Structure and dynamics of the hydrated palladium(II) ion in aqueous solution A QMCF MD simulation and EXAFS spectroscopic study

Chemical Physics Letters 445 (2007) 193–197 www.elsevier.com/locate/cplett

Structure and dynamics of the hydrated palladium(II) ion in aqueous solution A QMCF MD simulation and EXAFS spectroscopic study Thomas S. Hofer a

a,*

, Bernhard R. Randolf a, S. Adnan Ali Shah a, Bernd M. Rode a, Ingmar Persson b

Theoretical Chemistry Division, Institute of General, Inorganic and Theotrical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria b Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden Received 14 December 2006; in final form 2 August 2007 Available online 7 August 2007

Abstract The pharmacologically and industrially important palladium(II) ion is usually characterised as square-planar structure in aqueous solution, similar to the platinum(II) ion. Our investigations by means of the most modern experimental and theoretical methods give ˚ plus clear indications, however, that the hydrated palladium(II) ion is hexa-coordinated, with four ligands arranged in a plane at 2.0 A ˚ two additional ligands in axial positions showing an elongated bond distance of 2.7–2.8 A. The second shell consists in average of 8.0 ˚ . This structure provides a new basis for the interpretation of the kinetic properties of palladium(II) ligands at a mean distance of 4.4 A complexes.  2007 Elsevier B.V. All rights reserved.

1. Introduction Palladium(II) and platinum(II) complexes are utilised in numerous industrial processes because of their catalytic properties [1,2]. They have also cytotoxic properties, and several types of palladium(II) and platinum(II) complexes are employed as anticancer drugs [3]. The hydrated palladium(II) and platinum(II) ions are so far only known in acidic aqueous solution and they hydrolyse readily with pKa values of 2.3 and 2.5 [4,5], respectively. No solid-state structures containing fully hydrated palladium(II) and platinum(II) ions are reported so far. This is most probably due to the fact that the water molecules are too loosely bound, in a similar way as found for the equally soft silver(I) ion [6]. Electronic spectra [7] and the physico-chemical and kinetic substitution behaviour [8–10] appeared compatible with square-planar configuration. The water exchange rate of

*

Corresponding author. Fax: +43 512 507 2714. E-mail address: [email protected] (T.S. Hofer).

0009-2614/$ - see front matter  2007 Elsevier B.V. All rights reserved. doi:10.1016/j.cplett.2007.08.009

the hydrated palladium(II) and platinum(II) ions differs by six orders of magnitude, kex = 5.6 · 102 [11] and 4.4 · 104 s1 [12,13], respectively. The volume of activation of the water exchange in the hydrated palladium(II) and platinum(II) ions are small and negative, 2.2 and 4.6 cm3 mol1, respectively, strongly indicating a weak associative interchange, Ia, mechanism for the water exchange of both ions [11–13]. The structure of the hydrated palladium(II) ion in aqueous solution was reported recently with four tightly bound water molecules in the equatorial plane with the oxygens forming a square-plane with a Pd–O bond dis˚ . Additionally two (or one) water moletance of 2.00(1) A ˚ [14]. cule(s) are weakly bound in the axial positions at 2.5 A A vast majority of the crystal structures of the palladium(II) complexes and compounds display a squareplanar configuration around palladium [15,16]. The dimethylsulfoxide solvated palladium(II) ion is the only solvate structure studied by X-ray methods in solution showing a square-planar configuration with two oxygenand two sulphur-bound dimethylsulfoxide molecules [17]. This clearly shows the soft binding properties of the

