Chapter 1 : nucleobases with designed patterns of hydrogen bonding

The chemistry used in key bond-forming steps to prepare nucleobases with designed patterns of hydrogen bonding is surveyed. Incorporation of the nucleobases into DNA and RNA oligomers is achieved either chemically using building blocks such as nucleoside phosphoramidites or enzymatically using nucleotide triphosphates. By varying the hydrogen bonding pattern within nucleobases, and by incorporating additional substituents, new structures have been designed that "reach over" so that contacts with both strands in targeted duplex DNA can be made in antigene strategies to control gene expression. Various new base-pairing systems have been evaluated that expand the genetic alphabet beyond Watson-Crick base pairs A.T and G.C. For example, benzo-homologated analogs of the natural DNA bases represent a new genetic set of orthogonal, size-expanded derivatives that have been shown to encode amino acids of a protein in a living organism.

Special classes of iron(II) azole spin-crossover compounds

In this chapter, selected results obtained so far on Fe(II) spin crossover compounds of 1,2,4-triazole, isoxazole and tetrazole derivatives are summarized and analysed. These materials include the only compounds known to have Fe(II)N6 spin crossover chromophores consisting of six chemically identical heterocyclic ligands. Particular attention is paid to the coordination modes for substituted 1,2,4-triazole derivatives towards Fe(II) resulting in polynuclear and mononuclear compounds exhibiting Fe(II) spin transitions. Furthermore, the physical properties of mononuclear Fe(II) isoxazole and 1-alkyl-tetrazole compounds are discussed in relation to their structures. It will also be shown that the use of α,β- and α,ω-bis(tetrazol-1-yl)alkane type ligands allowed a novel strategy towards obtaining polynuclear Fe(II) spin crossover materials.

Intermediate pyrolysis of biomass energy pellets for producing sustainable liquid, gaseous and solid fuels

This work describes the use of intermediate pyrolysis system to produce liquid, gaseous and solid fuels from pelletised wood and barley straw feedstock. Experiments were conducted in a pilot-scale system and all products were collected and analysed. The liquid products were separated into an aqueous phase and an organic phase (pyrolysis oil) under gravity. The oil yields were 34.1 wt.% and 12.0 wt.% for wood and barley straw, respectively. Analysis found that both oils were rich in heterocyclic and phenolic compounds and have heating values over 24 MJ/kg. The yields of char for both feedstocks were found to be about 30 wt.%, with heating values similar to that of typical sub-bituminous class coal. Gas yields were calculated to be approximately 20 wt.%. Studies showed that both gases had heating values similar to that of downdraft gasification producer gas. Analysis on product energy yields indicated the process efficiency was about 75%. © 2014 Elsevier Ltd. All rights reserved.

Síntese e reatividade de derivados de quinoxalina visando aplicações como quimiossensores e estudo cinético por análise de imagens

Synthesis of heterocyclic compounds, as quinoxaline derivatives, has being shown to be relevant and promissor due to expressive applications in biological and technological areas. This work was dedicated to the synthesis, characterization and reactivity of quinoxaline derivatives in order to obtain new chemosensors. (L)-Ascorbic acid (1) and 2,3-dichloro-6,7- dinitroquinoxalina (2) were explored as synthetic precursors. Starting from synthesis of 1 and characterization of compounds derived from (L)-ascorbic acid, studies were performed investigating the application of products as chemosensors, in which compound 36 demonstrated selective affinity for Cu2+ íons in methanolic solution, by naked-eye (colorimetric) and UVvisible analyses. Further, initial analysis suggests that 39 a Schiff’s base derived from 36 also presents this feature. Five quinoxaline derivatives were synthesized from building block 2 through nucleophilic aromatic substitution by aliphatic amines, in which controlling the experimental conditions allows to obtain both mono- and di-substituted derivatives. Reactivity studies were carried out with two purposes: i) investigate the possibility of 47 compound being a chemosensor for anion, based on its interaction with sodium hydroxide in DMSO, using image analysis and UV-visible spectroscopy; ii) characterize kinetically the conversion of compound 44 into 46 based on RGB and multivariate image analysis from TLC data, as a simple and inexpensive qualitative and quantitative tool.

