Juan Sanz García

Furimamide, the light-emitting chromophore of the NanoLuc bioluminescent system, exhibits photophysical properties whose dependence on conformational flexibility and solute–solvent interactions in aqueous solution are not yet fully understood. Here, we present a multiscale computational study combining classical and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations with ensemble-averaged time-dependent density functional theory (TD-DFT) calculations. QM/MM derived spectra from both MM and QM/MM sampling reproduce the experimental absorption maximum, yet differ in the relative contributions of the two lowest excited states. Natural transition orbital analysis and the topological index Φₛ were performed for analyzing the transitions. Emission spectra computed from 10 ps excited-state QM/MM trajectories show excellent agreement with experiment in peak position without empirical shifting. These results establish a transferable computational framework for simulating condensed-phase spectroscopy of bioluminescent chromophores and highlight the sensitivity of predicted spectral features to the level of theory used to describe chromophore–solvent interactions.

Etude théorique de nouveaux complexes de ruthénium à ligand nitrosyle : mécanisme de photoisomérisation et de photolibération de NO: Au cours des dernières années, l'intérêt pour les complexes métalliques à ligand nitrosyle n'a pas cessé de croître dans les communautés pharmaceutique, chimique et en science des matériaux. Cet intérêt s'explique par leurs uniques propriétés physico-chimiques, plus concrètement par leur réponse aux perturbations lumineuses. Sous irradiation, ces composés sont capables de libérer NO, molécule qui a un rôle important dans le système vasculaire, ainsi que dans d'autres systèmes physiologiques importants. Ce n'est donc pas surprenant que de telles molécules aient attiré l'attention de la communauté médicale par sa potentielle application dans le traitement par photothérapie dynamique de plusieurs maladies tel que le cancer. La libération d'oxyde nitrique peut aussi être contrôlée par des réactions redox sans aucune perturbation électromagnétique. La réduction de la partie M-NO peut déclencher le départ de NO. En effet, les molécules qui présentent des bandes de transfert de charge depuis un ligand vers la partie M-NO dans leurs spectres d'absorption UV-Vis ont des rendements quantiques de photolibération plus élevés que celles qui n'en présentent pas. Ces transferts de charge peuvent être considérés comme une réduction de la partie M-NO. Une autre propriété extraordinaire de ces complexes métalliques à ligand nitrosyle est leur réponse photochromique à l'irradiation électromagnétique. Dans un cristal, le changement de couleur est dû à un réarrangement du ligand NO entre sa forme nitrosyle (lié par l'azote) et sa forme isonitrosyle (lié par l'oxygène). Avec la longueur d'onde appropriée, le sens de la photoisomérisation d'enchainement (aller et retour) peut être contrôlé. Cette caractéristique est vraiment intéressante pour la conception des nouveaux dispositifs optiques de stockage massif. Un des objectifs fondamentaux de cette thèse concerne la modélisation des mécanismes de réactions qui décrivent les phénomènes de photoisomérisation et photolibération de NO dans les complexes de ruthénium à ligand nitrosyle. Pour éclaircir la nature de ces processus, une caractérisation complète des structures électroniques ainsi que des surfaces d'énergie potentielle de l'état fondamental et des états excités de plus basse énergie est nécessaire. Des calculs réalisés avec la Théorie de la Fonctionnelle de la Densité ont permis de rationaliser le mécanisme de photoisomérisation d'enchainement du trans-[RuCl(NO)(py)4]2+, un complexe qui permet d'obtenir un taux de photoconversion (ca. 100%) parmi les plus élevés dans cette famille de complexes. La caractérisation de l'état fondamental singulet et de l'état excité triplet de plus basse énergie ainsi que l'identification de plusieurs croisements ont permis d'établir un mécanisme séquentiel à deux photons, avec un intermédiaire métastable d'hapticité deux.

