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).

Stereoselective Catalytic Processes for the Synthesis of Polycyclic Aromatic Compounds

In this PhD-thesis, two methodologies for enantioselective intramolecular ring closing reaction on indole cores are presented. The first methodology represents a highly stereoselective alkylation of the indole N1-nitrogen, leading to 3,4-dihydro-pyrazinoindol-1-ones – a structural class which is known for its activity on the CNS and therefore of high pharmacological interest concerning related diseases. In this approach, N-benzyl cinchona-alkaloids were used for the efficient catalysis of intramolecular aza-Michael reactions. Furthermore, computational studies in collaboration with the research group Prof. Andrea Bottoni (Department of Chemistry “G. Ciamician”, Bologna) were accomplished in order to get insight into the key interactions between catalyst and substrate, leading to enantiomeric excesses up to 91%. The results of the calculations on a model system are in accordance with the experimental results and demonstrate the high sensibility of the system towards structural modifications. The second project deals with a metal catalyzed, intramolecular Friedel-Crafts (FC)-reaction on indolyl substrates, carrying a side chain which on its behalf is furnished with an allylic alcohol unit. Allylic alcohols are part of the structural class of “π-activated alcohols” – alcohols, which are more easily activated due to the proximity to a π-unit (allyl-, propargyl-, benzyl-). The enantioselective intramolecular cyclization event is catalyzed efficiently by employment of a chiral Au(I)-catalyst, leading to 1-vinyl- or 4-vinyl-tetrahydrocarbazoles (THCs) under the formation of water as byproduct. This striking and novel process concerning the direct activation of alcohols in catalytic FC-reactions was subsequently extended to similar precursors, leading to functionalized tetrahydro-β-carbolines. These two methodologies represent highly efficient approaches towards the synthesis of scaffolds, which are of enormous pharmaceutical interest and amplify the spectra of enantioselective catalytic functionalisations of indoles.

Stereoselective synthesis of heterocycles as intermediates of biologically active compounds

The aim of this thesis was to investigate the synthesis of enantiomerically enriched heterocycles and dehydro-β-amino acid derivatives which can be used as scaffolds or intermediates of biologically active compounds, in particular as novel αvβ3 and α5β1 integrin ligands. The starting materials of all the compounds here synthesized are alkylideneacetoacetates. Alkylidene derivates are very usefull compounds, they are usually used as unsaturated electrophiles and they have the advantage of introducing different kind of functionality that may be further elaborated. In chapter 1, regio- and stereoselective allylic amination of pure carbonates is presented. The reaction proceeds via uncatalyzed or palladium-catalyzed conditions and affords enantiopure dehydro-β-amino esters that are useful precursor of biologically active compounds. Chapter 2 illustrates the synthesis of substituted isoxazolidines and isoxazolines via Michael addition followed by intramolecular hemiketalisation. The investigation on the effect of the Lewis acid catalysis on the regioselectivity of the addition it also reported. Isoxazolidines and isoxazolines are interesting heterocyclic compounds that may be regarded as unusual constrained -amino acids or as furanose mimetics. The synthesis of unusual cyclic amino acids precursors, that may be envisaged as proline analogues, as scaffolds for the design of bioactive peptidomimetics is presented in chapter 3. The synthesis of 2-substituted-3,4-dehydropyrrole derivatives starting from allylic carbonates via a two step allylic amination/ring closing metathesis (RCM) protocol is carried out. The reaction was optimized by testing different Grubbs’ catalysts and carbamate nitrogen protecting groups. Moreover, in view of a future application of these dehydro-β-amino acids as central core of peptidomimetics , the malonate chain was also used to protect nitrogen prior to RCM. Finally, chapter 4 presents the synthesis of two novel different classes of integrin antagonists, one derived from dehydro-β-amino acid prepared as described in chapter 1 and the other one has isoxazolidines synthesized in chapter 2 as rigid constrained core. Since that these compounds are promising RGD mimetics for αvβ3 and α5β1 integrins, they have been submitted to biological assay. and to interpret on a molecular basis their different affinities for the αvβ3 receptor, docking studies were performed using Glide program.

N-Heterocyclic carbene complexes of rhodium: structures, dynamics and catalysis

A series of imidazolium salts of the type [BocNHCH2CH2ImR]X (Boc = t-Bu carbamates; Im = imidazole) (R = Me, X = I, 1a; R = Bn, X = Br, 1b; R = Trityl, X = Cl, 1c) and [BnImR’]X (R’ = Me, X = Br, 1d; R’ = Bn, X = Br, 1e; R’ = Trityl, X = Cl, 1g; R’ = tBu, X = Br, 1h) bearing increasingly bulky substituents were synthetized and characterized. Subsequently, these precursors were employed in the synthesis of silver(I)-N-heterocyclic (NHC) complexes as transmetallating reagents for the preparation of rhodium(I) complexes [RhX(NBD)(NHC)] (NHC = 1-(2-NHBoc-ethyl)-3-R-imidazolin-2-ylidene; X = Cl; R = Me, 4a; R = Bn, 4b; R = Trityl, 4c; X = I, R = Me, 5a; NHC = 1-Bn-3-R’-imidazolin-2-ylidene; X = Cl; R’ = Me, 4d, R’ = Bn, 4e, R’ = Trityl, 4g; R’ = tBu, 4h). VT NMR studies of these complexes revealed a restricted rotation barriers about the metal-carbene bond. While the rotation barriers calculated for the complexes in which R = Me, Bn (4a,b,d,e and 5a) matched the experimental values, this was not true for the complexes 4c,g, bearing a trityl group for which the values are much smaller than the calculated ones. Energy barriers for 4c,g, derived from a line shape simulation, showed a strong dependence on the temperature while for 4h the rotational energy barrier is stopped at room temperature. The catalytic activity of the new rhodium compounds was investigated in the hydrosilylation of terminal alkynes and in the addition of phenylboronic acid to benzaldehyde. The imidazolium salts 1d,e were also employed in the synthesis of new iron(II)-NHC complexes. Finally, during a six-months stay at the University of York a new ligand derived from Norharman was prepared and employed in palladium-mediated cross-coupling.

