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tk5137 scheme

Acta Cryst. (2012). E68, m1144    [ doi:10.1107/S1600536812033946 ]

(Di-2-pyridylamine-[kappa]2N2,N2')diiodidopalladium(II)

K. Ha

Abstract top

The PdII ion in the title complex, [PdI2(C10H9N3)], is four-coordinated in a distorted square-planar environment defined by the two pyridine N atoms of the chelating di-2-pyridylamine (dpa) ligand and two I- anions. The dpa ligand is not planar, the dihedral angle between the pyridine rings being 51.2 (2)°. In the crystal, pairs of complex molecules are assembled through intermolecular N-H...I hydrogen bonds into dimeric species. The complexes are stacked in columns along the b axis and display several intermolecular [pi]-[pi] interactions between the pyridine rings, with a shortest ring centroid-centroid distance of 3.957 (3) Å.

Comment top

The title complex, [PdI2(dpa)] (dpa = di-2-pyridylamine, C10H9N3), is isomorphous with the previously reported PtII complex [PtI2(dpa)] (Ha, 2012).

The PdII ion is four-coordinated in a distorted square-planar environment defined by the two pyridine N atoms of the chelating dpa ligand and two I- anions (Fig. 1). In the crystal, the dpa ligand is not planar. The dihedral angle between the least-squares planes of the pyridine rings is 51.2 (2)°. The nearly planar pyridine rings [maximum deviation = 0.031 (3) Å] are considerably inclined to the least-squares plane of the PdI2N2 unit [maximum deviation = 0.081 (1) Å], making dihedral angles of 46.5 (1)° and 51.6 (1)°. The Pd—N and Pd—I bond lengths are nearly equivalent, respectively (Table 1). Pairs of complex molecules are assembled through intermolecular N—H···I hydrogen bonds into dimeric species. (Fig. 2 and Table 2). The complexes are stacked in columns along the b axis and display several intermolecular π-π interactions between the pyridine rings, with a shortest ring centroid-centroid distance of 3.957 (3) Å.

Related literature top

For the crystal structure of the related PtII complex [PtI2(dpa)], see: Ha (2012).

Experimental top

To a solution of Na2PdCl4 (0.1461 g, 0.497 mmol) and KI (0.7811 g, 4.705 mmol) in MeOH (30 ml) was added di-2-pyridylamine (0.0862 g, 0.519 mmol) followed by stirring at room temperature for 5 h. The formed precipitate was separated by filtration and washed with H2O and acetone, and dried at 50 °C, to give a dark-orange powder (0.2322 g). Crystals suitable for X-ray analysis were obtained by slow evaporation from a CH3NO2 solution held at room temperature.

Refinement top

Carbon-bound H atoms were positioned geometrically and allowed to ride on their respective parent atoms: C—H = 0.95 Å and Uiso(H) = 1.2Ueq(C). The nitrogen-bound H atom was located from a Fourier difference map and then allowed to ride on its parent atom in the final cycles of refinement with N—H = 0.92 Å and Uiso(H) = 1.5Ueq(N). The highest peak (1.17 e Å-3) and the deepest hole (-0.78 e Å-3) in the difference Fourier map are located 1.99 Å and 0.82 Å, respectively, from the atoms H4 and I2. A number of reflections were omitted from the final cycles of refinement owing to poor agreement.

