Theoretical Modeling of Water Exchange on [Pd(H(2)O)(4)](2+), [Pt(H(2)O)(4)](2+), and trans-[PtCl(2)(H(2)O)(2)]

Modelling ligand exchange in metal complexes with machine learning potentials

Metal ions are irreplaceable in many areas of chemistry, including (bio)catalysis, self-assembly and charge transfer processes. Yet, modelling their structural and dynamic properties in diverse chemical environments remains challenging for both force fields and ab initio methods. Here, we introduce a strategy to train machine learning potentials (MLPs) using MACE, an equivariant message-passing neural network, for metal-ligand complexes in explicit solvents. We explore the structure and ligand exchange dynamics of Mg2+ in water and Pd2+ in acetonitrile as two illustrative model systems. The trained potentials accurately reproduce equilibrium structures of the complexes in solution, including different coordination numbers and geometries. Furthermore, the MLPs can model structural changes between metal ions and ligands in the first coordination shell, and reproduce the free energy barriers for the corresponding ligand exchange. The strategy presented here provides a computationally efficient approach to model metal ions in solution, paving the way for modelling larger and more diverse metal complexes relevant to biomolecules and supramolecular assemblies.

Theoretical investigation on hydrolysis mechanism of cis-platin analogous Pt(II)/Pd(II) complex by DFT calculation and molecular docking approach for their interaction with DNA & HSA

The properties to be an active drug candidate of the complex Pt(TEEDA)Cl₂, C1; Pd(TEEDA)Cl₂, C2 and their hydrolysed product [Pt(TEEDA)(OH₂)₂]²⁺, C1' and [Pd(TEEDA)(OH₂)₂]²⁺, C2' were predicted by Lipinski's rule of 5 and PASS (prediction of activity spectra for substances) web tool. Their structural profile, HOMO-LUMO energy and electronic potential surface ware analysed by DFT calculation. Their TD-DFT spectra were compared with experimental UV-Vis spectra. The hydrolysis mechanisms of C1 & C2 to the diaqua form C1' and C2' were extensively investigated by DFT method in different levels of theory and using CPCM/water model and compared with recognised Pt based anticancer drugs. All the stationary states, including the transition state for the reactions were identified by the DFT calculation. The IRC calculation confirmed that the transition states are well connected and corelate with reactants and products. Interaction of the complexes with DNA & HSA was also investigated by molecular docking study.

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

Abstract

Nucleobases serve as ideal targets where drugs bind and exert their anticancer activities. Cisplatin (cisPt) preferentially coordinates to 2′-deoxyguanosine (dGuo) residues within DNA. The dGuo adducts that are formed alter the DNA structure, contributing to inhibition of function and ultimately cancer cell death. Despite its success as an anticancer drug, cisPt has a number of drawbacks that reduce its efficacy, including repair of adducts and drug resistance. Some approaches to overcome this problem involve development of compounds that coordinate to other purine nucleobases, including those found in RNA. In this work, amino acid-linked platinum(II) (AAPt) compounds of alanine and ornithine (AlaPt and OrnPt, respectively) were studied. Their reactivity preferences for DNA and RNA purine nucleosides (i.e., 2′-deoxyadenosine (dAdo), adenosine (Ado), dGuo, and guanosine (Guo)) were determined. The chosen compounds form predominantly monofunctional adducts by reacting at the N1, N3, or N7 positions of purine nucleobases. In addition, features of AAPt compounds that impact the glycosidic bond stability of Ado residues were explored. The glycosidic bond cleavage is activated differentially for AlaPt-Ado and OrnPt-Ado isomers. Formation of unique adducts at non-canonical residues and subsequent destabilization of the glycosidic bonds are important features that could circumvent platinum-based drug resistance.

Graphic abstract

Electronic supplementary material

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Platinum(ii)-catalyzed dehydrative C3-benzylation of electron-deficient indoles with benzyl alcohols

A synthetic strategy for the water-promoted direct dehydrative coupling of indoles with benzyl alcohols catalyzed by PtCl₂(PhCN)₂ in 1,2-dichloroethane has been developed.

Square planar or octahedral after all? The indistinct solvation of platinum(ii)

The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.

