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.

Advanced Spectroscopy for the Study of Colourants in Cultural Heritage

Colourants are substances used to change the colour of something, and are classified in three typology of colorants: a) pigments, b) dyes, and c) lakes and hybrid pigments. Their identification is very important when studying cultural heritage; it gives information about the artistic technique, can help in dating, and offers insights on the condition of the object. Besides, the study of the degradation phenomena constitutes a framework for the preventive conservation strategies, provides evidence of the object's original appearance, and contributes to the authentication of works of art. However, the complexity of these systems makes it impossible to achieve a complete understanding using a single technique, making necessary a multi-analytical approach. This work focuses on the set-up and application of advanced spectroscopic methods for the study of colourants in cultural heritage. The first chapter presents the identification of modern synthetic organic pigments using Metal Underlayer-ATR (MU-ATR), and the characterization of synthetic dyes extracted from wool fibres using a combination of Thin Layer Chromatography (TLC) coupled to MU-ATR using AgI@Au plates. The second chapter presents the study of the effect of metallic Ag in the photo-oxidation process of orpiment, and the influence of the different factors, such as light and relative humidity. We used a combination of vibrational and synchrotron radiation-based X-ray microspectroscopy techniques: µ-ATR-FT-IR, µ-Raman, SR-µ-XRF, µ-XANES at S K-, Ag L3- and As K-edges and SR-µ-XRD. The third chapter presents the study of metal carboxylates in paintings, specifically on the formation of Zn and Pb carboxylates in three different binders: stand linseed oil, whole egg, and beeswax. We used micro-ATR-FT-IR, macro FT-IR in total reflection (rMA-FT-IR), portable Near-Infrared spectroscopy (NIR), macro X-ray Powder Diffraction (MA-XRPD), XRPD, and Gas Chromatography Mass-Spectrometry (GC-MS). For the data processing, we explored the data from rMA-FT-IR and NIR with the Principal Component Analysis (PCA).

Development and optimization of fibre-shaped dye-sensitized solar cells employing an innovative fully organic sensitizer

The quality of human life depends to a large degree on the availability of energy. In recent years, photovoltaic technology has been growing extraordinarily as a suitable source of energy, as a consequence of the increasing concern over the impact of fossil fuels on climate change. Developing affordable and highly efficiently photovoltaic technologies is the ultimate goal in this direction. Dye-sensitized solar cells (DSSCs) offer an efficient and easily implementing technology for future energy supply. Compared to conventional silicon solar cells, they provide comparable power conversion efficiency at low material and manufacturing costs. In addition, DSSCs are able to harvest low-intensity light in diffuse illumination conditions and then represent one of the most promising alternatives to the traditional photovoltaic technology, even more when trying to move towards flexible and transparent portable devices. Among these, considering the increasing demand of modern electronics for small, portable and wearable integrated optoelectronic devices, Fibre Dye-Sensitized Solar Cells (FDSSCs) have gained increasing interest as suitable energy provision systems for the development of the next-generation of smart products, namely “electronic textiles” or “e-textiles”. In this thesis, several key parameters towards the optimization of FDSSCs based on inexpensive and abundant TiO2 as photoanode and a new innovative fully organic sensitizer were studied. In particular, the effect of various FDSSCs components on the device properties pertaining to the cell architecture in terms of photoanode oxide layer thickness, electrolytic system, cell length and electrodes substrates were examined. The photovoltaic performances of the as obtained FDSSCs were fully characterized. Finally, the metal part of the devices (wire substrate) was substituted with substrates suitable for the textile industry as a fundamental step towards commercial exploitation.