Computer assisted synthesis and in-vitro cytotoxic evaluation of new pyrazole-fused isoquinolinoquinones derivatives as PI3K receptor antagonist with promising antitumoral activity

The importance of pyrazole and isoquinoline-5,8-dione scaffolds in medical chemistry is underlined by the high number of drugs currently on trading that contains these active ingredients. Due to their cytotoxic capability, the interest of medicinal chemists in these heterocyclic rings has grown exponentially especially, for cancer therapy. In this project, the first synthesis of pyrazole-fused isoquinoline-5,8-diones has been developed. 1,3-Dipolar cycloaddition followed by oxidative aromatization, established by our research group, has been employed. Screening of reaction conditions and characterization studies about the regioselectivity have been successfully performed. A remote control of regioselectivity, to achieve the two possible regioisomers has been accomplished. Through Molecular Docking studies, Structure-Activity relationship of differently substituted scaffolds containing our central core proved that a family of PI3K inhibitors have been discovered. Finally, in order to verify the promising antitumor activity, a first test of cell viability in vitro on T98G cell line of a solid brain tumor, the Glioblastoma Multiforme, showed cytotoxic inhibition comparable to currently trade anticancer drugs.

Catalyst and substrate effects in enantioselective C–H insertion reactions of α-diazosulfones

This thesis describes a systematic investigation of the mechanistic and synthetic aspects of intramolecular reactions of a series of α-diazo-β-oxo sulfone derivatives using copper and, to a lesser extent, rhodium catalysts. The key reaction pathways explored were C–H insertion and cyclopropanation, with hydride transfer competing in certain instances. Significantly, up to 98% ee has been achieved in the C–H insertion processes using copper-NaBARF-bisoxazoline catalysts, with the presence of the additive NaBARF critical to the efficiency of the transformations. This novel synthetic methodology provides access to a diverse range of enantioenriched heterocyclic compounds including thiopyrans, sulfolanes, β- and γ-lactams, in addition to carbocycles such as fused cyclopropanes. The synthesis of the α-diazosulfones required for subsequent investigations is initially described. Of the twenty seven diazo sulfones described, nineteen are novel and are fully characterised in this work. The discussion is subsequently focused on a study of the copper and rhodium catalysed reactions of the α-diazosulfones with Chapter Four concentrated on highly enantioselective C–H insertion to form thiopyrans and sufolanes, Chapter Five focused on C–H insertion to form fused sulfolanes, Chapter Six focused on C–H insertion in sulfonyl α-diazoamides where both lactam formation and / or thiopyran / sulfolane formation can result from competing C–H insertion pathways, while Chapter Seven focuses on cyclopropanation to yield fused cyclopropane derviatives. One of the key outcomes of this work is an insight into the steric and / or electronic factors on both the substrate and the catalyst which control regio-, diastereo- and enantioselectivity patterns in these synthetically powerful transformations. Full experimental details for the synthesis and spectral characterisation of the compounds are included at the end of each Chapter, with details of chiral stationary phase HPLC analysis and assignment of absolute stereochemistry included in the appendix.

Design and Synthesis of 4-N-Alkanoyl and 4-N-Alkyl Gemcitabine Analogues Suitable for Positron Emission Tomography

