metal-organic compounds
Dichlorido(o-phenylenediamine)palladium(II)
aDepartment of Chemistry, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902, Japan, and bDepartment of Chemistry and Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan
*Correspondence e-mail: cnmatsu@rikkyo.ac.jp
The PdII atom in the title compound, [PdCl2{(C6H4)(NH2)2}], lies on a twofold rotation axis and has a square-planar coordination environment defined by two N atoms of an o-phenylenediamine ligand and two Cl− ions. In the crystal, the planar Pd complex molecules are stacked parallel to the c axis, resulting in a columnar structure. In the column, an infinite almost straight Pd chain is formed, suggesting weak metal–metal interactions. The crystal packing is stabilized by a three-dimensional N—H⋯Cl hydrogen-bonding network between the amino groups and the Cl ligands of adjacent molecules.
Keywords: crystal structure; columnar structure; infinite metal chain; palladium(II) complex; hydrogen bonding.
CCDC reference: 1055178
Structure description
The molecular structure of the title compound is displayed in Fig. 1. Its comprises half of a [PdCl2{(C6H4)(NH2)2}] molecule, the other half being completed by application of a twofold rotation operation. The PdII atom is coordinated by two N atoms of an o-phenylenediamine molecule and two Cl− ions in a slightly distorted square-planar configuration (Table 1). The r.m.s. deviation of the least-squares plane formed by atoms Pd1, N1, C1, C2 and C3 is 0.0176 Å. The Pd1—N1 [2.0297 (13) Å] and Pd1—Cl1 [2.3159 (4) Å] bond lengths are consistent with those reported for cis-[PdCl2(NH3)2] [Pd—N = 1.99 (4) and 2.13 (4) Å, Pd—Cl = 2.26 (2) and 2.29 (2) Å; Kirik et al., 1996], for [PdCl2(en)] [en is ethylenediamine; Pd—N = 1.978 (12) Å, Pd—Cl = 2.309 (3) Å; Iball et al., 1975] or for [PdCl2(tn)] [tn is 1,3-diaminopropane; Pd—N = 2.036 (2) Å, Pd—Cl = 2.3296 (15) Å; Odoko & Okabe, 2006]. Bond lengths and angles of the o-phenylenediamine moiety (Table 1) are not significantly different from those of the bis(o-phenylenediamine)platinum(II) complex, [Pt(C6H8N2)2]Cl2·2H2O [N—C = 1.450 (2) Å, C—C = 1.365 (6)–1.389 (4) Å; Konno & Matsushita, 2006].
As shown in Fig. 2, the neutral planar molecules of the title compound stack parallel to the c axis, resulting in a columnar structure. The planar [PdCl2{(C6H4)(NH2)2}] units are arranged in parallel and the o-phenylenediamine moieties alternate with each other owing to the c-glide operation. In the column, an infinite almost straight [Pd⋯Pd⋯Pd = 179.232 (7)°] Pd chain is formed with a short interatomic distance [Pd⋯Pd = 3.3510 (6) Å], suggesting weak metal–metal interactions. The Pd⋯Pd distance of the title compound is slightly shorter than those of cis-[PdCl2(NH3)2] [3.3886 (1) Å; Kirik et al., 1996] or [PdCl2(en)] [3.369 Å; Iball et al., 1975], which have similar columnar structures.
The shorter intermolecular Pd⋯Pd distance of the title compound suggests that the columnar structure is stabilized by weak metal–metal interactions. The columnar structure of the title compound is further stabilized by intermolecular N—H⋯Cl hydrogen bonds between adjacent molecules in the column (Fig. 2 and Table 2). Intercolumnar hydrogen bonds also help to stabilize the crystal packing of the columns (Fig. 3 and Table 2).
Synthesis and crystallization
To an aqueous HCl solution (1.0 M, 20 ml) of K2[PdCl4] (0.050 mmol, 16 mg) was slowly added an aqueous HCl solution (1.0 M, 20 ml) of o-phenylenediamine (0.050 mmol, 5 mg), and then the solution was sealed in a screw-cap vial and was kept at 323 K for 24 h in the dark. Pale-yellow needle-like crystals suitable for X-ray analysis were obtained (yield 28%). Elemental analysis: found: C, 25.17; H, 2.93; N, 9.64%, calculated for C6H8Cl2N2Pd: C, 25.24; H, 2.82; N, 9.81%. Elemental analysis was carried out by Laboratory of Organic Elemental Analysis, Department of Chemistry, Graduate School of Science, The University of Tokyo.
