research communications
(μ-Methylenediphosphonato-κ4O,O′:O′′,O′′′)bis[(ethylenediamine-κ2N,N′)palladium(II)] tetrahydrate
aSSI "Institute for Single Crystals", National Academy of Sciences of Ukraine, Nauki Ave 60, Kharkiv 61001, Ukraine, bV.I. Vernadsky Institute of General and Inorganic Chemistry of the National Academy of Sciences of Ukraine, Kyiv, Ukraine, and cNational University of Life and Environmental Science of Ukraine, Kyiv, Ukraine
*Correspondence e-mail: vika@xray.isc.kharkov.com
The title compound, [Pd2(C2H8N2)2(CH2O6P2)]·4H2O, comprises of a binuclear molecule (point group symmetry 2), with a twofold rotation axis running through the central C atom of the methylenediphosphonate (MDP) anion. The PdII atom has a square-planar coordination environment defined by the N atoms of a bidentate ethylenediamine (en) ligand and two O atoms of the bridging MDP anion. In the metal complexes are arranged in layers parallel (001) and are sandwiched between layers containing disordered water molecules of crystallization. Extensive intralayer hydrogen bonds of the type N—H⋯O in the metal complex layer and O—H⋯O in the water layer, as well as O—H⋯O hydrogen bonds between the two types of layers, lead to the formation a three-dimensional network structure. The two lattice water molecules are each equally disordered over two positions.
Keywords: crystal structure; ethylenediamine palladium; methylenediphosphonate; anticancer agents.
CCDC reference: 1879750
1. Chemical context
Platinum drugs are some of the most important and clinically applied anti-cancer agents. Diphosphonic acids are therapeutic agents for treating osteoporosis and metastatic bone diseases. Therefore new complexes designed with a combination of platinum group metals with diphosphonic acid (or derivatives thereof) as bone-targeting groups can improve the chemotherapeutic efficacy in the treatment of bone cancer and can reduce adverse effects. Methylenediphosphonic acid (medronic acid, MDP, H4L) is the smallest bisphosphonate, which accumulates on the sites of osteoid mineralization and can be used in combination with platinum metals to treat cancer and metastatic bone diseases. Platinum–bisphosphonate complexes, including bis{ethylenediamine)platinum(II)}medronate, as novel Pt-prodrugs in the local treatment of bone tumors have been reported (Wani et al., 2016; Iafisco et al., 2009; Palazzo et al., 2007; Iafisco & Margiotta, 2012; Margiotta et al., 2009). The preparation and of [Pt2(cis-diaminohexane)2(methylenediphosphonate)] was reported by Bau et al. (1988).
In this work, we synthesized a new platinum metal complex, viz. [Pd2(C2H8N2)2(CH2O6P2)]·4H2O or [Pd2(en)2(MDP)]·4H2O, and report here its molecular and crystal structures.
2. Structural commentary
The binuclear [Pd2(en)2(MDP)] complex molecule is uncharged and exhibits symmetry 2, with the twofold rotation axis passing through the central C atom of the MDP ligand (Fig. 1). The PdII atom has a square-planar environment defined by two nitrogen atoms (N1 and N2) of the chelating en ligand and two oxygen atoms (O2 and O3) of the bis-bidentately coordinating MDP ligand that bridges two symmetry-related PdII atoms into the binuclear complex. The deviation of the Pd1 site from the least-squares plane involving the ligand atoms N1, N2, O2 and O3 is 0.06 Å. The Pd—N and Pd—O bond lengths are in typical ranges whereby the Pd—N bonds are about 0.02 Å shorter than the Pd—O bonds (Table 1). The O—Pd—O, N—Pd—N and O—Pd—N bond angles vary within 84.5 (2)°–93.3 (2)° (Table 1) and indicate a slight distortion from a square-planar coordination. In general, the structural features of the [Pd2(en)2(MDP)] complex are similar to those of the related complex [Pd2(en)2EDP] where EDP is 1-hydroxyethane 1,1-diphosphonate or etidronate (Kozachkova et al., 2018).
