metal-organic compounds
(Di-2-pyridylamine-κ2N2,N2′)diiodidopalladium(II)
aSchool of Applied Chemical Engineering, The Research Institute of Catalysis, Chonnam National University, Gwangju 500-757, Republic of Korea
*Correspondence e-mail: hakwang@chonnam.ac.kr
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 π–π interactions between the pyridine rings, with a shortest ring centroid–centroid distance of 3.957 (3) Å.
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 2000); cell 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.
Supporting information
10.1107/S1600536812033946/tk5137sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812033946/tk5137Isup2.hkl
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.
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
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 owing to poor agreement.Data collection: SMART (Bruker, 2000); cell
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).[PdI2(C10H9N3)] | F(000) = 968 |
Mr = 531.40 | Dx = 2.697 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 4274 reflections |
a = 8.2846 (8) Å | θ = 2.4–28.3° |
b = 9.7782 (9) Å | µ = 6.11 mm−1 |
c = 16.5355 (14) Å | T = 200 K |
β = 102.344 (2)° | Block, red |
V = 1308.5 (2) Å3 | 0.18 × 0.14 × 0.08 mm |
Z = 4 |
Bruker SMART 1000 CCD diffractometer | 3152 independent reflections |
Radiation source: fine-focus sealed tube | 2304 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.032 |
ϕ and ω scans | θmax = 28.3°, θmin = 2.4° |
Absorption correction: multi-scan (SADABS; Bruker, 2000) | h = −10→11 |
Tmin = 0.797, Tmax = 1.000 | k = −13→11 |
9135 measured reflections | l = −22→18 |
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)] = 0.028 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.065 | H-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 parameters | Δρmax = 1.17 e Å−3 |
0 restraints | Δρmin = −0.78 e Å−3 |
[PdI2(C10H9N3)] | V = 1308.5 (2) Å3 |
Mr = 531.40 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 8.2846 (8) Å | µ = 6.11 mm−1 |
b = 9.7782 (9) Å | T = 200 K |
c = 16.5355 (14) Å | 0.18 × 0.14 × 0.08 mm |
β = 102.344 (2)° |
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 = 1.000 | Rint = 0.032 |
9135 measured reflections |
R[F2 > 2σ(F2)] = 0.028 | 0 restraints |
wR(F2) = 0.065 | H-atom parameters constrained |
S = 1.01 | Δρmax = 1.17 e Å−3 |
3152 reflections | Δρmin = −0.78 e Å−3 |
145 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Pd1 | 0.07287 (4) | 0.84262 (4) | 0.15317 (2) | 0.02380 (10) | |
I1 | −0.13829 (4) | 0.86318 (4) | 0.24664 (2) | 0.03867 (11) | |
I2 | 0.24276 (4) | 1.04417 (4) | 0.230708 (19) | 0.03719 (11) | |
N1 | −0.0699 (5) | 0.6997 (4) | 0.0777 (2) | 0.0248 (9) | |
N2 | −0.0086 (5) | 0.8273 (4) | −0.0325 (2) | 0.0273 (9) | |
H2N | −0.0376 | 0.8473 | −0.0881 | 0.041* | |
N3 | 0.2299 (5) | 0.8278 (4) | 0.0718 (2) | 0.0269 (9) | |
C1 | −0.1482 (6) | 0.5937 (5) | 0.1053 (3) | 0.0288 (11) | |
H1 | −0.1266 | 0.5751 | 0.1630 | 0.035* | |
