Synthetic and mechanistic investigation of new radical processes: reaction of organic azides with group-XIII Lewis acids

Dichloroindium hydride revealed to be a valid alternative to tributyltin hydride for radical reduction of organic (alkyl, aryl, acyl, solfonyl) azides. The new approach entails mild reaction conditions and provides high yields of the corresponding amines and amides, also showing high degrees of selectivity. The system dichloroindium hydride / azides can be utilised in fivemembered ring closures of g-azidonitriles, as a new source of aminyl radicals for the attractive synthesis of interesting amidine compounds in the absence of both toxic reagents and tedious purification procedures. Allylindium dichloride seems a good substitute for dichloroindium hydride for generation of indium centred radicals under photolytic conditions, since it allows allylation of electrophilic azides (e.g. phenylsulfonyl azide) and halogen or ester δ-substituted azides, the latter through a 1,5-H transfer rearrangement mechanism. Evidences of the radical nature of the reactions mechanism were provided by ESR spectroscopy, furthermore the same technique, allowed to discover that the reaction of azides with indium trichloride and other group XIII Lewis acids, in particular gallium trichloride, gives rise to strongly coloured, persistent paramagnetic species, whose structure is consistent with the radical cation of the head-to-tail dimer of the aniline corresponding to the starting azide.

In situ real-time investigation of Organic Ultra-Thin-Film transistors: growth, electrical properties and biosensing applications

Organic electronics has grown enormously during the last decades driven by the encouraging results and the potentiality of these materials for allowing innovative applications, such as flexible-large-area displays, low-cost printable circuits, plastic solar cells and lab-on-a-chip devices. Moreover, their possible field of applications reaches from medicine, biotechnology, process control and environmental monitoring to defense and security requirements. However, a large number of questions regarding the mechanism of device operation remain unanswered. Along the most significant is the charge carrier transport in organic semiconductors, which is not yet well understood. Other example is the correlation between the morphology and the electrical response. Even if it is recognized that growth mode plays a crucial role into the performance of devices, it has not been exhaustively investigated. The main goal of this thesis was the finding of a correlation between growth modes, electrical properties and morphology in organic thin-film transistors (OTFTs). In order to study the thickness dependence of electrical performance in organic ultra-thin-film transistors, we have designed and developed a home-built experimental setup for performing real-time electrical monitoring and post-growth in situ electrical characterization techniques. We have grown pentacene TFTs under high vacuum conditions, varying systematically the deposition rate at a fixed room temperature. The drain source current IDS and the gate source current IGS were monitored in real-time; while a complete post-growth in situ electrical characterization was carried out. At the end, an ex situ morphological investigation was performed by using the atomic force microscope (AFM). In this work, we present the correlation for pentacene TFTs between growth conditions, Debye length and morphology (through the correlation length parameter). We have demonstrated that there is a layered charge carriers distribution, which is strongly dependent of the growth mode (i.e. rate deposition for a fixed temperature), leading to a variation of the conduction channel from 2 to 7 monolayers (MLs). We conciliate earlier reported results that were apparently contradictory. Our results made evident the necessity of reconsidering the concept of Debye length in a layered low-dimensional device. Additionally, we introduce by the first time a breakthrough technique. This technique makes evident the percolation of the first MLs on pentacene TFTs by monitoring the IGS in real-time, correlating morphological phenomena with the device electrical response. The present thesis is organized in the following five chapters. Chapter 1 makes an introduction to the organic electronics, illustrating the operation principle of TFTs. Chapter 2 presents the organic growth from theoretical and experimental points of view. The second part of this chapter presents the electrical characterization of OTFTs and the typical performance of pentacene devices is shown. In addition, we introduce a correcting technique for the reconstruction of measurements hampered by leakage current. In chapter 3, we describe in details the design and operation of our innovative home-built experimental setup for performing real-time and in situ electrical measurements. Some preliminary results and the breakthrough technique for correlating morphological and electrical changes are presented. Chapter 4 meets the most important results obtained in real-time and in situ conditions, which correlate growth conditions, electrical properties and morphology of pentacene TFTs. In chapter 5 we describe applicative experiments where the electrical performance of pentacene TFTs has been investigated in ambient conditions, in contact to water or aqueous solutions and, finally, in the detection of DNA concentration as label-free sensor, within the biosensing framework.