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The Pd1—O1—P1—C3—P1i—O1i [symmetry code: (i) − x, − y, z] six-membered metallacycle adopts a chair conformation; the puckering parameters (Cremer & Pople, 1975; Zefirov et al., 1990) are S = 1.19, ψ = 16.52°, θ = 3.02°. The Pd1 and C3 atoms deviate by −0.95 and 0.82 Å, respectively, from the least-squares plane of the remaining atoms of this metallacycle with an s.u. of 0.01 Å. The Pd1—N1—C2—C1—N2 five-membered metallacycle involving the en ligand adopts an The N1 atom deviates by 0.27 Å from the mean plane of the remaining atoms (the s.u. of this plane is 0.005 Å).
3. Supramolecular features
In the crystal, [Pd2(en)2(MDP)] molecules are linked via (en)N1—H1A⋯O1ii(MDP) hydrogen bonds (Fig. 2, Table 2), forming chains parallel to [010]. Neighboring chains are connected to each other through (en)N2—H2A⋯O3iii(MDP) and (en)N1—H1B⋯O3iv(MDP) hydrogen bonds, forming layers parallel to (001). The disordered water molecules O4 and O5 are located between these layers and are connected to each other by O—H⋯O hydrogen bonds (Table 2), forming a sandwich-type structure. The structural disorder of the water molecules is probably caused by different possibilities of possible positions favourable for hydrogen bonding with neighbouring molecules. Alternating layers containing [Pd2(en)2(MDP)] complexes and water molecules are stacked along [001] and are linked to each other by a series of O—H⋯O hydrogen bonds (O5A—H5AB⋯O3 and O4B—H4BB⋯O3; Table 2).
4. Database survey
A search of the Cambridge Structural Database (CSD, Version 5.39, update November 2017; Groom et al., 2016) for complexes containing the Pd(en) moiety yielded 226 hits with a mean Pd—N bond lengths of 2.028 Å. A search for Pd complexes with MPD as a ligand revealed only one entry (Kutsenko et al., 2014) with Pd—O bond lengths of 1.999 and 2.004 Å.
5. Synthesis and crystallization
[Pd2(C2H8N2)2(CH2O6P2)]·4H2O was prepared as previously reported in the literature (Kozachkova et al., 2018). A solution of AgNO3 (0.4 mmol, 0.0679 g) in water (3 ml) was added to a suspension of [Pd(en)Cl2] (0.2 mmol, 0.0474 g) in water (6 ml) under constant stirring and heating at 333 K for 30 min. The resulting suspension was refrigerated to facilitate the precipitation of AgCl. The solid material was removed by suction filtration. MDP (0.1 mmol, 0.0176 g) was added to the filtrate, and the pH was adjusted to 6 by addition of KOH (0.1 mol l−1). The obtained slightly yellow solution was heated at 333 K for 20 min and then left to evaporate at room temperature. Yellow rectangular crystals of the title compound suitable for crystallographic studies were grown by slow evaporation of an aqueous solution at room temperature.
Compound [Pd2(en)2(MDP)]·4H2O: yield 86%. Analysis found: C, 11.5; H, 3.6; N, 10.9; P, 11.8; Pd, 40.8. Calculated for C5H26N4O6P2Pd2: C, 11.9; H, 3.9; N, 11.1; P, 12.3; Pd, 41.9%. The 31P-{H} NMR spectrum of an aqueous solutions of the synthesized compound exhibited a singlet with δP 35.0 ppm.
6. Refinement
Crystal data, data collection and structure . Hydrogen atoms of the metal complex were located from difference-Fourier syntheses. The H atom of the central CH2 bridge of the MDP ligand was refined freely, and the methylene and NH2 hydrogen atoms of the en ligand were treated in the riding-model approximation with C—H = 0.97 Å (N—H = 0.89 Å) and Uiso(H) = 1.2Ueq(C,N). The two lattice water molecules (O4 and O5) are each disordered over two positions and were refined with occupancies 0.5:0.5 each. Their hydrogen atoms were calculated, taking into account the direction of expected hydrogen bonds. The positions of these hydrogen atoms were fixed at the last steps of with O—H = 0.85 Å, and with Uiso(H) = 1.5Ueq(O).