C2 | −0.2578 (6) | 0.5121 (5) | 0.0525 (3) | 0.0340 (12) | |
H2 | −0.3109 | 0.4381 | 0.0735 | 0.041* | |
C3 | −0.2900 (6) | 0.5389 (5) | −0.0318 (3) | 0.0336 (12) | |
H3 | −0.3679 | 0.4853 | −0.0692 | 0.040* | |
C4 | −0.2078 (6) | 0.6437 (5) | −0.0604 (3) | 0.0299 (11) | |
H4 | −0.2266 | 0.6625 | −0.1180 | 0.036* | |
C5 | −0.0973 (5) | 0.7219 (5) | −0.0047 (3) | 0.0227 (10) | |
C6 | 0.1623 (6) | 0.8357 (5) | −0.0085 (3) | 0.0267 (11) | |
C7 | 0.2600 (6) | 0.8499 (5) | −0.0670 (3) | 0.0301 (12) | |
H7 | 0.2097 | 0.8615 | −0.1238 | 0.036* | |
C8 | 0.4280 (6) | 0.8469 (5) | −0.0424 (3) | 0.0352 (13) | |
H8 | 0.4961 | 0.8574 | −0.0815 | 0.042* | |
C9 | 0.4975 (6) | 0.8284 (5) | 0.0412 (3) | 0.0343 (12) | |
H9 | 0.6138 | 0.8203 | 0.0597 | 0.041* | |
C10 | 0.3965 (6) | 0.8219 (5) | 0.0962 (3) | 0.0293 (11) | |
H10 | 0.4446 | 0.8130 | 0.1535 | 0.035* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.0271 (2) | 0.0261 (2) | 0.01677 (18) | −0.00202 (16) | 0.00160 (15) | 0.00029 (15) |
I1 | 0.0427 (2) | 0.0497 (3) | 0.02587 (19) | 0.00181 (17) | 0.01239 (16) | −0.00231 (16) |
I2 | 0.0485 (2) | 0.0335 (2) | 0.02414 (18) | −0.00877 (16) | −0.00439 (15) | −0.00119 (14) |
N1 | 0.027 (2) | 0.023 (2) | 0.023 (2) | 0.0005 (17) | 0.0030 (17) | 0.0009 (17) |
N2 | 0.030 (2) | 0.031 (3) | 0.018 (2) | −0.0062 (18) | 0.0007 (17) | 0.0053 (17) |
N3 | 0.030 (2) | 0.026 (2) | 0.023 (2) | −0.0013 (18) | 0.0020 (18) | −0.0016 (17) |
C1 | 0.032 (3) | 0.024 (3) | 0.032 (3) | 0.002 (2) | 0.010 (2) | 0.005 (2) |
C2 | 0.036 (3) | 0.028 (3) | 0.039 (3) | −0.007 (2) | 0.011 (2) | −0.002 (2) |
C3 | 0.032 (3) | 0.029 (3) | 0.039 (3) | −0.009 (2) | 0.006 (2) | −0.011 (2) |
C4 | 0.042 (3) | 0.028 (3) | 0.019 (2) | −0.001 (2) | 0.006 (2) | −0.004 (2) |
C5 | 0.024 (2) | 0.026 (3) | 0.018 (2) | 0.002 (2) | 0.0038 (19) | −0.0044 (19) |
C6 | 0.036 (3) | 0.019 (3) | 0.025 (3) | 0.000 (2) | 0.005 (2) | 0.000 (2) |
C7 | 0.043 (3) | 0.023 (3) | 0.028 (3) | −0.004 (2) | 0.015 (2) | 0.003 (2) |
C8 | 0.040 (3) | 0.029 (3) | 0.043 (3) | −0.004 (2) | 0.022 (3) | −0.003 (2) |
C9 | 0.031 (3) | 0.029 (3) | 0.043 (3) | 0.000 (2) | 0.008 (2) | 0.001 (2) |
C10 | 0.024 (2) | 0.022 (3) | 0.038 (3) | 0.000 (2) | −0.001 (2) | −0.001 (2) |
Pd1—N1 | 2.068 (4) | C2—H2 | 0.9500 |
Pd1—N3 | 2.067 (4) | C3—C4 | 1.370 (7) |
Pd1—I1 | 2.5780 (5) | C3—H3 | 0.9500 |
Pd1—I2 | 2.5957 (5) | C4—C5 | 1.382 (6) |
N1—C5 | 1.351 (5) | C4—H4 | 0.9500 |
N1—C1 | 1.353 (6) | C6—C7 | 1.394 (6) |
N2—C6 | 1.389 (6) | C7—C8 | 1.365 (7) |
N2—C5 | 1.399 (6) | C7—H7 | 0.9500 |
N2—H2N | 0.9200 | C8—C9 | 1.390 (7) |
N3—C6 | 1.329 (6) | C8—H8 | 0.9500 |
N3—C10 | 1.354 (6) | C9—C10 | 1.362 (7) |
C1—C2 | 1.372 (7) | C9—H9 | 0.9500 |
C1—H1 | 0.9500 | C10—H10 | 0.9500 |
C2—C3 | 1.388 (7) | ||
N3—Pd1—N1 | 85.31 (15) | C2—C3—H3 | 120.5 |
N3—Pd1—I1 | 176.37 (11) | C3—C4—C5 | 119.4 (4) |
N1—Pd1—I1 | 92.33 (10) | C3—C4—H4 | 120.3 |
N3—Pd1—I2 | 91.40 (11) | C5—C4—H4 | 120.3 |
N1—Pd1—I2 | 172.21 (11) | N1—C5—C4 | 121.9 (4) |