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palladium(II) ion in its square-planar binding positions. A search in the CSD data base [15] shows several palladium(II) complexes with the coordination numbers five and six in strongly square-pyramidal and tetragonally elongated octahedral configurations, and with axial Pd–O bond ˚ [18–20]. The presence of additional distances of ca. 2.7 A one or two fast-exchanging water molecules in the axial position(s) had been proposed based on theoretical investigations without any experimental proofs [21]. The very long axial Pd–O bond distances in the five- and six-coordinated palladium(II) complexes observed in the solid state strongly indicate that these bonds have mainly electrostatic character, and they are therefore difficult to observe with kinetic and thermodynamic experimental methods. Density functional theory at the local density approximation level (LDA-DFT) calculations have been applied to model the water exchange of the [Pd(H2O)4]2+ complex in gaseous phase in order to correlate with experimental observations [10]. However, the experimentally determined exchange rates refer to the in-plane water molecules which exchange too slow to be investigated by molecular dynamics, in particular with hybride quantum mechanical/molecular mechanical (QM/MM) methods. More recently, a classical molecular dynamics (MD) study of the palladium(II) ion in water by Sanchez-Marcos [22] gave strong indications that two more ligands are coordinated at longer distance to the ion, forming a tetragonally elongated octahedron. As different potentials were employed for equatorial and axial positions in this study, one cannot determine, however, to what extent this results could be ‘biased’ by the potentials. A subsequent ab initio QM/ MM MD simulation of the same system predicted only one additional (axial) ligand and thus a square-pyramidal structure, but it was concluded that inclusion of only one hydration shell in the quantum mechanical treatment could not have been sufficient for this system [23]. In the present study we have performed a simulation with the ab initio quantum mechanical charge field (QMCF) MD formalism [24], which works without potential functions except the one for solvent–solvent interactions and includes two full hydration layers into the quantum mechanical treatment. Experimentally, a 40 mmol dm3 Pd(ClO4)2 solution in 1.0 mol dm3 HClO4, in order to supress hydrolysis, was investigated by extended X-ray absorbtion fine structure (EXAFS) methods, and the X-ray spectroscopic data were analysed on the basis of different models for the hydrate complex. 2. Methods 2.1. Theoretical The ab initio QMCF MD simulation was performed for one palladium(II) ion in a cubic box containing 499 water molecules, applying periodic boundary conditions and maintaining the NVT ensemble at room temperature by the Berendsen algorithm [25]. The starting structure was

obtained from a previous ab initio QM/MM MD simulation of the same system [22], and after re-equilibration of 4 ps, a total simulation time of 12 ps was used for sampling, which is sufficient to obtain reliable data for structural parameters as well as short time dynamics such as the exchange of weakly bound ligands. The quantum mechanical region contained the palladium(II) ion and two full hydration layers (in average 14 water molecules), the calculation of forces was performed at Hartree–Fock level employing the LANL2DZ plus ECP basis set for palladium(II) [26] and Dunning double zeta plus polarisation basis sets for water [27]. For solvent–solvent interactions in the MM region of the box the flexible BJH-CF2 potential was used [28]. Details of the simulation protocol are given in literature [23]. All calculations were performed on a cluster of 10 AMD Opteron 246 processors with the QMCF MD code [29], interfaced to the parallel TURBOMOLE program for the quantum mechanical calculations [16]. The total computing time for the simulation amounted to approximately 3 months. 2.2. Experimental Palladium K-edge X-ray absorption spectra were recorded at the bending magnet beam line 2–3 at the Stanford Synchrotron Radiation Laboratory (SSRL). The EXAFS station was equipped with a Si[2 2 0] double crystal monochromator. SSRL operated at 3.0 GeV and a maximum current of 100 mA. The data collections were performed in transmission mode at ambient temperature. Higher order harmonics were reduced by detuning the second monochromator to 70% of maximum intensity at the end of the scans. The aqueous solution was kept in a sample cell made of a 10 mm Teflon spacer and Mylar tape windows. The energy scale of the X-ray absorption spectra was calibrated by assigning the first inflection point of the K-edge of a palladium foil to 24 350 eV [30]. Eight scans were collected and averaged. The EXAFSPAK program package was used for the primary data treatment [31]. The data analyses were performed by means of the GNXAS code. The GNXAS code is based on the calculation of the EXAFS signal and a subsequent refinement of the structural parameters [32]. The GNXAS method accounts for multiple scattering (MS) paths, with correct treatment of the configurational average of all the MS signals to allow fitting of correlated distances and bond distance variances (Debye–Waller factors). A correct description of the first coordination sphere of the studied complex has to account for asymmetry in the distribution of the ion–solvent distances [33,34]. Therefore the Pd–O two-body signal associated with the first coordination shells was modelled with C-like distribution functions which depend on four parameters, the coordination number N, the average distance R, the mean-square variation r and the skewness b. The b term is related to the third cumulant C3 through the relationR C3 = r3b, and R is the first moment of the function 4p gðrÞ2 dr. It is important to stress that R is the average

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distance and not the position of the maximum of the distribution (Rm). The statistical error estimates provide a measure of the precision of the results and allow reasonable comparisons, e.g. of the significance of relative shifts in the distances. However, the variations in the refined parameters, including the shift in the E0 value (for which k = 0), using different models and data ranges, indicate that the absolute accuracy of the distances given for the separate complexes ˚ for well-defined interactions. The is within ±0.01 to 0.02 A given ‘standard deviations’ have been increased accordingly to include estimated additional effects of systematic errors.

