Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods

Ion Chiorescu; Dirk V Deubel; Vladimir B Arion; Bernhard K Keppler

doi:10.1021/ct700247g

Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods

J Chem Theory Comput. 2008 Mar;4(3):499-506. doi: 10.1021/ct700247g.

Authors

Ion Chiorescu¹, Dirk V Deubel¹, Vladimir B Arion¹, Bernhard K Keppler¹

Affiliation

¹ Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Vienna, Austria, and Laboratory of Physical Chemistry, D-CHAB, ETH Zurich, CH-8093 Zurich, Switzerland.

PMID: 26620790
DOI: 10.1021/ct700247g

Abstract

Two ruthenium(III) complexes {(HIm)[trans-RuCl4(DMSO)(Im)] (NAMI-A) and (HInd)[trans-RuCl4(Ind)2] (KP1019), DMSO = dimethyl sulfoxide, Im = imidazole, Ind = indazole} have been tested in phase I clinical trials as potential anticancer drugs. Ru(III) anticancer agents are likely activated in vivo upon reduction to their Ru(II) analogs. Aiming at benchmarking implicit solvation methods in DFT studies of ruthenium pharmaceuticals at the B3LYP level, we have calculated the standard redox potentials (SRPs) of Ru(III/II) pairs that were electrochemically characterized in the literature. 80 SRP values in four solvents were calculated using three implicit solvation methods and five solute cavities of molecular shape. Comparison with experimental data revealed substantial errors in some of the combinations of solvation method and solute cavity. For example, the overall mean unsigned error (MUE) with the PCM/UA0 combination, which is the popular default in Gaussian 03, amounts to 0.23 V (5.4 kcal/mol). The MUE with the CPCM/UAKS combination, which was employed by others for recent computational studies on the hydrolysis of NAMI-A and trans-[RuCl4(Im)2](-), amounts to 0.30 V (7.0 kcal/mol) for all compounds and to 0.60 V (13.9 kcal/mol) for a subset of compounds of the medicinally relevant type, trans-[RuCl4(L)(L')](-). The SRPs calculated with the PCM or CPCM methods in Gaussian 03 can be significantly improved by a more compact solute cavity constructed with Bondi's set of atomic radii. Earlier findings that CPCM performs better than PCM cannot be confirmed, as the overall MUE amounts to 0.19 V (4.3-4.4 kcal/mol) for both methods in combination with Bondi's set of radii. The Poisson-Boltzmann finite element method (PBF) implemented in Jaguar 7 together with the default cavity performs slightly better, with the overall MUE being 0.16 V (3.7 kcal/mol). Because the redox pairs considered in this study bear molecular charges from +3/+2 to -1/-2 and the prediction of solvation free energies is most challenging for highly charged species, the present work can serve as a general benchmarking of the implicit solvation methods.