Gemcitabine is a highly potent chemotherapeutic nucleoside agent used in the treatment of several cancers and solid tumors. However, it is therapeutically limitated because of toxicity to normal cells and its rapid intracellular deamination by cytidine deaminase into the inactive uracil derivative. Modification at the 4-(N) position of gemcitabine's exocyclic amine to an -amide functionality is a well reported prodrug strategy which has been that confers a resistance to intracellular deamination while also altering pharmacokinetics of the parent drug. Coupling of gemcitabine to carboxylic acids with varying terminal moieties afforded the 4-N-alkanoylgemcitabines whereas reaction of 4-N-tosylgemcitabine with the corresponding alkyl amines gave the 4-N-alkylgemcitabines. The 4-N-alkanoyl and 4-N-alkyl gemcitabine analogues with a terminal hydroxyl group on the 4-N-alkanoyl or 4-N-alkyl chain were efficiently fluorinated either with diethylaminosulfur trifluoride or under conditions that are compatible with the synthetic protocols for 18F labeling, such as displacement of the corresponding mesylate with KF/Kryptofix 2.2.2. The 4-N-alkanoylgemcitabine analogues displayed potent cytostatic activities against murine and human tumor cell lines with 50% inhibitory concentration (IC50) values in the range of low nM, whereas cytotoxicity of the 4-N-alkylgemcitabine derivatives were in the low to modest µM range. The cytostatic activity of the 4-N-alkanoylgemcitabines was reduced by several orders of magnitude in the 2'-deoxycytidine kinase (dCK)-deficient CEM/dCK- cell line while the 4-N-alkylgemcitabines were only lowered by 2-5 times. None of the 4-N-modified gemcitabines were found to be substrates for cytosolic dCK, however all were found to inhibit DNA synthesis. As such, the 4-N-alkanoyl gemcitabine derivatives likely need to be converted to gemcitabine prior to achieving their significant cytostatic potential, whereas the 4-N-alkylgemcitabines reach their modest activity without "measurable" conversion to gemcitabine. Thus, the 4-N-alkylgemcitabines provide valuable insight on the metabolism of 4-N-modified gemcitabine prodrugs.

THE DESIGN AND SYNTHESIS OF SILOXANE PRECURSORS FOR CHIRAL PERIODIC MESOPOROUS ORGANOSILICA MATERIALS

The development of cost-effective and reliable methods for the synthesis and separation of asymmetric compounds is paramount in helping to meet society’s ever-growing demand for chiral small molecules. Of these methods, chiral heterogeneous supports are particularly appealing as they allow for the reuse of the chiral source. One such support, based on the synergy between chiral organic units and structurally stable inorganic silicon scaffolds are periodic mesoporous organosilicas (PMOs). In the work described herein, I examine some of the factors governing the transmission of chirality between chiral dopants and prochiral bulk phases in chiral PMO materials. In particular, the exploration of 1,1’-binaphthalene-bridged chiral dopants with a focus on the point of attachment into the materials. Moreover, the effects of ordering in the materials are examined and reveal that chirality transfer is more facile in materials with molecular-scale order then those containing amorphous walls. Secondly, the issues surrounding the synthesis and purification of aryl-triethoxysilanes as siloxane precursors are addressed. Both the introduction of a two-carbon linker and the direct attachment of allyl and mixed allyldiethoxysilane species are explored. This work demonstrates that allyldiethoxysilanes are ideal, in that they are stable enough to permit facile synthesis, while still being able to hydrolyze completely to produce well-ordered materials. Lastly, the production of new bulk phases for chiral PMO materials is examined by introducing new prochiral nitrogen-containing siloxane precursors. Biphenyldiamine and bipyridine-bridged siloxane precursors are readily synthesized on reasonable scales. Their use as the bulk siloxane precursor in the production of PMO materials however, is precluded by insufficient gelation and additional siloxane precursors are necessary for the production of ordered materials. In addition to the research detailed above that forms the body of this thesis, two short works are appended. The first details the production of polythiophene assemblies mediated through coordination nanospaces, while the second explores the production of N-heterocyclic carbene functionalized gold nanoparticles through ligand exchange.