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Table 1 Maxima rM and minima rm of the Pd–O and Pd–H radial distribution ˚ and average coordination numbers CN in the first, functions in A extended first and second hydration shell

Pd(II)–O Pd(II)–H

rM1

rm1

rM,ext

rm,ext

CN1

rM2

rm2

CN2

2.02 2.69

2.33 3.07

2.7 3.3

3.45 4.0

5.94 12.1

4.4 5.0

4.96 6.0

8.0 31.5

3. Results and discussion The Pd–O and Pd–H radial distribution functions (RDFs) resulting from the QM/MM MD simulation, shown in Fig. 1 and Table 1, clearly show that the first hydration shell consists of four ligands located at an aver˚ , and two further water molecules age distance of 2.05 A ˚ away from the metal ion. A second shell peaking 2.71 A ˚ contains only eight ligands in average. A more at 4.4 A detailed analysis showed that only the four ligands in the plane are capable of forming this second hydration shell, not the two axial ligands at the larger distance. The Pd– H RDF is fully consistent with this structure, and it further shows a dipole orientation of all (also the axial) ligands. The Pd–O–H angular distribution of the equatorial water molecules peaks at 121 confirming the dominant dipole orientation of the ligands. The axial ligands’ considerably lower bond strength resulted in the occurrence of two exchange events along the simulation time of 12 ps, associated with five- and seven-fold hydration structures. Fitting of the newly collected EXAFS data to a squareplanar model was good, but not perfect. Therefore, models with one and two water molecules in the axial positions at ˚ , were applied in order to improve long distance, ca. 2.7 A the fit. The Pd–O bond distance in the square plane is ˚ in all models, and this scattering pathway is 2.00–2.01 A strongly dominating the total scattering, illustrated in

Fig. 1. Pd–O (solid line) and Pd–H (dashed line) radial distribution functions and their running integration numbers.

Fig. 2. k2-weighted EXAFS data of experimental (thin solid line) and theoretical (thick solid line) data using a tetragonally elongated octahedral model of the hydrated palladium(II) ion in aqueous solution, and the individual contributions of the equatorial and axial Pd–O bonds, the multiple scattering within the square-planar PdO4 core, and the Pd–H single scattering and Pd–O–H three-leg scattering path to the hydrogens in water molecules bound in the square plane.

Fig. 2. A model with two axial water molecules in a tetrag˚ improves onally elongated octahedral model at 2.77(4) A the fit in comparison with a square-planar model, while a model with only one axial water molecule does not (cf. Table 2 and Supplementary data). The bond distance distribution of the equatorially bound water molecules is symmetric with a C3 value being ˚ 3), at or below the methodical accuracy limit (1.0 · 106 A while the axially bound ones display a significant asymme˚ 3, and peak maximum of try with C3 = (6.3 ± 0.4) · 104 A ˚ . The Pd–O bond distance distribution of the axial 2.73(4) A water molecule in the square-pyramidal model becomes ˚ 3, with a mean very asymmetric, C3 = (2.1 ± 0.5) · 103 A ˚ and an Rm value of 2.73(5) A ˚ . The multivalue of 2.81(5) A ple scattering within the equatorial PdO4 core gives a significant contribution to the EXAFS function with O–Pd– O angles very close to 90 and 180, Fig. 2. The Pd–H single and Pd–O–H multiple scattering of the water molecules bound in the square plane has been refined to a Pd–H dis˚ , and a Pd–O–H bond angle of 122, tance of 2.73(3) A which is consistent with a dipole-oriented arrangement of these ligands, as expected for a metal ion with a polarization power (q/r) of about 3 [24]. The tested square-planar and square-pyramidal models show somewhat higher error squares sums, Table 2, and the Pd–O bond distances becomes somewhat asymmetric with Rm values very close to the symmetric bond distance obtained in the tetragonally elongated octahedral model, Table 2. The Pd–O