Non-ambient solid-state characterization of crystalline molecular organic semiconductors

The research project is focused on the investigation of the polymorphism of crystalline molecular material for organic semiconductor applications under non-ambient conditions, and the solid-state characterization and crystal structure determination of the different polymorphic forms. In particular, this research project has tackled the investigation and characterization of the polymorphism of perylene diimides (PDIs) derivatives at high temperatures and pressures, in particular N,N’-dialkyl-3,4,9,10-perylendiimide (PDI-Cn, with n = 5, 6, 7, 8). These molecules are characterized by excellent chemical, thermal, and photostability, high electron affinity, strong absorption in the visible region, low LUMO energies, good air stability, and good charge transport properties, which can be tuned via functionalization; these features make them promising n-type organic semiconductor materials for several applications such as OFETs, OPV cells, laser dye, sensors, bioimaging, etc. The thermal characterization of PDI-Cn was carried out by a combination of differential scanning calorimetry, variable temperature X-ray diffraction, hot-stage microscopy, and in the case of PDI-C5 also variable temperature Raman spectroscopy. Whereas crystal structure determination was carried out by both Single Crystal and Powder X-ray diffraction. Moreover, high-pressure polymorphism via pressure-dependent UV-Vis absorption spectroscopy and high-pressure Single Crystal X-ray diffraction was carried out in this project. A data-driven approach based on a combination of self-organizing maps (SOM) and principal component analysis (PCA) is also reported was used to classify different π-stacking arrangements of PDI derivatives into families of similar crystal packing. Besides the main project, in the framework of structure-property analysis under non-ambient conditions, the structural investigation of the water loss in Pt- and Pd- based vapochromic potassium/lithium salts upon temperature, and the investigation of structure-mechanical property relationships in polymorphs of a thienopyrrolyldione endcapped oligothiophene (C4-NT3N) are reported.

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.

Fabrication and characterization of hybrid ferromagnetic-organic heterostructures for spintronics application

Recent research in the field of organic spintronics highlighted the peculiar spin-dependent properties of the interface formed by an organic semiconductor (OSC) chemisorbed over a 3d ferromagnetic metal, also known as spinterface. The hybridization between the molecular and metallic orbitals, typically π orbitals of the molecule and the d orbitals of the ferromagnet, give rise to spin dependent properties that were not expected by considering the single components of interfaces, as for example the appearance of a magnetic moment on non-magnetic molecules or changes in the magnetic behavior of the ferromagnet. From a technological viewpoint these aspects provide novel engineering schemes for spin memory and for spintronics devices, featuring unexpected interfacial magnetoresistance, spin-filtering effects and even modulated magnetic anisotropy. Applications of these concepts to devices require nevertheless to transfer the spinterface effects from an ideal interface to room temperature operating thin films. In this view, my work presents for the first time how spinterface effects can be obtained even at room temperature on polycrystalline ferromagnetic Co thin films interfaced with organic molecules. The considered molecules were commercial and widely used in the field of organic electronics: Fullerene (C60), Gallium Quinoline (Gaq3) and Sexithiophene (T6). An increase of coercivity, up to 100% at room temperature, has been obtained on the Co ultra-thin films by the deposition of an organic molecule. This effect is accompanied by a change of in-plane anisotropy that is molecule-dependent. Moreover the Spinterface effect is not limited to the interfacial layer, but it extends throughout the whole thickness of the ferromagnetic layer, posing new questions on the nature of the 3d metal-molecule interaction.

Theoretical and experimental study of novel hybrid composite and metal-composites interfaces

The growing demand for lightweight solutions in every field of engineering is driving the industry to seek new technological solutions to exploit the full potential of different materials. The combination of dissimilar materials with distinct property ranges embodies a transparent allocation of component functions while allowing an optimal mix of their characteristics. From both technological and design perspectives, the interaction between dissimilar materials can lead to severe defects that compromise a multi-material hybrid component's performance and its structural integrity. This thesis aims to develop methodologies for designing, manufacturing, and monitoring of hybrid metal-composite joints and hybrid composite components. In Chapter 1, a methodology for designing and manufacturing hybrid aluminum/composite co-cured tubes is assessed. In Chapter 2, a full-field methodology for fiber misalignment detection and stiffness prediction for hybrid, long fiber reinforced composite systems is shown and demonstrated. Chapter 3 reports the development of a novel technology for joining short fiber systems and metals in a one-step co-curing process using lattice structures. Chapter 4 is dedicated to a novel analytical framework for the design optimization of two lattice architectures.

