Catalytic upgrading of carboxylic acids and esters to bio fuels and bio chemicals

The research activity was focused on the transformation of methyl propionate (MP) into methyl methacrylate (MMA), avoiding the use of formaldehyde (FAL) thanks to a one-pot strategy involving in situ methanol (MeOH) dehydrogenation over the same catalytic bed were the hydroxy-methylation/dehydration of MP with FAL occurs. The relevance of such research line is related to the availability of cheap renewable bio-glycerol from biodiesel production, from which MP can be obtained via a series of simple catalytic reactions. Moreover, the conventional MMA synthesis (Lucite process) suffers from safety issues related to the direct use of carcinogenic FAL and depends on non-renewable MP. During preliminary studies, ketonization of carboxylic acids and esters has been recognized as a detrimental reaction which hinders the selective synthesis of MMA at low temperature, together with H-transfer hydrogenation with FAL or MeOH as the H-donor at higher temperatures. Therefore, ketonization of propionic acid (PA) and MP was investigated over several catalysts (metal oxides and metal phosphates), to obtain a better understanding of the structure-activity relationship governing the reaction and to design a catalyst for MMA synthesis capable to promote the desired reaction while minimizing ketonization and H-transfer. However, ketonization possesses scientific and industrial value itself and represents a strategy for the upgrade of bio oils from fast pyrolysis of lignocellulosic materials, a robust and versatile technology capable to transform the most abundant biomass into liquid biofuels. The catalysts screening showed that ZrO2 and La2O3 are the best catalysts, while MgO possesses low ketonization activity, but still, H-transfer parasitic hydrogenation of MMA reduces its yield over all catalysts. Such study resulted in the design of Mg/Ga mixed oxides that showed enhanced dehydrogenating activity towards MeOH at low temperatures. It was found that the introduction of Ga not only minimize ketonization, but also modulates catalyst basicity reducing H-transfer hydrogenations.

Synthesis of Modified Amino Acids and Insertion in Peptides and Mimetics. Structural Aspects and Impact on Biological Activity.

I studied the effects exerted by the modifications on structures and biological activities of the compounds so obtained. I prepared peptide analogues containing unusual amino acids such as halogenated, alkylated (S)- or (R)-tryptophans, useful for the synthesis of mimetics of the endogenous opioid peptide endomorphin-1, or 2-oxo-1,3-oxazolidine-4-carboxylic acids, utilized as pseudo-prolines having a clear all-trans configuration of the preceding peptide bond. The latter gave access to a series of constrained peptidomimetics with potential interest in medicinal chemistry and in the field of the foldamers. In particular, I have dedicated much efforts to the preparation of cyclopentapeptides containing D-configured, alfa-, or beta-aminoacids, and also of cyclotetrapeptides including the retro-inverso modification. The conformational analyses confirmed that these cyclic compounds can be utilized as rigid scaffolds mimicking gamma- or beta-turns, allowing to generate new molecular and 3D diversity. Much work has been dedicated to the structural analysis in solution and in the receptor-bound state, fundamental for giving a rationale to the experimentally determined bioactivity, as well as for predicting the activity of virtual compounds (in silico pre-screen). The conformational analyses in solution has been done mostly by NMR (2D gCosy, Roesy, VT, molecular dynamics, etc.). A special section is dedicated to the prediction of plausible poses of the ligands when bound to the receptors by Molecular Docking. This computational method proved to be a powerful tool for the investigation of ligand-receptor interactions, and for the design of selective agonists and antagonists. Another practical use of cyclic peptidomimetics was the synthesis and biological evaluation of cyclic analogues of endomorphin-1 lacking in a protonable amino group. The studies revealed that a inverse type II beta-turn on D-Trp-Phe constituted the bioactive conformation.

