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I. Efforts Toward the Synthesis of (–)-Tetracycline. A macrocyclic approach toward (–)-tetracycline is described. Traditional approaches towards the synthesis of tetracycline antibiotics employ the linear construction of the core structure starting with either the A- or D-rings. In contrast to this iterative annulation-based strategy, we have sought to employ a chiral macrocycle in our approach. Key to the success of our synthesis endeavor is the execution of two key steps: (1) a transannular Michael addition, which forms the A-ring and sets the C4a-stereogenic center; and (2) an isoxazole substitution reaction, which effects a ring contraction to produce both the B- and C-rings. This work describes our implementation of the strategy and focuses on the stereochemical interplay between the C4-, C4a-, C6-, and C12a-stereocenters within the context of the key steps. II. Analysis of the Peripheral Attack Model. The application of the peripheral attack model to 34 literature examples of intermolecular macrocyclic stereocontrol is described. While the peripheral attack model has been broadly applied in complex molecule synthesis, the validity of the model has not been subjected to analysis since being proposed in the early 1980’s. In order to assess the value of the model to organic chemists, we have developed a systematic method for probing the conformational profile of macrocycles. Using this tool, we then analyzed each of the 34 literature substrates and concluded whether the peripheral attack model predicts the correct stereochemical outcome in both a binary- and magnitude-based capacity. Analysis of both the bulk dataset and subsets of the dataset is included. / Chemistry and Chemical Biology

Norzoanthamine is a complex heptacyclic marine alkaloid isolated from colonial zoanthids. It potently inhibits loss of bone weight and strength in a postmenopausal osteoporosis mouse model, but its mode-of-action remains unknown. The scarcity of this natural product from its natural source and the need to access analogs for structure-activity relationship (SAR) study make it necessary to chemically synthesize this compound. However, the complex molecular skeleton, especially the highly functionalized and stereochemically complex ABC core structure of the natural product poses a significant challenge. As part of our efforts to develop a practical synthetic route to norzoanthamine, we systematically explored a transannular Michael reaction cascade in the context of the synthesis of angular 6-6-6 tricyclic ring system, a mimic of the ABC core structure of norzoanthamine. Using 1,7-bis-enones in the form of 14-membered macrocyclic lactone as model substrates, we demonstrated that both E,Z- and E,E-macrocycles underwent facile transannular reactions to give cis-syn-cis and trans-anti-trans ring systems, respectively. However, Z,E- and Z,Z- macrocycles did not cyclize under similar reactions. The similarities and differences between transannular Diels-Alder reactions and this transannular cyclization process were also disclosed. Building upon these preliminary studies, we developed a 12-linear step synthesis of the ABC carbocyclic core of norzoanthamine. It features an organocatalytic asymmetric intramolecular aldolization to set the stereochemistry of the entire molecule, a fragment coupling based on selective alkylation of a bis-enolate, and a transannular Michael reaction cascade for rapid and stereoselective synthesis of the polycyclic core. Subsequent Claisen rearrangement enabled installation of a handle for introduction of the bottom piece to complete the total synthesis. Other efforts toward the total synthesis have also been discussed.

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This thesis is concerned with the development of transannular iodoamination methodology for the synthesis of pyrrolizidine, indolizidine and tropane alkaloids. Chapter 1 introduces the concept of a ‘transannular cyclisation’ and outlines the utility of such cyclisations in the synthesis of a range of [x.y.z]-azabicyclic alkaloids. Chapter 2 describes the development of a three step lithium amide conjugate addition, ring-closing metathesis and transannular iodoamination protocol for the preparation of the pyrrolizidine scaffold ([3.3.0]-azabicycle). Cyclisation of a hexahydroazocine occurs with concomitant N-debenzylation to give a single diastereoisomer of the corresponding C(7)-iodopyrrolizidine product, which is then elaborated to the known pyrrolizidine, (−)-7a-epi-hyacinthacine A1. Chapter 3 delineates an extension of the methodology described in Chapter 2, and an investigation into accessing alternate diastereoisomeric pyrrolizidine scaffolds via the transannular iodoamination process. These studies culminate in the synthesis of two pyrrolizidine alkaloids, (−)-hyacinthacine A1 and (−)-hyacinthacine A2. Chapter 4 details investigations into the further elaboration of the C(7)-iodopyrrolizidine scaffold synthesised in Chapter 2. A nucleophilic displacement reaction with azide leads to the synthesis of novel 7-deoxy-7-aminoalexine analogues, whilst radical-mediated substitution of the iodide by oxygen allows the synthesis and isolation of the pyrrolizidine alkaloid (−)-1-epi-alexine. Chapter 5 outlines the development of the transannular iodoamination reaction to facilitate the synthesis of the tropane architecture ([3.2.1]-azabicycle). A tandem lithium amide conjugate addition and aldol reaction sequence is followed by ring-closing metathesis to give the required aminocycloheptene. Subsequent treatment with iodine results in transannular cyclisation to give a single iodotropane product which, following elaboration culminates in the synthesis of (+)-pseudococaine. Chapter 6 contains full experimental procedures and characterisation data for all compounds synthesised in Chapters 2, 3, 4 and 5.

