Treatment of dichloromaleic anhydride and 1,8-diaminonaphthalene in either benzene or toluene under refluxing conditions gives low yields of the new heterocyclic compound 8,9-dichloropyrrolo[1,2-a]perimidin-10-one. This product has been isolated and characterized in solution by NMR, IR, and UV/vis spectroscopies, and the solid-state structure of 8,9-dichloropyrrolo[1,2-a]perimidin-10-one has been established by X-ray crystallography. The nature of the HOMO and LUMO levels of 8,9-dichloropyrrolo[1,2-a]perimidin-10-one has been studied by extended Hückel molecular orbital calculations.

<strong>Introduction</strong> The introduction describes the importance of arylamine compounds to society and provides a brief overview of the methods available for their synthesis. The application of metathesis catalysis to the de novo synthesis of heteroaromatic compounds is also described. <strong>Results and discussion</strong> The first section describes efforts towards the de novo synthesis of arylamines using a cross metathesis/oxidation protocol to form a 1,5-unsaturated dicarbonyl followed by an amine mediated cyclisation. The scope with respect to the 1,5-unsaturated dicarbonyl and amine is covered as well as the utility of some of the products. The section concludes with a modification of the Bohlmann Rahtz pyridine synthesis to furnish arylamines. The next section describes the applications of our methodology to the synthesis of naphthylamines, specifically using the palladium catalysed &alpha;-arylation reaction. A discussion of the α-arylation reaction is included as well as our efforts to explore the scope of the reaction. The third section follows our efforts to apply this methodologyy to the synthesis of five benzo[c]phenanthridine alkaloids including the first reported synthesis of maclekarpine B and C. The final section concludes with a discussion of our efforts towards the de novo synthesis of furans bearing a benzylic stereocentre.

Bioinorganic chemistry strives to understand the roles of metals in biological systems, whether in the form of naturally occurring or addition of non-essential metals to natural systems. Metal ions play vital roles in many cellular functions such as gene expression/regulation and DNA transcription and repair. The study of metal-protein-DNA/RNA interactions has been relatively unexplored. It is important to understand the role of metalloprotein interactions with DNA/RNA as this enhanced knowledge may lead to better understanding of diseases and therefore more effective treatments. A major milestone in the development of this field was the discovery of the cytotoxic properties of cisplatin in 1965 and its FDA approval in 1978. Since then, two other chemotherapeutic drugs containing platinum, carboplatin and oxaliplatin, have been used in the clinic. These three compounds are all bifunctional with the ligands surrounding platinum In the cis conformation and rearrangement of the ligands to the trans orientation results in a loss of cytotoxic properties due to rapid deactivation through binding to S-containing proteins. This enhanced reactivity yields new opportunities to study the reactions between proteins and DNA. One of the first crosslinking experiments used transplatin to crosslink NCp7 to viral RNA in order to understand how/where the protein bound to RNA. We have studied the interaction between cis and trans dinuclear platinum complexes and the C-terminal zinc finger (ZF). The trans complex reacts at a faster rate than the cis isomer and causes N- terminal specific cleavage of the ZF. The dinuclear structure plays a critical role in the peptide cleavage as studies with transplatin (the mononuclear derivative) does not result in cleavage. Monofunctional trans platinum-nucleobase complexes (MPNs) serve as a model for the binding of transplatin to DNA. This provides an interesting opportunity to study their reactions with S-containing proteins, such as HIV1 NCp7. MPNs have been shown to bind to the C-terminal ZF of HIV1 NCp7, resulting in zinc ejection. This occurs through a two-step process where the nucleobase π-stacks with Trp37 on the ZF, followed by covalent binding at the labile Cl site to Cys. MPNs have also shown antiviral activity in vitro. The labile Cl on MPNs reduces specificity of these compounds, as it leaves an available coordination site on the platinum center for binding to other S-proteins or DNA. Therefore, we have moved to an inert PtN4 coordination sphere, [Pt(dien)L]2+ (dien= diethylenetri- amine). Due to the strong bond between platinum and nitrogen, covalent reactions are highly unlikely to occur at rapid rates. The strength of the pi-stacking interaction between nucleobases (free and platinated) and the aromatic amino acid, tryptophan (Trp), showed an enhanced binding constant for platinated nucleobases. This was confirmed by density functional theory (DFT) calculations as the difference in energy between the HOMO of Trp and the LUMO of the nucleobase was smaller for the platinum complex. The studies were extended to the Trp-containing C-terminal ZF of HIV1 NCp7 and an increase in association constant was seen compared to free Trp. Reaction of PtN4 nucleobases compounds with a short amino acid sequence con- taining either Ala (no pi-stacking capabilities) or Trp (pi-stacking interactions) revealed an enhanced rate of reactivity for the Trp-containing peptide. This result supports the theory of a two-step reaction mechanism where the platinum-nucleobase complex recognizes the pep- tide through a pi-stacking interaction with Trp followed by covalent binding to the platinum center. The [Pt(dien)L]2+ motif allows for systematic modification of the structural elements surrounding platinum in a search for the most effective compound. Methylation of the dien ligand should, in theory, increase lipophilicity of the compounds, however, due to 2+ charge of the compounds, this simple association does not hold true. Analysis of the cellular accumulation profiles showed little change in the uptake with the addition of methyl groups to the dien ligand, in agreement with the non-linear change in lipophilicity. Modification of L using different nucleobases allows for the tuning of the strength of the π-stacking interaction between Trp and the platinum complex. The addition of inosine (which lacks a H-bonding donor/acceptor at the C2 position) resulted in a lower association constant with both N-AcTrp and the C-terminal zinc finger of HIV1 NCp7. Interestingly, the addition of xanthosine resulted in an ehanced pi-stacking interaction with the C-terminal zinc finger of HIV1 NCp7; likely as a results of the addition of a H-bonding donor (double-bonded O) at the C2 position. The ability of PtN4 nucleobase complexes to inhibit formation of the NCp7 complexation with viral RNA was studied by mass spectrometry and gel electrophoresis. Dissociation of the NCp7-RNA complex was seen upon addition of PtN4 compounds. These compounds were also able to retard formation of the NCp7-RNA complex when pre-incubated with the protein. These results have important implications as inhibition of complex formation between NCp7 and viral RNA has negative implications for viral replication. Despite the success of platinum-nucleobase compounds, it is important to evaluate all potential pi-stacking ligands. A series of pyridine- and thiazole-based compounds were evaluated for the strength of the pi-stacking interaction with N-AcTrp and the C-terminal ZF of HIV1 NCp7. There was notable increase in association constant for the platinum- DMAP (4-dimethylaminopyridine) complex compared to other ligands studied. This result highlights the importance of exploring multiple avenues for the design of specifically targeted inhibitors and further confirms the viability of the medicinal chemistry dual approach of target recognition (non-covalent) followed by target fixation (covalent).