Design and synthesis of novel non peptidomimtic beta-secretase inhibitors in the treatment of Alzheimer's disease

The aspartic protease BACE1 (β-amyloid precursor protein cleaving enzyme, β-secretase) is recognized as one of the most promising targets in the treatment of Alzheimer's disease (AD). The accumulation of β-amyloid peptide (Aβ) in the brain is a major factor in the pathogenesis of AD. Aβ is formed by initial cleavage of β-amyloid precursor protein (APP) by β-secretase, therefore BACE1 inhibition represents one of the therapeutic approaches to control progression of AD, by preventing the abnormal generation of Aβ. For this reason, in the last decade, many research efforts have focused at the identification of new BACE1 inhibitors as drug candidates. Generally, BACE1 inhibitors are grouped into two families: substrate-based inhibitors, designed as peptidomimetic inhibitors, and non-peptidomimetic ones. The research on non-peptidomimetic small molecules BACE1 inhibitors remains the most interesting approach, since these compounds hold an improved bioavailability after systemic administration, due to a good blood-brain barrier permeability in comparison to peptidomimetic inhibitors. Very recently, our research group discovered a new promising lead compound for the treatment of AD, named lipocrine, a hybrid derivative between lipoic acid and the AChE inhibitor (AChEI) tacrine, characterized by a tetrahydroacridinic moiety. Lipocrine is one of the first compounds able to inhibit the catalytic activity of AChE and AChE-induced amyloid-β aggregation and to protect against reactive oxygen species. Due to this interesting profile, lipocrine was also evaluated for BACE1 inhibitory activity, resulting in a potent lead compound for BACE1 inhibition. Starting from this interesting profile, a series of tetrahydroacridine analogues were synthesised varying the chain length between the two fragments. Moreover, following the approach of combining in a single molecule two different pharmacophores, we designed and synthesised different compounds bearing the moieties of known AChEIs (rivastigmine and caproctamine) coupled with lipoic acid, since it was shown that dithiolane group is an important structural feature of lipocrine for the optimal inhibition of BACE1. All the tetrahydroacridines, rivastigmine and caproctamine-based compounds, were evaluated for BACE1 inhibitory activity in a FRET (fluorescence resonance energy transfer) enzymatic assay (test A). With the aim to enhancing the biological activity of the lead compound, we applied the molecular simplification approach to design and synthesize novel heterocyclic compounds related to lipocrine, in which the tetrahydroacridine moiety was replaced by 4-amino-quinoline or 4-amino-quinazoline rings. All the synthesized compounds were also evaluated in a modified FRET enzymatic assay (test B), changing the fluorescent substrate for enzymatic BACE1 cleavage. This test method guided deep structure-activity relationships for BACE1 inhibition on the most promising quinazoline-based derivatives. By varying the substituent on the 2-position of the quinazoline ring and by replacing the lipoic acid residue in lateral chain with different moieties (i.e. trans-ferulic acid, a known antioxidant molecule), a series of quinazoline derivatives were obtained. In order to confirm inhibitory activity of the most active compounds, they were evaluated with a third FRET assay (test C) which, surprisingly, did not confirm the previous good activity profiles. An evaluation study of kinetic parameters of the three assays revealed that method C is endowed with the best specificity and enzymatic efficiency. Biological evaluation of the modified 2,4-diamino-quinazoline derivatives measured through the method C, allow to obtain a new lead compound bearing the trans-ferulic acid residue coupled to 2,4-diamino-quinazoline core endowed with a good BACE1 inhibitory activity (IC50 = 0.8 mM). We reported on the variability of the results in the three different FRET assays that are known to have some disadvantages in term of interference rates that are strongly dependent on compound properties. The observed results variability could be also ascribed to different enzyme origin, varied substrate and different fluorescent groups. The inhibitors should be tested on a parallel screening in order to have a more reliable data prior to be tested into cellular assay. With this aim, preliminary cellular BACE1 inhibition assay carried out on lipocrine confirmed a good cellular activity profile (EC50 = 3.7 mM) strengthening the idea to find a small molecule non-peptidomimetic compound as BACE1 inhibitor. In conclusion, the present study allowed to identify a new lead compound endowed with BACE1 inhibitory activity in submicromolar range. Further lead optimization to the obtained derivative is needed in order to obtain a more potent and a selective BACE1 inhibitor based on 2,4-diamino-quinazoline scaffold. A side project related to the synthesis of novel enzymatic inhibitors of BACE1 in order to explore the pseudopeptidic transition-state isosteres chemistry was carried out during research stage at Università de Montrèal (Canada) in Hanessian's group. The aim of this work has been the synthesis of the δ-aminocyclohexane carboxylic acid motif with stereochemically defined substitution to incorporating such a constrained core in potential BACE1 inhibitors. This fragment, endowed with reduced peptidic character, is not known in the context of peptidomimetic design. In particular, we envisioned an alternative route based on an organocatalytic asymmetric conjugate addition of nitroalkanes to cyclohexenone in presence of D-proline and trans-2,5-dimethylpiperazine. The enantioenriched obtained 3-(α-nitroalkyl)-cyclohexanones were further functionalized to give the corresponding δ-nitroalkyl cyclohexane carboxylic acids. These intermediates were elaborated to the target structures 3-(α-aminoalkyl)-1-cyclohexane carboxylic acids in a new readily accessible way.