details are summarized in Table 3
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Supporting information
CCDC reference: 1879750
https://doi.org/10.1107/S2056989018016419/wm5473sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018016419/wm5473Isup2.hkl
Data collection: CrysAlis PRO (Rigaku OD, 2018); cell
CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).[Pd2(C2H8N2)2(CH2O6P2)]·4H2O | Dx = 2.140 Mg m−3 |
Mr = 577.04 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Fddd | Cell parameters from 2899 reflections |
a = 11.8871 (6) Å | θ = 3.2–30.1° |
b = 12.5405 (6) Å | µ = 2.24 mm−1 |
c = 48.052 (2) Å | T = 294 K |
V = 7163.2 (6) Å3 | Block, colourless |
Z = 16 | 0.6 × 0.4 × 0.2 mm |
F(000) = 4576 |
Rigaku Oxford Diffraction Xcalibur, Sapphire3 diffractometer | 2065 independent reflections |
Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source | 1746 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.075 |
Detector resolution: 16.1827 pixels mm-1 | θmax = 27.5°, θmin = 3.2° |
ω scans | h = −15→8 |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018) | k = −16→16 |
Tmin = 0.418, Tmax = 1.000 | l = −58→62 |
14597 measured reflections |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.063 | H-atom parameters constrained |
wR(F2) = 0.175 | w = 1/[σ2(Fo2) + (0.0908P)2 + 141.6934P] where P = (Fo2 + 2Fc2)/3 |
S = 1.14 | (Δ/σ)max = 0.002 |
2065 reflections | Δρmax = 1.69 e Å−3 |
126 parameters | Δρmin = −2.06 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
Pd1 | 0.37981 (4) | 0.24678 (4) | 0.61611 (2) | 0.0284 (2) | |
P1 | 0.24784 (12) | 0.37098 (12) | 0.66205 (3) | 0.0273 (4) | |
O1 | 0.2537 (4) | 0.2699 (4) | 0.64405 (11) | 0.0346 (10) | |
O2 | 0.2468 (4) | 0.4739 (4) | 0.64479 (10) | 0.0322 (10) | |
O3 | 0.1464 (4) | 0.3667 (4) | 0.68076 (9) | 0.0362 (10) | |
N2 | 0.4951 (5) | 0.2116 (5) | 0.58694 (13) | 0.0387 (13) | |
H2A | 0.542935 | 0.265756 | 0.585250 | 0.046* | |
H2B | 0.533949 | 0.154405 | 0.592230 | 0.046* | |
N1 | 0.2672 (5) | 0.2073 (5) | 0.58635 (12) | 0.0355 (12) | |
H1A | 0.235915 | 0.144735 | 0.590388 | 0.043* | |
H1B | 0.212909 | 0.256180 | 0.585660 | 0.043* | |
C3 | 0.375000 | 0.375000 | 0.68243 (19) | 0.0299 (17) | |
H3 | 0.373 (6) | 0.437 (6) | 0.6938 (17) | 0.036* | |
C1 | 0.3239 (8) | 0.2011 (11) | 0.55937 (18) | 0.073 (3) | |
H1C | 0.293176 | 0.140753 | 0.549266 | 0.087* | |
H1D | 0.305487 | 0.264816 | 0.548883 | 0.087* | |
C2 | 0.4418 (8) | 0.1906 (13) | 0.5599 (2) | 0.089 (4) | |
H2C | 0.473610 | 0.239097 | 0.546319 | 0.107* | |
H2D | 0.461070 | 0.118672 | 0.554208 | 0.107* | |
