geometrically and allowed to ride on their respective parent atoms [C—H = 0.95 Å and U_iso(H) = 1.2U_eq(C)]. Nitrogen-bound H atom was located from Fourier difference maps then allowed to ride on its parent atom in the final cycles of refinement with N—H = 0.92 Å and U_iso(H) = 1.5 U_eq(N). The NO₃^- anion displayed relatively large displacement factors and low electron density peaks so that the anion appears to be highly disordered. The atom O3 was modelled anisotropically as disordered over two sites with a site-occupancy factor of 0.55 (10) for the major component. The highest peak (0.91 e Å^-3) and the deepest hole (-0.94 e Å^-3) in the difference Fourier map are located 0.68 Å and 0.85 Å from the atoms N3 and Pd1, respectively.

Figures

Fig. 1.

Molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level for non-H atoms. Unlabelled atoms are related to the reference atoms by the (-x, -y, -z) symmetry transformation. The minor bond of the disordered anion is drawn as a dashed line.

Fig. 2.

A view of the unit-cell contents of the title compound. Intermolecular N—H···O hydrogen-bond interactions are drawn as dashed lines.

Crystal data

[Pd(C10H9N3)2](NO3)2	F(000) = 576
Mr = 572.82	Dx = 1.764 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 4149 reflections
a = 8.5760 (8) Å	θ = 2.4–28.3°
b = 16.8916 (16) Å	µ = 0.92 mm−1
c = 7.4893 (7) Å	T = 200 K
β = 96.296 (2)°	Block, yellow
V = 1078.37 (18) Å3	0.29 × 0.23 × 0.14 mm
Z = 2

Data collection

Bruker SMART 1000 CCD diffractometer	2626 independent reflections
Radiation source: fine-focus sealed tube	1932 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.025
φ and ω scans	θmax = 28.3°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −9→11
Tmin = 0.890, Tmax = 1.000	k = −22→20
7678 measured reflections	l = −9→4

Refinement

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086	H-atom parameters constrained
S = 1.16	w = 1/[σ2(Fo2) + (0.011P)2 + 2.4328P] where P = (Fo2 + 2Fc2)/3
2626 reflections	(Δ/σ)max < 0.001
170 parameters	Δρmax = 0.91 e Å−3
0 restraints	Δρmin = −0.94 e Å−3

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	Occ. (<1)
Pd1	0.0000	0.0000	0.0000	0.02988 (11)
N1	0.1491 (3)	0.08511 (16)	0.1032 (4)	0.0310 (6)
N2	−0.0576 (4)	0.14664 (17)	0.2356 (4)	0.0365 (7)
H2N	−0.0894	0.1943	0.2789	0.055*
N3	−0.1005 (3)	0.00901 (17)	0.2323 (4)	0.0300 (6)
C1	0.3025 (4)	0.0847 (2)	0.0763 (5)	0.0377 (8)
H1	0.3437	0.0388	0.0251	0.045*
C2	0.4012 (5)	0.1469 (2)	0.1189 (6)	0.0445 (10)
H2	0.5082	0.1445	0.0973	0.053*
C3	0.3411 (5)	0.2138 (2)	0.1947 (6)	0.0456 (10)
H3	0.4055	0.2590	0.2214	0.055*
C4	0.1882 (5)	0.2140 (2)	0.2306 (5)	0.0397 (9)
H4	0.1461	0.2588	0.2852	0.048*
C5	0.0942 (4)	0.1478 (2)	0.1864 (5)	0.0339 (8)
C6	−0.1315 (4)	0.0808 (2)	0.2959 (5)	0.0315 (7)
C7	−0.2348 (4)	0.0899 (2)	0.4275 (5)	0.0410 (9)
H7	−0.2600	0.1412	0.4681	0.049*
C8	−0.2983 (5)	0.0241 (3)	0.4962 (5)	0.0453 (10)
H8	−0.3703	0.0293	0.5832	0.054*
C9	−0.2576 (5)	−0.0503 (2)	0.4390 (5)	0.0429 (9)
H9	−0.2977	−0.0966	0.4897	0.052*
C10	−0.1587 (4)	−0.0558 (2)	0.3084 (5)	0.0375 (8)
H10	−0.1299	−0.1068	0.2697	0.045*
N4	0.7615 (4)	0.32688 (19)	0.3476 (5)	0.0396 (7)
O1	0.7104 (4)	0.39245 (17)	0.3829 (4)	0.0598 (9)
O2	0.9002 (4)	0.3157 (2)	0.3252 (5)	0.0657 (10)
O3A	0.683 (2)	0.2662 (8)	0.380 (8)	0.078 (7)	0.55 (10)
O3B	0.6702 (18)	0.278 (2)	0.282 (10)	0.073 (10)	0.45 (10)