Archaeological Baltic amber: degradation mechanisms and conservation measures

The aim of this project was to achieve a deep understanding of the mechanisms by which Baltic amber degrades, in order to develop techniques for preventive conservation of archaeological amber objects belonging to the National Museum of Denmark’s collections. To examine deterioration of Baltic amber, a starting point was to identify and monitor surface and bulk properties which are affected during degradation. The way to operate consisted of the use of accelerated ageing to initiate degradation of raw Baltic amber samples in different conditions of relative humidity, oxygen exposure or pH and, successively, of the use of non/micro-destructive techniques to identify and quantify changes in visual, chemical and structural properties. A large piece of raw Baltic amber was used to prepare several test samples for two different kinds of accelerated ageing: thermal-ageing and photo-ageing. During the ageing, amber samples were regularly examined through several analytical techniques related to different information: appearance/colour change by visual examination, photography and colorimetry; chemical change by infrared spectroscopy, Raman spectroscopy and elemental analysis; rate of oxidation by oxygen measurement; qualitative analysis of released volatiles by gas chromatography – mass spectrometry. The obtained results were analysed through both critical evaluation and statistical study. After the interpretation of the achieved data, the main relations between amber and environmental factors during the degradation process became clearer and it was possible to identify the major pathways by which amber degrades, such as hydrolysis of esters into alcohols and carboxylic acids, thermal-oxidation and photo-oxidation of terpenoid components, depolymerisation and decomposition of the chemical structure. At the end it was possible to suggest a preventive conservation strategy based on the control of climatic, atmospheric and lighting parameters in the environment where Baltic amber objects are stored and displayed.

Polymorphs solvates and co-crystals of molecular materials

The scope of my research project is to produce and characterize new crystalline forms of organic compounds, focusing the attention on co-crystals and then transferring these notions on APIs to produce co-crystals of potential interest in the pharmaceutical field. In the first part of this work co-crystallization experiments were performed using as building blocks the family of aliphatic dicarboxylic acids HOOC-(CH2)n-COOH, with n= 2-8. This class of compounds has always been an object of study because it is characterized by an interesting phenomenon of alternation of melting points: the acids with an even number of carbon atoms show a melting point higher than those with an odd one. The acids were co-crystallized with four dipyridyl molecules (formed by two pyridine rings with a different number of bridging carbon atoms) through the formation of intermolecular interactions N•••(H)O. The bases used were: 4,4’-bipyridine (BPY), 1,2-bis(4-pyridyl)ethane (BPA), 1,2-(di-4-pyridyl)ethylene (BPE) and 1,2-bis(4-pyridyl)propane (BPP). The co-crystals obtained by solution synthesis were characterized by different solid-state techniques to determine the structure and to see how the melting points in co-crystals change. In the second part of this study we tried to obtain new crystal forms of compounds of pharmaceutical interest. The APIs studied are: O-desmethylvenlafaxine, Lidocaine, Nalidixic Acid and Sulfadiazine. Each API was subjected to Polymorph Screening and Salt/Co-crystal Screening experiments to identify new crystal forms characterized by different properties. In a typical Salt/Co-crystal Screening the sample was made to react with a co-former (solid or liquid) through different methods: crystallization by solution, grinding, kneading and solid-gas reactions. The new crystal forms obtained were characterized by different solid state techniques (X-ray single crystal diffraction, X-ray powder diffraction, Differential Scanning Calorimetry, Thermogravimetric Analysis, Evolved gas analysis, FT-IR – ATR, Solid State N.M.R).