Refinement
Crystal data, data collection and structure . The maximum and minimum electron density peaks are located 1.68 Å from atom Pd1 and 0.78 Å from atom Pd1, respectively.
details are summarized in Table 3
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Structural data
CCDC reference: 1055178
https://doi.org/10.1107/S2414314617001444/wm4038sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617001444/wm4038Isup2.hkl
Data collection: RAPID-AUTO (Rigaku, 1998); cell
RAPID-AUTO (Rigaku, 1998); data reduction: RAPID-AUTO (Rigaku, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2017); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).[PdCl2(C6H8N2)] | F(000) = 276 |
Mr = 285.44 | Dx = 2.150 Mg m−3 |
Monoclinic, P2/c | Mo Kα radiation, λ = 0.71075 Å |
Hall symbol: -P 2yc | Cell parameters from 6414 reflections |
a = 7.0734 (8) Å | θ = 3.9–32.2° |
b = 10.4076 (12) Å | µ = 2.65 mm−1 |
c = 6.7019 (12) Å | T = 296 K |
β = 116.683 (4)° | Needle, pale yellow |
V = 440.83 (11) Å3 | 0.22 × 0.11 × 0.07 mm |
Z = 2 |
Rigaku R-AXIS RAPID imaging-plate diffractometer | 1578 independent reflections |
Radiation source: X-ray sealed tube | 1449 reflections with F2 > 2σ(F2) |
Graphite monochromator | Rint = 0.022 |
Detector resolution: 10.00 pixels mm-1 | θmax = 32.5°, θmin = 3.2° |
ω scans | h = −10→10 |
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | k = −15→15 |
Tmin = 0.611, Tmax = 0.824 | l = −9→10 |
11439 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.020 | H-atom parameters constrained |
wR(F2) = 0.053 | w = 1/[σ2(Fo2) + (0.032P)2 + 0.0862P] where P = (Fo2 + 2Fc2)/3 |
S = 1.09 | (Δ/σ)max < 0.001 |
1578 reflections | Δρmax = 1.07 e Å−3 |
52 parameters | Δρmin = −0.77 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.126 (4) |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane) - 2.4031 (0.0035) x + 0.0000 (0.0000) y + 6.6544 (0.0013) z = 0.4621 (0.0016) * 0.0000 (0.0000) Pd1 * -0.0263 (0.0008) Cl1 * 0.0315 (0.0013) N1 * 0.0022 (0.0014) C1 * -0.0016 (0.0015) C2 * 0.0034 (0.0028) C3 * 0.0263 (0.0008) Cl1_$6 * -0.0315 (0.0013) N1_$6 * -0.0022 (0.0014) C1_$6 * 0.0016 (0.0015) C2_$6 * -0.0034 (0.0028) C3_$6 Rms deviation of fitted atoms = 0.0176 |
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 > 2sigma(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 | 0.5000 | 0.498921 (11) | 0.2500 | 0.03038 (8) | |
Cl1 | 0.23288 (6) | 0.65031 (4) | 0.14958 (7) | 0.04182 (10) | |
N1 | 0.2865 (2) | 0.35440 (13) | 0.1776 (2) | 0.0406 (3) | |
H1A | 0.2218 | 0.3604 | 0.2662 | 0.049* | |
H1B | 0.1874 | 0.3613 | 0.0349 | 0.049* | |
C1 | 0.3920 (2) | 0.23028 (14) | 0.2113 (2) | 0.0412 (3) | |
C2 | 0.2807 (4) | 0.11529 (17) | 0.1706 (3) | 0.0571 (4) | |
H2 | 0.1345 | 0.1157 | 0.1169 | 0.069* | |
C3 | 0.3889 (6) | 0.00139 (14) | 0.2104 (5) | 0.0720 (10) | |
H3 | 0.3161 | −0.0760 | 0.1853 | 0.086* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.02747 (9) | 0.03112 (10) | 0.02949 (10) | 0.000 | 0.01007 (6) | 0.000 |