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Pd1	0.03068 (19)	0.02516 (18)	0.0353 (2)	−0.00072 (16)	0.01034 (15)	−0.00249 (17)
N1	0.0332 (15)	0.0272 (14)	0.0335 (16)	−0.0007 (12)	0.0078 (13)	−0.0013 (12)
N2	0.0405 (17)	0.0276 (15)	0.0430 (18)	0.0000 (13)	0.0123 (15)	−0.0075 (13)
N3	0.0306 (14)	0.0337 (16)	0.0263 (13)	−0.0011 (12)	0.0053 (11)	−0.0025 (12)
C1	0.0331 (19)	0.043 (2)	0.038 (2)	−0.0019 (16)	0.0103 (16)	0.0033 (17)
C2	0.035 (2)	0.052 (2)	0.047 (2)	−0.0079 (18)	0.0044 (18)	0.0068 (19)
C3	0.048 (2)	0.038 (2)	0.051 (3)	−0.0123 (18)	0.004 (2)	0.0012 (19)
C4	0.049 (2)	0.0308 (19)	0.040 (2)	−0.0059 (16)	0.0049 (18)	−0.0019 (16)
C5	0.0367 (19)	0.0319 (18)	0.0335 (19)	−0.0007 (15)	0.0065 (16)	0.0019 (15)
C6	0.0332 (18)	0.0342 (18)	0.0266 (17)	0.0027 (14)	0.0015 (15)	−0.0057 (15)
C7	0.035 (2)	0.049 (2)	0.039 (2)	−0.0002 (17)	0.0079 (17)	−0.0094 (18)
C8	0.037 (2)	0.065 (3)	0.035 (2)	−0.0025 (19)	0.0103 (17)	0.0022 (19)
C9	0.044 (2)	0.050 (2)	0.035 (2)	−0.0117 (19)	0.0055 (18)	0.0070 (18)
C10	0.043 (2)	0.0353 (19)	0.035 (2)	−0.0049 (16)	0.0053 (17)	0.0057 (16)
N4	0.0394 (18)	0.0362 (17)	0.0433 (19)	−0.0002 (14)	0.0051 (15)	−0.0024 (15)
O1	0.079 (2)	0.0378 (16)	0.066 (2)	0.0150 (15)	0.0226 (18)	0.0034 (15)
O2	0.0398 (17)	0.089 (3)	0.071 (2)	0.0008 (17)	0.0179 (16)	−0.0229 (19)
O3A	0.076 (6)	0.035 (4)	0.12 (2)	−0.016 (4)	0.006 (9)	0.008 (6)
O3B	0.051 (6)	0.048 (7)	0.12 (3)	−0.020 (5)	−0.006 (8)	−0.007 (11)

Geometric parameters (Å, º)