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 view of the unit-cell contents of the title complex. Intermolecular N—H···I hydrogen-bond interactions are drawn with dashed lines.
(Di-2-pyridylamine-κ2N2,N2')diiodidopalladium(II) top
Crystal data top
[PdI2(C10H9N3)]F(000) = 968
Mr = 531.40Dx = 2.697 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 4274 reflections
a = 8.2846 (8) Åθ = 2.4–28.3°
b = 9.7782 (9) ŵ = 6.11 mm1
c = 16.5355 (14) ÅT = 200 K
β = 102.344 (2)°Block, red
V = 1308.5 (2) Å30.18 × 0.14 × 0.08 mm
Z = 4
Data collection top
Bruker SMART 1000 CCD
diffractometer
3152 independent reflections
Radiation source: fine-focus sealed tube2304 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
φ and ω scansθmax = 28.3°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 1011
Tmin = 0.797, Tmax = 1.000k = 1311
9135 measured reflectionsl = 2218
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)] = 0.028Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.065H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0239P)2]
where P = (Fo2 + 2Fc2)/3
3152 reflections(Δ/σ)max = 0.001
145 parametersΔρmax = 1.17 e Å3
0 restraintsΔρmin = 0.78 e Å3
Crystal data top
[PdI2(C10H9N3)]V = 1308.5 (2) Å3
Mr = 531.40Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.2846 (8) ŵ = 6.11 mm1
b = 9.7782 (9) ÅT = 200 K
c = 16.5355 (14) Å0.18 × 0.14 × 0.08 mm
β = 102.344 (2)°
Data collection top
Bruker SMART 1000 CCD
diffractometer
3152 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
2304 reflections with I > 2σ(I)
Tmin = 0.797, Tmax = 1.000Rint = 0.032
9135 measured reflectionsθmax = 28.3°
Refinement top
R[F2 > 2σ(F2)] = 0.028H-atom parameters constrained
wR(F2) = 0.065Δρmax = 1.17 e Å3
S = 1.01Δρmin = 0.78 e Å3
3152 reflectionsAbsolute structure: ?
145 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
Pd10.07287 (4)0.84262 (4)0.15317 (2)0.02380 (10)
I10.13829 (4)0.86318 (4)0.24664 (2)0.03867 (11)
I20.24276 (4)1.04417 (4)0.230708 (19)0.03719 (11)
N10.0699 (5)0.6997 (4)0.0777 (2)0.0248 (9)
N20.0086 (5)0.8273 (4)0.0325 (2)0.0273 (9)
H2N0.03760.84730.08810.041*
N30.2299 (5)0.8278 (4)0.0718 (2)0.0269 (9)
C10.1482 (6)0.5937 (5)0.1053 (3)0.0288 (11)
H10.12660.57510.16300.035*
C20.2578 (6)0.5121 (5)0.0525 (3)0.0340 (12)
H20.31090.43810.07350.041*
C30.2900 (6)0.5389 (5)0.0318 (3)0.0336 (12)
H30.36790.48530.06920.040*
C40.2078 (6)0.6437 (5)0.0604 (3)0.0299 (11)
H40.22660.66250.11800.036*
C50.0973 (5)0.7219 (5)0.0047 (3)0.0227 (10)
C60.1623 (6)0.8357 (5)0.0085 (3)0.0267 (11)
C70.2600 (6)0.8499 (5)0.0670 (3)0.0301 (12)
H70.20970.86150.12380.036*
C80.4280 (6)0.8469 (5)0.0424 (3)0.0352 (13)
H80.49610.85740.08150.042*
C90.4975 (6)0.8284 (5)0.0412 (3)0.0343 (12)
H90.61380.82030.05970.041*
C100.3965 (6)0.8219 (5)0.0962 (3)0.0293 (11)
H100.44460.81300.15350.035*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.0271 (2)0.0261 (2)0.01677 (18)0.00202 (16)0.00160 (15)0.00029 (15)
I10.0427 (2)0.0497 (3)0.02587 (19)0.00181 (17)0.01239 (16)0.00231 (16)
I20.0485 (2)0.0335 (2)0.02414 (18)0.00877 (16)0.00439 (15)0.00119 (14)
N10.027 (2)0.023 (2)0.023 (2)0.0005 (17)0.0030 (17)0.0009 (17)