The mixed gold-palladium polyoxo-noble-metalate [NaAu(III)4Pd(II)8O8(AsO4)8](11-)

The first fully inorganic, discrete gold-palladium-oxo complex [NaAu(III) 4 Pd(II) 8 O8 (AsO4 )8 ](11-) has been synthesized in aqueous medium. The combination of single-crystal XRD, elemental analysis, mass spectrometry, and DFT calculations allowed establishing the structure and composition of the novel polyanion, and UV/Vis studies suggest that it is stable in neutral aqueous media.

THE HYDROLYSIS MECHANISM OF THE ANTICANCER AGENT trans-DICHLORO(AMMINE)(QUINOLINE)PLATINUM COMPLEX: A THEORETICAL STUDY

Hydrolysis of trans-dichloro(ammine)(quinoline)platinum, a novel potential anticancer drug, is believed to be the key activation step before the drug reaches its intracellular target DNA. To obtain an accurate hydrolysis mechanism for this nonclassical class of square-planar Pt (II) complex, five different models were used at the experimental temperature with the solvent effect B3LYP/PCM using hybrid density functional theory. The stationary points on the potential energy surfaces for the first and second hydrolysis steps, proceeding via a five-coordinate trigonal-bipyramidal (TBP)-like structure of transition state, were fully optimized and characterized. The most remarkable structural variations in the hydrolysis process were found to occur in the equatorial plane of the TBP-like structures of the intermediates and transition states. It was found that the explicit solvent effect originating from the inclusion of extra water molecules into the system is significantly stronger than those arising from the bulk aqueous medium, especially for the first aquation step, which emphasizes the use of appropriate models for these types of problems. The results give detailed energy profiles for the mechanism of hydrolysis of trans-dichloro(ammine)(quinoline)platinum, which may assist in understanding the reaction mechanism of the drug with DNA target and in the design of novel platinum-based anticancer drugs with trans geometries.

Characterizing Pt-derived anticancer drugs from first principles: the case of oxaliplatin in aqueous solution

The molecular compound ethyldiamine-oxalatoplatinum(II), EDO-Pt, is used as a model to study the oxaliplatin anticancer drug in aqueous solution by means of ab initio computer simulation. Gas-phase structure optimizations have been performed for both oxaliplatin and its EDO-Pt mimic along with Car-Parrinello molecular dynamics simulations of EDO-Pt in gas phase and in aqueous solution. The coordination of Pt(II) is square-planar on average, with Pt-N and Pt-O(I) distances of 2.04 A in solution. The diamine ligand has a bent structure, while the oxalate ligand is planar on average. The complex features a very rigid structure during the simulation and the charge distribution describes a dipole with its negative pole on the oxalate ligand and the positive pole on the Pt-diamine side. The solvation pattern of EDO-Pt is most well-defined around the amine and oxalate groups and is quantified by means of radial and spatial distribution functions of water molecules around the complex. Decomposition of radial distribution functions into their contributions from different regions (axial and equatorial) reveals an "anionic hydration" pattern of the metal cation by the solvent, which is analogous in nature to the bare Pt(II) aqua ion. A qualitative prediction on the kinetics of ligand exchange in oxaliplatin is derived based on its axial hydration pattern.

Computational insights into the O2-evolving complex of photosystem II

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies.

QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II

This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The model OEC involves a cuboidal Mn3CaO4Mn metal cluster with three closely associated manganese ions linked to a single mu4-oxo-ligated Mn ion, often called the 'dangling manganese'. Two water molecules bound to calcium and the dangling manganese are postulated to be substrate molecules, responsible for dioxygen formation. It is found that the energy barriers for the Mn(4)-bound water agree nicely with those of model complexes. However, the barriers for Ca-bound waters are substantially larger. Water binding is not simply correlated to the formal oxidation states of the metal centres but rather to their corresponding electrostatic potential atomic charges as modulated by charge-transfer interactions. The calculations of structural rearrangements during water exchange provide support for the experimental finding that the exchange rates with bulk 18 O-labelled water should be smaller for water molecules coordinated to calcium than for water molecules attached to the dangling manganese. The models also predict that the S1-->S2 transition should produce opposite effects on the two water-exchange rates.

