De Novo Design of secondary structures: Synthesis and conformational studies

Chemists have long sought to extrapolate the power of biological catalysis and recognition to synthetic systems. These efforts have focused largely on low molecular weight catalysts and receptors; however, biological systems themselves rely almost exclusively on polymers, proteins and RNA, to perform complex chemical functions. Proteins and RNA are unique in their ability to adopt compact, well-ordered conformations, and specific folding provides precise spatial orientation of the functional groups that comprise the “active site”. These features suggest that identification of new polymer backbones with discrete and predictable folding propensities (“foldamers”) will provide a basis for design of molecular machines with unique capabilities. The foldamer approach complements current efforts to design unnatural properties into polypeptides and polynucleotides. The aim of this thesis is the synthesis and conformational studies of new classes of foldamers, using a peptidomimetic approach. Moreover their attitude to be utilized as ionophores, catalysts, and nanobiomaterials were analyzed in solution and in the solid state. This thesis is divided in thematically chapters that are reported below. It begins with a very general introduction (page 4) which is useful, but not strictly necessary, to the expert reader. It is worth mentioning that paragraph I.3 (page 22) is the starting point of this work and paragraph I.5 (page 32) isrequired to better understand the results of chapters 4 and 5. In chapter 1 (page 39) is reported the synthesis and conformational analysis of a novel class of foldamers containing (S)-β3-homophenylglycine [(S)-β3-hPhg] and D- 4-carboxy-oxazolidin-2-one (D-Oxd) residues in alternate order is reported. The experimental conformational analysis performed in solution by IR, 1HNMR, and CD spectroscopy unambiguously proved that these oligomers fold into ordered structures with increasing sequence length. Theoretical calculations employing ab initio MO theory suggest a helix with 11-membered hydrogenbonded rings as the preferred secondary structure type. The novel structures enrich the field of peptidic foldamers and might be useful in the mimicry of native peptides. In chapter 2 cyclo-(L-Ala-D-Oxd)3 and cyclo-(L-Ala-DOxd) 4 were prepared in the liquid phase with good overall yields and were utilized for bivalent ions chelation (Ca2+, Mg2+, Cu2+, Zn2+ and Hg2+); their chelation skill was analyzed with ESI-MS, CD and 1HNMR techniques and the best results were obtained with cyclo-(L-Ala-D-Oxd)3 and Mg2+ or Ca2+. Chapter 3 describes an application of oligopeptides as catalysts for aldol reactions. Paragraph 3.1 concerns the use of prolinamides as catalysts of the cross aldol addition of hydroxyacetone to aromatic aldeydes, whereas paragraphs 3.2 and 3.3 are about the catalyzed aldol addition of acetone to isatins. By means of DFT and AIM calculations, the steric and stereoelectronic effects that control the enantioselectivity in the cross-aldol addition of acetone to isatin catalysed by L-proline have been studied, also in the presence of small quantities of water. In chapter 4 is reported the synthesis and the analysis of a new fiber-like material, obtained from the selfaggregation of the dipeptide Boc-L-Phe-D-Oxd-OBn, which spontaneously forms uniform fibers consisting of parallel infinite linear chains arising from singleintermolecular N-H···O=C hydrogen bonds. This is the absolute borderline case of a parallel β-sheet structure. Longer oligomers of the same series with general formula Boc-(L-Phe-D-Oxd)n-OBn (where n = 2-5), are described in chapter 5. Their properties in solution and in the solid state were analyzed, in correlation with their attitude to form intramolecular hydrogen bond. In chapter 6 is reported the synthesis of imidazolidin-2- one-4-carboxylate and (tetrahydro)-pyrimidin-2-one-5- carboxylate, via an efficient modification of the Hofmann rearrangement. The reaction affords the desired compounds from protected asparagine or glutamine in good to high yield, using PhI(OAc)2 as source of iodine(III).

