The aim of my Ph.D. research was to study the new synthetic ways for the production of adipic acid. Three different pathways were studied: i) oxidation of cyclohexanone with molecular oxygen using Keggin – heteropolycompounds as the catalyst, ii) Baeyer – Villiger oxidation of cyclohexanone with hydrogen peroxide in the presence of two different heterogeneous catalysts, titanium silicalite and silica grafted decatungstate, iii) two step synthesis of adipic acid starting from cyclohexene via 1,2-cyclohexanediol. The first step was catalyzed by H2WO4 in the presence of the phase transfer catalyst, the oxidant was hydrogen peroxide. The second step, oxidation of 1,2 – cyclohexanediol was performed in the presence of oxygen and the heterogeneous catalyst – ruthenium on alumina. The results of my research showed that: i) Oxidation of cyclohexanone with molecular oxygen using Keggin heteropolycompounds is possible, anyway the conversion of ketone is low and the selectivity to adipic acid is lowered by the consecutive reaction to from lower diacids. Moreover it was found out, that there are two mechanisms involved: redox type and radicalic chain-reaction autoxidation. The presence of the different mechanism is influenced by the reaction condition. ii) It is possible to perform thermally activated oxidation of cyclohexanone and obtain non negligible amount of the products (caprolactone and adipic acid). Performing the catalyzed reaction it was demonstrated that the choice of the reaction condition and of the catalyst plays a crucial role in the product selectivity, explaining the discrepancies between the literature and our research. iii) Interesting results can be obtained performing the two step oxidation of cyclohexene via 1,2-cyclohexanediol. In the presence of phase transfer catalyst it is possible to obtain high selectivity to alcohol with stoichiometric amount of oxidant. In the second step of the synthesis, the conversion of alcohol is rather low with modest selectivity to adipic acid

Carbonyl compounds are very important volatil organic compounds receiving increasing attention due to their critical role in tropospheric organic chemistry and to their effects on human health. They are first photo-oxidation stage of almost all organic compounds and originators of free radicals (OH, O3...). Therfore, continuous determination of their atmospheric concentrations is essential. Currently, field measurements are very limited mainly because of the analytical challenges posed by trace concentrations and interferences arising from atmospheric co-pollutants. Additionally, hydroxyl radical (OH) plays a central role in atmospheric chemistry processes. The measurement of atmospheric OH concentrations is essential for the comprehension of atmospheric chemical and photochemical processes. In this context, objectives of this work were: To perform a continuous survey of atmospheric concentrations of carbonyl compounds on different sites around the area of Bologna. For this purpose, an automatic instrument for the continuous measurement (one hour of time resolution) was developed and used. Additionally, the development of a complete and original analytical method was realised. To develop an original OH generation system in order to evaluate the effect of OH and the reactivity of solid and/or liquid materials of interest. This included the validation of an analytical method for the quantification of OH concentrations generated. Effect of OH on ceramic materials and reactivity of snow surface samples, involved as sink of OH in atmospheric chemistry, were evaluated.

Regenerative medicine claims for a better understanding of the cause-effect relation between cell behaviour and environment signals. The latter encompasses topographical, chemical and mechanical stimuli, electromagnetic fields, gradients of chemo-attractants and haptotaxis. In this perspective, a spatial control of the structures composing the environment is required. In this thesis I describe a novel approach for the multiscale patterning of biocompatible functional materials in order to provide systems able to accurately control cell adhesion and proliferation. The behaviour of different neural cell lines in response to several stimuli, specifically chemical, topographical and electrical gradients is presented. For each of the three kind of signals, I chose properly tailored materials and fabrication and characterization techniques. After a brief introduction on the state of art of nanotechnology, nanofabrication techniques and regenerative medicine in Chapter 1 and a detailed description of the main fabrication and characterization techniques employed in this work in Chapter 2, in Chapter 3 an easy route to obtain accurate control over cell proliferation close to 100% is described (chemical control). In Chapter 4 (topographical control) it is shown how the multiscale patterning of a well-established biocompatible material as titanium dioxide provides a versatile and robust method to study the effect of local topography on cell adhesion and growth. The third signal, viz. electric field, is investigated in Chapter 5 (electrical control), where the very early stages of neural cell adhesion are studied in the presence of modest steady electric fields. In Chapter 6 (appendix) a new patterning technique, called Lithographically Controlled Etching (LCE), is proposed. It is shown how LCE can provide at the same time the micro/nanostructuring and functionalization of a surface with nanosized objects, thus being suitable for applications both in regenerative medicine in biosensing.