Non-Covalent Interaction: Revealed by Rotational Spectroscopy

The pulsed jet Fourier transform microwave spectroscopy have been applied to several molecular complexes involving H2O, freons, methane, carboxylic acids, and rare gas. The obtained results showcase the suitability of this technique for studying the intermolecular interactions. The rotational spectra of three water adducts of halogenated organic molecules, i.e. chlorotrifluoroethylene, isoflurane and alfa,alfa,alfa,-trifluoroanisole, have been investigated. It has been found that, the halogenation of the partner molecules definitely changes the way in which water will link to the partner molecule. Quadrupole hyperfine structures and/or the tunneling splittings have been observed in the rotational spectra of difluoromethane-dichloromethane, chlorotrifluorometane-fluoromethane, difluoromethane-formaldehyde and trifluoromethane-benzene. These features have been useful to describe their intermolecular interactions (weak hydrogen bonds or halogen bonds), and to size the potential energy surfaces of their internal motions. The rotational spectrum of pyridine-methane pointed out that methane prefers to locate above the ring and link to pyridine through a C-H•••π weak hydrogen bond, rather than the C-H•••n interaction. This behavior, typical of complexes of pyridine with rare gases, suggests classifying CH4, in relation to its ability to form molecular complexes with aromatic molecules, as a pseudo rare gas. The conformational equilibria of three bi-molecules of carboxylic acids, acrylic acid-trifluoroacetic acid, difluoroacetic acid-formic acid and acrylic acid-fluoroacetic acid have been studied. The increase of the hydrogen bond length upon H→D isotopic substitution (Ubbelohde effect) has been deduced from the elongation of the carboxylic carbons C•••C distance. The van der Waals complex tetrahydrofuran-krypton shows that the systematic doubling of the rotational lines has been attributed to the residual pseudo-rotation of tetrahydrofuran in the complex, based on the values of the Coriolis coupling constants, and on the type (mu_b) of the interstate transitions.

Synthesis and electronic properties of luminescent silicon nanocrystals and copper indium sulphide quantum dots

In the last decades, nanomaterials, and in particular semiconducting nanoparticles (or quantum dots), have gained increasing attention due to their controllable optical properties and potential applications. Silicon nanoparticles (also called silicon nanocrystals, SiNCs) have been extensively studied in the last years, due to their physical and chemical properties which render them a valid alternative to conventional quantum dots. During my PhD studies I have planned new synthetical routes to obtain SiNCs functionalised with molecules which could ameliorate the properties of the nanoparticle. However, this was certainly challenging, because SiNCs are very susceptible to many reagents and conditions that are often used in organic synthesis. They can be irreversibly quenched in the presence of alkalis, they can be damaged in the presence of oxidants, they can modify their optical properties in the presence of many nitrogen-containing compounds, metal complexes or simple organic molecules. If their surface is not well-passivated, the oxygen can introduce defect states, or they can aggregate and precipitate in several solvents. Therefore, I was able to functionalise SiNCs with different ligands: chromophores, amines, carboxylic acids, poly(ethylene)glycol, even ameliorating functionalisation strategies that already existed. This thesis will collect the experimental procedures used to synthesize silicon nanocrystals, the strategies adopted to functionalise effectively the nanoparticle with different types of organic molecules, and the characterisation of their surface, physical properties and luminescence (mostly photogenerated, but also electrochemigenerated). I also spent a period of 7 months in Leeds (UK), where I managed to learn how to synthesize other cadmium-free quantum dots made of copper, indium and sulphur (CIS QDs). During my last year of PhD, I focused on their functionalisation by ligand exchange techniques, yielding the first example of light-harvesting antenna based on those quantum dots. Part of this thesis is dedicated to them.

Catalytic reduction of levulinic acid derivatives to bio-fuel components

Levulinic Acid and its esters are polyfunctional molecules obtained by biomass conversion. The most investigated strategy for the valorization of LA is its hydrogenation towards fuel additives, solvents and other added-value bio-based chemicals and, in this context, heterogeneous and homogeneous catalysts are widely used. Most commonly, it is typically performed with molecular hydrogen (H2) in batch systems, with high H2 pressures and noble metal catalysts. Several works reported the batch liquid-phase hydrogenation of LA and its esters by heterogenous catalysts which contained support with Brønsted acidity in order to obtain valeric acid and its esters. Furthermore, bimetallic and monometallic systems composed by both a metal for hydrogen activation and a promoter were demonstrated to be suitable catalysts for reduction of carboxylic group. However, there were no studies in the literature reporting the hydrogenation of alkyl levulinates to 1-pentanol (1-PAO). Therefore, bimetallic and monometallic catalysts were tested for one-pot hydrogenation of methyl levulinate to 1-PAO. Re-based catalysts were investigated, this way proving the crucial role of the support for promoting the ring-opening of GVL and its consecutive reduction to valeric compounds. All the reactions were performed in neat without the need of any additional solvents. In these conditions, bimetallic Re-Ru-O/HZSM-5 afforded methyl valerate and valeric acid (VA) with a productivity of 512 mmol gmetal-1 h-1, one of the highest reported in literature to date. Rhenium can also promote the reduction of valeric acid/esters to PV through the formation of 1-pentanol and its efficient esterification/transesterification with the starting material. However, it was proved that Re-based catalysts may undergo leaching of active phase in presence of carboxylic acids, especially by working in neat with VA. Furthermore, the over-reduction of rhenium affects catalytic performance, suggesting not only that a pre-reduction step is unnecessary but also that it could be detrimental for catalyst’s activity.