Outcome a lungo termine dei pazienti pediatrici con rene singolo. Valutazione di marker laboratoristici e strumentali di danno renale

Obiettivi: valutare in pazienti con rene singolo congenito la correlazione tra il filtrato glomerulare misurato con il DTPA (DTPA-VFG) e 1) marker laboratoristici di danno renale (creatinina, cistatinaC, proteinuria) 2) formule per stimare il filtrato glomerulare 3) parametri di valutazione della crescita renale ecografica. Materiali e metodi: Sono stati arruolati 118 pazienti con rene singolo congenito tra 0 e 18 anni. Sono stati valutati a ogni visita altezza, creatinina, cistatinaC, proteinuria e lunghezza ecografica renale. E’ stato calcolato il filtrato stimato con formule basate sulla creatinina (Schwartz), sulla cistatina C (Zappitelli, Filler, Grubb e Bokenkamp) e su entrambe (equazione di Zappitelli). La crescita renale è stata valutata come rapporto lunghezza ecografica/altezza corporea (USL/H), differenza percentuale tra lunghezza renale misurata e attesa per età (delta%) e presenza o meno d’ipertrofia compensatoria. In 74 bambini è stata misurata la DTPA-VFG. Risultati: Il follow-up è di 2.1 ± 0.9 anni. Il 65% sono maschi. Nessun paziente ha sviluppato danno renale cronico. La media del DTPA-VFG era di 135±44ml/min/1.73m², il valore medio della creatinina 0.47±0.17mg/dl e di cistatinaC di 1±0.4mg/L. La lunghezza ecografica renale media era di 100±17 mm, il rapporto USL/H medio di 0.8±0,1 e il delta% di 1,13±11,4, il 66% presentava ipertrofia renale. Le uniche correlazioni significative con DTPA-VFG sono inversa con la creatinina (p=<.001) e lineare con USL/H (p=<.001). Discussione: Lo studio ha mostrato che come per altre nefrouropatie, la creatina e l’ecografia renale siano due strumenti validi per il follow-up dei pazienti con rene singolo congenito. Il limite principale è dovuto al fatto che nessuno dei pazienti ha sviluppato danno renale cronico e pertanto non è stato possibile stabilire dei cutt-off di rischio per parametri quali USL/H.

Risk assessment to improve food safety along different food chains

The great challenges of today pose great pressure on the food chain to provide safe and nutritious food that meets regulations and consumer health standards. In this context, Risk Analysis is used to produce an estimate of the risks to human health and to identify and implement effective risk-control measures. The aims of this work were 1) describe how QRA is used to evaluate the risk for consumers health, 2) address the methodology to obtain models to apply in QMRA; 3) evaluate solutions to mitigate the risk. The application of a QCRA to the Italian milk industry enabled the assessment of Aflatoxin M1 exposure, impact on different population categories, and comparison of risk-mitigation strategies. The results highlighted the most sensitive population categories, and how more stringent sampling plans reduced risk. The application of a QMRA to Spanish fresh cheeses evidenced how the contamination of this product with Listeria monocytogenes may generate a risk for the consumers. Two risk-mitigation actions were evaluated, i.e. reducing shelf life and domestic refrigerator temperature, both resulting effective in reducing the risk of listeriosis. A description of the most applied protocols for data generation for predictive model development, was provided to increase transparency and reproducibility and to provide the means to better QMRA. The development of a linear regression model describing the fate of Salmonella spp. in Italian salami during the production process and HPP was described. Alkaline electrolyzed water was evaluated for its potential use to reduce microbial loads on working surfaces, with results showing its effectiveness. This work showed the relevance of QRA, of predictive microbiology, and of new technologies to ensure food safety on a more integrated way. Filling of data gaps, the development of better models and the inclusion of new risk-mitigation strategies may lead to improvements in the presented QRAs.

Application-oriented Mixed Integer Non-Linear Programming

In the most recent years there is a renovate interest for Mixed Integer Non-Linear Programming (MINLP) problems. This can be explained for different reasons: (i) the performance of solvers handling non-linear constraints was largely improved; (ii) the awareness that most of the applications from the real-world can be modeled as an MINLP problem; (iii) the challenging nature of this very general class of problems. It is well-known that MINLP problems are NP-hard because they are the generalization of MILP problems, which are NP-hard themselves. However, MINLPs are, in general, also hard to solve in practice. We address to non-convex MINLPs, i.e. having non-convex continuous relaxations: the presence of non-convexities in the model makes these problems usually even harder to solve. The aim of this Ph.D. thesis is to give a flavor of different possible approaches that one can study to attack MINLP problems with non-convexities, with a special attention to real-world problems. In Part 1 of the thesis we introduce the problem and present three special cases of general MINLPs and the most common methods used to solve them. These techniques play a fundamental role in the resolution of general MINLP problems. Then we describe algorithms addressing general MINLPs. Parts 2 and 3 contain the main contributions of the Ph.D. thesis. In particular, in Part 2 four different methods aimed at solving different classes of MINLP problems are presented. Part 3 of the thesis is devoted to real-world applications: two different problems and approaches to MINLPs are presented, namely Scheduling and Unit Commitment for Hydro-Plants and Water Network Design problems. The results show that each of these different methods has advantages and disadvantages. Thus, typically the method to be adopted to solve a real-world problem should be tailored on the characteristics, structure and size of the problem. Part 4 of the thesis consists of a brief review on tools commonly used for general MINLP problems, constituted an integral part of the development of this Ph.D. thesis (especially the use and development of open-source software). We present the main characteristics of solvers for each special case of MINLP.