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.

Novel catalytic systems and methidologies for organocatalysis and photocatalysis

The thesis is divided into two main parts. In the first one organocatalysis is briefly introduced. Then, new enantiopure trityl pyrrolidines modified with an ionic tag are described. All the catalysts are tested in the benchmark Michael addition reaction to prove their activity and stereoselectivity. In the second part, photocatalysis is first introduced. Then, four different research projects are described. At first, the construction of a hybrid metal-organo-photoredox catalyst is described. The hybrid photocatalysts obtained were employed in the benchmark photoredox alkylation of aldehydes. Then, the use of visible light and a photocatalytic system for the cyclization of iodoaryl vinyl derivatives to tetrahydroquinoline structures is described. In addition, the reaction can also be performed using flow-chemistry. Finally, a mechanistic proposal based on some mechanistic studies is described. Third, a new photoredox catalyzed transformation for the synthesis of 2,3-dihydrofurans is reported. Depending on the involved starting materials, different pathways have arisen. A mechanistic proposal based on reported literatures and experimental data is described. At last, a new photoredox catalyzed transformation for the synthesis of 2-aminofurans is described. Electrophilic radical addition on allenamides and subsequential intramolecular cyclization are exploited. The reaction proceeds under very mild conditions and in 2-aminofurans are obtained in good to high yield. It represents one of the few applications of allenamides in photoredox catalysis. A mechanistic proposal is described. Finally, preliminary investigations on the applicability of the developed transformation under flow chemistry conditions.

Photoredox Catalysis and Nucleophilic Organometallic Reagents – Application in Organic Synthesis

The main purpose of my PhD was the combination of the principles of transition metal catalysis with photoredox catalysis. We focused our attention on the development of novel dual catalytic protocols for the functionalization of carbonyl compounds through the generation of transient nucleophilic organometallic species. Specifically, we focused on the development of new methodologies combining photoredox catalysis with titanium and nickel in low oxidation state. Firstly, a Barbier-type allylation of aromatic and aliphatic aldehydes –catalytic in titanium– in the presence of a blue photon-absorbing dye was developed. Parallelly, we were pleased to observe that the developed methodology could also be extended to the propargylation of aldehydes under analogous conditions. After an extensive re–optimization of all the reaction parameters, we developed an enantioselective and diastereoselective pinacol coupling of aromatic aldehydes promoted by non-toxic, cheap and easy to synthetize titanium complexes. The key feature, that allows the complete (dia)stereocontrol played by titanium, is the employment of a red-absorbing organic dye. The tailored (photo)redox properties of the red-absorbing organic dye [nPr–DMQA+][BF4–] promote the selective reduction of Ti(IV) to Ti(III). Moreover, even if the major contribution in dual photoredox and nickel catalysis is devoted to the realization of cross-coupling-type reactions, we wanted to evaluate different possible scenarios. Our focus was on the possibility of exploiting intermediates arising from the oxidative addition of nickel complexes as transient nucleophilic species. The first topic considered regarded the possibility to perform allylation of aldehydes by dual photoredox and nickel catalysis. In the first instance, a non–stereocontrolled version of the reaction was presented. Finally, after a long series of drastic modification of the reaction conditions, a highly enantioselective variant of the protocol was also reported. All the reported methodologies are supported by careful photophysical analysis and, in some cases, computational modelling.

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.

Organic photosensitizers and nanostructured semiconductors for photoredox catalysis and artificial photosynthesis

Over the course of evolution, Nature has elegantly learned to use light to drive chemical reactions. On the other hand, humans have only recently started learning how to play with this powerful tool to carry out chemical transformations. In particular, a step forward was possible thanks to molecules and materials that can absorb light and trigger a series of processes that can drive chemical reactions. However, scarce elements are extensively employed in the design of most of these compounds and considerations on their scarcity and toxicity have sparked interest on alternatives based on earth-abundant elements. In this framework, the focus of this thesis has been the development and employment of heavy-metal free chromophores and of earth-abundant oxides. The first chapter regards the functionalization of boron-dipyrromethenes (BODIPYs) so as to allow access to their triplet excited state and tune their redox potentials, which was achieved thanks to the design of orthogonal donor-acceptor dyads. The BODIPY dyads were used to promote a photoredox reaction, and the mechanism of the reaction was clarified. In the second chapter, organic chromophores that display thermally-activated delayed fluorescence (TADF) were studied. These were used to perform enantioselective photoredox reactions, and a mechanistic investigation allowed to elucidate the fate of these photosensitizers in the reaction. Thanks to their stronger reducing power, it was possible to demonstrate the employability of TADF dyes in artificial photosynthesis, as well. Last, the oxidation of biomass-derived compounds was studied in a photoelectrochemical cell. For this purpose, hematite photoanodes were synthesized in collaboration with Prof. Caramori’s group at the University of Ferrara (Italy) and they were tested in the presence of a redox mediator. In addition to this, the possibility of repurposing a copper(II) water oxidation catalyst for the oxidation of biomass was investigated in collaboration with Prof. Llobet’s group at ICIQ (Tarragona, Spain).