Pd1—N1i	2.021 (3)	C3—H3	0.9500
Pd1—N1	2.021 (3)	C4—C5	1.397 (5)
Pd1—N3	2.030 (3)	C4—H4	0.9500
Pd1—N3i	2.030 (3)	C6—C7	1.404 (5)
N1—C5	1.340 (4)	C7—C8	1.363 (6)
N1—C1	1.353 (4)	C7—H7	0.9500
N2—C6	1.381 (4)	C8—C9	1.384 (6)
N2—C5	1.391 (4)	C8—H8	0.9500
N2—H2N	0.9200	C9—C10	1.366 (5)
N3—C6	1.341 (4)	C9—H9	0.9500
N3—C10	1.355 (4)	C10—H10	0.9500
C1—C2	1.364 (5)	N4—O3B	1.204 (15)
C1—H1	0.9500	N4—O1	1.231 (4)
C2—C3	1.390 (6)	N4—O2	1.234 (4)
C2—H2	0.9500	N4—O3A	1.264 (17)
C3—C4	1.367 (5)
N1i—Pd1—N1	180.00 (19)	C3—C4—H4	120.2
N1i—Pd1—N3	94.06 (11)	C5—C4—H4	120.2
N1—Pd1—N3	85.94 (11)	N1—C5—N2	119.9 (3)
N1i—Pd1—N3i	85.94 (11)	N1—C5—C4	121.3 (3)
N1—Pd1—N3i	94.06 (11)	N2—C5—C4	118.7 (3)
N3—Pd1—N3i	180.0	N3—C6—N2	119.7 (3)
C5—N1—C1	118.0 (3)	N3—C6—C7	120.9 (3)
C5—N1—Pd1	120.0 (2)	N2—C6—C7	119.3 (3)
C1—N1—Pd1	121.7 (2)	C8—C7—C6	119.0 (4)
C6—N2—C5	125.1 (3)	C8—C7—H7	120.5
C6—N2—H2N	115.1	C6—C7—H7	120.5
C5—N2—H2N	113.8	C7—C8—C9	120.0 (4)
C6—N3—C10	119.0 (3)	C7—C8—H8	120.0
C6—N3—Pd1	119.5 (2)	C9—C8—H8	120.0
C10—N3—Pd1	120.7 (2)	C10—C9—C8	118.7 (4)
N1—C1—C2	123.4 (4)	C10—C9—H9	120.6
N1—C1—H1	118.3	C8—C9—H9	120.6
C2—C1—H1	118.3	N3—C10—C9	122.1 (4)
C1—C2—C3	118.3 (4)	N3—C10—H10	118.9
C1—C2—H2	120.9	C9—C10—H10	118.9
C3—C2—H2	120.9	O3B—N4—O1	118.3 (11)
C4—C3—C2	119.2 (4)	O3B—N4—O2	115.7 (10)
C4—C3—H3	120.4	O1—N4—O2	122.6 (4)
C2—C3—H3	120.4	O1—N4—O3A	118.7 (9)
C3—C4—C5	119.5 (4)	O2—N4—O3A	116.2 (8)
N3—Pd1—N1—C5	−43.5 (3)	C6—N2—C5—N1	36.1 (5)
N3i—Pd1—N1—C5	136.5 (3)	C6—N2—C5—C4	−141.9 (4)
N3—Pd1—N1—C1	142.8 (3)	C3—C4—C5—N1	−2.5 (6)
N3i—Pd1—N1—C1	−37.2 (3)	C3—C4—C5—N2	175.4 (4)
N1i—Pd1—N3—C6	−133.9 (3)	C10—N3—C6—N2	172.0 (3)
N1—Pd1—N3—C6	46.1 (3)	Pd1—N3—C6—N2	−18.3 (4)
N1i—Pd1—N3—C10	35.6 (3)	C10—N3—C6—C7	−6.0 (5)
N1—Pd1—N3—C10	−144.4 (3)	Pd1—N3—C6—C7	163.7 (3)
C5—N1—C1—C2	−4.4 (6)	C5—N2—C6—N3	−33.2 (5)
Pd1—N1—C1—C2	169.4 (3)	C5—N2—C6—C7	144.9 (4)
N1—C1—C2—C3	0.4 (6)	N3—C6—C7—C8	2.9 (6)
C1—C2—C3—C4	2.6 (6)	N2—C6—C7—C8	−175.1 (4)
C2—C3—C4—C5	−1.6 (6)	C6—C7—C8—C9	1.5 (6)
C1—N1—C5—N2	−172.5 (3)	C7—C8—C9—C10	−2.7 (6)
Pd1—N1—C5—N2	13.6 (5)	C6—N3—C10—C9	4.9 (5)
C1—N1—C5—C4	5.4 (5)	Pd1—N3—C10—C9	−164.7 (3)
Pd1—N1—C5—C4	−168.5 (3)	C8—C9—C10—N3	−0.5 (6)

Symmetry code: (i) −x, −y, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···O2ii	0.92	2.08	2.964 (4)	160
N2—H2N···O3Aii	0.92	2.49	3.274 (17)	144
C2—H2···O1iii	0.95	2.57	3.409 (5)	148
C3—H3···O3A	0.95	2.55	3.23 (4)	129
C4—H4···O2ii	0.95	2.37	3.152 (5)	140
C7—H7···O3Aii	0.95	2.25	3.07 (2)	144
C10—H10···O2iv	0.95	2.53	3.334 (5)	142

Symmetry codes: (ii) x−1, y, z; (iii) x, −y+1/2, z−1/2; (iv) −x+1, y−1/2, −z+1/2.