Electrochemistry of carbon based engineered structures

The main aims of my PhD research work have been the investigation of the redox, photophysical and electronic properties of carbon nanotubes (CNT) and their possible uses as functional substrates for the (electro)catalytic production of oxygen and as molecular connectors for Quantum-dot Molecular Automata. While for CNT many and diverse applications in electronics, in sensors and biosensors field, as a structural reinforcing in composite materials have long been proposed, the study of their properties as individual species has been for long a challenging task. CNT are in fact virtually insoluble in any solvent and, for years, most of the studies has been carried out on bulk samples (bundles). In Chapter 2 an appropriate description of carbon nanotubes is reported, about their production methods and the functionalization strategies for their solubilization. In Chapter 3 an extensive voltammetric and vis-NIR spectroelectrochemical investigation of true solutions of unfunctionalized individual single wall CNT (SWNT) is reported that permitted to determine for the first time the standard electrochemical potentials of reduction and oxidation as a function of the tube diameter of a large number of semiconducting SWNTs. We also established the Fermi energy and the exciton binding energy for individual tubes in solution and, from the linear correlation found between the potentials and the optical transition energies, one to calculate the redox potentials of SWNTs that are insufficiently abundant or absent in the samples. In Chapter 4 we report on very efficient and stable nano-structured, oxygen-evolving anodes (OEA) that were obtained by the assembly of an oxygen evolving polyoxometalate cluster, (a totally inorganic ruthenium catalyst) with a conducting bed of multiwalled carbon nanotubes (MWCNT). Here, MWCNT were effectively used as carrier of the polyoxometallate for the electrocatalytic production of oxygen and turned out to greatly increase both the efficiency and stability of the device avoiding the release of the catalysts. Our bioinspired electrode addresses the major challenge of artificial photosynthesis, i.e. efficient water oxidation, taking us closer to when we might power the planet with carbon-free fuels. In Chapter 5 a study on surface-active chiral bis-ferrocenes conveniently designed in order to act as prototypical units for molecular computing devices is reported. Preliminary electrochemical studies in liquid environment demonstrated the capability of such molecules to enter three indistinguishable oxidation states. Side chains introduction allowed to organize them in the form of self-assembled monolayers (SAM) onto a surface and to study the molecular and redox properties on solid substrates. Electrochemical studies on SAMs of these molecules confirmed their attitude to undergo fast (Nernstian) electron transfer processes generating, in the positive potential region, either the full oxidized Fc+-Fc+ or the partly oxidized Fc+-Fc species. Finally, in Chapter 6 we report on a preliminary electrochemical study of graphene solutions prepared according to an original procedure recently described in the literature. Graphene is the newly-born of carbon nanomaterials and is certainly bound to be among the most promising materials for the next nanoelectronic generation.

Riconversione degli impianti saccariferi per la valorizzazione della filiera agro-energetica: analisi di impatto sul comprensorio agricolo