N20.030 (2)0.031 (3)0.018 (2)0.0062 (18)0.0007 (17)0.0053 (17)
N30.030 (2)0.026 (2)0.023 (2)0.0013 (18)0.0020 (18)0.0016 (17)
C10.032 (3)0.024 (3)0.032 (3)0.002 (2)0.010 (2)0.005 (2)
C20.036 (3)0.028 (3)0.039 (3)0.007 (2)0.011 (2)0.002 (2)
C30.032 (3)0.029 (3)0.039 (3)0.009 (2)0.006 (2)0.011 (2)
C40.042 (3)0.028 (3)0.019 (2)0.001 (2)0.006 (2)0.004 (2)
C50.024 (2)0.026 (3)0.018 (2)0.002 (2)0.0038 (19)0.0044 (19)
C60.036 (3)0.019 (3)0.025 (3)0.000 (2)0.005 (2)0.000 (2)
C70.043 (3)0.023 (3)0.028 (3)0.004 (2)0.015 (2)0.003 (2)
C80.040 (3)0.029 (3)0.043 (3)0.004 (2)0.022 (3)0.003 (2)
C90.031 (3)0.029 (3)0.043 (3)0.000 (2)0.008 (2)0.001 (2)
C100.024 (2)0.022 (3)0.038 (3)0.000 (2)0.001 (2)0.001 (2)
Geometric parameters (Å, º) top
Pd1—N12.068 (4)C2—H20.9500
Pd1—N32.067 (4)C3—C41.370 (7)
Pd1—I12.5780 (5)C3—H30.9500
Pd1—I22.5957 (5)C4—C51.382 (6)
N1—C51.351 (5)C4—H40.9500
N1—C11.353 (6)C6—C71.394 (6)
N2—C61.389 (6)C7—C81.365 (7)
N2—C51.399 (6)C7—H70.9500
N2—H2N0.9200C8—C91.390 (7)
N3—C61.329 (6)C8—H80.9500
N3—C101.354 (6)C9—C101.362 (7)
C1—C21.372 (7)C9—H90.9500
C1—H10.9500C10—H100.9500
C2—C31.388 (7)
N3—Pd1—N185.31 (15)C2—C3—H3120.5
N3—Pd1—I1176.37 (11)C3—C4—C5119.4 (4)
N1—Pd1—I192.33 (10)C3—C4—H4120.3
N3—Pd1—I291.40 (11)C5—C4—H4120.3
N1—Pd1—I2172.21 (11)N1—C5—C4121.9 (4)
I1—Pd1—I290.598 (16)N1—C5—N2117.5 (4)
C5—N1—C1118.3 (4)C4—C5—N2120.6 (4)
C5—N1—Pd1116.8 (3)N3—C6—N2117.9 (4)
C1—N1—Pd1124.6 (3)N3—C6—C7121.1 (4)
C6—N2—C5121.6 (4)N2—C6—C7121.0 (4)
C6—N2—H2N107.8C8—C7—C6119.8 (5)
C5—N2—H2N116.2C8—C7—H7120.1
C6—N3—C10119.0 (4)C6—C7—H7120.1
C6—N3—Pd1117.2 (3)C7—C8—C9118.6 (5)
C10—N3—Pd1123.6 (3)C7—C8—H8120.7
N1—C1—C2122.1 (4)C9—C8—H8120.7
N1—C1—H1118.9C10—C9—C8119.1 (5)
C2—C1—H1118.9C10—C9—H9120.4
C1—C2—C3119.2 (5)C8—C9—H9120.4
C1—C2—H2120.4N3—C10—C9122.1 (5)
C3—C2—H2120.4N3—C10—H10118.9
C4—C3—C2119.1 (5)C9—C10—H10118.9
C4—C3—H3120.5
N3—Pd1—N1—C546.2 (3)C3—C4—C5—N11.3 (7)
I1—Pd1—N1—C5131.0 (3)C3—C4—C5—N2178.3 (4)
N3—Pd1—N1—C1139.7 (4)C6—N2—C5—N152.2 (6)
I1—Pd1—N1—C143.0 (4)C6—N2—C5—C4127.4 (5)
N1—Pd1—N3—C648.2 (4)C10—N3—C6—N2173.5 (4)
I2—Pd1—N3—C6124.7 (3)Pd1—N3—C6—N211.9 (6)
N1—Pd1—N3—C10137.4 (4)C10—N3—C6—C75.6 (7)
I2—Pd1—N3—C1049.7 (4)Pd1—N3—C6—C7169.1 (4)
C5—N1—C1—C22.3 (7)C5—N2—C6—N350.6 (6)
Pd1—N1—C1—C2171.7 (4)C5—N2—C6—C7128.5 (5)
N1—C1—C2—C30.1 (8)N3—C6—C7—C84.2 (7)
C1—C2—C3—C41.9 (8)N2—C6—C7—C8174.8 (5)
C2—C3—C4—C51.2 (8)C6—C7—C8—C90.6 (8)
C1—N1—C5—C43.0 (7)C7—C8—C9—C103.9 (8)
Pd1—N1—C5—C4171.4 (4)C6—N3—C10—C92.2 (7)
C1—N1—C5—N2176.6 (4)Pd1—N3—C10—C9172.1 (4)
Pd1—N1—C5—N29.0 (5)C8—C9—C10—N32.6 (8)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···I2i0.922.803.656 (4)155
Symmetry code: (i) x, y+2, z.
Selected bond lengths (Å) top
Pd1—N12.068 (4)Pd1—I12.5780 (5)
Pd1—N32.067 (4)Pd1—I22.5957 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···I2i0.922.803.656 (4)154.5
Symmetry code: (i) x, y+2, z.
Acknowledgements top

This work was supported by 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.

Ha, K. (2012). Acta Cryst. E68, m479.

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

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