O aumento do conhecimento sobre os mecanismos macromoleculares de diversas doenças tem permitido a identificação de vários alvos terapêuticos, porém o desenvolvimento de fármacos para esses alvos não seguiu na mesma velocidade. Além disso, a presença de padrões estruturais inovadores nesses fármacos é baixa. Neste cenário, buscamos, ao mapear o espaço químico medicinal de compostos heteroaromáticos, introduzir novos fragmentos úteis no desenvolvimento de compostos bioativos inovadores. Para tanto, duas abordagens foram avaliadas: 1) Estudo da viabilidade de síntese de dois núcleos heteroaromáticos sem síntese descrita na literatura. 2) Estudo de uma nova rota sintética para obtenção do núcleo furo[2,3-b]piridina, bem como a viabilidade de sua funcionalização e aplicação no desenvolvimento de compostos com atividade antituberculose. Em relação a primeira abordagem (Capítulo 1), para o núcleo 22 (piridazina-piridona) foi possível explorar uma rota sintética que, embora, ainda não tenha sido possível obter o composto desejado, o mesmo necessita apenas de uma etapa de aromatização para ser obtido. Já para o núcleo 20 (pirido-piridazinona), após o estudo de diversas estratégias sintéticas, foi possível obtê-lo, em baixos rendimentos, e, portanto, a otimização da rota sintética, bem como a completa caracterização dele, ainda serão necessários. Durante a exploração das diversas estratégias para a síntese do núcleo 20, foi possível, a partir de resultado inesperado em uma delas, verificar uma nova rota sintética para compostos furo[2-3-b]piridina substituídos nas posições C-2 e C-3, o que foi objeto de estudo da segunda abordagem descrita nesta tese (Capítulo 2). Utilizando condições brandas e livre de metais, foi possível obter diversas furanopiridinas com diferentes substituições em C-2 (arílico ou alquílico), utilizando diversos cloretos de ácidos ou anidridos. Além disso, foi verificado que o anel furânico do núcleo furanopiridínico é estável na reação de hidrólise do éster em C-3, porém quando na presença de hidrazina é formado um novo padrão estrutural com anel pirazolona, proveniente da abertura do anel furano. Em relação a reatividade química da porção piridínica desse núcleo, em reações de ativação da ligação C-H, foi possível realizar a borilação seguida de acoplamento cruzado de Suzuki na posição C-5. Já arilação radicalar ocorreu em C-4 e a fluorinação direta em C-6. Porém, os rendimentos destas reações não foram satisfatórios. Com isso, foi avaliado a reatividade do derivado N-óxido da furanopiridina com diferentes agentes ativantes e nucleófilos. Com o uso de anidrido tríflico como agente ativante, foi possível a iodação em C-5, bromação em C-4 e hidroxilação em C-4 e C-6. Já utilizando PyBroP, como ativante, foi possível realizar reações de aminação nas posições C-4, C-5 e C-6. Esses compostos tiveram a atividade biológica contra Mycobacterium tuberculosis avaliada, onde um dos compostos apresentou atividade promissora, tanto contra cepas laboratoriais, quanto cepas de isolados clínicos multirresistentes. Além disso, esse composto apresentou alto índice de seletividade, e por ser um fragmento, permitirá futuras otimização estruturais. / The increasing knowledge about the macromolecular mechanisms of different diseases allowed the identification of several therapeutic targets over the years. However, the development of drugs to these targets did not follow the same rate. In addition, the introduction of innovative frameworks in new drugs is unsatisfactory. In this scenario, we aim to introduce new useful fragments for application in the development of innovative bioactive compounds, by charting the medicinal chemical space of heteroaromatic compounds. For this purpose, two approaches were evaluated: 1) Develop a feasible synthetic strategy to obtain two new heteroaromatic cores (Cores 20 and 22); 2) Develop a new synthetic route to obtain the furo[2,3-b]pyridine core, chemical elaborate it and screening it against Mycobacterium tuberculosis. For the first approach (Chapter 1), one aromatization step is needed to obtain core 22 (pyridazine-pyridone). On the other hand, after evaluating several synthetic strategies, it was possible to obtain core 20 (pyrido-pyridazinone) in low yields. Therefore, a synthetic route optimization and a complete characterization are still required for 20. An unexpected result in attempt to obtain core 20, resulted in a new synthetic route to furo[2-3-b]pyridine, C-2 and C- 3 substituted, that was explored in the second approach (Chapter 2). Using mild and metal-free conditions, it was possible to obtain various furopyridines with different substitutions patterns at C-2 (aryl or alkyl) using either acyl chlorides or anhydrides. In addition, the furan moiety in this core, showed to be stable under the C-3-ester hydrolysis, however, in solution, hydrazine opens the furan ring to form a new pyrazolone ring. Regarding the chemical reactivity of the pyridine moiety in the furopyridine core, it was possible to perform the C-H borylation followed by Suzuki coupling reaction at the C-5 position. Furthermore, radical arylation at C-4 and direct fluorination at C-6 had not satisfactory yields. Therefore, the reactivity of the furopyridine N-oxide derivative with nucleophiles using different activating agents was studied. Using triflic anhydride, as an activating agent, it was possible to iodinate at C-5, brominated at C-4 and hydroxylated at C-4 and C-6. Using PyBroP, as an activator, it was possible to perform amination reactions at positions C-4, C-5 and C-6. In the end, our in-house library of furopyridines was screened against Mycobacterium tuberculosis and it was found a promising selective bioactive compound against different multidrug-resistant strains of this mycobacteria. Furthermore, this compound is a fragment, which will allow future structural optimization.