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Table 2 ˚ , number of distances, N, Debye-Waller coefficients, r2/A ˚ 2, the third cumulation factor, C3/A ˚ 3, and the peak maximum of Mean Pd–O bond distances, d/A ˚ , of the hydrated palladium(II) ion in aqueous solution as determined by EXAFS at room temperature, using three the bond distance distribution, Rm/A different models, tetragonally elongated octahedral (Teo), square-pyramidal (Spy) and square-planar (Spl) Model Teo Spy Spl

d 2.006(4) 2.77(4) 2.018(5) 2.81(5) 2.013(5)

F is the error square sum as defined in the a Accuracy limit of the method.

r2

N

0.0029(2) 0.011(3) 0.0033(3) 0.022(4) 0.0025(3) GNXAS

4 2 4 1 4

C3 6 a

<1.0 · 10 (6.3 ± 0.4) · 104 (7.4 ± 0.3) · 105 (2.1 ± 0.5) · 103 (2.7 ± 0.3) · 105

Rm

F

2.006 2.73 2.004 2.74 2.005

6.57 · 108 8.43 · 108 8.16 · 108

program.

bond distance of the axial water molecule in the square pyramidal model becomes very asymmetric with a mean ˚ and an Rm value of 2.73 A ˚ . The tetragvalue of 2.81(5) A onally elongated octahedral model seems to fit the experimental data best of the applied models. At the same time only this model results in a symmetric bond distance distribution to the strongly bound water molecules. The EXAFS data in this study give a significantly longer Pd–O bond distance to the water molecules in the axial positions, ˚ , than in the previous study, 2.5(1) A ˚ [14]. The 2.77(4) A reason for this discrepancy is not obvious. These experimental results are in full agreement with the data from the ab initio QMCF MD simulation, except for ˚ in the distance of the small discrepancy of less than 0.1 A the axial ligands, which could be attributed to the slightly different conditions, as the experiments have been performed with counterions and in 1 M perchloric acid solution. Another possible reason is the lability of the axial ligands: in the course of the simulation’s duration of 12 picoseconds, two exchange processes of axial ligands with bulk water were observed, indicating a ligand exchange rate below the measurability of the NMR time scale. Such fast exchange processes also add some uncertainty to the determination of structural parameters. On the basis of all data presented here, the tetragonally elongated octahedral structure of the palladium(II) ion in water seems unambiguous, and the weak binding of the two axial ligands explains the difficulty to experimentally identify them. At the same time, it provides a good reason for the enhanced ligand exchange rate of this ion and confirms the good quality of the 2-potential approach by Sanchez-Marcos in his classical description of this hydrate [21]. The clarification of the structure of hydrated palladium(II) ion in aqueous environment also provides a new basis for the interpretation of the catalytic and pharmacological activity of this ion. Although the experimental data give strong indications towards the existence of two axial water ligands their unambiguous identification is only possible on the basis of the quantum mechanical simulation, which by the ultrafast exchange processes also explains the difficulties of the experimental identification of these ligands. The combination of ab initio simulation methods with experimental methods proved a very successful approach for the elucidation of structural entities in solution. This