Une stratégie de synthèse efficace de différents composés de type azabicyclo[X.Y.0]alkanone fonctionnalisés a été développée. La stratégie synthétique implique la préparation de dipeptides par couplage avec des motifs vinyl-, allyl-, homoallyl- et homohomoallylglycine suivi d’une réaction de fermeture de cycle par métathèse permettant d’obtenir des lactames macrocycliques de 8, 9 et 10 membres, qui subissent une iodolactamisation transannulaire menant à l’obtention de mimes peptidiques bicycliques portant un groupement iode. Des couplages croisés catalysés par des métaux de transition ont été développés pour la synthèse d’acides aminés ω-insaturés énantiomériquement purs à partir de l’iodoanaline. L’étude du mécanisme suggère que l’iodure subit une attaque du coté le moins stériquement encombré de la lactame macrocyclique insaturée pour mener à l’obtention d’un intermédiaire iodonium. La cyclisation se produit ensuite par une route minimisant les interactions diaxiales et la tension allylique. L’iodolactamisation des différentes lactames macrocycliques insaturées a mené à l’obtention regio- et diastéréosélective d’acides aminés 5,5- et 6,6-iodobicycicliques. De plus, une imidate azabicyclo[4.3.1]alkane pontée de type anti-Bredt fut synthétisée à partir d’une lactame macrocyclique insaturé à neuf membres. Les analyses cristallographiques et spectroscopiques des macrocycles à 8, 9 et 10 membres, du composé iodobicyclique 5,5 ainsi que de l’imidate pontée, montrent bien le potentiel de ces dipeptides rigidifiés de servir en tant que mimes des résidus centraux de tours β de type I, II’, II et VI. / An efficient strategy has been developed for the synthesis of different functionalized azabicyclo[X.Y.0]alkanone amino acids. The synthetic sequence features preparation of dipeptides by coupling respectively vinyl-, allyl-, homoallyl- and homohomoallylglycine building blocks, followed by ring closing metathesis to produced 8-, 9-, and 10-member unsaturated macrocyclic lactams, and transannular iodolactamization to make the bicyclic dipeptide surrogates bearing iodine on the lactam ring. Transition metal cross-coupling methods were developed to make enantiomerically pure ω-unsaturated amino acid building blocks from iodoalanine. Mechanistic considerations suggest that attack of iodine from the least hindered face of the unsaturated macrocyclic lactam provides an iodonium intermediate and cyclization occurs by a route that minimizes allylic strain and diaxial interactions. Iodolactamization of the unsaturated macrocyclic lactams gave regio- and diastereoselectively fused 5,5- and 6,6-iodo-bicylic amino acids. Moreover, an anti-Bredt bridgehead imidate azabicyclo[4.3.1]alkane was synthesized from a 9-membered unsaturated macrocyclic lactam precursor. X-ray crystallographic and spectroscopic analyses of the 8-, 9-, and 10-member macrocycles, as well as the 5,5-bicycle and bridgehead imidate demonstrate the potential of these constrained dipeptides to mimic the central residues of ideal type I, II’, II and VI β-turn geometry.