Neste trabalho promovemos a síntese de sulfóxidos vinílicos ?-substituídos através da reação de acoplamento cruzado de Suzuki-Miyaura. Também foi feita a síntese de sulfóxidos enínicos inéditos, pela adição do nucleófilo no carbono &#946;-sulfóxido. Esses compostos eram passíveis de serem submetidos a reação de rearranjo de Pummerer aditivo e assim gerarem uma pequena biblioteca de compostos &#945;-tioaldeídos. Um desses aldeídos sintetizados foi empregado na reação de formação de uma imina propargílica, com consequente reação de CuAAC formando iminas triazólicas. Outras iminas arílicas foram sintetizadas, passando por uma etapa de redução, com intuito de se obter a amina livre, para que fosse feita a reação de ciclização com auxílio de um agente eletrofílico. Outra classe de composto organoenxofre foi sintetizada, as N-sulfinil imina, que após a reação de acoplamento cruzado de Sonogashira, com consequente remoção de um grupo protetor e a formação do anel heterocíclico, foram obtidos compostos triazólicos N-sulfinil imínicos. / In this work we promote the synthesis of &#945;-substituted vinylic sulfoxides through the Suzuki-Miyaura cross coupling reaction. Also the synthesis of unpublished enynic sulfoxides was made, by the addition of the nucleophile in the &#946;-sulfoxide carbon. These compounds were susceptible to additive Pummerer rearragement reaction and thus generated a small library of compounds. One of these aldehydes synthesized was used in the formation reaction of a propargyl imine, with consequent CuAAC reaction, forming triazol imines. Other aryl imines were synthesized, undergoing a reduction step, in order to obtain the free amine, so that the cyclization reaction was carried out with the aid of an electrophilic agent. Another class of organosulfur compound was synthesized, the N-sulfinyl imine, which after the Sonogashira cross-coupling reaction, with consequent removal of a protecting group and formation of the heterocyclic ring, N-sulfinyl imine triazolic compounds were obtained.