combined study clearly demonstrates that a square-planar model is an incomplete description of the hydrated palladium(II) ion. The findings for structure and dynamics of the palladium(II) ion will be a suitable basis for the treatment of the hydrated platinum(II) ion at the same level of theory and accuracy. This simulation is in progress of preparation and should allow a detailed composition of the experimentally observed differences between the dynamics of these ions. Acknowledgement Financial support by the Austrian Science Foundation (Project 18429) and the Swedish Research Council is gratefully acknowledged. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/ j.cplett.2007.08.009. References [1] S.S. Stahl, Angew. Chem. 43 (2004) 3400. [2] D. Bianchi, R. Bortolo, R. D’Aloisio, M. Ricci, Angew. Chem. 38 (1990) 706. [3] Y.-P. Ho, S.C.F. Au-Yeung, K.K.W. To, Med. Res. Rev. 23 (2003) 633. [4] B.I. Nabivanits, L.V. Kalabina, Russ. J. Inorg. Chem. 15 (1970) 818. [5] L.I. Elding, Inorg. Chim. Acta 20 (1976) 65. [6] I. Persson, K.B. Nilsson, Inorg. Chem. 45 (2006) 7428. [7] L.I. Elding, L.F. Olsson, J. Phys. Chem. 82 (1978) 69. [8] L.I. Elding, Inorg. Chim. Acta 6 (1972) 647, and references therein. [9] L.I. Elding, Inorg. Chim. Acta 6 (1972) 683. [10] R.J. Deeth, L.I. Elding, Inorg. Chem. 35 (1996) 5019, and references therein. [11] L. Helm, L.I. Elding, A.E. Merbach, Helv. Chim. Acta 67 (1984) 1453. [12] L. Helm, L.I. Elding, A.E. Merbach, Inorg. Chem. 24 (1985) 1719. ¨ . Gro¨ning, L.I. Elding, Inorg. Chem. 28 (1989) 3366. [13] O [14] J. Purans, B. Fourest, C. Cannes, V. Sladkov, F. David, L. Venault, M. Lecomte, J. Phys. Chem. B 109 (2005) 11074. [15] F.H. Allen et al., Acta Crystallogr. B 35 (1979) 2331, and references therein. [16] Inorganic Crystal Structure Data Base, National Institute of Standards and Technology, Fachinformationszentrum, Karlsruhe, Release 06/1.

T.S. Hofer et al. / Chemical Physics Letters 445 (2007) 193–197 [17] B. Hellquist, L. Bengtsson, B. Homberg, B. Hedman, I. Persson, L.I. Elding, Acta Chem. Scand. 45 (1991) 449. [18] K.R. Dunbar, J.-S. Sun, Chem. Commun. (1994) 2387; J.-S. Sun, C.E. Uzelmeier, D.L. Ward, K.R. Dunbar, Chem. Commun. (1994) 2387. [19] S. Okeya, T. Miyamoto, S. Ooi, Y. Nakamura, S. Kawaguchi, Inorg. Chim. Acta 45 (1980) L135; S. Okeya, T. Miyamoto, S. Ooi, Y. Nakamura, S. Kawaguchi, Bull. Chem. Soc. Jpn. 57 (1984) 395. [20] A.M. Grevtsev, N.N. Zheligovskaya, L.V. Popov, V.I. Spitsyn, Vestn. Mosk. Univ. Ser. Khim. 19 (1978) 490. ¨ . Gro¨ning, T. Drakenberg, L.I. Elding, Inorg. Chem. 21 (1982) [21] O 1820. [22] J.M. Martinez, F. Torrico, R.R. Pappalardo, E.S. Marcos, J. Phys. Chem. A 108 (2004) 15851. [23] S.A.A. Shah, T.S. Hofer, M.Q. Fatmi, B.R. Randolf, B.M. Rode, Chem. Phys. Lett. 426 (2006) 301. [24] B.M. Rode, T.S. Hofer, B.R. Randolf, C.F. Schwenk, D. Xenides, V. Vchirawongkwin, Theor. Chem. Acc. 116 (2006) 77.

197

[25] H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, J.R. Haak, J. Chem. Phys. 81 (1984) 3684. [26] P.J. Hay, W.R. Wadt, Chem. Phys. 82 (1985) 299. [27] T.H. Dunning Jr., J. Chem. Phys. 53 (1970) 2823. [28] P. Bopp, G. Jansco, K. Heinzinger, Chem. Phys. Lett. 98 (1983) 129. [29] R. Ahlrichs, M. von Arnim, In Methods and Techniques in Computational Chemistry: METECC-95. [30] A. Thompson et al., X-ray Data Booklet, LBNL/PUB-490 Rev. 2, Lawrence Berkeley National Laboratory, Berkeley, California 94720, 2001. [31] G.N. George, I.J. Pickering, EXAFSPAK – A Suite of Computer Programs for Analysis of X-ray Absorption Spectra, SSRL, Stanford, CA, 1993. [32] A. Filipponi, A. Di Cicco, C.R. Natoli, Phys. Rev. B 52 (1995) 15122. [33] A. Filipponi, J. Phys.: Condens. Mat. 6 (1994) 8415. [34] L. Hedin, B.I. Lundqvist, J. Phys. C: Solid State Phys. 4 (1971) 2064.