O4A | 0.1779 (11) | 0.1374 (12) | 0.7512 (3) | 0.072 (4) | 0.5 |
H4AA | 0.162933 | 0.203516 | 0.754198 | 0.108* | 0.5 |
H4AB | 0.115953 | 0.105016 | 0.747549 | 0.108* | 0.5 |
O5B | 0.1617 (16) | 0.5219 (16) | 0.7487 (5) | 0.108 (7) | 0.5 |
H5BA | 0.226607 | 0.542097 | 0.753922 | 0.163* | 0.5 |
H5BB | 0.118927 | 0.574297 | 0.752362 | 0.163* | 0.5 |
O5A | 0.1535 (13) | 0.3512 (16) | 0.7363 (3) | 0.064 (4) | 0.5 |
H5AA | 0.084422 | 0.344140 | 0.740362 | 0.096* | 0.5 |
H5AB | 0.154092 | 0.358020 | 0.718632 | 0.096* | 0.5 |
O4B | 0.1903 (15) | 0.2992 (16) | 0.7344 (4) | 0.069 (5) | 0.5 |
H4BA | 0.228698 | 0.242206 | 0.733009 | 0.104* | 0.5 |
H4BB | 0.164928 | 0.316206 | 0.718439 | 0.104* | 0.5 |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.0273 (3) | 0.0295 (4) | 0.0285 (4) | 0.00014 (16) | −0.00047 (18) | −0.00197 (17) |
P1 | 0.0229 (7) | 0.0320 (8) | 0.0270 (8) | −0.0004 (5) | 0.0012 (6) | 0.0012 (6) |
O1 | 0.028 (2) | 0.041 (3) | 0.035 (3) | −0.0021 (18) | 0.0028 (19) | −0.005 (2) |
O2 | 0.028 (2) | 0.035 (2) | 0.034 (2) | 0.0019 (17) | 0.0010 (18) | 0.0029 (19) |
O3 | 0.026 (2) | 0.051 (3) | 0.031 (2) | 0.0004 (18) | 0.0045 (18) | −0.001 (2) |
N2 | 0.032 (3) | 0.047 (3) | 0.036 (3) | 0.000 (2) | 0.002 (2) | 0.000 (3) |
N1 | 0.031 (3) | 0.040 (3) | 0.035 (3) | −0.003 (2) | −0.006 (2) | −0.005 (2) |
C3 | 0.028 (4) | 0.036 (5) | 0.025 (4) | −0.001 (3) | 0.000 | 0.000 |
C1 | 0.061 (6) | 0.126 (10) | 0.031 (4) | 0.010 (6) | −0.010 (4) | −0.013 (5) |
C2 | 0.047 (5) | 0.176 (13) | 0.045 (5) | −0.020 (7) | 0.009 (4) | −0.028 (7) |
O4A | 0.058 (7) | 0.081 (10) | 0.077 (10) | 0.006 (7) | −0.006 (7) | −0.007 (8) |
O5B | 0.074 (11) | 0.117 (15) | 0.134 (17) | −0.013 (10) | 0.010 (11) | −0.061 (13) |
O5A | 0.046 (8) | 0.114 (16) | 0.032 (6) | 0.000 (8) | 0.002 (5) | −0.002 (8) |
O4B | 0.064 (11) | 0.097 (14) | 0.047 (8) | 0.001 (9) | 0.009 (7) | 0.002 (9) |
Pd1—Pd1i | 3.2180 (9) | C3—H3 | 0.95 (8) |
Pd1—Pd1ii | 3.1715 (9) | C3—H3i | 0.95 (8) |
Pd1—O1 | 2.033 (5) | C1—H1C | 0.9700 |
Pd1—O2i | 2.046 (5) | C1—H1D | 0.9700 |
Pd1—N2 | 2.009 (6) | C1—C2 | 1.408 (14) |
Pd1—N1 | 2.021 (5) | C2—H2C | 0.9700 |
P1—O1 | 1.536 (5) | C2—H2D | 0.9700 |
P1—O2 | 1.534 (5) | O4A—H4AA | 0.8600 |
P1—O3 | 1.506 (4) | O4A—H4AB | 0.8590 |
P1—C3 | 1.802 (5) | O4A—H4ABiii | 0.56 (2) |
N2—H2A | 0.8900 | O5B—H5BA | 0.8503 |
N2—H2B | 0.8900 | O5B—H5BB | 0.8504 |
N2—C2 | 1.468 (11) | O5A—H5AA | 0.8495 |
N1—H1A | 0.8900 | O5A—H5AB | 0.8515 |
N1—H1B | 0.8900 | O4B—H4BA | 0.8502 |
N1—C1 | 1.464 (11) | O4B—H4BB | 0.8500 |
Pd1ii—Pd1—Pd1i | 164.246 (17) | Pd1—N1—H1B | 109.8 |