Design and Implementation of Tools for STM Studies in UHV and at the Solid-Liquid Interface

This thesis presents details of the design and development of novel tools and instruments for scanning tunneling microscopy (STM), and may be considered as a repository for several years' worth of development work. The author presents design goals and implementations for two microscopes. First, a novel Pan-type STM was built that could be operated in an ambient environment as a liquid-phase STM. Unique features of this microscope include a unibody frame, for increased microscope rigidity, a novel slider component with large Z-range, a unique wiring scheme and damping mechanism, and a removable liquid cell. The microscope exhibits a high level of mechanical isolation at the tunnel junction, and operates excellently as an ambient tool. Experiments in liquid are on-going. Simultaneously, the author worked on designs for a novel low temperature, ultra-high vacuum (LT-UHV) instrument, and these are presented as well. A novel stick-slip vertical coarse approach motor was designed and built. To gauge the performance of the motor, an in situ motion sensing apparatus was implemented, which could measure the step size of the motor to high precision. A new driving circuit for stick-slip inertial motors is also presented, that o ffers improved performance over our previous driving circuit, at a fraction of the cost. The circuit was shown to increase step size performance by 25%. Finally, a horizontal sample stage was implemented in this microscope. The build of this UHV instrument is currently being fi nalized. In conjunction with the above design projects, the author was involved in a collaborative project characterizing N-heterocyclic carbene (NHC) self-assembled monolayers (SAMs) on Au(111) films. STM was used to characterize Au substrate quality, for both commercial substrates and those manufactured via a unique atomic layer deposition (ALD) process by collaborators. Ambient and UHV STM was then also used to characterize the NHC/Au(111) films themselves, and several key properties of these films are discussed. During this study, the author discovered an unexpected surface contaminant, and details of this are also presented. Finally, two models are presented for the nature of the NHC-Au(111) surface interaction based on the observed film properties, and some preliminary theoretical work by collaborators is presented.

Novel Synthesis of Carbocycles and Heterocycles Employing Zwitterions Derived from Allenic Esters

Carbon-carbon and carbon-heteroatom bond formations constitute the central events in organic synthesis. In view of this, much of the research in organic synthesis has been focused on devising novel and efficient methods for such bond constructions. In general, polar, pericyclic and radical methodologies are employed for this purpose. The polar and radical reactions proceed via reactive intermediates such as carbanions, enols/enolates, enamines, carbocations, radical cations, radical anions, carbenes, zwitterions etc. In recent years, there has been enormous interest in the chemistry of zwitterionic species largely from the standpoint of their applications in multicomponent reactions (MCRs) and organocatalytic reactions. Zwitterions formed by the addition of nucleophiles to electrophilic π-systems such as acetylenic esters and azoesters have been the subject of extensive investigations; their synthetic utility, however, remained largely unexplored. Investigations in a number of laboratories, including our own, have shown that zwitterions of the type mentioned above on reaction with electrophiles give rise to carbo- and heterocyclic products by 1,3- or 1,4-dipolar cycloadditions. Recently, allenoates, another class of active π-systems were introduced to this field. Against this background, a systematic investigation of the reactions of various zwitterions derived from allenoates with different electrophiles especially 1,2-diones, were carried out. The results of these studies are embodied in the thesis entitled “Novel Synthesis of Carbocycles and Heterocycles Employing Zwitterions Derived from Allenic Esters”.

Nucleophilic addition of Nitrones to Electron deficient acetylenes and related studies