Carbocyanine dyes are organic compounds containing chains of conjugated methine groups with electron-donating and electron-withdrawing substituents at the terminal heterocycles of the general formula [R1-(CH)n-R2]+X-. The synthetic methodology and optical properties of carbocyanines will be discussed. This thesis consists of two parts: (A) synthesis and optical properties of novel carbocyanine dyes substituted with various amines and the synthesis of unsymmetrical carbocyanine dyes containing monofunctional groups for bioconjugation. (B) synthesis of heptamethine carbocyanine dyes to be used for image-guided surgery. In part A, the synthesis of carbocyanine dyes functionalized with various amines and studies of their optical properties with respect to absorbance, fluorescence, quantum yield and extinction coefficient will be presented. These property studies will aid in designing efficient dyes for future biomedical applications. Part A will also include a one pot synthesis of unsymmetrical carbocyanine dyes functionalized with mono carboxylic acid chains, useful for biomolecule (i.e. proteins, amino acids, etc.) conjugation. Part B will describe the synthesis of novel carbocyanine dyes to be used for cancer image-guided surgery. Cancers are thus far incurable diseases, i.e. there are no drugs currently available to cure cancer; however, by designing a dye to visualize tumor cells will greatly increase the efficiency of cancer removal and hopefully increase the survival rate of cancer patients. The dyes reported in this thesis are superior to commercially available dyes used to visualize and identify various tumors invisible to the naked eye of surgeons with regards to biodistribution and clearance through kidney filtration.

The last decade has been marked by a large increase of demand for green chemistry processes. Consequently, chemists have focused their efforts on the development of more direct routes toward different classes of targets. In that regard catalysis has played a crucial role at enabling key bond formations that were otherwise inaccessible or very energy and resources consuming. The central theme of this body of work concerns the formation of C–N bonds, either through transition metal catalysis or organocatalysis. These structural units being highly recurrent in biologically active molecules, the establishment of more efficient routes for their construction is indispensable. The first part of this thesis describes a new method for the synthesis of isoquinolines from the oxidative coupling/annulation of alkynes with N-tert-butyl benzaldimines via Rh(III) catalysis (Chapter 2). Preliminary mechanistic investigations of this system pointed to the involvement of Rh(III) in the C–H bond cleavage step as well as in the C–N bond reductive elimination that provides the desired heterocycle. Following this oxidative process, a Rh(III)-catalyzed redox-neutral approach to isoquinolones from the reaction of benzhydroxamic acids with alkynes is presented (Chapter 3). The discovery that an N–O bond contained in the substrate can act as an internal oxidant was found to be very enabling. Indeed, it allowed for milder reaction conditions, broader scope (terminal alkyne and alkene compatible) and low catalyst loadings (0.5 mol%). Mechanistic investigations on this system were also conducted to identify the nature of the C–N bond formation/N–O bond cleavage as well as the rate-determining step. The second part of this work presents mechanistic investigations performed on a recently developed intermolecular hydroamination reaction catalyzed through tethering organocatalysis (Chapter 4). This transformation operates via the reversible covalent attachment of two reactants, a hydroxylamine and an allylamine, to an aldehyde catalyst by the formation of a mixed aminal. This allows a difficult intermolecular Cope-type hydroamination to be performed intramolecularly. The main kinetic parameters associated with this reaction were determined and they allowed the generation of a more accurate catalytic cycle for this transformation. Attempts at developing new families of organocatalysts are also discussed.