Computational studies of the O(2)-evolving complex of photosystem II and biomimetic oxomanganese complexes

In recent years, there has been considerable interest in studies of catalytic metal clusters in metalloproteins based on Density Functional Theory (DFT) quantum mechanics/molecular mechanics (QM/MM) hybrid methods. These methods explicitly include the perturbational influence of the surrounding protein environment on the structural/functional properties of the catalytic centers. In conjunction with recent breakthroughs in X-ray crystallography and advances in spectroscopic and biophysical studies, computational chemists are trying to understand the structural and mechanistic properties of the oxygen-evolving complex (OEC) embedded in photosystem II (PSII). Recent studies include the development of DFT-QM/MM computational models of the Mn(4)Ca cluster, responsible for photosynthetic water oxidation, and comparative quantum mechanical studies of biomimetic oxomanganese complexes. A number of computational models, varying in oxidation and protonation states and ligation of the catalytic center by amino acid residues, water, hydroxide and chloride have been characterized along the PSII catalytic cycle of water splitting. The resulting QM/MM models are consistent with available mechanistic data, Fourier-transform infrared (FTIR) spectroscopy, X-ray diffraction data and extended X-ray absorption fine structure (EXAFS) measurements. Here, we review these computational efforts focused towards understanding the catalytic mechanism of water oxidation at the detailed molecular level.

On the anomalous adsorption of [Pd(edta)]2- at the water/Goethite interface: spectroscopic evidence for two types of surface complexes

The structure of palladium(II) ethylenediaminetetraacetate (edta) in aqueous solutions and its adsorption on the surface of goethite (alpha-FeOOH) were studied using extended X-ray absorption fine structure spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy. The obtained results show that in aqueous solutions, Pd-edta exists as a 1:1 complex, [Pd(edta)]2-, with edta acting as a quadridentate ligand. On the surface of goethite, [Pd(edta)]2- forms two different types of complexes over a pH range of 3.40-8.12. At pH < 5, [Pd(edta)]2- adsorbs as an outer-sphere species with possible hydrogen bonding. At higher pH values, the formation of inner-sphere complexes of the cation-type sets in after a cleavage of one glycinate ring and the formation of an (edta)Pd-O-Fe linkage.

Bifunctional binding of cisplatin to DNA: why does cisplatin form 1,2-intrastrand cross-links with ag but not with GA?

The bifunctional binding of the anticancer drug cisplatin to two adjacent nucleobases in DNA is modeled using density functional theory. Previous experimental studies revealed that cisplatin binding to adjacent guanine and adenine is sensitive to nucleobase sequence. Whereas AG 1,2-intrastrand cross-links are commonly observed, the analogous GA adducts are not known. This study focuses on understanding this directional preference by constructing a full reaction profile using quantum chemical simulation methods. Monofunctional and bifunctional cisplatin adducts were generated, and the transition states that connect them were located for the dinucleotides d(pApG) and d(pGpA), assuming that initial platination takes place at the guanine site. Our computer simulations reveal a significant kinetic preference for formation of the AG over the GA adduct. The activation free energies of approximately 23 kcal/mol for AG and approximately 32 kcal/mol for GA suggest that bifunctional closure is approximately 6 orders of magnitude faster for AG than for GA. A strong hydrogen bond between one of the ammine ligands of cisplatin and the 5' phosphate group of the DNA backbone is responsible for the stabilization of the transition state that affords the AG adduct. This interaction is absent in the transition state that leads to the GA adduct because the right-handed helix of the DNA backbone places the phosphate out of reach for the ammine ligand. We found only an insignificant thermodynamic difference between AG and GA adducts and conclude that the preference of AG over GA binding is largely under kinetic control. The puckering of the deoxyribose ring plays an important role in determining the energetics of the bifunctional platination products. Whereas the 3'-nucleoside remains in the native C2'-endo/C3'-exo form of B-DNA, the deoxyribose of the 5'-nucleoside always adopts the C2'-exo/C3'-endo puckering in our simulations. A detailed analysis of the energies and structures of the bifunctional adducts revealed that the observed sugar puckering patterns are necessary for platinum to bind in a relaxed coordination geometry.