Design of luminescent metal complexes for polymer science

The program of my PhD studies has been dealing with the investigation of the research outcomes that may result from the use of luminescent Iridium(III) cyclometalated complexes in the field of polymer science. In particular, my activity has been focused on exploring two main applicative contexts, i.e. Ir(III) complexes for preparing polymers and in combination with polymers. In the first part, a new set of luminescent Ir(III) complexes was exploited as photocatalysts for light-assisted atom transfer radical polymerization of methyl methacrylate. The decoration of both cyclometalated and ancillary ligands with sp3 hybridized nitrogen substituents together with the use of specific counterions, imparted suitable photophysical and redox properties for an efficient photocatalyzed process. The second part has been focused on the employment of Ir(III) tetrazole complexes as phosphorescent dyes in polymeric materials. Colourless luminescent solar concentrators were prepared blending two Ir(III) cyclometalates with acrylate polymers. Their performances were investigated, leading to promising outcomes comparable, or superior, to those obtained from colourless LSCs based on organic fluorophores. As a complementary approach, Ir(III) complexes were covalently linked to polymers in the side chain, to obtain a new class of metallopolymers. To this extent, a bifunctional tetrazolate molecule, equipped with a coordination site and a polymerizable unit, was designed. The photophysical properties of the resultant luminescent polymeric films were discussed. In the end, an additional project involving both polymers and metal compounds was carried out during my experience as a visiting PhD student at Humboldt – University of Berlin. Polystyrene and polyethylene glycol -based ion-exchange resins were functionalized with peptides through a ligation pathway, for the selective chelation of Copper(II) in aqueous solutions. The coordinating capability of the materials towards Cu2+ ions was tested by ICP-MS analysis. The resins strategically modified with ion-selective peptides, may be exploited in the preparation of water-processing devices.

Geochemistry Of Acid Mine Drainage From A Coal Mining Area And Processes Controlling Metal Attenuation In Stream Waters, Southern Brazil.

Acid drainage influence on the water and sediment quality was investigated in a coal mining area (southern Brazil). Mine drainage showed pH between 3.2 and 4.6 and elevated concentrations of sulfate, As and metals, of which, Fe, Mn and Zn exceeded the limits for the emission of effluents stated in the Brazilian legislation. Arsenic also exceeded the limit, but only slightly. Groundwater monitoring wells from active mines and tailings piles showed pH interval and chemical concentrations similar to those of mine drainage. However, the river and ground water samples of municipal public water supplies revealed a pH range from 7.2 to 7.5 and low chemical concentrations, although Cd concentration slightly exceeded the limit adopted by Brazilian legislation for groundwater. In general, surface waters showed large pH range (6 to 10.8), and changes caused by acid drainage in the chemical composition of these waters were not very significant. Locally, acid drainage seemed to have dissolved carbonate rocks present in the local stratigraphic sequence, attenuating the dispersion of metals and As. Stream sediments presented anomalies of these elements, which were strongly dependent on the proximity of tailings piles and abandoned mines. We found that precipitation processes in sediments and the dilution of dissolved phases were responsible for the attenuation of the concentrations of the metals and As in the acid drainage and river water mixing zone. In general, a larger influence of mining activities on the chemical composition of the surface waters and sediments was observed when enrichment factors in relation to regional background levels were used.

Bacterial Diversity Assessment In Soil Of An Active Brazilian Copper Mine Using High-throughput Sequencing Of 16s Rdna Amplicons.

Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences.

An Integrated Framework To Improve The Concept Of Resource Specialisation.