Nitrones or azomethine-N-oxides are important precursors for the synthesis of several heterocyclic systems. They belong to the allyl anion type 1,3-dipoles and possess unique structural features which make them extraordinarily useful synthons. They behave as 1,3-dipoles in 1,3-dipolar cycloaddition reactions and as electrophiles in reactions with organometallic reagents. These are the two basic reactions given by nitrones. Nitrones also act as ‘spin traps’ in which they react with short-lived radicals to furnish stable nitroxide radicals which can be detected and identified by electron paramagnetic resonance (EPR) spectroscopy. Recently SmI2 catalysed reductive cross-coupling reactions of nitrones have gained significant interest in which the reactions are initiated by single electron transfer (SET) to nitrones. Apart from these reactions, nitrones are also known to participate in reactions which are initiated by the nucleophilic attack of nitrone-oxygen. In our group, we have also explored the nucleophilic character of nitrones through various reactions. The results obtained enabled us to develop a novel two-step one-pot strategy for quinolines and indoles - the heterocycles renowned for their pharmacological applications, from nitrones and electron deficient acetylenes. Using dibenzoylacetylene and phenylbenzoylacetylene as dipolarophiles, we could introduce a desired functional group at a predetermined position of the quinolines or indoles to be synthesised. In this context, the thesis entitled “NUCLEOPHILIC ADDITION OF NITRONES TO ELECTRON DEFICIENT ACETYLENES AND RELATED STUDIES” portrays our attempt to expand the scope of our x novel synthetic protocol using ester functionalised acetylenes: dimethyl acetylenedicarboxylate (DMAD) and methyl propiolate. The thesis is organised in to five chapters. The first chapter briefly describes the different classes of reactions that nitrone functionality can tolerate. The research problem is defined at the end of this chapter. The second chapter describes the synthesis of different nitrones used for the present study. The optimisation and expansion of scope of the novel strategy towards quinoline synthesis is discussed in the third chapter. The fourth chapter portrays the synthesis of indole-3-carboxylates using the novel strategy. In the fifth chapter, the reaction of N-(2,6-dimethylphenyl) and N-(2,4,6-trimethylphenyl)nitrones are discussed. Here we also discuss the mechanistic reinvestigation of Baldwin’s proposal in the isoxazoline-oxazoline rearrangement. The major outcome of the work is given at the end of the thesis. The structural formulae, schemes, tables and figures are numbered chapter-wise since each chapter of the thesis is organized as an independent unit. All new compounds (except two compounds reported in fourth chapter) are fully characterised on the basis of spectral and analytical data and single crystal X-ray analysis on representative examples. Relevant references are included at the end of individual chapters.

Transition metal complexes of some N4-phenylsemicarbazones: crystal structures and spectral studies

The work embodied in this thesis was carried out by the author in the Department of Applied Chemistry, CUSAT, Kochi, during the period 2009-2012. The thesis is an introduction to our attempts to evaluate the coordination behavior of some compounds of our interest. The biological activities of semicarbazones and their metal complexes have been an active area of research during the past years because of their significant role in naturally occurring biological systems. Tridentate NNO and ONO semicarbazone systems formed from heterocyclic and aromatic carbonyl compounds and their transition metal complexes are wellauthenticated compounds in this field and their synthesis, crystal structures and spectral studies are well desirable. Hence, we decided to develop a research program aimed at the syntheses, crystal structures and spectral studies of new N4- phenylsemicarbazones derived from 2-formylpyridine and 3-ethoxysalicylaldehyde and their transition metal complexes and new transition metal complexes of 2- benzoylpyridine-N4-phenylsemicarbazone. In addition to various physicochemical methods of analysis, single crystal X-ray diffraction studies were also used for the characterization of the complexes.

Sintesi e Caratterizzazione di Elettrodi Modificati Chimicamente con nuovi complessi Carbenici del Ferro

The Chemically Modified Electrodes (CME) are widely used in electroanalytical chemistry as chemical sensors. The interest in the covalent anchoring of a redox mediator on the electrode surface is increasing, because it allows the sensibility and the selectivity of this kind of systems to improve. My work is situated in this field of research and involves the synthesis of new Iron(0) complexes that contain cyclopentadienone, N-heterocyclic carbene (NHC) and carbonyl ancillary ligands. These complexes have shown electrochemical properties similar to those of ferrocene (organometallic compound widely used as electrochemical sensor). These complexes have been properly functionalized with a EDOT group in the NHC ligand side chain that it was after used for the realization of Electrochemically Modified PEDOT thanks to copolymerization reaction between the functionalized complex and the EDOT in different amounts. All the synthetic steps were assisted by suitable characterizations (NMR, IR, ESI-MS, cyclic voltammetry and X-ray for the monomeric compound as imidazolium salt and NHC functionalized complexes; cyclic voltammetry, IR e SEM for the copolymers). The properties of the polymer as a selective sensor was preliminarily investigated for dopamine and 2-propanol.

