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This PhD thesis focuses on the employment of computational approaches for the study of the interactions between biomolecules, a broad term that accounts for different molecular species ranging from proteins to small ligands. Understanding how biomolecules recognize each other, thus giving rise to complexes or assemblies, is a key point for the comprehension of biological mechanisms in living organisms and for application purposes in a variety of fields, among which drug design. These difficult and multidisciplinary issues strongly exploit in silico approaches, which, in the last decades, have become increasingly efficient and essential for supporting and guiding the experiments. The research activity carried out during my PhD work has mainly dealt with two projects. The first one revolves around protein-protein interactions and concerns a specific use-case, namely the necessity to predict how two affitins bind the human epidermal growth factor receptor 2 (HER2). This project has been carried out in collaboration with Dr. Alessandro Maiocchi (Bracco S.p.A – owner of two patents that cover the use of the two affitins as molecular probes targeting HER2), and Dr. Elisabetta Moroni (SCITEC, Italian National Research Council). The second project has been conducted at the Computational Structural Biology group (Bijvoet Centre for Biomolecular Research, Universiteit Utrecht) under the supervision of Prof. Alexandre Bonvin and Dr. Marco Giulini. It aims at building a reliable protocol, based on the software HADDOCK3, which is developed at the CSB group, for the prediction of protein-glycan complexes., This PhD thesis focuses on the employment of computational approaches for the study of the interactions between biomolecules, a broad term that accounts for different molecular species ranging from proteins to small ligands. Understanding how biomolecules recognize each other, thus giving rise to complexes or assemblies, is a key point for the comprehension of biological mechanisms in living organisms and for application purposes in a variety of fields, among which drug design. These difficult and multidisciplinary issues strongly exploit in silico approaches, which, in the last decades, have become increasingly efficient and essential for supporting and guiding the experiments. The research activity carried out during my PhD work has mainly dealt with two projects. The first one revolves around protein-protein interactions and concerns a specific use-case, namely the necessity to predict how two affitins bind the human epidermal growth factor receptor 2 (HER2). This project has been carried out in collaboration with Dr. Alessandro Maiocchi (Bracco S.p.A – owner of two patents that cover the use of the two affitins as molecular probes targeting HER2), and Dr. Elisabetta Moroni (SCITEC, Italian National Research Council). The second project has been conducted at the Computational Structural Biology group (Bijvoet Centre for Biomolecular Research, Universiteit Utrecht) under the supervision of Prof. Alexandre Bonvin and Dr. Marco Giulini. It aims at building a reliable protocol, based on the software HADDOCK3, which is developed at the CSB group, for the prediction of protein-glycan complexes.

The aerobic oxidation of carbon monoxide to carbon dioxide is catalysed by the Mo/Cu-containing CO-dehydrogenase enzyme in the soil bacterium Oligotropha carboxidovorans, enabling the organism to grow on the small gas molecule as carbon and energy source. It was shown experimentally that silver can be substituted for copper in the active site of Mo/Cu CODH to yield a functional enzyme. In this study, we employed QM/MM calculations to investigate whether the reaction mechanism of the silver-substituted enzyme is similar to that of the native enzyme. Our results suggest that the Ag-substituted enzyme can oxidize CO and release CO2 following the same reaction steps as the native enzyme, with a computed rate-limiting step of 10.4 kcal/mol, consistent with experimental findings. Surprisingly, lower activation energies for C-O bond formation have been found in the presence of silver. Furthermore, comparison of rate constants for reduction of copper- and silver-containing enzymes suggests a discrepancy in the transition state stabilization upon silver substitution. We also evaluated the effects that differences in the water-active site interaction may exert on the overall energy profile of catalysis. Finally, the formation of a thiocarbonate intermediate along the catalytic pathway was found to be energetically unfavorable for the Ag-substituted enzyme.

Sodium chloride (NaCl) represents the principal component of atmospheric particulates of marine origin. To gain a molecular-level understanding of the adsorption process of water vapor on the NaCl surface, Monte Carlo simulations performed in the Grand Canonical ensemble were carried out, considering the water adsorption at different water pressures on a NaCl(001) surface. The calculated adsorption isotherm shows four different regions, whose coverages correspond to those of the low-, transition-, high-, and pre-solution-coverage regions experimentally observed. Detailed analysis reveals how the structure of the adsorbed water molecules (islands, layer, and multi-layer) changes depending on water pressure, and how their orientation with respect to the surface varies with the distance from the surface. This detailed information further supports the picture coming from previous experimental IR absorption spectroscopy studies.

Nitrogen gas is a highly inert molecule and its activation under mild conditions represents a crucial goal in current research. In a recent study, the discovery of low-valence Ca(i) compounds capable of coordinating and reducing N2 was reported [B. Rösch, T. X. Gentner, J. Langer, C. Färber, J. Eyselein, L. Zhao, C. Ding, G. Frenking and S. Harder, Science, 2021, 371, 1125]. The study of low-valence alkaline earth complexes represents a new horizon in inorganic chemistry and demonstrates examples of spectacular reactivity. For example, complexes of the [BDI]2Mg2 type are selective reducing reagents in both organic and inorganic synthesis reactions. To date, however, no activity of Mg(i) complexes in the activation of the nitrogen molecule has been reported. By computational studies, in the present work, we investigated the analogies and differences of low-valence Ca(i) and Mg(i) complexes in the coordination, activation and protonation of N2. We have shown that the possibility of alkaline earth metals to employ atomic orbitals of the d type is reflected in the differences in the N2 binding energy and its coordination mode (end-on vs. side-on), as well as in the spin state of the resulting adduct (singlet vs. triplet). These divergences are finally observed in the subsequent protonation reaction, which turned out to be prohibitive in the presence of Mg.

Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of enormous interest and urgent relevance: the properties of metalloenzymes involved in the degradation and valorization of natural biopolymers and synthetic plastics on the basis of both circular biofuel production and bioremediation strategies. In particular, we will focus on lytic polysaccharide monooxygenase, laccases, and various heme peroxidases involved in the processing of polysaccharides, lignins, rubbers, and some synthetic polymers. Special attention will be dedicated to the interaction between these enzymes and their substrate studied at different levels of theory, starting from classical molecular docking and molecular dynamics techniques up to techniques based on quantum chemistry.

La tesi esplora le correlazioni fra composizione chimica del particolato emesso in frenata e alcuni fattori quali: i) le combinazioni di materiali che compongono l'interfaccia tribologica; ii) le condizioni di guida; iii) le frazioni dimensionali in cui vengono prodotti i particolati, This thesis reports on the correlations between the compositional features of the particulates produced by brakes and several determining or modulating factors, such as: i) The starting material composing the friction couple; ii) the driving conditions; and iii) the dimensional fractions in which the particulates are generated and emitted.

Lo sviluppo di tessuti biologici 3D artificiali richiede che cellule specifiche siano ospitate da uno scaffold sintetico che imita al meglio la matrice extracellulare (ECM) del tessuto, contenente specifiche molecole di segnalazione bioattive, che svolgono un ruolo importante nell'omeostasi cellulare. Più un modello ECM 3D in vitro replica queste condizioni, più le cellule all'interno replicheranno i comportamenti e i segnali delle cellule in vivo. Infatti, il microambiente cellulare è specifico per ogni organo e tessuto e svolge un ruolo fondamentale nella crescita cellulare, nel differenziamento e nella comunicazione tra cellule ed è coinvolto nella patogenesi. Lo scopo del progetto di dottorato è la progettazione, la sintesi, la caratterizzazione e la reticolazione di polimeri biocompatibili impiegabili come matrice cellula-specifica per lo sviluppo di modelli 3D tissutali in vitro utili per la validazione di farmaci e nuove terapie. A questo scopo sono state studiate reazioni chemoselettive per funzionalizzare e reticolare biomateriali polimerici al fine di generare "bioinchiostri" adatti per la biostampa 3D di ECM artificiale. Considerando il ruolo rilevante degli zuccheri come molecole di segnalazione in ECM, in grado di indurre anche eventi patologici, abbiamo deciso di generare ECM artificiali coniugati covalentemente con diversi zuccheri opportunamente selezionati. In questa tesi vengono descritti tre diversi approcci sintetici per generare modelli tissutali con caratteristiche diverse: (i) idrogel coniugato con zuccheri ottenuto dalla reticolazione di glico-gelatine e acido ialuronico strain – promoted azide-alkyne cycloaddition (SPAAC); (ii) elastina – acido ialuronico reticolato tramite la reazione di addizione di Michael; (iii) alginato – idrogel di gelatina ottenuto mediante doppia reticolazione statico-dinamica (tramite HRP e acido boronico). Gli idrogel glicoconiugati sono stati testati come modello tissutale in vitro di cancro al colon in colla, The production of artificial 3D biological tissues requires that specific cells are hosted by a synthetic scaffold mimicking at the best the extracellular matrix (ECM) of the tissue, containing specific bioactive signaling molecules, which play an important role in the cellular homeostasis. The more closely a 3D in vitro ECM model replicates those conditions, the more closely the cells inside will replicate the behaviours and responses of cells in vivo. Indeed, the cell microenvironment is tissue and organ specific and play a fundamental role in cell growth, cell differentiation and communication, and is involved in pathogenesis. Aim of the PhD project is the design, the synthesis, the characterization and crosslinking of biocompatible polymers employable as cell-specific matrix for the development of 3D tissue in vitro models useful for drug and new therapies validation. To this purpose chemoselective reactions have been investigated to functionalize and crosslink polymeric biomaterials in order to generate suitable “bioinks” for 3D bioprinting of artificial ECM. Considering the relevant role of glycans as signalling molecules in ECM, able to also induce pathological event, we decided to generate artificial ECMs covalently conjugated with different, properly selected glycans. In this thesis three different synthetic approaches are described to generate tissue models with different characteristics: (i) glycol-conjugate hydrogel obtained by the crosslinking of glyco-gelatins and hyaluronic acid via strain – promoted azide-alkyne cycloaddition (SPAAC); (ii) elastin – hyaluronic acid crosslinked via Michael addition reaction; (iii) alginate – gelatin hydrogel obtained by dual static-dynamic crosslinking (via HRP and boronic acid). The glycoconjugate hydrogels have been tested as colon cancer in vitro tissue model in collaboration with San Gerardo Hospital (Monza, Italy) and as gastric cancer in vitro tissue model in collaboration with i3S - Institute for Research and I

The photon upconversion based on triplet–triplet annihilation (TTA) is a mechanism that converts the absorbed low-energy electromagnetic radiation into higher energy photons also at extremely low excitation intensities, but its use in actual technologies is still hindered by the limited availability of efficient annihilator moieties. We present here the results obtained by the synthesis and application of two new fluorinated chromophores based on phenazine and acridine structures, respectively. Both compounds show upconverted emission demonstrating their ability as TTA annihilator. More interesting, the acridine-based chromophore shows an excellent TTA yield that overcomes the one of some of best model systems. By correlating the experimental data and the quantum mechanical modeling of the investigated compound, we propose an alternative efficient pathway for the generation of the upconverted emissive states involving the peculiar high-energy triplet levels of the dye, thus suggesting a new development strategy for TTA annihilators based on the fine tuning of their high-energy excited states properties.