Resource specialisation, although a fundamental component of ecological theory, is employed in disparate ways. Most definitions derive from simple counts of resource species. We build on recent advances in ecophylogenetics and null model analysis to propose a concept of specialisation that comprises affinities among resources as well as their co-occurrence with consumers. In the distance-based specialisation index (DSI), specialisation is measured as relatedness (phylogenetic or otherwise) of resources, scaled by the null expectation of random use of locally available resources. Thus, specialists use significantly clustered sets of resources, whereas generalists use over-dispersed resources. Intermediate species are classed as indiscriminate consumers. The effectiveness of this approach was assessed with differentially restricted null models, applied to a data set of 168 herbivorous insect species and their hosts. Incorporation of plant relatedness and relative abundance greatly improved specialisation measures compared to taxon counts or simpler null models, which overestimate the fraction of specialists, a problem compounded by insufficient sampling effort. This framework disambiguates the concept of specialisation with an explicit measure applicable to any mode of affinity among resource classes, and is also linked to ecological and evolutionary processes. This will enable a more rigorous deployment of ecological specialisation in empirical and theoretical studies.

Bipolar Tribocharging Signal During Friction Force Fluctuations At Metal-insulator Interfaces.

Friction and triboelectrification of materials show a strong correlation during sliding contacts. Friction force fluctuations are always accompanied by two tribocharging events at metal-insulator [e.g., polytetrafluoroethylene (PTFE)] interfaces: injection of charged species from the metal into PTFE followed by the flow of charges from PTFE to the metal surface. Adhesion maps that were obtained by atomic force microscopy (AFM) show that the region of contact increases the pull-off force from 10 to 150 nN, reflecting on a resilient electrostatic adhesion between PTFE and the metallic surface. The reported results suggest that friction and triboelectrification have a common origin that must be associated with the occurrence of strong electrostatic interactions at the interface.

Seven-membered Rings Through Metal-free Rearrangement Mediated By Hypervalent Iodine.

A versatile and metal-free approach for the synthesis of carbocycles and of heterocycles bearing seven- and eight-membered rings is described. The strategy is based on ring expansion of 1-vinylcycloalkanols (or the corresponding silyl or methyl ether) mediated by the hypervalent iodine reagent HTIB (PhI(OH)OTs). Reaction conditions can be easily adjusted to give ring expansion products bearing different functional groups. A route to medium-ring lactones was also developed.

Metal Ions Bound To The Human Milk Immunoglobulin A: Metalloproteomic Approach.

The presence of calcium, iron, and zinc bound to human milk secretory IgA (sIgA) was investigated. The sIgA components were first separated by two-dimensional polyacrylamide gel electrophoresis and then identified by electrospray ionization-tandem mass spectrometry (ESI MS MS). The metal ions were detected by flame atomic absorption spectrometry after acid mineralization of the spots. The results showed eight protein spots corresponding to the IgA heavy chain constant region. Another spot was identified as the transmembrane secretory component. Calcium was bound to both the transmembrane component and the heavy chain constant region, while zinc was bound to the heavy chain constant region and iron was not bound with the identified proteins. The association of a metal ion with a protein is important for a number of reasons, and therefore, the findings of the present study may lead to a better understanding of the mechanisms of action and of additional roles that sIgA and its components play in human milk.

Engineered Nanoparticles And Organic Matter: A Review Of The State-of-the-art.

Growth in the development and production of engineered nanoparticles (ENPs) in recent years has increased the potential for interactions of these nanomaterials with aquatic and terrestrial environments. Carefully designed studies are therefore required in order to understand the fate, transport, stability, and toxicity of nanoparticles. Natural organic matter (NOM), such as the humic substances found in water, sediment, and soil, is one of the substances capable of interacting with ENPs. This review presents the findings of studies of the interaction of ENPs and NOM, and the possible effects on nanoparticle stability and the toxicity of these materials in the environment. In addition, ENPs and NOM are utilized for many different purposes, including the removal of metals and organic compounds from effluents, and the development of new electronic sensors and other devices for the detection of active substances. Discussion is therefore provided of some of the ways in which NOM can be used in the production of nanoparticles. Although there has been an increase in the number of studies in this area, further progress is needed to improve understanding of the dynamic interactions between ENPs and NOM.