Synthetic approaches towards modified peptide nucleic acids (PNAs) for biomimetical nanostructured surfaces

†œThere is plenty of room at the bottom†�. These were the famous words of Richard P. Feynman in 1959 that led to the birth of nanotechnology and nanoscience. Electronic devices based on inorganic semiconductors have been part of our daily lives for the last 60 years. Their miniaturisation has occurred gradually over the years, however, according to Moore's law the contemporary microelectronic industry's †œtop-down†� manufacturing technique will soon reach its limits. Therefore, the recent development and increased knowledge of organic semiconductors has led to a tendency to explore alternative avenues with a focus on the creation of electronic devices based on organic molecules. The invention of techniques such STM (1981) and AFM (1986) have facilitated this research, allowing the imaging and manipulation of surfaces and molecules at the nanometre scale (0.1-100 nm). The next step is therefore the development of methods for the controlled fabrication of molecular assemblies and their integration into usable macroscopic systems. In this respect, the †œbottom-up†� approach offers considerable advantages over any other methodology (i.e. †œtop-down†�) for the construction of nanoscale functional materials and devices. This approach generally exploits the hierarchical self-assembly of functional molecules through multiple non-covalent interactions to prepare long range ordered and defect-free assemblies barely accessible through conventional covalent synthesis. However, an intrinsic drawback of investigating such systems in solution or in a crystal is that molecular components cannot be directly addressed on a nanometric scale. As a consequence, the best engineering methodology involves modifying the surfaces of bulk materials such as metals or semiconductors by deposition of functional organic materials. The modified surfaces are then characterised using scanning probe microscopies (e.g. STM, AFM). To this end, surface-confined, supramolecularly constructed, bi-dimensional (2D) networks, featuring regular porous domains (controllable both in shape and size) are of particular significance in this research domain because their cavities can be used as receptors for the confinement of other remotely controlled functional molecules (e.g. molecular switches, luminescent chromophores). Since these complex nanostructures could ultimately find applications as optoelectronic devices, research efforts in this domain have been gathering momentum in recent years. In Chapter 1, the reader is introduced to the methods employed to construct porous networks on surfaces via supramolecular interactions. The second part of the chapter deals with recent examples of recognition, selection and immobilisation of guest molecules within the cavities of the networks, which is followed in the third part with a discussion about surface assemblies that display structural features or functionality in the third dimension. The last section of the chapter is devoted to the construction of porous networks on surfaces via the interactions of biomimetic molecules (e.g. DNA), which leads to the objectives of the present doctoral project. Inspired by the self-assembly of DNA into nanoporous arrays, it was postulated that the Watson-Crick base pairing of oligonucleotide's nucleobases would be ideal in preparing 2D porous networks with large receptor cavities. The idea was to covalently attach complementary single stranded oligonucleotides to rigid angular and linear unit core modules respectively, and then allow the two units to self-assemble on surfaces. However, instead of using DNA oligonucleotides, the use of peptide nucleic acid (PNA) oligonucleotides was proposed since more robust architectures would be obtained due to the higher duplex stability displayed by this class of biomimetic molecules. This doctoral dissertation describes the synthetic steps taken towards achieving this goal. The design of the angular and linear units bearing complementary PNA oligomers, required for the preparation of self-assembled nanoporous arrays are described. However, prior to synthesizing these complex molecules, a simpler proof of principle was required to confirm that PNA duplexes could be formed on surfaces and also, whether the presence of chromophoric moieties (e.g. porphyrin) appended to the PNA strands had any effect on duplex formation and duplex stability. The molecule designed for this proof of principle was a self-complementary PNA dodecamer bearing a porphyrin adduct. The synthesis of the self-complementary PNA oligomer required for the preparation of the PNA-porphyrin adduct is described in the first part of Chapter 2. The main synthetic routes and protecting-group strategies used to prepare PNA monomers and oligomers are described first. This is followed by a discussion of the orthogonal protecting group strategies chosen for our project that would allow the isolation of PNA oligomers bearing protected nucleobases following resin-cleavage. This is contrary to the general norm in existing strategies wherein resin-cleavage and nucleobase deprotection is carried out in situ, however, it was required in our synthetic strategy since the terminal amino group of the PNA oligomers was required for further solution phase reactions. To this end, two protecting group strategies were proposed, a Fmoc/Mmt and Fmoc/Cbz-protecting group strategies. The solid support chosen for the Fmoc/Mmt strategy was Tentagel featuring a base-cleavable linker. Due to the failure to hydrolyse the linker during the resin-cleavage step, the Fmoc/Mmt strategy was abandoned. In the second strategy, an acid-cleavable Rink amide resin was chosen as the solid support, therefore a Fmoc/Cbz-protecting group strategy was chosen since it would allow the TFA-mediated cleavage of the oligomer from the resin, without the deprotection of the Cbz groups from the nucleobases. The preparation of the target PNA oligomer (sequence: TTAATTAATTAA) using the Fmoc/Cbz strategy is described in the next section. First, the required monomers for the oligomer synthesis were prepared using established procedures. Then, following reports of the advances in microwave assisted solid phase peptide synthesis claiming improved purity of oligomer products using short coupling times, the solid phase PNA oligomerisation was attempted using microwave irradiation. Three attempts were performed. The first, using a standard laboratory microwave, resulted in a complex mixture of products at the dodecamer stage. An improvement was observed in the results using the CEM discover SPS microwave which was specifically designed for solid phase synthesis, however, the crude dodecamer obtained was still inseparable from the by-products. Similar results were obtained with the CEM liberty microwave, which was an automated solid phase synthesis setup. Finally, utilising manual solid phase synthesis, the target PNA dodecamer was obtained. The HPLC chromatogram of crude PNA dodecamer obtained following resin cleavage displayed a single major product, which was subsequently purified. The oligomer was then deprotected by treatment with TMSI, and was analysed by mass spectrometry, which confirmed that the target dodecamer had been isolated. Section 2.2 described our efforts to prepare PNA-chromophore adducts. Following the isolation of the PNA dodecamer, attempts to covalently attach a porphyrin moiety to the resin-bound oligomer via an amide linkage failed, possibly due to steric hindrance. Subsequently, an azide linker was appended to the oligomer, and attempts to attach an acetylene functionalised porphyrin using a Cu(I)-catalysed 1,3-dipolar cycloaddition were performed. Unfortunately, this approach also did not yield the target adduct. These unsuccessful results paved the way to the development of a Cu(I)-free 1,3-dipolar cycloaddition that enabled the attachment of chromophores to the PNA oligomer. Recently published reports of Cu(I)-free 1,3-dipolar cycloaddition reactions applied on DNA oligomers offered inspiration towards this goal. The reported strategies involved the generation of a nitrile oxide species, which then reacted with either an alkene or an alkyne to form an isoxazoline or an isoxazole. Two methods of generating the nitrile oxide species were evaluated using anthracene derivatives.