Neste trabalho foram estudados computacionalmente os [2.2]ciclofanos ([2.2]paraciclofano (1), anti-[2.2]metaciclofano (2a), sin-[2.2]metaciclofano (2b) e [2.2]metaparaciclofano (3)), que são os [2n]ciclofanos mais simples, contendo dois anéis fenílicos conectados por duas pontes etilênicas. Os ciclofanos têm apresentado inúmeras aplicações importantes, podendo atuar como auxiliares em sínteses assimétricas e como catalisadores que simulam funções enzimáticas, apresentando seletividade em relação aos substratos. Eles são empregados tanto em químicab supramolecular quanto em áreas biomédicas. Estudos que empregam ressonância de spin eletrônico ou que investigam propriedades ópticas não-lineares dos [2.2]ciclofanos indicam que os mesmos apresentam interações transanulares, que ocorrem através de recobrimento direto entre orbitais pertencentes a anéis diferentes, through-space, ou através de recobrimento entre orbitais dos anéis e das pontes, through-bond. As interações transanulares possuem um papel fundamental na química dos ciclofanos, alterando o comportamento reacional destes compostos e as transições espectroscópicas. Apesar dos métodos de preparação de ciclofanos, desde os mais simples aos mais complexos, serem intensamente investigados, estudos computacionais, que busquem compreender as correlações entre tensão e aromaticidade, estrutura eletrônica e o mecanismo de ocorrência das interações transanulares, são raramente encontrados na literatura. Desse modo, o objetivo deste trabalho foi estudar as interações transanulares, bem como correlacionar as diferenças estruturais, a tensão sobre anéis e pontes, cargas atômicas, aromaticidade e os deslocamentos químicos, não apenas para os isômeros dos [2.2]ciclofanos, mas também seus derivados fluorados (perfluoração de um dos anéis dos [2.2]ciclofanos), bem como avaliar os efeitos de diversos substituintes (CN, Cl, C=O, NH2 e NO2) e da protonação na estrutura eletrônica do isômero [2.2]paraciclofano. As otimizações de geometria de 1, realizadas com diferentes métodos e conjuntos de funções de base, mostraram que os modelos MP2/6-31+G(d,p) e B3PW91/6-31+G(d,p) fornecem os melhores resultados em comparação com os dados de raios-x. Buscas conformacionais mostraram que 2a e 2b são confôrmeros com energias diferentes e que 3 possui dois confôrmeros degenerados. As energias relativas e de tensão das pontes, seguiram a mesma ordem, indicando que a tensão sobre as pontes e a repulsão entre as nuvens ? dos anéis aromáticos são determinantes para a estabilidade dos [2.2]ciclofanos. As reações isodésmicas indicaram que os anéis comportam-se como absorvedores de tensão. NICS e HOMA mostraram que apesar das perdas de planaridade dos anéis a aromaticidade é mantida. O método NBO confirmou que todos os [2.2]ciclofanos apresentam interações through-bond, mas apenas 2a e 2b apresentaram interações through-space significantes. A análise AIM mostrou que as interações transanulares observadas são do tipo camada fechada (iônica ou ligação de hidrogênio) e que estabilizam os [2.2]ciclofanos. Para os derivados fluorados as principais alterações geométricas observadas foram para os diedros das pontes. As reações isodésmicas revelaram que as tensões das pontes e as energias relativas são afetadas pela fluoração. Além disso, os anéis dos isômeros fluorados absorvem mais tensão que os anéis dos isômeros não fluorados. NICS e HOMA mostraram que a substituição por flúor aumenta a aromaticidade dos [2.2]ciclofanos. A análise NBO indicou que a perfluoração aumentou o número e a intensidade das interações through-space, mas as mesmas ficaram restritas principalmente aos derivados fluorados de 2a e 2b. A mesma análise evidenciou que há uma conjugação dos pares de elétrons dos átomos de flúor com o sistema ?. Por outro lado, a análise AIM sugeriu que a substituição não aumenta o número de interações through-space, mas confirmou a conjugação dos pares de elétrons dos átomos de flúor. Os demais substituintes empregados afetam os parâmetros geométricos do [2.2]paraciclofano (1) de maneira diferenciada. A análise particionada das reações isodésmicas mostrou que as tensões nos anéis e nas pontes dependem não apenas do substituinte empregado, mas também da posição da substituição. NICS e HOMA indicaram que a aromaticidade no anel não-substituído dos derivados substituídos é maior que em 1. A análise NBO revelou que a substituição e a protonação aumentam a ocorrência de interações transanulares through-space. O método AIM indicou a presença de interações transanulares apenas para o derivado substituído com NH2 e CN e para a espécie protonada. No entanto, tais interações apresentaram características de interações de camada fechada. com pequenas estabilizações. As cargas atômicas e os deslocamentos químicos confirmaram as mudanças