Cl1 | 0.03435 (16) | 0.03968 (17) | 0.0480 (2) | 0.00551 (12) | 0.01543 (14) | 0.00033 (14) |
N1 | 0.0340 (6) | 0.0396 (6) | 0.0424 (6) | −0.0047 (5) | 0.0120 (5) | −0.0018 (5) |
C1 | 0.0559 (8) | 0.0341 (6) | 0.0324 (6) | −0.0043 (5) | 0.0188 (6) | −0.0011 (5) |
C2 | 0.0783 (12) | 0.0449 (8) | 0.0486 (9) | −0.0199 (8) | 0.0288 (9) | −0.0076 (7) |
C3 | 0.132 (3) | 0.0362 (9) | 0.0565 (15) | −0.0183 (8) | 0.0496 (19) | −0.0068 (6) |
Pd1—N1 | 2.0297 (13) | N1—H1B | 0.9000 |
Pd1—N1i | 2.0297 (13) | C1—C1i | 1.375 (3) |
Pd1—Cl1i | 2.3159 (4) | C1—C2 | 1.391 (2) |
Pd1—Cl1 | 2.3159 (4) | C2—C3 | 1.371 (3) |
Pd1—Pd1ii | 3.3510 (6) | C2—H2 | 0.9300 |
Pd1—Pd1iii | 3.3510 (6) | C3—C3i | 1.416 (8) |
N1—C1 | 1.458 (2) | C3—H3 | 0.9300 |
N1—H1A | 0.9000 | ||
N1—Pd1—N1i | 84.36 (8) | C1—N1—Pd1 | 110.22 (10) |
N1—Pd1—Cl1i | 174.81 (4) | C1—N1—H1A | 109.6 |
N1i—Pd1—Cl1i | 90.71 (4) | Pd1—N1—H1A | 109.6 |
N1—Pd1—Cl1 | 90.71 (4) | C1—N1—H1B | 109.6 |
N1i—Pd1—Cl1 | 174.81 (4) | Pd1—N1—H1B | 109.6 |
Cl1i—Pd1—Cl1 | 94.26 (2) | H1A—N1—H1B | 108.1 |
N1—Pd1—Pd1ii | 95.75 (4) | C1i—C1—C2 | 120.62 (12) |
N1i—Pd1—Pd1ii | 84.83 (4) | C1i—C1—N1 | 117.58 (8) |
Cl1i—Pd1—Pd1ii | 85.393 (12) | C2—C1—N1 | 121.80 (16) |
Cl1—Pd1—Pd1ii | 94.083 (12) | C3—C2—C1 | 119.3 (2) |
N1—Pd1—Pd1iii | 84.83 (4) | C3—C2—H2 | 120.4 |
N1i—Pd1—Pd1iii | 95.75 (4) | C1—C2—H2 | 120.4 |
Cl1i—Pd1—Pd1iii | 94.083 (12) | C2—C3—C3i | 120.13 (16) |
Cl1—Pd1—Pd1iii | 85.393 (12) | C2—C3—H3 | 119.9 |
Pd1ii—Pd1—Pd1iii | 179.232 (7) | C3i—C3—H3 | 119.9 |
N1i—Pd1—N1—C1 | −0.57 (7) | Pd1—N1—C1—C1i | 1.8 (2) |
Cl1i—Pd1—N1—C1 | −18.8 (5) | Pd1—N1—C1—C2 | −179.16 (12) |
Cl1—Pd1—N1—C1 | 177.81 (10) | C1i—C1—C2—C3 | 0.6 (3) |
Pd1ii—Pd1—N1—C1 | 83.63 (10) | N1—C1—C2—C3 | −178.4 (2) |
Pd1iii—Pd1—N1—C1 | −96.89 (10) | C1—C2—C3—C3i | −0.7 (5) |
Symmetry codes: (i) −x+1, y, −z+1/2; (ii) −x+1, −y+1, −z; (iii) −x+1, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···Cl1iv | 0.90 | 2.54 | 3.3508 (15) | 151 |
N1—H1B···Cl1v | 0.90 | 2.74 | 3.3860 (15) | 129 |
N1—H1B···Cl1vi | 0.90 | 2.66 | 3.3278 (15) | 132 |
Symmetry codes: (iv) x, −y+1, z+1/2; (v) x, −y+1, z−1/2; (vi) −x, −y+1, −z. |
Acknowledgements
This work was partly supported by a MEXT-Supported Program for the Strategic Research Foundation at Private Universities (project No. S1311027) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.
References
Brandenburg, K. (2017). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Iball, J., MacDougall, M. & Scrimgeour, S. (1975). Acta Cryst. B31, 1672–1674. CSD CrossRef CAS IUCr Journals Web of Science Google Scholar
Kirik, S. D., Solovyov, L. A., Blokhin, A. I., Yakimov, I. S. & Blokhina, M. L. (1996). Acta Cryst. B52, 909–916. CrossRef CAS Web of Science IUCr Journals Google Scholar
Konno, Y. & Matsushita, N. (2006). Bull. Chem. Soc. Jpn, 79, 1046–1053. Web of Science CSD CrossRef CAS Google Scholar
Odoko, M. & Okabe, N. (2006). Acta Cryst. C62, m136–m139. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar
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