Structure-Property Relationships and Charge Transport Modeling of Organic Molecular Materials

From the perspective of a new-generation opto-electronic technology based on organic semiconductors, a major objective is to achieve a deep and detailed knowledge of the structure-property relationships, in order to optimize the electronic, optical, and charge transport properties by tuning the chemical-physical characteristics of the compounds. The purpose of this dissertation is to contribute to such understanding, through suitable theoretical and computational studies. Precisely, the structural, electronic, optical, and charge transport characteristics of several promising organic materials recently synthesized are investigated by means of an integrated approach encompassing quantum-chemical calculations, molecular dynamics and kinetic Monte Carlo simulations. Particular care is addressed to the rationalization of optical and charge transport properties in terms of both intra- and intermolecular features. Moreover, a considerable part of this project involves the development of a home-made set of procedures and parts of software code required to assist the modeling of charge transport properties in the framework of the non-adiabatic hopping mechanism applied to organic crystalline materials. As a first part of my investigations, I mainly discuss the optical, electronic, and structural properties of several core-extended rylene derivatives, which can be regarded to as model compounds for graphene nanoribbons. Two families have been studied, consisting in bay-linked perylene bisimide oligomers and N-annulated rylenes. Beside rylene derivatives, my studies also concerned electronic and spectroscopic properties of tetracene diimides, quinoidal oligothiophenes, and oxygen doped picene. As an example of device application, I studied the structural characteristics governing the efficiency of resistive molecular memories based on a derivative of benzoquinone. Finally, as a second part of my investigations, I concentrate on the charge transport properties of perylene bisimides derivatives. Precisely, a comprehensive study of the structural and thermal effects on the charge transport of several core-twisted chlorinated and fluoro-alkylated perylene bisimide n-type semiconductors is presented.

Design, Synthesis and Characterization of N-Containing Organic Compounds

The needed of new intermediates/products for screening in the fields of drug discovery and material science is the driving force behind the development of new methodologies and technologies. Organic scaffolds are privileged targets for this scouting. Among them a priority place must be attributed to those including nitrogen functionalities in their scaffolds. It comes out that new methodologies, allowing the introduction of the nitrogen atom for the synthesis of an established target or for the curiosity driven researches, will always be welcome. The target of this PhD Thesis’ work is framed within this goal. Accordingly, Chapter 1 reports the preparation of new N-Heteroarylmethyl 3-carboxy-5-hydroxy piperidine scaffold, as potential and selective α-glucosidase inhibitors. The proposed reversible uncompetitive mechanism of inhibition makes them attractive as interesting candidate for drug development. Chapter 2 is more environmentally method-driven research. Eco-friendly studies on the synthesis of enantiomerically pure 1,4-dihydropyridines using “solid” ammonia (magnesium nitride) is reported via classical Hantzch method. Chapter 3 and Chapter 4 may be targeted as the core of the Thesis’s research work. Chapter 3 reports the studies addressed to the synthesis of N-containing heterocycles by using N-trialkylsilylimine/hetero-Diels–Alder (HAD) approach. New eco-friendly methodology as MAOS (Microwave Assisted Organic Synthesis) has been used as witness of our interest to a sustainable chemistry. Theoretical calculations were adopted to fully clarify the reaction mechanism. Chapter 4 is dedicated to picture the most recent studies performed on the application of N-Metallo-ketene imines (metallo= Si, Sn, Al), relatively new intermediates which are becoming very popular, in the preparation of highly functionalized N-containing derivatives, accordingly to the Thesis’ target. Derivatives obtained are designed in such a way that they could be of interest in the field of drug and new material chemistry.

In-situ and real time scanning probe microscopy of organic ultra thin films

In recent decades, Organic Thin Film Transistors (OTFTs) have attracted lots of interest due to their low cost, large area and flexible properties which have brought them to be considered the building blocks of the future organic electronics. Experimentally, devices based on the same organic material deposited in different ways, i.e. by varying the deposition rate of the molecules, show different electrical performance. As predicted theoretically, this is due to the speed and rate by which charge carriers can be transported by hopping in organic thin films, transport that depends on the molecular arrangement of the molecules. This strongly suggests a correlation between the morphology of the organic semiconductor and the performance of the OTFT and hence motivated us to carry out an in-situ real time SPM study of organic semiconductor growth as an almost unprecedent experiment with the aim to fully describe the morphological evolution of the ultra-thin film and find the relevant morphological parameters affecting the OTFT electrical response. For the case of 6T on silicon oxide, we have shown that the growth mechanism is 2D+3D, with a roughening transition at the third layer and a rapid roughening. Relevant morphological parameters have been extracted by the AFM images. We also developed an original mathematical model to estimate theoretically and more accurately than before, the capacitance of an EFM tip in front of a metallic substrate. Finally, we obtained Ultra High Vacuum (UHV) AFM images of 6T at lying molecules layer both on silicon oxide and on top of 6T islands. Moreover, we performed ex-situ AFM imaging on a bilayer film composed of pentacene (a p-type semiconductor) and C60 (an n-type semiconductor).