Nucleic acid biosensors represent a powerful tool for clinical and environmental pathogens detection. For applications such as point-of-care biosensing, it is fundamental to develop sensors that should be automatic, inexpensive, portable and require a professional skill of the user that should be as low as possible. With the goal of determining the presence of pathogens when present in very small amount, such as for the screening of pathogens in drinking water, an amplification step must be implemented. Often this type of determinations should be performed with simple, automatic and inexpensive hardware: the use of a chemical (or nanotechnological) isothermal solution would be desirable. My Ph.D. project focused on the study and on the testing of four isothermal reactions which can be used to amplify the nucleic acid analyte before the binding event on the surface sensor or to amplify the signal after that the hybridization event with the probe. Recombinase polymerase amplification (RPA) and ligation-mediated rolling circle amplification (L-RCA) were investigated as methods for DNA and RNA amplification. Hybridization chain reaction (HCR) and Terminal deoxynucleotidil transferase-mediated amplification were investigated as strategies to achieve the enhancement of the signal after the surface hybridization event between target and probe. In conclusion, it can be said that only a small subset of the biochemical strategies that are proved to work in solution towards the amplification of nucleic acids does truly work in the context of amplifying the signal of a detection system for pathogens. Amongst those tested during my Ph.D. activity, recombinase polymerase amplification seems the best candidate for a useful implementation in diagnostic or environmental applications.

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Supramolecular chemistry is a multidisciplinary field which impinges on other disciplines, focusing on the systems made up of a discrete number of assembled molecular subunits. The forces responsible for the spatial organization are intermolecular reversible interactions. The supramolecular architectures I was interested in are Rotaxanes, mechanically-interlocked architectures consisting of a "dumbbell shaped molecule", threaded through a "macrocycle" where the stoppers at the end of the dumbbell prevent disassociation of components and catenanes, two or more interlocked macrocycles which cannot be separated without breaking the covalent bonds. The aim is to introduce one or more paramagnetic units to use the ESR spectroscopy to investigate complexation properties of these systems cause this technique works in the same time scale of supramolecular assemblies. Chapter 1 underlines the main concepts upon which supramolecular chemistry is based, clarifying the nature of supramolecular interactions and the principles of host-guest chemistry. In chapter 2 it is pointed out the use of ESR spectroscopy to investigate the properties of organic non-covalent assemblies in liquid solution by spin labels and spin probes. The chapter 3 deals with the synthesis of a new class of p-electron-deficient tetracationic cyclophane ring, carrying one or two paramagnetic side-arms based on 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO) moiety. In the chapter 4, the Huisgen 1,3-dipolar cycloaddition is exploited to synthesize rotaxanes having paramagnetic cyclodextrins as wheels. In the chapter 5, the catalysis of Huisgen’s cycloaddition by CB[6] is exploited to synthesize paramagnetic CB[6]-based [3]-rotaxanes. In the chapter 6 I reported the first preliminary studies of Actinoid series as a new class of templates in catenanes’ synthesis. Being f-block elements, so having the property of expanding the valence state, they constitute promising candidates as chemical templates offering the possibility to create a complex with coordination number beyond 6.

Proper ion channels’ functioning is a prerequisite for a normal cell and disorders involving ion channels, or channelopathies, underlie many human diseases. Long QT syndromes (LQTS) for example may arise from the malfunctioning of hERG channel, caused either by the binding of drugs or mutations in HERG gene. In the first part of this thesis I present a framework to investigate the mechanism of ion conduction through hERG channel. The free energy profile governing the elementary steps of ion translocation in the pore was computed by means of umbrella sampling simulations. Compared to previous studies, we detected a different dynamic behavior: according to our data hERG is more likely to mediate a conduction mechanism which has been referred to as “single-vacancy-like” by Roux and coworkers (2001), rather then a “knock-on” mechanism. The same protocol was applied to a model of hERG presenting the Gly628Ser mutation, found to be cause of congenital LQTS. The results provided interesting insights about the reason of the malfunctioning of the mutant channel. Since they have critical functions in viruses’ life cycle, viral ion channels, such as M2 proton channel, are considered attractive targets for antiviral therapy. A deep knowledge of the mechanisms that the virus employs to survive in the host cell is of primary importance in the identification of new antiviral strategies. In the second part of this thesis I shed light on the role that M2 plays in the control of electrical potential inside the virus, being the charge equilibration a condition required to allow proton influx. The ion conduction through M2 was simulated using metadynamics technique. Based on our results we suggest that a potential anion-mediated cation-proton exchange, as well as a direct anion-proton exchange could both contribute to explain the activity of the M2 channel.