Il presente lavoro trae origine dagli obiettivi e dalle relative misure applicative della riforma dell’OCM zucchero del 2006 e nello specifico dal Piano nazionale per la razionalizzazione e riconversione della produzione bieticolo-saccarifera approvato dal MIPAF nel 2007. Lo studio riguarda la riconversione dello zuccherificio di Finale Emilia (MO), di appartenenza del Gruppo bieticolo-saccarifero Co.Pro.B, in un impianto di generazione di energia elettrica e termica che utilizza biomassa di origine agricola per la combustione diretta. L'alimentazione avviene principalmente dalla coltivazione dedicata del sorgo da fibra (Sorghum bicolor), integrata con risorse agro-forestali. Lo studio mostra la necessità di coltivazione di 4.400 ettari di sorgo da fibra con una produzione annua di circa 97.000 t di prodotto al 75% di sostanza secca necessari per l’alimentazione della centrale a biomassa. L’obiettivo é quello di valutare l’impatto della nuova coltura energetica sul comprensorio agricolo e sulla economia dell’impresa agricola. La metodologia adottata si basa sulla simulazione di modelli aziendali di programmazione lineare che prevedono l’inserimento del sorgo da fibra come coltura energetica nel piano ottimo delle aziende considerate. I modelli predisposti sono stati calibrati su aziende RICA al fine di riprodurre riparti medi reali su tre tipologie dimensionali rappresentative: azienda piccola entro i 20 ha, media da 20 a 50 ha e grande oltre i 50 ha. La superficie di entrata a livello aziendale, se rapportata alla rappresentatività delle aziende dell’area di studio, risulta insufficiente per soddisfare la richiesta di approvvigionamento dell’impianto a biomassa. Infatti con tale incremento la superficie di coltivazione nel comprensorio si attesta sui 2.500 ettari circa contro i 4.400 necessari alla centrale. Lo studio mostra pertanto che occorre un incentivo superiore, di circa 80-90 €/ha, per soddisfare la richiesta della superficie colturale a livello di territorio. A questi livelli, la disponibilità della coltura energetica sul comprensorio risulta circa 9.500 ettari.

Synthesis and aplication of linear and macrocyclic nitrogen ligand

Linear and macrocyclic nitrogen ligands have been found wide application during the years. Nitrogen has a much strong association with transition-metal ions because the electron pair is partucularly available for complexing purposes. We started our investigation with the synthesis of new chiral perazamacrocycles containing four pyrrole rings. This ligand was synthesized by the [2+2]condensation of (R,R)-diaminocyclohexane and dipirranedialdehydes and was tested, after a complexation with Cu(OAc)2, in Henry reactions. The best yields (96%) and higher ee’s (96%) were obtained when the meso-substituent on the dipyrrandialdehyde was a methyl group. The positive influence of the pyrrole-containing macrocyclic structure on the efficiency/enantioselectivity of the catalytic system was demonstrated by comparison with the Henry reactions performed using analogous ligands. Henry product was obtain in good yield but only 73% of ee, when the dialdehyde unit was replaced by a triheteroaromatic dialdehye (furan-pyrrol-furan). Another well known macrocyclic ligand is calix[4]pyrrole. We decided to investigate, in collaboration with Neier’s group, the metal-coordinating properties of calix[2]pyrrole[2]pyrrolidine compounds obtained by the reduction of calix[4]pyrrole. We focused our attention on the reduction conditions, and tested different Pd supported (charcoal, grafite) catalysts at different condition. Concerning the synthesis of linear polyamine ligands. We focused our attention to the synthesis of 2-heteroaryl- and 2,5-diheteroarylpyrrolidines. The reductive amination reaction of diarylketones and aryl-substitutedketo-aldehydes with different chiral amines was exploited to prepare a small library of diastereo-enriched substituted pyrrolidines. We have also described a new synthetic route to 1,2-disubstituted 1,2,3,4-tetrahydropyrrole[1,2-a]pyrazines, which involves the diastereoselective addition of Grignard reagents to chiral oxazolidines. The best diastereoselectivity (98:2) was dependent on the nature of both the chiral auxiliary, (S)-1-phenylglycinol, and the nature of the organometallic reagent (MeMgBr).

Quantum Integrability in Non-Linear Sigma Models related to Gauge/String Correspondences

The Thermodynamic Bethe Ansatz analysis is carried out for the extended-CP^N class of integrable 2-dimensional Non-Linear Sigma Models related to the low energy limit of the AdS_4xCP^3 type IIA superstring theory. The principal aim of this program is to obtain further non-perturbative consistency check to the S-matrix proposed to describe the scattering processes between the fundamental excitations of the theory by analyzing the structure of the Renormalization Group flow. As a noteworthy byproduct we eventually obtain a novel class of TBA models which fits in the known classification but with several important differences. The TBA framework allows the evaluation of some exact quantities related to the conformal UV limit of the model: effective central charge, conformal dimension of the perturbing operator and field content of the underlying CFT. The knowledge of this physical quantities has led to the possibility of conjecturing a perturbed CFT realization of the integrable models in terms of coset Kac-Moody CFT. The set of numerical tools and programs developed ad hoc to solve the problem at hand is also discussed in some detail with references to the code.