Exciton Localization on Ru-Based Photosensitizers Induced by Binding to Lipid Membranes

Binding modes of a flexible ruthenium polypyridyl complex to DNA

Ruthenium(II) polypyridyl complexes are attractive binders to DNA. Modifying the hydrophobicity, shape, or size of the ancillary ligands around the central ruthenium atom can induce changes in the binding mode to the DNA double helix. In this paper, we investigate the binding modes of [Ru(2,2'-bipyridine)2 (5-{4-[(pyren-1-yl)methyl]-1H-1,2,3-triazol-4-yl}-1,10-phenanthroline)]2+ (RuPy for short), a metal complex featuring a flexible pyrene moiety known for its intercalative properties. Classical molecular dynamics simulations are employed to gain insight into the non-covalent binding interactions of RuPy with two different 20 base pair DNA sequences, poly(dA)poly(dT) (AT) and poly(dC)poly(dG) (CG). In addition to examining the intercalation of the pyrene moiety from the major groove, the stability of RuPy-DNA adducts is investigated when the metal complex interacts externally with the DNA and with the major and minor groove pockets. The results indicate that external interaction and major groove binding are not stable, whereas intercalation consistently forms stable adducts. Minor groove binding showed less stability than intercalation and more variability, with some trajectories transitioning to intercalation, involving either the pyrene moiety or a bipyridine ligand. Pyrene intercalation, especially from the minor groove, was the most stable, while bipyridine intercalation was less favorable and associated with higher binding free energies.

Characterization of cisplatin/membrane interactions by QM/MM energy decomposition analysis

We extend for the first time a quantum mechanical energy decomposition analysis scheme based on deformation electron densities to a hybrid electrostatic embedding quantum mechanics/molecular mechanics framework. The implemented approach is applied to characterize the interactions between cisplatin and a dioleyl-phosphatidylcholine membrane, which play a key role in the permeation mechanism of the drug inside the cells. The interaction energy decomposition into electrostatic, induction, dispersion and Pauli repulsion contributions is performed for ensembles of geometries to account for conformational sampling. It is evidenced that the electrostatic and repulsive components are predominant in both polar and non-polar regions of the bilayer.

The importance of finite temperature and vibrational sampling in the absorption spectrum of a nitro-functionalized Ru(ii) water oxidation catalyst

Consideration of finite temperature and vibrational motion can be an essential component for accurate simulations of absorption spectra. Here we use finite-temperature Wigner phase-space sampling to investigate the intense absorption of the water oxidation catalyst Ru(dppip-NO2) in the visible (vis) region. The influence of vibrational and torsional motions as well as temperature effects are addressed for the different protonation forms of the pH-sensitive dppip-NO2 ligand of the catalyst. Excitations to the nitrophenyl group and π-system of dppip-NO2, which characterize the absorption band in the equilibrium spectra, experience energy shifts and a significant decrease in oscillator strength when nuclear motion is considered. The importance of excitations to the nitrophenyl group for the vis band is reduced in the spectra computed from the 300 K ensembles, which feature broad distributions of the corresponding dihedral angles. The effects of vibrational sampling on the absorption spectra may be attributed to nitrophenyl and, in particular, to NO2 torsional motions. We expect finite temperature and vibrational sampling to be important for simulating the absorption spectra of other transition metal complexes with flexible ligands or nitro-aromatic motifs.

The Permeation Mechanism of Cisplatin Through a Dioleoylphosphocholine Bilayer*

The investigation of the intermolecular interactions between platinum-based anticancer drugs and lipid bilayers is of special relevance to unveil the mechanisms involved in different steps of the anticancer mode of action of these drugs. We have simulated the permeation of cisplatin through a model membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling classical molecular dynamics simulations. The initial physisorption of cisplatin into the polar region of the lipid membrane is controlled by long-range electrostatic interactions with the choline groups in a first step and, in a second step, by long-range electrostatic and hydrogen bond interactions with the phosphate groups. The second half of the permeation pathway, in which cisplatin diffuses through the nonpolar region of the bilayer, is characterized by the drop of the interactions with the polar heads and the rise of attractive interactions with the non-polar tails, which are dominated by van der Waals contributions. The permeation free-energy profile is explained by a complex balance between the drug/lipid interactions and the energy and entropy contributions associated with the dehydration of the drug along the permeation pathway and with the decrease and increase of the membrane ordering along the first and second half of the mechanism, respectively.

Molecular Photochemistry: Recent Developments in Theory

Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light-induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non-adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.

Orbital-free photophysical descriptors to predict directional excitations in metal-based photosensitizers

The development of dye-sensitized solar cells, metalloenzyme photocatalysis or biological labeling heavily relies on the design of metal-based photosensitizes with directional excitations. Directionality is most often predicted by characterizing the excitations manually via canonical frontier orbitals. Although widespread, this traditional approach is, at the very least, cumbersome and subject to personal bias, as well as limited in many cases. Here, we demonstrate how two orbital-free photophysical descriptors allow an easy and straightforward quantification of the degree of directionality in electron excitations using chemical fragments. As proof of concept we scrutinize the effect of 22 chemical modifications on the archetype [Ru(bpy)3]2+ with a new descriptor coined "substituent-induced exciton localization" (SIEL), together with the concept of "excited-electron delocalization length" (EEDL n ). Applied to quantum ensembles of initially excited singlet and the relaxed triplet metal-to-ligand charge-transfer states, the SIEL descriptor allows quantifying how much and whereto the exciton is promoted, as well as anticipating the effect of single modifications, e.g. on C-4 atoms of bpy units of [Ru(bpy)3]2+. The general applicability of SIEL and EEDL n is further established by rationalizing experimental trends through quantification of the directionality of the photoexcitation. We thus demonstrate that SIEL and EEDL descriptors can be synergistically employed to design improved photosensitizers with highly directional and localized electron-transfer transitions.

Charge-Transfer versus Charge-Separated Triplet Excited States of [ReI (dmp)(CO)3 (His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.

Novel Molecular-Dynamics-Based Protocols for Phase Space Sampling in Complex Systems

The adequate exploration of the phase space of a chromophore is a fundamental necessity for the simulation of their optical and photophysical properties, taking into account the effects of vibrational motion and, most importantly, the coupling with a (non-homogeneous) molecular environment. A representative set of conformational snapshots around the Franck-Condon region is also required to perform non-adiabatic molecular dynamics, for instance in the framework of surface hopping. Indeed, in the latter case one needs to prepare a set of initial conditions providing a meaningful and complete statistical base for the subsequent trajectory propagation. In this contribution, we propose two new protocols for molecular dynamics-based phase space sampling, called "local temperature adjustment" and "individual QM/MM-based relaxation." These protocols are intended for situations in which the popular Wigner distribution sampling procedure is not applicable-as it is the case when anharmonic or nonlinear vibrations are present-and where regular molecular dynamics sampling might suffer from an inaccurate distribution of internal energy or from inaccurate force fields. The new protocols are applied to the case of phase space sampling of [Re(CO)3(Im)(Phen)]+ (im, imidazole; phen, phenanthroline) in aqueous solution, showing the advantages and limitations of regular Wigner and molecular dynamics sampling as well as the strengths of the new protocols.