na densidade eletrônica, observadas através do método AIM. / In this work, the [2.2]cyclophanes ([2.2]paracyclophane (1), anti-[2.2]metacyclophane (2a), syn-[2.2]metacyclophane (2b) e [2.2]metaparacyclophane (3)), which are the simplest [2n] cyclophanes that contain two phenyl rings connected by two ethanediyl linkages, were studied computationally. Cyclophanes have presented several important applications, such as auxiliary in asymmetric synthesis, catalysts that simulate enzymatic functions, presenting selectivity in relation to the substrates. They are employed either in supramolecular chemistry or in biomedical areas. Studies that apply electron spin resonance or that investigate the non-linear optical properties of [2.2]cyclophanes, indicate that these compounds present transannular interactions, which occur through direct overlap of orbitals lying in different rings, throughspace, or through overlap between orbitals from rings and bridges, through-bond. The transannular interactions have a fundamental role in cyclophane chemistry, changing the reactional behavior of these compounds, and the spectroscopic transitions. Despite the fact that the well known methods of preparation, from the simplest to the most complex cyclophanes, have been studied intensively, computational studies that intent to comprehend the correlations between tension and aromaticity, electronic structure, and the mechanism of the transannular interactions are rarely found in the literature. Therefore, the aim of this work was not only to study the transannular interactions, correlating the structural differences, tension in rings and bridges, atomic charges, aromaticity, and chemical shifts of the [2.2]cyclophanes isomers but also to extent a similar treatment to the fluorinated derivatives. In addition, the effects of substituents such as (CN, Cl, C=O, NH2, and NO2) and the protonation on the electronic structure of [2.2]paracyclophane were also evaluated. The geometry optimizations of 1, carried out by using different methods and basis set, showed that the models MP2/6-31+G(d,p) and B3PW91/6-31+G(d,p) provide the best results in comparison with the x-ray data. Conformational searches showed that 2a and 2b are the conformers that present the same energy and the isomer 3 has two degenerated conformers. The strain energies of the bridges followed the same tendency as the relative energies, indicating that the tension on the bridges and the repulsions between the ? clouds of the aromatic rings are the key factors that determine the [2.2]cyclophane stabilities. The isodesmic reactions indicated that the rings are absorbents of tension. NICS and HOMA showed that the aromaticity of the rings is preserved despite the changes on the planarity. The NBO method confirmed that all [2.2]cyclophanes present through-bond interactions, but only 2a and 2b exhibit noteworthy through-space interactions. The AIM analysis pointed out that the transannular interactions behave as closed shell interactions (ionic or hydrogen bond), stabilizing the [2.2]cyclophanes. The main geometric changes, observed to the fluorinated derivatives, were those related with the dihedral angle of bridges. The isodesmic reactions pointed out that the tensions of bridges and the relative energies are affected by the fluorination. In addition, the fluorinated rings absorb more tension than the non-fluorinated rings. NICS and HOMA showed that the substitution by fluorine increases the aromaticity of the [2.2]cyclophanes. The NBO analysis indicated that the number of through-space interactions increase with the fluorination, but it is restrict to the derivatives of 2a and 2b. In addition, the same analysis pointed out a conjugation of the fluorine lone pairs with the ? system. On the other hand, the AIM analysis suggested that the substitution do not increase the number of through-space interactions, but confirmed the conjugation of the fluorine lone pairs. The other substituents can affect the geometric parameter of 1 noticeably. The partitioned analysis of isodesmic reactions showed that the tensions in bridges and rings not only depend on the substituents employed but also on the position of substitution. NICS and HOMA pointed out that the aromaticity is bigger in the non-substituted rings of [2.2]paracyclophane derivatives than in 1. The NBO analysis showed that the substitution and protonation increase the number of through-space interactions. AIM method indicated the transannular interactions occur only to the derivate substituted by NH2 and CN, and to the protonated specie. However, these interactions presented features of closed shell interactions with small stabilizations. The atomic charges and the chemical shifts confirmed the changes of the electronic density, observed through the AIM method.