Reactivity of activated electrophiles and nucleophiles: labile intermediates and properties of the reaction products

The main topic of my Ph.D. thesis is the study of nucleophilic and electrophilic aromatic substitution reaction, in particular from a mechanistic point of view. The research was mainly focused on the reactivity of superactivated aromatic systems. In spite of their high reactivity (hence the high reaction’s rate), we were able to identify and in some case to isolate -complexes until now only hypothesized. For example, interesting results comes from the study of the protonation of the supernucleophiles tris(dialkylamino)benzenes. However, the best result obtained in this field was the isolation and structural characterization of the first stables zwitterionic Wheland-Meisenheimer complexes by using 2,4-dipyrrolidine-1,3-thiazole as supernucleophile and 4,6-dinitrobenzofuroxan or 4,6-dinitrotetrazolepyridine as superelectrophile. These reactions were also studied by means of computational chemistry, which allowed us to better investigate on the energetic and properties of the reactions and reactants studied. We also discovered, in some case fortuitously, some relevant properties and application of the compounds we synthesized, such as fluorescence in solid state and nanoparticles, or textile dyeing. We decided to investigate all these findings also by collaborating with other research groups. During a period in the “Laboratoire de Structure et Réactivité des Systèmes Moléculaires Complexes-SRSMC, Université de Lorraine et CNRS, France, I carried out computational studies on new iron complexes for the use as dyes in Dye Sensitized Solar Cells (DSSC). Furthermore, thanks to this new expertise, I was involved in a collaboration for the study of the ligands’ interaction in biological systems. A collaboration with University of Urbino allowed us to investigate on the reactivity of 1,2-diaza-1,3-dienes toward nucleophiles such as amino and phosphine derivatives, which led to the synthesis of new products some of which are 6 or 7 member heterocycles containing both phosphorus and nitrogen atoms.

A multidisciplinary approach to the study of protein dynamics and signal transmission

Allostery is a phenomenon of fundamental importance in biology, allowing regulation of function and dynamic adaptability of enzymes and proteins. Despite the allosteric effect was first observed more than a century ago allostery remains a biophysical enigma, defined as the “second secret of life”. The challenge is mainly associated to the rather complex nature of the allosteric mechanisms, which manifests itself as the alteration of the biological function of a protein/enzyme (e.g. ligand/substrate binding at the active site) by binding of “other object” (“allos stereos” in Greek) at a site distant (> 1 nanometer) from the active site, namely the effector site. Thus, at the heart of allostery there is signal propagation from the effector to the active site through a dense protein matrix, with a fundamental challenge being represented by the elucidation of the physico-chemical interactions between amino acid residues allowing communicatio n between the two binding sites, i.e. the “allosteric pathways”. Here, we propose a multidisciplinary approach based on a combination of computational chemistry, involving molecular dynamics simulations of protein motions, (bio)physical analysis of allosteric systems, including multiple sequence alignments of known allosteric systems, and mathematical tools based on graph theory and machine learning that can greatly help understanding the complexity of dynamical interactions involved in the different allosteric systems. The project aims at developing robust and fast tools to identify unknown allosteric pathways. The characterization and predictions of such allosteric spots could elucidate and fully exploit the power of allosteric modulation in enzymes and DNA-protein complexes, with great potential applications in enzyme engineering and drug discovery.

New Gold(I) complexes: from ligand design to homogeneous catalysis

This PhD thesis summarize the work carried out during three years of PhD course. Several thematic concerning gold(I) chemistry are analysed by crossing data from different chemistry areas as: organic chemistry, organometallic chemistry, inorganic chemistry and computational chemistry. In particular, the thesis focuses its attention on the evaluation of secondary electronic interactions, subsisting between ligand and Au(I) metal centre in the catalyst, and their effects on catalytic activity. The interaction that has been taken in consideration is the Au…Ar π-interaction which is known to prevent the decomposition of catalyst, but exhaustive investigations of further effects has never been done so far. New libraries of carbene (ImPy) and biarylphosphine ligands have been designed and synthetized for the purpose and subsequently utilized for the synthesis of corresponding Au(I) complexes. Resulting catalysts are tested in various catalytic processes involving different intermediates and in combination with solid state information from SC-XRD revealed an unprecedented activation mode which is only explained by considering both electronic nature and strength of Au…Ar π-interaction. DFT calculation carried on catalysis intermediates are in agreement with experimental ones, giving robustness to the theory. Moreover, a new synthetic protocol for the lactonization of N-allenyl indole-2-carboxylic acids is presented. Reaction conditions are optimized with the newly synthetized ImPy-Au(I) catalysts and different substrates are also tested providing a quite broad reaction scope. Chiral ImPy ligands have also been developed for the asymmetric variant of the same reaction and encouraging enantiomeric excess are obtained.