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.

The bright routes to five-membered heterocycles: a photoredox catalytic approach

Synthetic chemists constantly strive to develop new methodologies to access complex molecules more sustainably. The recently developed photocatalytic approach results in a valid and greener alternative to the classical synthetic methods. Here we present three protocols to furnish five-membered rings exploiting photoredox catalysis. We firstly obtained 4,5-dihydrofurans (4,5-DHFs) from readily available olefins and α-haloketones employing fac-Ir(ppy)3 as a photocatalyst under blue-light irradiation (Figure 1, top). This transformation resulted very broad in scope, thanks to its mild conditions and the avoidance of stoichiometric amounts of oxidants or reductants. Moreover, similar conditions could lead to β,γ-unsaturated ketones, or highly substituted tetrahydrofurans (THFs) by carefully differentiating the substitution pattern on the starting materials and properly adjusting the reaction parameters. We then turned our attention to the reactivity of allenamides employing analogous photocatalytic conditions to access 2-aminofurans (Figure 1, bottom). α-Haloketones again provided the radical generated by fac-Ir(ppy)3 under visible-light irradiation, which added to the π-system and furnished the cyclic molecule. The addition of a second molecule of the α-haloketone moiety led to the formation of the final highly functionalized furan, which might be further elaborated to afford more complex products. The two works were both supplied with mechanistic investigations supported by experimental and computational methods. As our last project, we developed a methodology to achieve cypentanonyl-fused N-methylpyrrolidines (Figure 2), exploiting N,N-dimethylamines and carboxylic acids as radical sources. In two separated photocatalytic steps, both functionalities are manipulated through the photoredox catalysis by 4CzIPN to add to an α,β-enone system, furnishing the bicyclic product.

Study of the genes involved in Naphthenic acids (NAs) degradation by Rhodococcus spp.

Naphthenic acids (NAs) are an important group of organic pollutants mainly found in hydrocarbon deposits. Although these compounds are toxic, recalcitrant, and persistent in the environment, we are just learning the diversity of microbial communities involved in NAs- degradation and the mechanisms by which NAs are biodegraded. Studies have shown that naphthenic acids are susceptible to biodegradation, which decreases their concentration and reduces toxicity. Nevertheless, little is still known about their biodegradability. The present PhD Thesis’s work is aimed to study the biodegradation of simple model NAs using bacteria strains belonging to the Rhodococcus genus. In particular, Rh. sp. BCP1 and Rh. opacus R7 were able to utilize NAs such as cyclohexane carboxylic acid and cyclopentane carboxylic acid as the sole carbon and energy sources, even at concentrations up to 1000 mg/L. The presence of either substituents or longer carboxylic acid chains attached to the cyclohexane ring negatively affected the growth by pure bacterial cultures. Moreover, BCP1 and R7 cells incubated in the presence of CHCA or CPCA show a general increase of saturated and methyl-substituted fatty acids in their membrane, while the cis-mono-unsaturated ones decrease, as compared to glucose-grown cells. The observed lipid molecules modification during the growth in the presence of NAs is suggested as a possible mechanism to decrease the fluidity of the cell membrane to counteract NAs toxicity. In order to further evaluate this toxic effect on cell features, the morphological changes of BCP1 and R7 cells were also assessed through Transmission Electron Microscopy (TEM), revealing interesting ultrastructural changes. The induction of putative genes, and the construction of a random transposon mutagenesis library were also carried out to reveal the mechanisms by which these Rhodococcus strains can degrade toxic compounds such as NAs.