New 9-Terpenyl(7-Terpenyl)Purines: synthesis and cytotoxicity

The purine ring system is one of the most widely distributed N-heterocycles in Nature [1] and many structurally modified purine nucleosides and nucleotides have activities ranging from antineoplastic and antiviral to antihypertensive, antiasthmatic, antituberculosis, etc [2]. Among the purine derivatives, we have put our attention on natural N-alkylpurines such as the asmarines or agelasimines, a group of secondary metabolites isolated from marine sponges with very interesting biological properties [3]. They have a diterpenoid moiety attached to the N-7 nitrogen atom of an adenine and are usually isolated in very small quantities, which limited their structure-activity relationship studies. Our research group has been involved for years in the design, synthesis and biological evaluation of cytotoxic compounds related to natural products, including the chemoinduction of bioactivity on inactive terpenoids [4]. These diterpenoid include compounds such as communic or cupressic acids that bear decaline moieties very close to those present in the above-mentioned marine natural products. These facts prompted us to design and prepare new terpenylpurine derivatives starting from natural monoterpenoids and diterpenoids, commercially available or isolated from their natural sources and transformed into appropriate alkylated agents. Thus, we have prepared purines alkylated at N-7 and N-9 positions with isoprenoids, monoterpenoids and diterpenoids, using two different synthetic approaches: from 6-chloropurine or from 4,5-diamine-6-chloropyrimidine. The structure of the synthesized purines are shown in the following figure. The purine analogues synthesized have been evaluated for their cytotoxicity against four tumour human cell lines (breast, non-small lung, cervical and hepatocellular carcinoma) and non-tumour cells (porcine liver primary cells). The most cytotoxic derivatives were those with a diterpenoid rest on the purine. The results obtained allowed to draw conclusions on the structure-activity relationship of the compounds in order to evaluate the influence of the terpenyl size on their cytotoxic properties.

Applications of Photoinduced Electron Transfer Chemistry: Photoremovable Protecting Groups and Carbon Dioxide Conversion

Traditional organic chemistry has long been dominated by ground state thermal reactions. The alternative to this is excited state chemistry, which uses light to drive chemical transformations. There is considerable interest in using this clean renewable energy source due to concerns surrounding the combustion byproducts associated with the consumption of fossil fuels. The work presented in this text will focus on the use of light (both ultraviolet and visible) for the following quantitative chemical transformations: (1) the release of compounds containing carboxylic acid and alcohol functional groups and (2) the conversion of carbon dioxide into other useable chemicals. Chapters 1-3 will introduce and explore the use of photoremovable protecting groups (PPGs) for the spatiotemporal control of molecular concentrations. Two new PPGs are discussed, the 2,2,2-tribromoethoxy group for the protection of carboxylic acids and the 9-phenyl-9-tritylone group for the protection of alcohols. Fundamental interest in the factors that affect C–X bond breaking has driven the work presented in this text for the release of carboxylic acid substrates. Product analysis from the UV photolysis of 2,2,2-tribromoethyl-(2′-phenylacetate) in various solvents results in the formation of H–atom abstraction products as well as the release of phenylacetic acid. The deprotection of alcohols is realized through the use of UV or visible light photolysis of 9-phenyl-9-tritylone ethers. Central to this study is the use of photoinduced electron transfer chemistry for the generation of ion diradicals capable of undergoing bond-breaking chemistry leading to the release of the alcohol substrates. Chapters 4 and 5 will explore the use of N-heterocyclic carbenes (NHCs) as a catalyst for the photochemical reduction of carbon dioxide. Previous experiments have demonstrated that NHCs can add to CO2 to form stable zwitterionic species known as N-heterocylic-2-carboxylates (NHC–CO2). Work presented in this text illustrate that the stability of these species is highly dependent on solvent polarity, consistent with a lengthening of the imidazolium to carbon dioxide bond (CNHC–CCO2). Furthermore, these adducts interact with excited state electron donors resulting in the generation of ion diradicals capable of converting carbon dioxide into formic acid.