The synthesis of 2,4-disubstituted pyrimidine derivatives is described. The synthetic route involved the addition reaction of lithiated intermediates, mostly heterocycles, to position 4 of 2-chloropyrimidine to give a dihydropyrimidine intermediate which was oxidized back to a pyrimidine. This was followed by nucleophilic aromatic substitution with various amines of the chlorine in the position 2. A number of compounds were prepared which showed binding towards various serotonin receptors in preliminary biological evaluation.

Microbe resistence is a serious issue, especially as they have become resistant to most well known drugs. Therefore this is considered as a global problem and is now dealt with at a poitical level. Since no new classes of antimicrobial agents have been discovered in the past three deacdes, the development of new drugs is extremely urgent. Therefore the aim of this project was to synthesise derivatives of benzimidazole, and then assesses their antimicrobial activities in vitro by using disc (well) diffusion and MICs tests. A total of 69 benzimidazole derivatives, with substituents at positions 1, 2, and 5, were synthesised, characterised and tested against selected bacteria and fungi. In addition, six bezimidazole silver complexes were prepared and evaluated for their antimicrobial behavior. The SAR showed that the antimicrobial activity of the compounds depended on the substituents attached to the bicyclic heterocycle. Some promising results were obtained. In particular, 5 compounds displayed antibacterial activity against two MRSA strains with MIC values corresponding to ciprofloxacin, which can be considered significant. The compounds have some common features; four possess 5-chloro or 5-bromo substituents; two are derivatives of (S)-2- ethanaminebenzimidazole and the others are derivative of one 2-(chloromethyl)-1Hbenzo[d]imidazole, (1H-benzo[d]imidazol-2-yl)methanethiol and 2-(methoxymethyl)-1-methyl-1H-benzo[d]imidazole. The results from the antifungal screening were very interesting as there were 26 compounds, including two silver complexes, which were potent fungicides against the selected fungal species. They showed equivalent or greater potentency in their MIC values than amphotericin B. In particular, the 5-fluoro, 5-chloro and 5-bromo benzimidazole showed broad spectrum activity.

This thesis is divided into four chapters that describe the new development in rhodium-catalyzed addition reactions and asymmetric ring opening (ARO) reactions of strained alkenes. Chapter 1 describes a regioselective Rh(I)-catalyzed addition reaction of arylboronic acids to unactivated alkenes - protected allylic amines and allyl sulfones. These formal hydroarylation processes have significantly advanced the substrate scope. Comprehensive studies were carried out to optimize the reaction conditions and a wide range of arylboronic acids were employed. The reaction was found to be linear-selective and a mechanism based on functional group- directing effects has been proposed. Chapter 2 discloses the discovery of Rh(I)-catalyzed addition of arylboronic acids to (benzyl- /arylsulfonyl)acetonitriles. Novel β-sulfonylvinylamine products were formed in a stereoselective fashion (Z-alkene). Upon hydrolysis, β-keto sulfones were obtained with a broad scope of aryl and sulfonyl substituents. These (Z)-β-sulfonylvinylamines were useful synthons in the synthesis of unsymmetrical polysubstituted pyridines via 1-aza-allyl anion intermediates as well as 1,4- benzothiazine derivatives via intramolecular cyclization. Chapter 3 reports the use of two new nucleophiles in Rh(I)-catalyzed ARO of oxabicyclic alkenes - water and triethylamine trihydrofluoride. In the water-induced ARO, an unprecedented domino ARO/isomerization process was discovered which led to the formation of 2-hydroxy-1- tetralones. By modifying the reaction conditions, trans-1,2-diols can be obtained in excellent enantioselectivity. Using triethylamine trihydrofluoride as a nucleophile, an aliphatic C-F bond was constructed enantioselectively in the ring-opening process which provided fluorinated building blocks containing both allylic fluoride and fluorohydrin units. Finally, Chapter 4 details the development of a one-pot synthesis of a chiral dihydrobenzofuran framework using Rh-catalyzed asymmetric ring opening and Pd-catalyzed C-O coupling. The product can be obtained in excellent enantioselectivity without isolation of intermediates. Systematic metal-ligand studies were carried out to investigate the compatibility of each catalytic system using product enantiopurity as an indicator.