We sought to determine the cyclodextrins (CDs) best suited to solubilize a patented succinimido-ferrocidiphenol (SuccFerr), a compound from the ferrociphenol family having powerful anticancer activity but low water solubility. Phase solubility experiments and computational modelling were carried out on various CDs. For the latter, several CD-SuccFerr complexes were built starting from combinations of one or two CD(s) where the methylation of CD oxygen atoms was systematically changed to end up with a database of ca. 13 k models. Modelling and phase solubility experiments seem to indicate the predominance of supramolecular assemblies of SuccFerr with two CDs and the superiority of randomly methylated β-cyclodextrins (RAMEβCDs). In addition, modelling shows that there are several competing combinations of inserted moieties of SuccFerr. Furthermore, the models show that ferrocene can contribute to high stabilization by making atypical hydrogen bonds between Fe and the hydroxyl groups of CDs (single bond with one OH or clamp with two OH of the same glucose unit).

Transition Metal Complexes (TMCs) are known for the rich variety of their excited states showing different nature and degrees of locality. Describing the energies of these excited states with the same degree of accuracy is still problematic when using time-dependent density functional theory in conjunction with the most current density functional approximations. In particular, the presence of unphysically low lying excited states possessing a relevant Charge Transfer (CT) character may significantly affect the spectra computed at such a level of theory and, more relevantly, the interpretation of their photophysical behavior. In this work, we propose an improved version of the M_AC index, recently proposed by the authors and collaborators, as a simple and computationally inexpensive diagnostic tool that can be used for the detection and correction of the unphysically predicted low lying excited states. The analysis, performed on five prototype TMCs, shows that spurious and ghost states can appear in a wide spectral range and that it is difficult to detect them only on the basis of their CT extent. Indeed, both delocalization of the excited state and CT extent are criteria that must be combined, as in the M_AC index, to detect unphysical states.

Luminescence of furimamide is 150 times brighter than oxidized luciferins in firefly and renilla luciferase. However, we do not have a clear understanding of the structure, function and dynamic behavior of the nanoluciferase-furimamide complex. Here, for the first time, the absorption and emission proprieties of eight different possible light emitter forms of furimamide were investigated using the TD-DFT method in the gas phase and aqueous solution. The emission oscillator strengths in the gas phase showed that emission transition may be forbidden for some forms, and fluorescence would not occur. Besides, the charge transfer (CT) as well as the orbitals involved in the transitions were analyzed. Furthermore, molecular docking results showed that furimamide is situated inside the central cavity (β-barrel) of nanoluciferase. Analysis of the trajectory of molecular dynamics (MD) simulations suggested a less compact structure of protein in the presence of furimamide in comparison to its apo form. The QM/MM spectroscopic proprieties of one form in the binding site of nanoluciferase were investigated. The evolution of the ESs of furimamide in the binding pocket of the protein confirmed that after photoexcitation and during the relaxation of the system, a crossing point between the first two singlet ESs exists. Thus, the initially populated S2 (a π→π* transition) becomes the first singlet excited state.

Analyzing the behavior of potential energy surfaces (PESs) of diabatic excited states (ESs) becomes of crucial importance for a complete understanding of complex photochemical reactions. Since the definition of a compact representation for the transition density matrix, the use of the natural transition orbitals (NTOs) has become a routine practice in time‐dependent density functional theory calculations. Their popularity has remarkably grown due to its simple orbital description of electronic excitations. Indeed, very recently, we have presented a new formalism used for the optimization of ESs by tracking the state of interest computing the NTO's overlap between consecutive steps of the procedure. In this new contribution, we generalize the use of this NTO's overlap‐based state‐tracking formalism for the analysis of all the desired diabatic states along any chemical reaction pathway. Determining the PES of the different diabatic states has been automatized by developing an extension of our recently presented algorithm, the so‐called SDNTO: “Steepest Descent minimization using NTOs.” This automatized overlap‐based procedure allows an agile and convenient analysis of the evolution of the ESs avoiding the intrinsic ambiguity of visualizing orbitals or comparing physical observables. The analysis of two photochemical reactions of the same nature with different PES landscapes perfectly illustrates the utility of this new tool.