Computational Methods in Biophysics and Medicinal Chemistry: Applications and Challenges

In this thesis I described the theory and application of several computational methods in solving medicinal chemistry and biophysical tasks. I pointed out to the valuable information which could be achieved by means of computer simulations and to the possibility to predict the outcome of traditional experiments. Nowadays, computer represents an invaluable tool for chemists. In particular, the main topics of my research consisted in the development of an automated docking protocol for the voltage-gated hERG potassium channel blockers, and the investigation of the catalytic mechanism of the human peptidyl-prolyl cis-trans isomerase Pin1.

Unconventional Catalysis in Organic Chemistry: a Computational Mechanistic Study

Catalysis plays a vital role in modern synthetic chemistry. However, even if conventional catalysis (organo-catalysis, metal-catalysis and enzyme-catalysis) has provided outstanding results, various unconventional ways to make chemical reactions more effective appear now very promising. Computational methods can be of great help to reach a deeper comprehension of these chemical processes. The methodologies employed in this thesis are Quantum-Mechanical (QM), Molecular Mechanics (MM) and hybrid Quantum-Mechanical/Molecular Mechanics (QM/MM) methods. In this abstract the results are briefly summarised. The first unconventional catalysis investigated consists in the application of Oriented External Electric Fields (OEEFs) to SN2 and 4e-electrocyclic reactions. SN2 reactions with back-side mechanism can be catalysed or inhibited by the presence of an OEEF. Moreover, OEEFs can inhibit back-side mechanism (Walden inversion of configuration) and promote the naturally unfavoured front-side mechanism (retention of configuration). Electrocyclic ring opening reaction of 3-substituted cyclobutene molecules can occur with inward or outward mechanisms depending on the nature of substituent groups on the cyclobutene structure (torquoselectivity principle). OEEFs can catalyse the naturally favoured pathway or circumvent the torquoselectivity principle leading to different stereoisomers. The second case study is based on Carbon Nanotubes (CNTs) working as nano-reactors: the reaction of ethyl chloride with chloride anion inside CNTs was investigated. In addition to the SN2 mechanism, syn and anti-E2 reactions are possible. These reactions inside CNTs of different radii were examined with hybrid QM/MM methods, finding that these processes can be both catalysed and inhibited by the CNT diameter. The results suggest that electrostatic effects govern the activation energy variations inside CNTs. Finally, a new biochemical approach, based on the use of DNA catalyst was investigated at QM level. Deoxyribozyme 9DB1 catalyses the RNA ligation allowing the regioselective formation of the 3'-5' bond, following an addition-elimination two-step mechanism.

Computational insight into materials properties

The aim of the work was to explore the practical applicability of molecular dynamics at different length and time scales. From nanoparticles system over colloids and polymers to biological systems like membranes and finally living cells, a broad range of materials was considered from a theoretical standpoint. In this dissertation five chemistry-related problem are addressed by means of theoretical and computational methods. The main results can be outlined as follows. (1) A systematic study of the effect of the concentration, chain length, and charge of surfactants on fullerene aggregation is presented. The long-discussed problem of the location of C60 in micelles was addressed and fullerenes were found in the hydrophobic region of the micelles. (2) The interactions between graphene sheet of increasing size and phospholipid membrane are quantitatively investigated. (3) A model was proposed to study structure, stability, and dynamics of MoS2, a material well-known for its tribological properties. The telescopic movement of nested nanotubes and the sliding of MoS2 layers is simulated. (4) A mathematical model to gain understaning of the coupled diffusion-swelling process in poly(lactic-co-glycolic acid), PLGA, was proposed. (5) A soft matter cell model is developed to explore the interaction of living cell with artificial surfaces. The effect of the surface properties on the adhesion dynamics of cells are discussed.