The studies conducted during my Phd thesis were focused on two different directions: 1. In one case we tried to face some long standing problems of the asymmetric aminocatalysis as the activation of encumbered carbonyl compounds and the control of the diastereoisomeric ratio in the diastero- and enantioselective construction of all carbon substituted quaternary stereocenters adjacent a tertiary one. In this section (Challenges) was described the asymmetric aziridination of ,-unsaturated ketones, the activation of ,-unsaturated -branched aldehydes and the Michael addition of oxindoles to enals and enones. For the activation via iminium ion formation of sterically demanding substrates, as ,-unsaturated ketones and ,-unsaturated -branched aldehydes, we exploited a chiral primary amine in order to overcome the problem of the iminium ion formation between the catalyst and encumbered carbonylic componds. For the control of diastereoisomeric ratio in the diastero- and enantioselective construction of all carbon substituted quaternary stereocenters adjacent a tertiary one we envisaged that a suitable strategy was the Michael addition to 3 substituted oxindoles to enals activated via LUMO-lowering catalysis. In this synthetic protocol we designed a new bifunctional catalyst with an amine moiety for activate the aldehyde and a tioureidic fragment for direct the approach of the oxindole. This part of the thesis (Challenges) could be considered pure basic research, where the solution of the synthetic problem was the goal itself of the research. 2. In the other hand (Molecules) we applied our knowledge about the carbonylic compounds activation and about cascade reaction to the synthesis of three new classes of spirooxindole in enantiopure form. The construction of libraries of these bioactive compounds represented a scientific bridge between medicinal chemistry or biology and the asymmetric catalysis.

Many physiological and pathological processes are mediated by the activity of proteins assembled in homo and/or hetero-oligomers. The correct recognition and association of these proteins into a functional complex is a key step determining the fate of the whole pathway. This has led to an increasing interest in selecting molecules able to modulate/inhibit these protein-protein interactions. In particular, our research was focused on Heat Shock Protein 90 (Hsp90), responsible for the activation and maturation and disposition of many client proteins [1], [2] [3]. Circular Dichroism (CD) spectroscopy, Surface Plasmon Resonance (SPR) and Affinity Capillary Electrophoresis (ACE) were used to characterize the Hsp90 target and, furthermore, its inhibition process via C-terminal domain driven by the small molecule Coumermycin A1. Circular Dichroism was used as powerful technique to characterize Hsp90 and its co-chaperone Hop in solution for secondary structure content, stability to different pHs, temperatures and solvents. Furthermore, CD was used to characterize ATP but, unfortunately, we were not able to monitor an interaction between ATP and Hsp90. The utility of SPR technology, on the other hand, arises from the possibility of immobilizing the protein on a chip through its N-terminal domain to later study the interaction with small molecules able to disrupt the Hsp90 dimerization on the C-terminal domain. The protein was attached on SPR chip using the “amine coupling” chemistry so that the C-terminal domain was free to interact with Coumermycin A1. The goal of the experiment was achieved by testing a range of concentrations of the small molecule Coumermycin A1. Despite to the large difference in the molecular weight of the protein (90KDa) and the drug (1110.08 Da), we were able to calculate the affinity constant of the interaction that was found to be 11.2 µm. In order to confirm the binding constant calculated for the Hsp90 on the chip, we decided to use Capillary Electrophoresis to test the Coumermycin binding to Hsp90. First, this technique was conveniently used to characterize the Hsp90 sample in terms of composition and purity. The experimental conditions were settled on two different systems, the bared fused silica and the PVA-coated capillary. We were able to characterize the Hsp90 sample in both systems. Furthermore, we employed an application of capillary electrophoresis, the Affinity Capillary Electrophoresis (ACE), to measure and confirm the binding constant calculated for Coumermycin on Optical Biosensor. We found a KD = 19.45 µM. This result compares favorably with the KD previously obtained on biosensor. This is a promising result for the use of our novel approach to screen new potential inhibitors of Hsp90 C-terminal domain.

The chief obstacle to understand the metabolic origin of life or RNA-based life is to identify a plausible mechanism for overcoming the clutter wrought by abiotic chemistry. Probably trough simple abiotic and then prebiotic reactions we could arrive to simple pre-RNA molecules. Here we report a possible preibiotic synthesis for heterocyclic compounds, and a self-assembling process of adenosine phosphates a constituent of RNA. In these processes we use a simple and prebiotic phosphorus cyclic compounds, as P4O10 and its derivatives. The processes are driven by the formation of hypercoordinated species that activate the processes by a factor of 106-8.