I1—Pd1—I2 | 90.598 (16) | N1—C5—N2 | 117.5 (4) |
C5—N1—C1 | 118.3 (4) | C4—C5—N2 | 120.6 (4) |
C5—N1—Pd1 | 116.8 (3) | N3—C6—N2 | 117.9 (4) |
C1—N1—Pd1 | 124.6 (3) | N3—C6—C7 | 121.1 (4) |
C6—N2—C5 | 121.6 (4) | N2—C6—C7 | 121.0 (4) |
C6—N2—H2N | 107.8 | C8—C7—C6 | 119.8 (5) |
C5—N2—H2N | 116.2 | C8—C7—H7 | 120.1 |
C6—N3—C10 | 119.0 (4) | C6—C7—H7 | 120.1 |
C6—N3—Pd1 | 117.2 (3) | C7—C8—C9 | 118.6 (5) |
C10—N3—Pd1 | 123.6 (3) | C7—C8—H8 | 120.7 |
N1—C1—C2 | 122.1 (4) | C9—C8—H8 | 120.7 |
N1—C1—H1 | 118.9 | C10—C9—C8 | 119.1 (5) |
C2—C1—H1 | 118.9 | C10—C9—H9 | 120.4 |
C1—C2—C3 | 119.2 (5) | C8—C9—H9 | 120.4 |
C1—C2—H2 | 120.4 | N3—C10—C9 | 122.1 (5) |
C3—C2—H2 | 120.4 | N3—C10—H10 | 118.9 |
C4—C3—C2 | 119.1 (5) | C9—C10—H10 | 118.9 |
C4—C3—H3 | 120.5 | ||
N3—Pd1—N1—C5 | −46.2 (3) | C3—C4—C5—N1 | −1.3 (7) |
I1—Pd1—N1—C5 | 131.0 (3) | C3—C4—C5—N2 | 178.3 (4) |
N3—Pd1—N1—C1 | 139.7 (4) | C6—N2—C5—N1 | 52.2 (6) |
I1—Pd1—N1—C1 | −43.0 (4) | C6—N2—C5—C4 | −127.4 (5) |
N1—Pd1—N3—C6 | 48.2 (4) | C10—N3—C6—N2 | 173.5 (4) |
I2—Pd1—N3—C6 | −124.7 (3) | Pd1—N3—C6—N2 | −11.9 (6) |
N1—Pd1—N3—C10 | −137.4 (4) | C10—N3—C6—C7 | −5.6 (7) |
I2—Pd1—N3—C10 | 49.7 (4) | Pd1—N3—C6—C7 | 169.1 (4) |
C5—N1—C1—C2 | −2.3 (7) | C5—N2—C6—N3 | −50.6 (6) |
Pd1—N1—C1—C2 | 171.7 (4) | C5—N2—C6—C7 | 128.5 (5) |
N1—C1—C2—C3 | −0.1 (8) | N3—C6—C7—C8 | 4.2 (7) |
C1—C2—C3—C4 | 1.9 (8) | N2—C6—C7—C8 | −174.8 (5) |
C2—C3—C4—C5 | −1.2 (8) | C6—C7—C8—C9 | 0.6 (8) |
C1—N1—C5—C4 | 3.0 (7) | C7—C8—C9—C10 | −3.9 (8) |
Pd1—N1—C5—C4 | −171.4 (4) | C6—N3—C10—C9 | 2.2 (7) |
C1—N1—C5—N2 | −176.6 (4) | Pd1—N3—C10—C9 | −172.1 (4) |
Pd1—N1—C5—N2 | 9.0 (5) | C8—C9—C10—N3 | 2.6 (8) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···I2i | 0.92 | 2.80 | 3.656 (4) | 155 |
Symmetry code: (i) −x, −y+2, −z. |
Experimental details
Crystal data | |
Chemical formula | [PdI2(C10H9N3)] |
Mr | 531.40 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 200 |
a, b, c (Å) | 8.2846 (8), 9.7782 (9), 16.5355 (14) |
β (°) | 102.344 (2) |
V (Å3) | 1308.5 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 6.11 |
Crystal size (mm) | 0.18 × 0.14 × 0.08 |
Data collection | |
Diffractometer | Bruker SMART 1000 CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2000) |
Tmin, Tmax | 0.797, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9135, 3152, 2304 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.667 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.028, 0.065, 1.01 |
No. of reflections | 3152 |
No. of parameters | 145 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 1.17, −0.78 |
Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···I2i | 0.92 | 2.80 | 3.656 (4) | 154.5 |
Symmetry code: (i) −x, −y+2, −z. |
Acknowledgements
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
Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Ha, K. (2012). Acta Cryst. E68, m479. CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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.