Ferrociphenols, especially those possessing a heterocycle at the terminus of an aliphatic chain, display strong anticancer activity through a novel redox mechanism that generates active metabolites such as quinone methides (QMs). X‐ray crystallography and UV/Vis spectroscopy reveal that the specific lone pair (lp)–π interaction between a carbonyl group of the imide and the quinone motif of the QM plays an important role in the exceptional cytotoxic behaviour of their imido‐ferrociphenol precursors. This intramolecular lp–π interaction markedly enhanced the stability of the QMs and lowered the pK_a values of the corresponding phenol/phenolate couples. As the first example of such a non‐covalent interaction that stabilizes QMs remotely, it not only expands the scope of the lp–π interaction in supramolecular chemistry, but also represents a new mode of stabilization of a QM. This unprecedented application of lp–π interactions in imido‐ferrociphenol anticancer drug candidates may also have great potential in drug discovery and organocatalyst design.

Ferrociphenols, especially those possessing a heterocycle at the terminus of an aliphatic chain, display strong anticancer activity through a novel redox mechanism that generates active metabolites such as quinone methides (QMs). X‐ray crystallography and UV/Vis spectroscopy reveal that the specific lone pair (lp)–π interaction between a carbonyl group of the imide and the quinone motif of the QM plays an important role in the exceptional cytotoxic behaviour of their imido‐ferrociphenol precursors. This intramolecular lp–π interaction markedly enhanced the stability of the QMs and lowered the pK_a values of the corresponding phenol/phenolate couples. As the first example of such a non‐covalent interaction that stabilizes QMs remotely, it not only expands the scope of the lp–π interaction in supramolecular chemistry, but also represents a new mode of stabilization of a QM. This unprecedented application of lp–π interactions in imido‐ferrociphenol anticancer drug candidates may also have great potential in drug discovery and organocatalyst design.

Taking advantage of the compensation between Basis Set Superposition Error and Basis Set Incompleteness Error, a new basis is developed to improve the performances of Double Hybrid (DH) functionals in reproducing interaction energies in weak noncovalent systems. Using a self-consistent formula, containing only energy terms computed for dimers and the corresponding monomers at the same level of theory, the exponents of the more external functions of the Def-2-SVPD basis wereoptimized on three systems extracted from the S22 set. The transferability of the obtained basis set, called DH-SVPD, is then tested on 5 benchmark sets, and it is assessed by considering 6 DH functionals, eventually corrected with empirical dispersion corrections (for a total of 11 methods). Our results show that this simple approach is able to provide accurate results for interactions energies of all the considered systems, and, in particular, to recover the performances obtained by coupling the DH functionals with empirical dispersion corrections.

The ability to locate minima on electronic excited states (ESs) potential energy surfaces both in the case of bright and dark states is crucial for a full understanding of photochemical reactions. This task has become a standard practice for small‐ to medium‐sized organic chromophores thanks to the constant developments in the field of computational photochemistry. However, this remains a very challenging effort when it comes to the optimization of ESs of transition metal complexes (TMCs), not only due to the presence of several electronic ESs close in energy, but also due to the complex nature of the ESs involved. In this article, we present a simple yet powerful method to follow an ES of interest during a structural optimization in the case of TMCs, based on the use of a compact hole‐particle representation of the electronic transition, namely the natural transition orbitals (NTOs). State tracking using NTOs is unambiguously accomplished by computing the mono‐electronic wave function overlap between consecutive steps of the optimization. Here, we demonstrate that this simple but robust procedure works not only in the case of the cytosine but also in the case of the ES optimization of a ruthenium nitrosyl complex which is very problematic with standard approaches. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.