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.

Simulation of photoinduced processes in organic chromophores: mapping photochemically relevant states for accurate dynamics

The simulation of ultrafast photoinduced processes is a fundamental step towards the understanding of the underlying molecular mechanism and interpretation/prediction of experimental data. Performing a computer simulation of a complex photoinduced process is only possible introducing some approximations but, in order to obtain reliable results, the need to reduce the complexity must balance with the accuracy of the model, which should include all the relevant degrees of freedom and a quantitatively correct description of the electronic states involved in the process. This work presents new computational protocols and strategies for the parameterisation of accurate models for photochemical/photophysical processes based on state-of-the-art multiconfigurational wavefunction-based methods. The required ingredients for a dynamics simulation include potential energy surfaces (PESs) as well as electronic state couplings, which must be mapped across the wide range of geometries visited during the wavepacket/trajectory propagation. The developed procedures allow to obtain solid and extended databases reducing as much as possible the computational cost, thanks to, e.g., specific tuning of the level of theory for different PES regions and/or direct calculation of only the needed components of vectorial quantities (like gradients or nonadiabatic couplings). The presented approaches were applied to three case studies (azobenzene, pyrene, visual rhodopsin), all requiring an accurate parameterisation but for different reasons. The resulting models and simulations allowed to elucidate the mechanism and time scale of the internal conversion, reproducing or even predicting new transient experiments. The general applicability of the developed protocols to systems with different peculiarities and the possibility to parameterise different types of dynamics on an equal footing (classical vs purely quantum) prove that the developed procedures are flexible enough to be tailored for each specific system, and pave the way for exact quantum dynamics with multiple degrees of freedom.

Novel developments of atropisomeric organic molecules. Design of atropisomeric drugs, fluorescent compounds and investigation of reaction mechanisms.

In recent years, the study of restricted rotation bonds in organic compounds has aroused increasing interest. The reason is that this characteristic can lead to obtaining new properties in organic compounds. In this research thesis, an intense investigation was carried out using DFT calculations and experimental evaluation of the barriers to rotational energies, in order to discover new properties deriving from the restricted rotation bonds. Research has been developed in various fields of organic chemistry, ranging from drugs (the atropisomeric atorvastatin in Chapter 3) to luminescent compounds (aryls amino borane in Chapter 4). Furthermore, an organocatalytic central to axial conversion mechanism was investigated through DFT calculations, finding out interesting outcomes (Chapter 5). Finally, a project in collaboration with Dr. Farran and Prof. Vanthuyne of the Aix-Marseille University was done to investigate the interactions in transition states of rotational barriers.

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).

Spectroscopic investigation on photoreactivity, structure and polymorphism of organic molecular crystals

The study of the spectroscopic phenomena in organic solids, in combination with other techniques, is an effective tool for the understanding of the structural properties of materials based on these compounds. This Ph.D. work was dedicated to the spectroscopic investigation of some relevant processes occurring in organic molecular crystals, with the goal of expanding the knowledge on the relationship between structure, dynamics and photoreactivity of these systems. Vibrational spectroscopy has been the technique of choice, always in combination with X-ray diffraction structural studies and often the support of computational methods. The vibrational study of the molecular solid state reaches its full potential when it includes the low-wavenumber region of the lattice-phonon modes, which probe the weak intermolecular interactions and are the fingerprints of the lattice itself. Microscopy is an invaluable addition in the investigation of processes that take place in the micro-meter scale of the crystal micro-domains. In chemical and phase transitions, as well as in polymorph screening and identification, the combination of Raman microscopy and lattice-phonon detection has provided useful information. Research on the fascinating class of single-crystal-to-single-crystal photoreactions, has shown how the homogeneous mechanism of these transformations can be identified by lattice-phonon microscopy, in agreement with the continuous evolution of their XRD patterns. On describing the behavior of the photodimerization mechanism of vitamin K3, the focus was instead on the influence of its polymorphism in governing the product isomerism. Polymorphism is the additional degree of freedom of molecular functional materials, and by advancing in its control and properties, functionalities can be promoted for useful applications. Its investigation focused on thin-film phases, widely employed in organic electronics. The ambiguities in phase identification often emerging by other experimental methods were successfully solved by vibrational measurements.