O1—Pd1—Pd1i | 80.27 (14) | H1A—N1—H1B | 108.2 |
O1—Pd1—Pd1ii | 87.69 (14) | C1—N1—Pd1 | 109.6 (5) |
O1—Pd1—O2i | 93.32 (19) | C1—N1—H1A | 109.8 |
O2i—Pd1—Pd1i | 81.11 (13) | C1—N1—H1B | 109.8 |
O2i—Pd1—Pd1ii | 89.54 (13) | P1—C3—P1i | 114.2 (5) |
N2—Pd1—Pd1i | 104.11 (19) | P1—C3—H3 | 108 (4) |
N2—Pd1—Pd1ii | 88.64 (19) | P1—C3—H3i | 108 (4) |
N2—Pd1—O1 | 174.2 (2) | P1i—C3—H3i | 108 (4) |
N2—Pd1—O2i | 91.2 (2) | P1i—C3—H3 | 108 (4) |
N2—Pd1—N1 | 84.5 (2) | H3—C3—H3i | 110 (10) |
N1—Pd1—Pd1ii | 87.42 (18) | N1—C1—H1C | 108.2 |
N1—Pd1—Pd1i | 102.77 (18) | N1—C1—H1D | 108.2 |
N1—Pd1—O1 | 90.8 (2) | H1C—C1—H1D | 107.3 |
N1—Pd1—O2i | 174.8 (2) | C2—C1—N1 | 116.5 (8) |
O1—P1—C3 | 106.9 (2) | C2—C1—H1C | 108.2 |
O2—P1—O1 | 113.0 (3) | C2—C1—H1D | 108.2 |
O2—P1—C3 | 106.1 (2) | N2—C2—H2C | 108.4 |
O3—P1—O1 | 110.1 (3) | N2—C2—H2D | 108.4 |
O3—P1—O2 | 110.3 (3) | C1—C2—N2 | 115.4 (8) |
O3—P1—C3 | 110.4 (3) | C1—C2—H2C | 108.4 |
P1—O1—Pd1 | 121.6 (3) | C1—C2—H2D | 108.4 |
P1—O2—Pd1i | 120.7 (3) | H2C—C2—H2D | 107.5 |
Pd1—N2—H2A | 109.4 | H4AA—O4A—H4AB | 108.2 |
Pd1—N2—H2B | 109.4 | H4AA—O4A—H4ABiii | 72.3 |
H2A—N2—H2B | 108.0 | H4AB—O4A—H4ABiii | 38.4 |
C2—N2—Pd1 | 111.2 (5) | H5BA—O5B—H5BB | 104.5 |
C2—N2—H2A | 109.4 | H5AA—O5A—H5AB | 104.4 |
C2—N2—H2B | 109.4 | H4BA—O4B—H4BB | 109.4 |
Pd1—N1—H1A | 109.8 | ||
Pd1—N2—C2—C1 | 1.3 (14) | O3—P1—O1—Pd1 | −179.9 (3) |
Pd1—N1—C1—C2 | 18.4 (13) | O3—P1—O2—Pd1i | −177.9 (3) |
O1—P1—O2—Pd1i | −54.3 (4) | O3—P1—C3—P1i | 179.4 (2) |
O1—P1—C3—P1i | 59.7 (2) | N1—C1—C2—N2 | −13.4 (17) |
O2—P1—O1—Pd1 | 56.3 (4) | C3—P1—O1—Pd1 | −60.0 (4) |
O2—P1—C3—P1i | −61.1 (2) | C3—P1—O2—Pd1i | 62.5 (4) |
Symmetry codes: (i) −x+3/4, −y+3/4, z; (ii) x, −y+1/4, −z+5/4; (iii) −x+1/4, −y+1/4, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O3iv | 0.89 | 2.07 | 2.932 (8) | 163 |
N1—H1A···O1ii | 0.89 | 2.21 | 3.006 (8) | 149 |
N1—H1B···O3v | 0.89 | 2.06 | 2.906 (8) | 159 |
O4A—H4AA···O5A | 0.86 | 2.05 | 2.79 (3) | 145 |
O5B—H5BA···O5Bvi | 0.85 | 1.56 | 2.17 (4) | 127 |
O5B—H5BA···O4Bvi | 0.85 | 2.29 | 2.97 (3) | 136 |
O5B—H5BB···O5Bvii | 0.85 | 1.97 | 2.73 (4) | 148 |
O5B—H5BB···O4Bviii | 0.85 | 2.24 | 2.78 (2) | 121 |
O5A—H5AA···O4Aviii | 0.85 | 1.98 | 2.786 (19) | 158 |
O5A—H5AB···O3 | 0.85 | 1.83 | 2.675 (16) | 176 |
O4B—H4BB···O3 | 0.85 | 1.93 | 2.761 (18) | 165 |
Symmetry codes: (ii) x, −y+1/4, −z+5/4; (iv) x+1/2, −y+3/4, −z+5/4; (v) −x+1/4, y, −z+5/4; (vi) −x+1/2, −y+1, −z+3/2; (vii) −x+1/4, −y+5/4, z; (viii) x−1/4, y+1/4, −z+3/2. |
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